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Buh duh fuh buh wha?

Today I am groggy. I was so relieved when I got home last night and discovered that scrottie had gone ahead and cooked dinner, a vegetarian-bastardized version of Chino Bandido's Emerald Chicken. After eating that and reclining on the sofa for a while to give Emma some much-needed lap time, we played a brief round of Super Mariokart and went to bed more-or-less on time. Even so, I slept in until 8:30 this morning. I brought leftovers for dinner tonight because tonight I'll run the hemolymph assay at 9 pm.

I am hoping I can keep the momentum going this week and still make it rowing tomorrow morning.

I'm also going to do another early morning set on Sunday. You know, just to keep things interesting.

It's tricky to bounce between this project and other things, but I'm still chipping away at the leafcutter manuscript, and have a status meeting in a bit to go over the state of work from Texas and Nebraska.

Power 10

The fun of circadian experiments: I got up at 4 this morning, made lunch, and headed in to work to remove food from today's group of 5-day-old adult crickets at 5 am. Then I took a 20-minute nap and after that I headed over to the boathouse to row.

Serious Double has reverted to a 6:30 am start time, so the boathouse was quiet at 6 aside from one guy on an ergometer.

I need to keep working on my catches. While we were in Sacramento, I took a look at the structure of the foot plate in the blue Hudson and determined that I could indeed raise the heels to a less atrocious height. I think I got the adjustment most of the way to where it needs to be for me, but maybe if I do another half-inch or so I'll have my feet in a rock-solid spot that will make it easier to release cleanly and come up to take good catches.

This morning, I did some alternating square-feather drills. The basic idea is that every other stroke is on the square, alternated with strokes on the feather. The feather strokes help keep things relaxed, while the square strokes help with cleaning up the catch and release because they ensure that the entry and exit of the oar to/from the water is separated from the motions of squaring and feathering the blade. This drill was all right but I am not sure that it is encouraging me to change bad habits or reinforce good habits. What I might need to do is more catch drills and half-slide pause drills.

After the square-feather drills, I did two sets of 10 strokes on, 10 strokes off, with an emphasis on high, high power through the water and low stroke rates. One of the things that Iz has had me do is strokes with 50-75% pressure at the catch, building to 100% pressure at the release, which helps emphasize acceleration through the water and good control when taking the catch. I could feel that, on the high-power strokes, I tend to hit the catch too hard, sending the blades too deep, and then I tend to wash out by the time I reach the release. Even so I managed to get in a few good strokes here and there.

Things to work on.

After a quick breakfast in the lab, I injected crickets with fluorescently-labeled inulin and then collected hemolymph samples 20 minutes later.

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Taking stock: Projects and chores

One of the things that scrottie and I didn't quite get to was updating our projects, chores, and fun activities lists.

We keep a lot of lists. But it seems to work pretty well to do so.

I think I'm actually due for a trip to slouch in a coffeeshop for this very reason - such thinkspaces tend to be the best places for me to think through who I am, where I am, and what I want to be doing.

Top of the lists:
-Travel. We need to make travel plans for RAGBRAI at the end of July, and also think about getting in more long bike rides to get ready. I also need to figure out how to work in visits with my parents and Riverside sibling over the remainder of the year. In the very least I should go up to a Seattle-area head race sometime around the end of October / beginning of November, methinks.

-Pants. Two pairs are on the mending pile, three pairs are about to meet their maker (including one on the mending pile), one pair is really only good for mucking around, and the other day I discovered that the last pair looks like it also has some sulfuric acid holes in it.

-Art: I want to finish the cat quilt but I don't seem to sit down for long enough while at home.

-Also art: I want to work on some insect art projects - mostly drawings.

-Plants: I bought a tiny fern at Berkeley Horticulture yesterday. I need to repot it and also some succulent babies from the yard so I have more pretty houseplants around.

-Furniture: I should work on refinishing the sewing machine table so as to help keep space clear in the workshop.

-Rowing: I have a big pile of miscellaneous rowing-related resources sitting on the desk, which need to get organized and put into binders. I should also put together a more defined training program.

-Gopher. There's a gopher in the backyard. It likes to gnaw on the roots of the artichoke plant, and it has pulled multiple tomato plants underground. S spent Saturday digging around to figure out its tunnel network and apply gopher repellant while RAC constructed root cages for some replacement tomato plants.
I can't do justice to telling you how the Gold Rush regatta went on Saturday, except to say I feel really lucky to get to hang out with the BPRC gang. They are great. Hopefully I can use them as inspiration/motivation to get in an even better rowing groove. I've continued to suffer predominantly from the problem of not managing to get myself out of bed and over to the boathouse.

The venue for the Gold Rush regatta is on Lake Natoma, in Sacramento. They host a whole series of regattas in May every year, and have all the pieces in place to run everything well, including a fancy starting platform where they can push out or pull in individual dock segments for each lane to align the bow balls.

Our Women's C quad came in first, and rowed well with good focus, but I still have this sense that we could squeeze out more speed. I had a pretty solid race in the 1x but got edged out by another rower who is apparently a professional mountain bike racer (Tara Walhart?). At least it was a good speed benchmark?

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One of the things that scrottie and I try to do every week is sit down to plan out the week. Initially, sytharin and L were hanging around while we tried to talk things through. L's preferred form of wordplay is the portmanteau, to the point where he's created an organization he calls The Departmanteau. If you hang around him long enough, you eventually find yourself inventing portmanteaus, too. Anyway, while sitting there, he started mumbling "Group...think...groupthink.." to himself, and, eventually, "Grink," which then led S to say, "Up a grink without a scrum!" in reference to our prior conversations about scrums (new to me because academics don't do that stuff).

Somehow that is a good summary of how Sunday went. I had to start a new experiment, which involved going to the lab to remove food from a cricket box at 1 pm, and then going back at 5 pm to inject the crickets with inulin and take hemolymph samples 25 minutes later. In between, RAC and I visited Berkeley Horticulture to make some decisions about a couple of plants, and I braved Monterey Market for some groceries. We also attended to a couple of the garden projects: repotting the pomegranate in a gorgeous giant planter, harvesting and processing carrots, harvesting the bolting lettuce, and harvesting onion greens. There's going to be a lull period now, up until the summer vegetables are ready to harvest.

This new experiment is going to take some work to finagle. It's the pilot phase of a project to study how metabolism changes across the circadian cycle in the wing-dimorphic crickets. Right now, we're measuring the baseline composition and volume of the cricket hemolymph at four different timepoints to get an idea of whether and how it changes. Two details are important: we're focusing on crickets at day 5 of adulthood, and they have to have food withheld for 4 hours prior to measurements. The 4-hour food withholding is what's going to be tricky, particularly for the 9 am crickets. I'm also going to have to think about how I want to handle the 9 pm hemolymph collection time. I'll probably just work late on those nights.

Doing science in public

While faffing around today in between productive bouts of working on the leafcutter manuscript (!), I came across a link to this article by Kieran Healey on social media and sociology. The excerpt posted on the Dynamic Ecology blog has convinced me to read and consider it further, and actually, it's relevant to the leafcutter manuscript in addition to being relevant to the act of blogging. Here's are some of those tantalizing excerpts:

"Here is also a natural connection here to the world of scholarly research. Although by now thoroughly professionalized, academic life has deep roots in the desire to talk about scholarly preoccupations in public, and in one’s spare time. It is in this sense an aspect of civil society. On a personal level, having the desire to go and tell people about your work is a good a sign that you are substantively absorbed by what you are doing. The point generalizes to disciplines. To the degree that thinking, talking, and arguing about research in one’s spare time and in public is a feature your field, it is a sign that your discipline is confident about what it does. Modern social media brings together these shared features of civil society and academic discourse in a new way. Social media platforms facilitate and accelerate the possibilities for talking about one’s
work in public, assuming we want to take advantage of it."

"In “Science as a Vocation”, Weber remarks that although we do not get our best
ideas while sitting at our desks all day doing regular work, we wouldn’t get any good ideas unless we sat at our desks all day doing regular work. In a similar way, successfully engaging with the public means doing it somewhat unsuccessfully very regularly. This fact is closely connected to the value of doing your everyday work somewhat publicly. You cannot drop a lump of text onto the Internet and expect anyone to pay attention if you have not been engaging with them in some ongoing way. You cannot put your work up on your website, or “do a blog”, or manufacture interest in your research like that. There is a demand side as well as a supply side to “content”, and most of the time the demand side does not care about what you have to say. This is why, in my view, one’s public work ought to be be continuous with the intellectual work you are intrinsically motivated to do. It is a mistake to think that there is a research phase and a publicity phase. Your employer might see it that way, but from a first-personal point of view it
is much better—both intrinsically and in terms of any public engagement you might
want—to think of yourself as routinely doing your work “slightly in public”. You write about it as you go, you are in regular conversation with other like-minded researchers or interested parties, and some of those people may have or be connected to larger audiences with a periodic interest in what you are up to."


...and so on.

Alchemy Collective

Alchemy Coffee

We finally found a coffeeshop that I liked enough to want to go back sometime to slouch and write in my journal.

It helped that I had enough spare mental capacity yesterday to browse for a couple more coffeeshop options. I was reminded that Okay-Oogley-Googley Maps isn't great in this department. Also, I find the south side of Berkeley to be way more fun and interesting than the north side.

We're reaching a point where I need to start keeping a spreadsheet. (this should cause my father to grin)

I also came to a decision yesterday evening. I am giving myself a one-month deadline for the leafcutter manuscript. Whatever shape it's in, I will submit it somewhere. OR I will drop working on it entirely. I have informed my advisor of this plan, so she's going to have to just deal with it. I have too many other things to attend to in the meantime, plus in a lot of respects at this stage I'd almost prefer to redo the experiment and do it better. Not that I'll ever have the time or energy to redo it. If anything, I would get a group of students to do it. But better. There comes a point where sitting on a thing no longer helps.

Dear draft

Dear draft,

I will set you down for now. I know you'll try to keep speaking to me, as I ride my bike home, as I try to sleep. I know you say something, in between saying nothing and saying everything. Nothing says nothing, and nothing says everything. There is no perfect experiment.

I have laid down a thousand tiny threads to try and tell your story, and I can never get it quite right because no story is ever perfect. I have tried to weave you together over the shouting of so many voices and interests and doubts, tried to figure out how you fit in, where you stand out. I am tired and frustrated but I will keep coming back. It is hard to know that the impact isn't proportional to the struggle after all. ["No one will ask how long it took. They will only ask, 'Who built it?']. I wish you did not cause me such feelings of sorrow and regret for your imperfections, but I hope I have the will to keep going.

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Blargh

I am getting really tired of the presidential election commentary on social media. Perhaps there's a silver lining, in that I have less motivation to use social media as a distraction tool? I recognize that it's important to be at least somewhat aware of what's going on in the political sphere, but there are limits to how much vitriol I can handle before I get too negative.

I did vote in the California primary election, by mail. Our county, Contra Costa, has these drop-off boxes called "CoCo Vote-N-Go," but I went the old-fashioned route with stamps. CoCo Vote-N-Go is the best part of the primary so far. There were some crazy candidates for the US Senator primary - 34 in total. A swift reading of the candidate statements quickly revealed that it would be pretty easy to pare down the choices to just a couple of individuals. I personally feel that Senators and Congresspeople are more important to choose wisely than figureheads.

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I managed to get up and go rowing this morning. It was windy. I was only able to convince myself to put in 2 laps (6k). Better than nothing.

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This piece on "What I Learned About Writing By Not" has gotten me thinking about the second point: "Figure out how you want the writing experience to feel." The leafcutter manuscript has been routinely sending me on a crazy and unnecessary emotional rollercoaster. The thing I struggle with the most is how to put all the pieces together into a coherent story. That makes me grateful for everything I've learned and experienced when working with my cricket collaborators. The crickets are just much more straightforward than the ants because I don't need to know things about leaves, ants, fungi, social evolution, or ecological vs. animal approaches to studying nutrient limitation to write about the crickets. I just have to write about nutrient limitation in animals and life-history trade-offs in wing-dimorphic insects.

Actually, I think the complexity in many social insect systems leads to a lot of incoherent writing in general.

Other statuses

Bean of the Month club has been more like Bean of the Week club, lately. Over the weekend, I picked up a big bag of Jacob's Cattle beans. After soaking they were big, plump things and were phenomenal in soup.

One of the things that was abandoned in the cupboard was most of a bag of dried lima beans. So I soaked them and tried making this Baghali-Ghatogh recipe. I chopped down a dill weed plant growing along the front walk. The beans had a poor texture after cooking, and the dill flavor was...strong. So the dish was fine, but not particularly exciting. I think I should probably eat more lima beans prepared in different fashions so as to decide how I feel about them.

At annikusrex's behest, I sent a strongly-worded letter to my former Lincoln landlord demanding the return of my rental deposit. It worked! Promptly, too. I am relieved that's over. The landlord included a Post-It note apologizing for the delay due to an accident and 2-month hospital stay. It's impossible to know whether or not the note was true. I hope for his sake that he gets his business affairs together. I miss that apartment, although I really don't miss the mildew or ancient furnace or lack of laundry facilities. Renting can be such a mixed bag. So can owning, of course.

I think I am going to buy some silly things for my cat. What do you think of this cat tree? Pricey, yes. I also want a tabletop fountain to stick in the bathroom so my cat has an elegant water supply.

She has a rough life.

Progress

This is a bit convoluted because I'm still working on how to pack meaningful parts of the information below into the leafcutter manuscript (or how to avoid having to pack them in).

A challenging part of writing about the leafcutter manuscript involves how different groups of people think about and write about nutrition. From a broad ecological perspective, it makes the most sense to use elements as a fundamental currency, and that's the perspective I started from originally. For those interested in animal nutrition, however, it makes more sense to think about elements in nutrient form, and to distinguish between things that can be readily digested and assimilated or not. So I have to be more nutrient-explicit than just talking about elements.

But where do fungi fit in? Many kinds of fungi can break down cellulose and lignin, which is why fungi are key for decomposition. I learned yesterday that in many ecosystems, decomposition often occurs in a two-stage process, with small soil organisms initially breaking down leaves into small particles, and then fungi can come in and colonize things: when tough leaves are put into a mesh bag with pores that are so small that only microbes can enter, the leaves don't break down. As soon as the pores are large enough to permit entry of soil arthropods, the leaves get decomposed. On the other hand, if leaves that are easy to break down are put into those same mesh bags (e.g. kale), there's no difference in decomposition rates between mesh bag types. But the jury's out with regards to the extent to which cellulose digestion is important in the leafcutter system specifically.

Anyway. Over the course of further extensive literature searching, I also determined that next to nothing is known about the ability of fungi to ingest and utilize lipids as an energy source. The vast majority of work has focused on the utilization of different carbohydrate sources. Typically, glucose is prioritized, but in mixtures, fungi (in general) will use different blends of things. This corresponds well with some of the studies that have been conducted on enzyme activities in leafcutter fungus gardens - gardens will shift enzyme production in response to changes in fungal substrate.

I got to thinking about all of this over the course of trying to determine why, from a biochemical standpoint, there are large differences in the carbon and nitrogen content of palo verde leaves as compared to polenta. I think the main reasons are because corn is mostly full of stored carbohydrates, whereas leaves are full of photosynthetic machinery. In addition, leaves of desert plants often have more waxy cuticles to prevent water loss. Waxes and and chlorophyll are high in carbon, and chlorophyll is somewhat high in nitrogen, so these are reasonable explanations for the differences.

It took a while to think this through and find good references for it, though, because I wasn't sure about how large the differences in N content were for leguminous vs. non-leguminous plants, or whether the differences are strongly tied to the production of plant secondary compounds. I also had to remember which kinds of plants use C3 versus C4 versus CAM photosynthesis. The literature informs me, however, that at least ~75% of the protein in plant leaves in general is associated with chlorophyll, so on a coarse level this explanation seems like it will hold unless a reviewer informs me otherwise.

I'm still not sure about how to justify my diet treatments, though, or if I even need to do much in the way of justification. I do, however, need to be able to talk about why it is that colonies in the wild collect foods that have more protein-biased ratios than the high-protein polenta treatment I used.

The answer really lies in the waste material. Unfortunately, I haven't been able to analyze the waste material for anything other than overall elemental composition. I also need to go back to working on comparisons of throughput rates for leaves versus polenta. Just knowing elemental composition doesn't reveal the full story in terms of nutrient utilization; I need to know things about both input rates and output rates. The main thing I know at the moment is that they aren't exactly steady-state in smaller colonies, which complicates things - there's variation in retention times within the fungus garden. If there was even a hint of steady-state rates, I could say, "Here's what goes in, here's what comes out, so here's what the ants and fungus and microbial community have used up."

I could design and conduct some really good experiments with what I know now, but I really don't have that luxury at the moment.

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