| Figure | Script | Output File |
|---|---|---|
| Figure 1 | closed-form-parameters.R | symbiont-subsets.pdf |
| Figure 2 | web-of-life-parameters.R | constraints.pdf |
| Figure 3 | estimate-viral-diversity.R | virus-diversity-wide.pdf |
| Figure 4 | virion-false-specialists.R | false-specialists_analytic_data.pdf |
| Figure 5 | scale-collapse-and-coextinction.R | coextinction.pdf |
| Figure S1 | decomposing-parameters.R | parameters.pdf |
| Figure S2 | web-of-life-parameters.R | power-law-exponents.pdf |
| Figure S3 | toju-again-no-problem.R | curve-fitting.pdf |
| Figure S4 | web-of-life-parameters.R | constraints2.pdf |
| Figure S5 | helminths-revisited.R | virion-change-through-time.pdf |
| Figure S6 | virion-time-change.R | poulin.pdf |
Note: virion-chao.R and false-specialist-functions.R conduct additional analyses shown in the text.
Q: Why is this repository called carlsonlab/straightlinewasalie?
A: The name comes from The Beths' 2025 album Straight Line Was a Lie, which is a very good album that I listened to a lot this year.
Q: So it has nothing to do with the research?
A: Well, it's also a little bit of a double entendre. Our work on this project started from critiquing a previous study, which assumed a linear relationship between hosts and viruses. It's a pretty terrible assumption, and at the time, we felt like it was intentionally misleading. So the straight line was a lie. But then it sort of comes full circle, because our work explains the sublinear scaling... with a linear relationship.
But then there's another layer, which is that we've been working on this project for a decade, and every time we think we have it figured out and we're making linear progress, it turns out we really don't.
Q: That's cool. It's kind of a triple entendre then.
A: Yeah, I guess so!
Q: Are there other little inside jokes like that in the paper?
A: Actually, yes - the album art was begging to be turned into a color palette, so we used those colors in most of the figures.
Q: You must really like this album.
A: Yeah, it's pretty good. I mean, there's a song called "Mosquitoes," which is just great. There's also a really pretty verse on "Metal" that's basically about symbiosis:
And I know I'm a collaboration
Bacteria, carbon, and light
A florid orchestration
A recipe of fortune and time
Q: Do you like any of their other stuff?
A: I got into The Beths thanks to the title track of Future Me Hates Me, which is a louder album like Straight Line Was a Lie, and also very good. I absolutely love their cover of "Brand New Colony" that they did with Pickle Darling for the 20th anniversary of The District Sleeps Tonight. And I really like their version of "Have Yourself a Merry Little Christmas," which is a song that I've always maintained should be a little sad, like the Coldplay version.
Q: The "Yellow" B-side?
A: Well, it's not really a B-side to "Yellow," they just bundled them on the Mince Spies EP.
Q: Oh, right. Sorry to interrupt.
There's also some really fantastic songs on Expert in a Dying Field. The title track uses the analogy of being an expert in a dying field for what it feels like when a relationship ends but it's still taking up all of your brainspace, which I think is really beautiful. "I Want To Listen" is also a really great song, because you can immediately tell that Elizabeth Stokes is a kiwi, in a way that is somehow not true on any other song they've written.
Q: Who's Elizabeth Stokes?
A: The lead singer of The Beths.
Q: Ah, got it. She's from New Zealand?
A: Yeah.
Q: Can you tell on any of their songs?
A: Yeah, "I Want to Listen" from Expert in a Dying Field.
Q: Oh, right.
A: They were also in a boat at one point. It was pretty obvious they were from New Zealand then, too.
Q: Because they were in a boat?
A: No, because they have New Zealand accents.
Q: Got it.
A: Yep.
Q: Do you feel like a bit of a pompous weenie for italicizing entendre?
A: This interview is over.