Microcosms are rigged the results can’t help but confirm the theory. (And if you insist that your system is so complex that it can’t be described with equations, how do you know humans can comprehend it?) The challenge in microcosms, just as in any other system, is to figure out what equations the organisms are solving, at least to a sufficiently good approximation to answer the scientific question of interest. Anything can be described with equations, and so all organisms can be said to ‘solve equations’. Microcosms just use organisms to solve equations. But those kinds of detailed considerations are of a very different character than the blanket objections to microcosms which I discuss below. It’s hard to study the bacteria in a typical protist microcosm, which means I (like many ecologists) mostly treat the bacterial portion of the system as a ‘black box’ whose effects I hope I can summarize implicitly (e.g., by treating bacterivorous ciliates as growing logistically, rather than actually modeling their interactions with the bacteria). Protists and other small organisms aren’t convenient for collecting individual-level data, and so if you want to scale up from individual-level data to population dynamics you need a different system (I understand that this is why my fellow Oikos editor Andre de Roos switched from working on zooplankton to working on fish). For instance, protists lack stage-structure, so you can’t study stage-structured population dynamics with protists. There are plenty of questions you just can’t ask using microcosms. I should also note that microcosms absolutely have their limitations. Indeed, one overarching problem I have with these objections is that they’re blanket objections, and those who raise them often don’t seem to pay attention to the various quite distinct reasons why microcosm experiments are conducted. Microcosm experiments are conducted for different reasons by different people, who would probably have different answers to these objections. I also emphasize that, in answering these objections in the way I do, I’m speaking only for myself. I emphasize that I really have encountered all these objections (sometimes in unsigned reviews, so I can’t link to the sources) I’m not setting up straw men here. So below are some objections to microcosms (in bold), and my own answers. Plus, although the debate over microcosms seems to have died down a while ago, who knows when it will flare up again, so I figured I might as well take a preemptive shot in the next Microcosm Wars. But over the years I’ve run into various objections that either haven’t been addressed publicly, or haven’t been addressed in quite the way I’d address them. The advantages and drawbacks of protist microcosms, and of artificially-assembled communities more generally, have been debated in various places (see, e.g., papers in the April 1996 issue of Ecology and chapters in Bernardo and Resetarits (eds.) 1998). For instance, how does productivity, in isolation from other factors, affect the occurrence of alternate stable states and assembly cycles ( Fox 2008 Oikos)? I tend to use the system to ask questions about the consequences of particular processes or combinations of processes that would be difficult or impossible to ask in other systems. You can control and manipulate features of the system that are difficult or impossible to control and manipulate in most other systems. Microcosms are easy and cheap to replicate highly, giving you a lot of statistical power. Protists have very short generation times (4-48 h), so you can collect hundreds of generations of data in a few months. Several features of this system combine to make it an excellent model system for asking fundamental questions about population and community dynamics. Then I (actually my research assistants) follow the resulting population dynamics. A typical experimental unit is a glass jar with 80 ml of nutrient medium, which I inoculate with bacteria, protists, and perhaps other microbes.
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