Even in Kyoto

So about a week after getting to Arizona, I finally finished a reasonably thorough draft revision to a manuscript I'll call the 2018 seed-harvester ant paper, and sent it over to my hosts, who are coauthors on it, for their review and feedback.

Then, while in the transition phase between that and the next writing project, I had one of those thinking-out-loud conversations that went, "Oh yeah, of course the next writing project I should work on is the next paper that's closest to being ready to submit."

...That would be a leafcutter manuscript rather than the next seed-harvester paper (the "2021 seed-harvester ant paper").

...the only major downside being that switching from seed-harvesters to leafcutter ants is kind of a big intellectual shift, for me, at least. To wit, I spent a bunch of time last week just trying to get my leafcutter ant annotated bibliographies better organized (yes, that's bibliographies, plural), to identify where I need to brush up on the literature, and since then I've been spending a bunch of time trying to find and read any information I can about how fungi might respond to excess nitrogen (protein).

Half of the challenge tends to be just figuring out how to dial in on what my question actually is, to figure out how to search for sufficiently specific information related to my question. "All fungi" is FAR too broad; I really just want to learn about saprotrophs - and soil saprotrophs rather than wood saprotrophs, but often they get studied in the context of "soil microbiota," which will also always include ectomycorrhizal fungi and bacteria, okay, rightly so. But the thing is, the context of other microbes might actually be really important, seeing as most leafcutter ants grow their fungus gardens underground. They do keep their gardens immaculately clean, but there are still bacteria in the mix.

Out of the papers I found, I only finished reading the best of them yesterday and today - a review article from 2014 that basically laid out a great framework for thinking mechanistically about how soil microbial communities could and do respond to C, N, or P limitation (so interesting and cool*), and a fun paper from 2024 that helps to clarify that there are some systematic patterns to fungal fruiting body element content, related to both fungal evolutionary history and ecology. The latter is important for being able to assert that fungi regulate their body element composition homeostatically.

Things I'm still not entirely clear about: in soil microbial communities, when there's an abundance of nitrogen around, it sounds like basically "microbes" (presumably mostly bacteria rather than fungi) produce and excrete "mineralized" nitrogen (ammonium) - a form of nitrogen readily available to plants. This basically means plants will renege on their deal with ectomycorrhizal fungi and just get their nitrogen directly. In contrast, when nitrogen is limited, microbes are said to "immobilize" it, which basically means they hold onto it and put it to use in forms that are not directly accessible to plants. (that would lead plants to barter with fungi for nitrogen in exchange for some sweet photosynthesized sugar).

But: do fungi also mineralize nitrogen? If there's too much nitrogen around and not enough carbon, are fungi more likely to die by way of simply running out of energy (can't get to enough organic carbon), or from some form of nitrogen toxicity, perhaps related to having lower tolerance to high nitrogen and getting outcompeted by microbes with higher nitrogen tolerance?

That's what I still don't really know and can't fully conjecture about.

This line of speculative thinking will probably only contribute to 1-2 sentences in the Discussion section of the leafcutter ant manuscript, but on the other hand, it's fun and interesting to think about.

...And so only eventually have I been able to get back to working on a coauthor's feedback on the 2018 seed-harvester ant manuscript.

I wasn't quite expecting so much of this time to get devoted to the writing step of reading papers and learning things, but here I am.




*Responses differ depending on the limiting element/nutrient (out of C, N, and P), because the extracellular enzymes that these organisms secrete in order to obtain nutrients require nitrogen and energy (but not phosphorus!) to synthesize. Fungi and microbes don't appear to store appreciable amounts of nitrogen, but they DO stockpile phosphorus! If nitrogen is limiting, that will then favor organisms that can burn a bunch of energy to get N (consider N fixation, for instance). If C (energy) is limiting, that will favor more energetically-thrifty organisms. P limitation will favor organisms that can store and transport phosphorus from one place to another (fungal hyphae FTW!).

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.

I spent a portion of the weekend trying to get myself mentally in gear for working on the leafcutter manuscript some more. I'm about ready to just give up on my advisor on that front. Instead, there's at least one person here who's willing to give the manuscript a good read-through, so now it's up to me to get it back into sufficiently non-embarrassing shape that I'm willing to show it to her.

Getting mentally in gear doesn't always happen in the way one wishes it would. I spent some of that time on social media sites, reminding myself about how annoying they can be (mostly FB). I spent some of it thinking about other life lists (things to cook, things to acquire, things to make). I spent some of it comforting the cat, who was Really Upset about getting accidentally locked in P's room (wind blew the door shut; basically she meow-yelled for a while). I spent some of it quilting another ant on the practice quilt. And I spent some of it on chores: sweeping the house, cooking food, getting groceries, washing dishes.

Oh, and I spent some of it thinking about how nice it would be to not have outside mental baggage distracting me. But then again, on the other hand, would I want to be that kind of singularly-focused person? Is it healthy to completely suppress outside interests? No and no.

So I am allowing myself to finish reading a book chapter that seems somewhat tangential to the manuscript, but which is important for perspective on how fungi take up, store, and use phosphorus. It's part of the broader context.

Wouldn't it be nice if demanding a revised draft of a manuscript NOW resulted in such a thing?

Sigh.

Instead it seems to just push me over the edge of the stress-performance inverted U-function.

To some degree, this has to do with how I process feedback from other people. It's an instinct to drag my heels and fight because I *know* that I know the literature way better than coauthors and am trying to think it through on a deeper level than they are. I refuse to turn in embarrassing and shoddy work. And I know this is to my detriment at a certain point, but I've also observed firsthand that turning in stuff that's half-baked is seriously embarrassing and an even larger waste of everyone's time.

I asked scrottie to help me budget some time to work on a long-neglected leafcutter ant manuscript, so yesterday evening we ate a quick dinner of leftovers and had a work date. My notes suggest that it has been about six months since I last sat down to touch this manuscript, coincident with my move from Texas to Nebraska. I'd spent the afternoon reading through a manuscript I agreed to review, which wound up putting me in the perfect frame of mind as I approached the leafcutter manuscript: time to go through the paper and murder some darlings. In a previous draft it had felt important to me to include certain bits of leafcutter-specific information, but at those points my advisor had written, more than once, "I don't see where you're going with these ideas." At the time, I still felt attached to them and was reluctant to change much. The six-month gap cured me of that notion, and the thing felt ready to send back over to my advisor last night. Hurrah, and FINALLY. It needs to get published because it's a good piece of science.

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While we were working, S and I heard my cat start horking up something. S says she threw up pretty much every single day while I was out of town, probably because she's a mama's kitty and barfs when she's stressed/anxious. He went to clean up, and discovered that she'd eaten some grass and a bit of clover, which is only odd when you realize that she's an indoor cat and I don't have any grass or clover growing inside at the moment.

I went over to the back screen door, and, sure enough, it was ajar, and as soon as I got over there a small gray form bolted back inside. The whole story is mostly hilarious because she snuck outside for a plant snack, then apparently snuck back inside to barf it up. Why do cats love to do this kind of thing, anyway?

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I bought oodles of sour cherries at the farmer's market the other week, and tried to pit and can most of them. However, a couple of the cans didn't seal properly, which is the perfect excuse to cook cherry-themed things, really. So we had some delectable cherry clafoutis for breakfast this morning. YUM.

As mentioned in my previous post, I spent a lot of time over the past week with I, a new graduate student. Interacting with her is reminding me of a number of little things that I have learned over my time as a scientist. A lot of those little things are obvious, in retrospect, but I always have to wonder if I would have spent less time flailing around if I'd known about or thought about many of them earlier in my career. A few examples:

1. Enter in your data as you collect it. (this is what I'm working on today, which is what made me think about this entry)

2. Along those same lines: Clean up as you go along.

3. While writing manuscripts, keep a text file with a "to do next" list. Actually, this should be started even before you start writing a manuscript. For me, it has been the simplest way to put down a project and then be able to pick it back up with minimal fuss.

4. When meeting with other people, put as much as you can into writing, but keep it simple. To have a focused meeting, have a goal for the meeting and put that at the top. Do you want feedback on a specific piece of writing? Do you want help with the experimental design? Do you want help figuring out the holes in your logic? Are you trying to figure out who to put on your committee or who to include in the project? The sooner you can get concrete specifics in writing, the easier it will be for others to help you make progress.

5. Have a plan for analyzing your data *before* you collect the data. You might change your mind later on, but this will save you many potential massive headaches. This means having a thorough outline of your experiment and its dependent variables. Is it frequency data? Continuous data? How many treatments are you comparing? How many figures in a paper will this translate into?

6. Consider keeping annotated bibliographies for projects. I don't know about you, but my brain and memory are small, and the amount of literature I need to be familiar with is large, and covers a wide range of themes. Annotated bibliographies are a shortcut for organizing your thoughts about the literature, and for staying on task with #3. I just keep mine in text files. No need to get fancy.

7. There are a lot of other useful sources of information that might be helpful. Don't skip over them. Read them in the evening before bed. This book comes highly recommended (although I haven't read it, I suspect if I read it I would do a lot of nodding). For academic writers in all walks of writing, I've found How to Write a Lot helpful, too.

8. For keeping the different parts of a research project organized, here's an idea of how I structure my files. I'll come up with a short name for the project and will make a directory (folder) for it. Within the directory, I'll have subdirectories for: datasheets, raw data (as it is entered in to the spreadsheet), figures, R scripts, and the manuscript. I'm not good at throwing things away, so whenever I generate new files, I make a directory within a folder, label it "Old," and stick the previous version in there.

9. I like Zotero as an open-source browser plugin for keeping track of references. I still download pdfs of references into a big (separate) folder, and label them with the authornames, year, and a few keywords. Note that this is completely separate from my annotated bibliographies.

I suspect I'll think of ten more pointers somewhere further down the line, but this should be a good starting list.

What work-organization insights have you wished you'd had at an earlier stage?

One of my fellow graduate students has an article taped up on the door to his/her office entitled "The importance of stupidity in scientific research," by Martin Schwartz. It was an essay published in the Journal of Cell Science in 2008 (volume 121, page 1771, just to ensure that all citation information is contained in this entry, even if I'm not including a separate References section), about the fact that science makes scientists feel stupid.*

Today, I am trying exceptionally hard to think about the Introduction for the Manuscript of Doom II: The Sequel. Trying to think is making me feel stupid, so I thought I'd take a break and write about what I know instead. As a reminder, this Manuscript is not part of my dissertation. The data to be included in this Manuscript are really interesting and novel, and by themselves, they tell a pretty good story. The challenge is the framework in which they are presented. I think we are stuck on figuring out how to use these data to help advance the field of social evolution. What I'm trying to imagine is, if a TeeVee News Crew stuck a camera in my face and asked me, "So, what have you done to advance science lately?", what would I say?

The joy and frustration of attempting to advance the field of social evolution is that it requires Great Thought. I've spent countless hours puzzling through the thoughts of other scientists who have attempted to study social evolution, so I think I have a pretty good idea of where they are coming from. The majority are devoting their time to defining and re-defining cooperation a thousand different ways. I have lessons to learn from the field of ecology, which has not really seen the emergence of any new Great Thoughts in quite some time (just a lot of spinning through a set of different trendy "approaches").

And I am armed with skepticism (is it actually possible to advance science, anyway, or is it all a political game?).

But ugh. I don't know where I'm going. At least it makes me grateful that the sphere of my dissertation research is not as all-encompassing. I wish, at times, I could work on something more concrete than this "social evolution" business. I don't want it to turn into the sort of pointless navelgazing that seems too prevalent in anthropological circles. But what's the point? I don't want to just say, "Here, have some interesting data and some patterns we discovered in some ant queens." There's more to it than that.

That's what I need to figure out.
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*I feel like I may have written about this before, because it's reminding me of what scrottie says his work is like - he is always on the lookout for "new" problems, because simply applying solutions to "old" problems is intellectually tedious. But the problem with "new" problems is that nobody has come up with any kind of strategy for solving them yet.

I'm finally getting back into the whole rowing/exercising/sporting activity thing now. Two weeks after the marathon. That isn't really all that bad. But it has been a bit rough to have to wake up at 4 am. I'm adjusting.

For the past couple of rows, I have been completing two laps around the lake (approximately 10k), but this morning I got in three whole laps before I had to rush home, rush bluepapercup out of the door, and rush off to school. From there, it was a nonstop day: tutoring, preparing for a presentation tomorrow, touring our new building (it looks quite industrial; I am going to call it The Cinderblock because it's concrete), going to class, etc. etc.

Oh. And I learned that the Manuscript of Doom has been accepted in a more finalized fashion. I just have to tweak it here and there. I can tell that the whole process was a bit much because every single time I get correspondence about the MOD my blood pressure goes up noticeably. It isn't the research itself that causes the change in BP; it's all of the people that I have to deal with. Oh, and also the fact that the whole manuscript submission process/acceptance/rejection involves judgment on something that I put a considerable amount of time into. The whole thing just preys on any lingering insecurities that I might feel over the type of data analysis I chose or the way I portrayed certain pieces of information. Science=objective? Sure. Keep telling yourself that. If you spend any duration of time trying to analyze data, you will quickly realize just how subjective science is. That doesn't mean that it's a waste of time, just that it's a culture just as much as any other discipline.

Then kihle and S came over for some tasty tostadas and snarkyness, which was quite fun. Operation: Bee Skirts is now underway (I will have to post pictures if they turn out okay) and it's time to go to sleep because it has been a loooong day.

Not that kind of cheese, you cheese fanatics you (you know who you are.). Although that would be fun, too.

I just want to say how much I appreciate all of my awesome (=reticulated argyle<--severe inside joke to people who don't even read my blog--just insert some other generic hip-to-the-fish word instead) friends here. You guys rock. And I don't think that it's just the caffeine talking. On my morning run with kihle, I somehow got around to talking about my friends in various places and about how hard it was for me to find people that I liked in Boston--I'd say it really took about four years for me to find people that appreciated me for who I was there. In great contrast, it's been easier to find people with similar (bizarre? No, eclectic is probably more appropriate. Or open-minded) interests here, people that are willing to sally forth and do all sorts of interesting things, be they expeditions to oriental grocery stores or coffeeshops or state fairs or what-have-you. Maybe the mundanity of this city inspires it. Maybe it's just because I've found a home amongst fellow nerds.

Regardless [irregardless], it seems that I've moved past whatever restless state was affecting me previously. There are so many good moments to savor instead. Not that I know anything more about what I'm doing with my life or anything, but oh well. :)

Okay, maybe it is just post-Manuscript-of-Doom euphoria + highly caffeinated state talking. Does it really matter?

In the past three days, I have managed to spill food on myself during six out of the past seven meals I've eaten. I think it's mostly because I've been a wee bit on the tired side. Nonetheless, it's an impressive record so far.

In other news, I ran the Race for the Cure (breast cancer...because who doesn't like boobies?) this morning--3 miles in 26:32.11. Apparently I can run faster than I thought I could! It felt good to stretch out a bit after yesterday's long run, and it was nice to feel like yes, I can be a runner, not just a rower. What with getting back on the water, the differences between the two sports are pretty salient for me right now. For instance, it's much more apparent to me just how difficult rowing can be from a cardiovascular standpoint relative to other sports; it takes years to develop the solid cardiovascular base and discipline that rowing demands.

Rowers and runners are also built completely differently--rowers tend to be much bulkier, while runners tend to be almost spindly--that has everything to do with the nature of the activities--the one being low-impact and more dependent on strength; the other being high-impact and dependent on quickness. While I think that rowing is the more demanding sport overall, I can still complete a rowing marathon without much immediate training, while the running marathon is going to require months of preparation because my body isn't used to the motion.

Ah well [why am I so fond of inserting phrases like that?].

There are chores to attend to, and the manuscript of doom deserves some more attention. Until next time, then.