What are you looking forward to as a semester break treat?

I’ve had a really busy fall, and am very happy to be in the home stretch!* There are a lot of things I’m looking forward to about the break between semesters, one of them being:

I loved Pullman’s His Dark Materials trilogy (which I first listened to — in audiobook form — as a grad student) and the first book in the new trilogy, The Book of Dust: La Belle Sauvage was a highlight of my semester break two years ago. I know that I will not be able to put down the second book once I get into it, so I’m saving it as a post-semester reward! I also got a book by Martha Grimes. I haven’t read any of her stuff before, but I suspect I’ll like it. Since I’ve decided to reread The Book of Dust prior to reading The Secret Commonwealth, that means I have three books that I’m saving for the semester break that I’m really looking forward to.

In conversations with a few folks lately, they’ve talked about what they have in mind as a semester break treat — I’m definitely not the only one with reading plans! I’m curious to hear what others have planned. Please share in the comments!

*I mostly feel like “Home stretch! Finish strong!” but other times this is more accurate:

Them: Just a few more weeks for you and your students. Finish strong!!

Me and my students: pic.twitter.com/ykLsYMz0GZ

— Julian Wamble (@jwamble25) November 21, 2019

An incomplete list of things that blow the minds of Intro Bio students

Early in the semester during an Intro Bio class, a student asked about whether it’s ever possible for individuals of two different species to breed. That led to discussion of zebroids and, at some point in the back and forth, I mentioned that Homo sapiens had successfully interbred with Neanderthals. At least a quarter of the students (maybe even half) were visibly surprised—and I didn’t even explain that the evidence is this happened repeatedly! (Don’t worry, we covered that in a later lecture.) That night, I was making lunch for my kids and thinking about that moment in class, and I thought “Just wait until I tell them how much of their genome is viral!”

There are parts of teaching Intro Bio that are hard or annoying or both. But there are some parts that I absolutely love, and one of those is routinely getting to introduce students to things that are literally jaw-dropping. It makes me think of this xkcd:

It is always a highlight of my day (week!) when we have one of those moments in class.

So, in that spirit, I present an incomplete list of things that blow the minds of Intro Bio students (many thanks to my colleague Cindee Giffen for helping me with this list!):

1. (Almost) all of your cells contain all of your genes
2. Humans interbred with Neanderthals (repeatedly)
3. About 8% of the human genome is viral in origin
4. Plants get infected by viruses. (This comes up because I show a thermal image of a plant leaf that has been infected by a virus when talking about respiration. Speaking of which…)
5. Plants respire
6. There are photosynthetic organisms that are not plants
7. Male anglerfish fuse to the female
8. Damselfly penises
9. Gerboas
10. Taxonomy, including humans are fish, whales are mammals not the things we generally mean by “fish”, and birds are dinosaurs. Or, to quote a former student, “So, sharks are fish, dolphins are mammals, whales are mammals too, and penguins are birds, and birds are dinosaurs, so penguins are dinosaurs?!?”
11. Fecal transplants
12. Judas goats

I sometimes think that, if we filmed students while introducing those things, we would get really, really good reaction gifs.

The above list are mostly factoid sorts of things, but there are some bigger conceptual things that are definitely mind-bending for some students. Three that immediately spring to mind are:

1. The same thing can be an ancestral or derived trait, depending on your frame of reference
2. The way you can zoom in through taxonomy, sort of like you’re zooming through Google Earth (for example, humans are eukaryotes and animals and deuterostomes and vertebrates and mammals and primates and apes and hominins)
3. Food webs — that something happening way over here in a food web can influence something way over there, and also the differences between how energy flows and matter cycles

Another thing that definitely blows their minds is that ecology involves math. I address this head on now at the start of the population ecology class, and my sense is that helps, but it still really surprises many of them when equations start appearing.

I initially started compiling this list because I thought it might be interesting to others. But I’ve found it has helped me during a very busy, challenging semester — it’s ended up being a really nice way of noting the little things that are fun that I might otherwise just blow right by in a frenzy of trying to get things done. (It’s also led to me adding notes to the front of my lecture notes that say things like “damselfly sex”, in an attempt to remember to add that to the list.)

So, I’m curious:

1. What things have you found blow your students’ minds (in a good way!) And
2. Do you have any routines or other things that help you note the little, fun things that occur while teaching?

 

How I think the start of the semester will go vs. how it actually goes

I’m not at ESA this week, and in some ways that’s good, because I’m currently being swamped by the beginning of semester deluge. Last week reminded me that I always misjudge what the start of the semester will be like, as I illustrated will some silly drawings:

 

And that last one doesn’t even include all the other stuff that always pops up (e.g., an uptick in requests for letters of recommendation, finding new undergrads to work in lab and getting them set up in the lab, etc.)

Related: at an event I went to this summer, they asked us to draw pie charts showing how we spend our time. After we attempted to draw them, we had some discussions about how the traditional teaching vs. research vs. service/admin split that we tend to talk about leaves out a lot of things that take up a lot of time. And, yes, this PhD Comics chart was discussed!

How professors spend their time #tbt https://t.co/zeOyDp1ERV pic.twitter.com/wYmXzVXRM6

— PHD Comics (@PHDcomics) February 23, 2016

 

Good luck to all of us trying to fit 200% as much stuff into the same amount of work time!

(For a previous installment in the “Meg draws things poorly” series, see this post on imposter syndrome)

What do you most think you should know but don’t?

I recently attended an event related to graduate student mental health. One point of emphasis was imposter syndrome (something I’ve blogged about before), and one thing the presenter stated was that it’s important to remind ourselves that it’s okay not to know what we’re doing. As a strategy for doing that, he suggested listing what you most think you should know but don’t. I thought this was an interesting idea, and thought it would be interesting to think about this question in three different areas:

1. a specific area of ecology
2. something that relates to my professional life but isn’t a content-related thing, and
3. something outside my professional life.

I then wrote Brian & Jeremy who were on board with thinking about those questions, too, leading to this post. Read on to see what we think we should know but don’t, and please tell us what your responses are in the comments!

Who is surprisingly well represented in your reference manager library?

As I worked on a manuscript recently, I wanted to add a reference to a paper by John K. Gilbert on concepts, misconceptions, and alternative conceptions and how they relate to science education (Gilbert & Watts, 1983). As I scrolled through my EndNote library, I was surprised by how many papers I had in there by the rotifer biologist John J. Gilbert—I felt like I was scrolling a long time to make it past Gilbert, J.J. in the database. This got me wondering: who else is surprisingly well-represented in my EndNote library? And who is in yours? (Feel free to substitute your preferred reference manager for “EndNote”, or to replace “EndNote library” with pdf library or, if you’re old school, folders in your filing cabinet.)

Manuscraps: on partially killing one’s manuscript darlings

If you here require a practical rule of me, I will present you with this: Whenever you feel an impulse to perpetrate a piece of exceptionally fine writing, obey it—whole-heartedly—and delete it before sending your manuscript to press. Murder your darlings.

– Arthur Quiller-Couch, “On Style”, 1914

“Murder your darlings” and its variants is common writing advice.* But what do you do if you’re not quite sure you’re ready to part with those darlings? My strategy is the same as Ethan White’s:

When writing I keep a separate file open where I cut and paste chunks text that I don't think fit any more but I'm worried I might decide I want later.

This helps me keep the main document clean because I'm not afraid to remove things "just in case".

— Ethan White (@ethanwhite) February 8, 2019

I suspect this is a common strategy (certainly the twitter responses suggest it is), though I don’t think it’s one that gets discussed much.

When did you realize you work on climate change?

Some ecologists start their careers planning to study climate change, and others make a decision to pivot towards that line of research. But something I find fascinating is that there are ecologists, myself included, who didn’t necessarily set out to study climate change, but who are accidental climate change biologists. To give just one example: if you work on a time series on natural populations, communities, or ecosystems that extends more than a few years, chances are you’ve found that climate change is now a part of what you’re studying.

I’ve thought about this over the years as projects we work on that started out as basic research into host-parasite interactions end up relating to climate change. Some links are obvious—wanting to understand how temperature influences host-parasite interactions leads pretty naturally to thinking about how climate change will influence host-parasite interactions. Some links are less obvious—for example, we wondered whether the light environment might be influencing when and where we saw parasite outbreaks. As I recall, our initial interest in this was not related to climate change. But lakes are getting browner, in part due climate change, so any work we do on how lake light levels influence disease naturally links with climate change. And we now have some data on host-parasite interactions in lakes that spans 1-2 decades. Once you’re into decadal time scales, you have to consider the impact of climate change on what you’re seeing.

I’ve also thought about this in terms of some projects I didn’t work on. When I started grad school, one of the projects I was thinking of working on related to what was going on under the ice in lakes in winter, and how things like snow cover influenced that. So, when I saw news articles about a new study showing that there will be an “extensive loss of lake ice…within the next generation”, I thought back to those grad school plans to work on lake ice & snow cover. My recollection is that my interest in that project was mainly wanting to understand the basic biology of lakes, but clearly it would have ended up being a study of climate change if I’d pursued it.

Based on conversations with colleagues, I know I’m not alone in coming to realize that I am an accidental climate change biologist.

So, I’m curious: for my fellow accidental climate change scientists, when did you realize you were studying climate change?

Less obvious signs of reaching a new career stage

Something I’ve been thinking about lately are the less obvious signs of reaching a new career stage. I don’t mean the obvious things like being accepted to grad school, or defending your PhD, or signing your first job contract. I mean things that aren’t generally listed as major milestones but that felt important or noteworthy to you (e.g., the first time you bought coffee for someone who was at an earlier career stage than you were).

I’ll give some more examples:

As a graduate student, I remember other students talking about the first time they did an experiment without running it by their advisor first. The two particular stories I can recall were both senior grad students (one may have been a postdoc) who had a hunch about an interesting thing that might be going on in their system. In one case, the person did the experiment, then went to talk to their advisor, proposing the idea. The advisor said it would never work, leading the advisee to get the extreme satisfaction of dropping a figure showing it did work on the table.

As another example, for me, the point that I felt solidified that I was no longer early career was when I was reviewing the application file of a graduate student applicant and saw that one of the letters of recommendation had come from someone who had been an undergrad in my lab (and who now has a faculty position).

To use some I’ve seen recently on twitter:

Having someone seek you out at a meeting to talk science:

👏 This happened to me last year and it was totally mind-bending.

— Noam Ross (@noamross) August 9, 2018

(And, since Rachel was my first PhD student, her experience also felt kind of significant for me!)

Your first paper is perhaps an obvious academic milestone, but your first last author paper also feels big!:

Hooray! My very first last-author paper! #AcademicMilestone https://t.co/nOzXdLmABi

— Josh Penalba (@JoshPenalba) August 15, 2018

(Related: I remember being extremely happy about the first paper that contained data collected entirely in my lab.)

Receiving your first review request is an academic milestone; a less obvious one is reaching the point where you receive too many review requests to handle:

I'm moving from the "yes, I accept all review invitations this is nice I feel validated" phase to the "sorryyyyy but I have to decline this one I need time to do science" phase, and I try to remember that @DynamicEcology post by @duffy_ma everytime I suggest reviewers

— Maxime Dahirel (@mdahirel) August 15, 2018

And here’s one based on a recent Eco-Evo, Evo-Eco blog post: being able to stand in one spot for a day and a half and have non-stop conversations seems to be a sign of having reached a particular (well-known!) career stage. (ht for this one goes to Jeremy!)

So, I’m curious: what were some of the less obvious milestones for you? (Update: If you want to tweet them, use #lessobviousmilestones)

Who is ecology’s equivalent of Erdős?

Paul Erdős was a prolific Hungarian mathematician who spent much of the later part of his career traveling to visit collaborators around the world. According to his Wikipedia biography,

Erdős published around 1,500 mathematical papers during his lifetime, a figure that remains unsurpassed. He firmly believed mathematics to be a social activity, living an itinerant lifestyle with the sole purpose of writing mathematical papers with other mathematicians. Erdős’s prolific output with co-authors prompted the creation of the Erdős number, the number of steps in the shortest path between a mathematician and Erdős in terms of co-authorships.

Or, to quote from Stephen Heard’s recent post on Erdős:

Paul Erdős (1913-1996) was a Hungarian mathematician who published somewhere around 1,500 papers (in mostly pure-math fields including set theory and number theory) and had somewhere around 500 coauthors.  He was a fascinating figure, and his biography The Man Who Loved Only Numbers is a great read.  He was famous both for brilliance and for broad collaboration.  Those two things in combination inspired mathematicians to invent the Erdős number as a metric of their collaborative closeness to Erdős.  Here’s how it works: Erdős’s own Erdős number is E = 0; those who have coauthored research papers with Erdős have E = 1; those who have coauthored with an E = 1 scientist have, as a result, E=2, and so on.

Stephen’s Erdős number is a very impressive 3. And, since I’ve coauthored a paper with Stephen, that means mine is 4, which I think it pretty neat. (That’s the same as Stephen Hawking’s!)

Right after reading Stephen’s post (or, more accurately, Jeremy’s link to Stephen’s post), I visited the University of Florida to give a seminar, hosted by Bob Holt. When I got my schedule ahead of time from Bob, it included a couple of people who are not at the University of Florida, but who are/were there visiting Bob. That was sort of surprising, but not very, as Bob is someone who has collaborated with lots of people – as just one indicator, I remember as a grad student hearing that Bob Holt and Andy Dobson were the two people who were involved in by far the most NCEAS working groups. Given the breadth of topics Bob has worked on, as well as the strength of his contributions, it’s not surprising that lots of people visit him to work on things.

This combination of events got me wondering: is there anyone in ecology who compares to Erdős in terms of being prolific and exceptionally well-connected (in terms of collaborations)?

I think Bob Holt is a great candidate. According to Google Scholar, he has 446 papers. By my count, he has had 574 different coauthors! (You can check the list I assembled here.) Should we have the Holt number in ecology*, or can you come up with someone who is even more connected to other ecologists?

 

*Clearly this could be expanded to a Holt-Erdős number, a Holt-Erdős-Bacon number, etc. Thanks to Hao Ye, I know that Bob Holt has an Erdős number of 4, so my Holt-Erdős number is 6. (Updated to fix error — I originally said 8, but my Holt number is 2, so I don’t know why I wrote 8!)

What’s the thing you’ve read recently that you enjoyed the most?

I just spent a few days of my semester break devouring Philip Pullman’s newest book, The Book of Dust: La Belle Sauvage (Amazon link, but supporting your local bookseller is great, if possible!) It’s the first book in a new trilogy that is a prequel to Pullman’s His Dark Materials trilogy. I listened to that trilogy while counting samples in grad school. Those books are among my all-time favorites*, so I was both excited and a little nervous about starting the new book. Could it possibly live up to my expectations?

It did. I loved it. I can’t wait for the next book in the new trilogy, and think I’ll reread the original trilogy and La Belle Sauvage as I wait for the new book. If you were a fan of His Dark Materials and haven’t gotten the new book yet, you should!

This made me wonder what books others have read recently that they loved, so I thought a quick post on the topic would be fun. I was originally thinking of non-work-related books, but, really whatever you read recently that you enjoyed the most (or found the most powerful, or whatever criterion you want to go with) works. And, if your favorite thing wasn’t a book, that’s fine, too.

I’m looking forward to what people say, even though I’m not exactly short on reading materials! My recent response to this tweet:

pic.twitter.com/kbA4lEBByY

— Mental Floss (@mental_floss) December 11, 2017

was:

I feel judged. https://t.co/LdaOZFvMeq

— Meghan Duffy (@duffy_ma) December 12, 2017

 

*The audiobooks are really well done! They are definitely my favorite audiobooks of all time.