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Standing up? Lying down? Apparently they're using some kind of nonspherical cow approximation.
Yes. They also use behavior differences between summer and winter to motivate the study, so an atmosphere is implicit.

Despite all its successes, we've known for years that someday we'd have to move beyond the Standard Model.

I hope we can avoid incorporating friction for a while.
Only if your farm is flat. Otherwise all your cows wind up at the bottom of the hill.
Actually this gives me an idea for a spherical-cow Farmville clone in which all cows are simulated with simple yet physically justifiable parameters...
Did you read the paper? In the text for Figure 4.3: "The spherical cow image was created for this paper by Yulian Ng and used with her permission." (Used to diagram cow neworks.)
I admit I had only read the abstract when I posted my comment. I had a bit of a look at the paper later.
The weird thing is that this appears to be quite serious (although it contains jokes, and quite right too), and motivated by a genuine need to understand the dynamics of coupled cow ensembles.

And there's an interesting and nonobvious result: you can increase the coupling between your cows and get their behaviour to synchronize less. (Although that's only true for a particular configuration of which cows interact with which others, and it's probably not realistic.) Their main example of this isn't quite as surprising as it sounds, to me at least: there's some lag in the influence of one cow on another, and the situation in which increased coupling reduces synchronization is one where there are long chains of mutually influencing cows.

I loved this sentence, from the second page: "Cattle are ruminants, so it is biologically plausible to view them as oscillators."

The paper actually has pictures in it showing spherical cows. The acknowledgements say: "We thank [...] Puck Rombach for assistance with cow puns, and Yulian Ng for drawing a spherical cow for us." Obviously it's a fair assumption that everyone reading their paper is familiar with the joke.

Consider a spherical cow...
I was trying to figure out if this model is Turing-complete but couldn't rapidly prove it either way. Still, with chaotic dynamics in the model I think the odds are pretty decent that something could be found, although it would of course require absurd levels of precision by the cows even if the model was simple, and could require truly absurd levels if it does end up requiring the chaos.