Who is doing interesting system-based research? And what is a model system anyway?

I will be organizing the American Society of Naturalists’ Vice Presidential Symposium next year, and think it would be fun to have the symposium focus on insights gained from system-based research. (Related: my old post on the merits of system-based research.) My thinking is to combine people who are working on well-established model systems (e.g., three spine sticklebacks, Arabidopsis, E. coli) with those working on more recently established systems (nascent model systems?). I’d like to include work that spans the breadth of the society (so, ecology, evolutionary biology, and behavior). I also want the symposium to feature the work of early career scientists. That’s where you come in! Tell me who you think is doing really interesting and exciting system-based research. I’m especially interested in hearing about early career folks, and am super duper interested in learning about early career folks who’ve done work to establish new model systems.

To give a few of examples:

  • María Rebolleda-Gómez has had a couple of recent papers using a well-established model system, Saccharomyces cerevisiae, to address really interesting questions about the reversibility of evolution and on how ecology matters for the evolution of multicellularity.
  • Ambika Kamath, one of the recipients of this year’s ASN Jasper Loftus-Hills Award, studied anoles for her dissertation research, including work finding that some early work on this model system may have led subsequent researchers astray. And
  • Nina Wale, a postdoc in my lab, has been doing a lot of work to establish a bacterial parasite as a model system for work on the ecology and evolution of infectious diseases, including revealing really interesting color variation.

Of course, this all raises the question of what is system-based research and what is a model system? This is something I’m hoping to explore more in the future, but for now I will go with this definition by my colleague Luis Zaman, who said:

I usually think of [model systems] as an organism/population/community/ecosystem/model that has been studied from many different angle and/or for different purposes leading up to a body of knowledge that is greater than one person can (or should) know.

I like that definition!

Please put your suggestions of early career folks who are doing interesting work with model systems in the comments! I’m especially interested in people who might have some interesting results they’d be interested in presenting at the 2020 Evolution meetings. And if you’re thinking, “hmmm, I think *I* fit that description”, send me an email (duffymeg at umich dot edu). (You can also put your own name in the comments! I’m just guessing most people would feel more comfortable emailing instead.) And, if you have thoughts on what makes something a model system, including signs that something seems to be on its way to becoming a new model system, I’d love to hear those, too!

11 thoughts on “Who is doing interesting system-based research? And what is a model system anyway?

  1. This post made something click for me. When I think of “system based” research, I think of it as contrasting with “question based” research, with the latter but not the former using model systems. But for you, research in model systems *is* system based.

    Your quoted definition of “model system” nicely highlights this contrast when I try to apply it to my own work. I think of myself as using a model system–protist microcosms–to study population and community dynamics. By that I just mean “if I want to answer questions about population dynamics, I need organisms with very short generation times and simple life histories, that can be grown in the lab”. That is, I decided what questions I wanted to ask, then picked a system that makes those questions tractable. But by the definition of “model system” in the post, protist microcosms are not a model system at all! Because they’re not really a model system for anything besides population dynamics, and we don’t have a massive body of knowledge about every aspect of protist microcosm biology.

    In my old post arguing for more model system-based research in ecology, I ran together your definition of “model system” and mine (https://dynamicecology.wordpress.com/2012/10/18/ecologists-should-quit-making-things-hard-for-themselves-and-focus-more-on-model-systems/). Now I think I shouldn’t have.

    Not that the two definitions are mutually exclusive, of course. For instance, I think of Maria Rebolleda-Gomez’s work as being “model system” work in the same sense as my protist microcosm work is model system work. You want to study the evolution of multicellularity experimentally? Ok, you have to pick an artificial lab environment that will select a unicellular organism to evolve multicellularity. In my mind, that’s picking a question and then picking a system that makes the question tractable, just like I do in protist microcosms. But on the other hand, her work would be much less tractable, and much less informative, if we didn’t also know a ton about yeast biology.

    Another difference between “model system” work of the sort I do, and “model system” work on threespine stickleback or yeast or whatever, is the ability to link up answers to different questions. I’m thinking for instance of eco-evolutionary work linking up selection for reduced lateral plating in freshwater populations of threespine stickleback (as compared to marine populations) with work on the genetics and development of lateral plates. That sort of linkage can’t happen if you work in a model system like mine; protist microcosms are *only* a model system for questions about population dynamics.

    Which in turn connects up to social aspects of science. Part of what makes, say, threespine stickleback or yeast a model system in the sense of the post is that there’s a huge critical mass of people working on those systems. That’s how we acquired all that cumulative background knowledge about every aspect of the system’s biology. And all those people work in those systems in part because they’re systems in which one can ask lots of different questions and link up the answers. There’s a positive feedback loop here. Whereas very few people work in protist microcosms, and even fewer make an entire career of it. Presumably in part because there aren’t *that* many questions you can ask in protist microcosms. And since few people work in the system, it never gets turned into a model system for other questions, which would then attract more people to work in the system.

    So I guess that’s my two cents suggestion for your symposium: I think it would be interesting to include people who define the terms “model system” and “system based research” in different ways.

    This is going to be a very interesting symposium, lots of directions you could go with it.

    • But aren’t a lot of the protists used in ecologists’ microcosm experiments (Tetrahymena, Bdelloid rotifers, Chlamydomonas) already widely-acknowledged model organisms for research on topics like photosynthesis, recombination, motility, etc?

      • Yeah, some of the protists I’ve used also have been used to study other questions, here and there. Chlamydomonas gets used in experimental evolution a decent amount, for instance. And yeah, Tetrahymena’s something of a model organism for various purposes. But I stand by my claim that none of those species is studied by a sufficiently large number of people asking a sufficient number of sufficiently interconnected questions to count as a “model organism” like Arabidopsis or C. elegans or E. coli or Daphnia or threespine stickleback or anoles or etc.

        Re: bdelloid rotifers, they are famous for being ancient asexuals, and so their genetics have been studied for that reason. But that hasn’t really made them a model organism, I don’t think, either in my sense or in Meghan’s. They’re a case study of the evolution of recombination, not a model organism. At least, that’s how I think of them–am I way off base? Am I embarrassingly ignorant of a massive community of bdelloid rotifer researchers?

      • Here’s another way to summarize my thinking: it’s a model organism in Meghan’s sense if you can imagine someone writing a book about how work on that organism is revolutionizing vast areas of biology. A la Carl Zimmer’s E. coli book: https://www.amazon.ca/Microcosm-Coli-Science-Life/dp/0307276864

        I can easily imagine a book like that about Arabidopsis or C. elegans or Drosophila or yeast. And I don’t know that you have to stretch *too* much to imagine a book like that about, say, threespine stickleback or Daphnia, either now or at some point in the near future. But Colpidium striatum? Paramecium spp.? Philodina spp.? Euplotes patella? (to name some of the protists and rotifers I often work with) No way.

  2. Interesting post Meghan.
    I use model systems (i.e., phytotelmata ecosystems) to test general ecological theory in community and ecosystem ecology. I think that Srivastava et al 2004 TREE doi:10.1016/j.tree.2004.04.010 give a nice perspective of the properties of a model system, in particular natural microcosms, such as tank bromeliads, pitcher plants (both phytotelmata), mosses patches. According to them “Model systems have three useful features: tractability, generality and realism, which enable future experiments to build on previous results. I know, this is a particular type of model system (not an organism per se), but something that they highlight, and with which I fully agree, is that natural microcosms offer a way to do not sacrifice realism and tractability.

    Phytotelmata communities are phylogenetically diverse and are comprised of aquatic invertebrates (mostly insect larvae) in several functional groups, including filter feeders (most Culicidae), shredders (Limoniidae, Trichoptera), scrapers (Scirtidae), collectors (Psychodidae, Chironomidae, Syrphidae, Ceratopogonidae), mesopredators (Corethrellidae, Tanypodinae, Hydrophylidae larvae, Ceratopogonidae), and top predators (Zygoptera in bromeliads, Sarcophagidae in pitcher plants). The communities also include small non-insect invertebrates, such as Oligochaeta, Ostracoda (both detritivores), Hirudinea, Turbellaria (predators), and aquatic Acari (multiple trophic groups). In practical terms, phytotelmata provide spatially discrete and highly-replicated ecosystems, facilitating surveys and manipulations of all components of the macro-invertebrate food web and its basal resources.

    The well-defined aquatic habitats created by phytotelmata and their broad geographic distribution also allows researchers to examine large-scale patterns of diversity, stoichiometry, and ecosystem function in a relatively invariant habitat. For example, tank bromeliads and pitcher plants have been successfully utilized to investigate organismal responses to environmental change (Gotelli & Ellison 2002, González et al. 2014), top down/bottom up processes (Gotelli & Ellison 2006, Peterman et al. 2015), community assembly (Gilbert et al. 2008), trophic cascades (Breviglieri et al. 2017, De Omena et al. 2017,), cross-ecosystem subsidies (Romero & Srivastava 2010), diversity and ecosystem functioning (Mouquet et al. 2008, Marino et al. 2015), energy pathways in aquatic food webs (Farjalla et al., 2016), predator-mediated nutrient dynamics (Ngai & Srivastava 2006, Atwood et al. 2013, Atwood et al. 2014), and community-level responses to changes in precipitation (Pires et al. 2016, Marino et al., 2017) and climate (Romero et al. 2016).

  3. Wow, this sounds really interesting! Makes me wish I could head back to grad school and work on ecological systems!

    Personally, though, I would deploy a much looser definition of “system” – something more along the lines of what’s traditionally used in physics and chemistry, from a quick Google for chemical systems: “the set of substances and energy that is being studied”, adding “organisms” to that for ecological work:

    “the set of organisms, substances and energy that is being studied”

    In geology study systems are chosen either to investigate specific phenomena or to use as an analog for a natural system to investigate the effects of natural variables. People tend to explore different systems for different reasons, and as the body of knowledge grows around a particular system, it may become useful for new or more sophisticated questions.

    I read María Rebolleda-Gómez’ abstract and wow, that’s cool stuff!

  4. I think Barro Colorado Island is a great example of a model tropical forest ecosystem. I think model ecosystems pretty much just need a research station and a few researchers tackling questions from different angles/organisms to become model systems. I work in Palau, which I think is just a few more studies away from emerging as a model system for understanding patterns of diversity (in freshwater, marine, and terrestrial habitats).

  5. So, do the Lotka-Volterra equations count as a “model system”? Their behavior has been studied by a large critical mass of people–everyone from applied mathematicians to ecologists to evolutionary biologists (the ‘replicator equation’ from evolutionary biology is a Lotka-Volterra equation). Those people have studied the Lotka-Volterra equations, and extensions thereof, using various techniques (analytical, numerical, graphical…). They’ve asked various questions (about competition and species coexistence, about predator-prey cycles, about species-abundance distributions, about community assembly…). And many questions that have been asked using the Lotka-Volterra equations aren’t tractable to ask using other models.

    Ok, I’ve convinced myself–the Lotka-Volterra equations are a model system, in the sense of the post. So now I really want this symposium of yours to include a theoretician who works with Lotka-Volterra models, Meghan!

  6. Some of the early career researchers building/establishing new models systems that I follow closely, even though some of these systems haven’t yet grown to the point of meeting Luis’ definition of a model system:
    -Kayla King and her group’s work building C. elegans into a model system for studying host-parasite-symbiont interactions over evolutionary time
    -Will Harcombe and his group’s work building simple crossfeeding and mutualistic bacterial communities
    -Alvaro Sanchez and his group’s work studying the ecological assembly of soil microbial communities (Disclaimer: I’m also at Yale so I hear about a lot of their ongoing work that’s not yet published)
    -Charles Ofria and others (including Luis Zaman) that have built AVIDA into a digital model system for all sorts of evolutionary questions
    -Kate Laskowski’s work using Sticklebacks and developing the Amazon molly as systems to study individual behavior and “personality”

  7. I’m hardly an ERC, but I thought I’d throw in my penny-worth…. Over the years I’ve tried to develop the plant family Apocynaceae as a model system for understanding the ecology of plant-pollinator interactions and how they evolve in large clades, biogeographic patterns and processes behind the interactions, etc. It’s met with moderate success and we’ve published quite a lot of papers and book chapters, but that’s been achieved through extensive international collaboration and a whole succession of relatively small grants (<£10,000). I know from conversations with colleagues in other parts of the world that this in turn has inspired them to work on the family and use it to answer more general questions in this field.

    That's great and I'm happy that it's been moderately successful. However I'm left with the feeling that we could have achieved a lot more if at least one of the large grants we'd applied for had been successful and had jump-started the work to a higher level. There's still time for this to happen but I think it's increasingly unlikely that I'll be the instigator, the UK funding system is just not receptive to the sorts of work I want to do with a family that has no native British representatives.

    If anyone's interested in learning more they can take a look at this post from last year: https://jeffollerton.wordpress.com/2018/08/21/the-evolution-of-pollination-systems-in-one-of-the-largest-plant-families-a-new-study-just-published-download-it-for-free/

    With best wishes from sunny Tenerife where I've been collecting data on some of the endemic Apocynaceae, a largely self-funded bit of field work 🙂

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