Questions from Jeremy Fox about the LTEE, part 2

EDIT (23 June 2015): PLOS Biology has published a condensed version of this blog-conversation.

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This is part 2, I guess, of my response to Jeremy Fox from his questions about the LTEE over at the Dynamic Ecology blog.

It’s not an answer to his 2nd question, but it’s a partial answer to the first part of his 3rd question? (Have I got you confused already? Me, too.) Well anyhow, Jeremy asked:

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  • Did the LTEE have any hypotheses initially, and if so, how were you going to test them? This question probably just reflects laziness on my part, not having gone back and read the first publications arising from the LTEE, sorry. 🙂 I ask because, with just one treatment and no quantitative a priori model of how the experiment should turn out, it’s not clear to me how it initially could’ve been framed as a hypothesis test. For instance, I don’t see how to frame it as a test of any hypothesis about the interplay of chance and determinism in evolution. It’s hard to imagine getting any result besides some mixture of the two, and there’s no “control” or a priori theoretical expectation to compare that mixture to. Am I being dense here? (in addition to being lazy…)

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Short answer: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. (What, did you think I was swimming completely naked?)

Medium answer that will be fleshed out in later responses: Before we get to specific hypotheses—those formal, testable suppositions and predictions—I like to begin with general questions about how and why things are they way they are. So, what were the questions the LTEE originally set out to answer? (I emphasize “originally” because new or substantially refined questions have arisen over the course of the project, as we’ve answered some questions, made new observations, framed new questions, etc.)

What follows below are three overarching sets of questions that I hoped, long ago, the LTEE could answer, at least in the context of the simple flask-world that it encompassed. I present all three sets of questions  in some of my talks about the LTEE. However, in my talks to broad public audiences – like my Darwin Day talk at the University of Calgary next week – I focus especially on the third set of questions – about the repeatability of evolution – because I think it is the most interesting to people who are not necessarily evolutionary biologists or even scientists, but who are curious about the world in which we live.

Motivating questions for the LTEE

A few more thoughts: The first set of questions, about the dynamics of adaptation, include ones where I had clear  expectations that were testable in a fairly standard hypothesis-driven framework. For example, I was pretty sure we would see the rate of fitness improvement decelerate over time (and it has), and I was also pretty sure we’d see a quasi-step-like dynamic to the early fitness increases (and we did). Nonetheless, these analyses have yielded surprises as well, including evidence (and my new strong conviction) that fitness can increase indefinitely, and essentially without limit, even in a constant environment. In regards to the second set of questions, about the dynamics of genome evolution and their coupling to phenotypic changes–I’m sure these were part of my original thinking, but I will readily admit that I had almost no idea how I would answer them. Hope sprung eternal, I guess; fortunately, wonderful collaborators—like the molecular microbiologist Dom Schneider—and brand new technologies—wow, sequencing entire genomes—saved the LTEE.

 

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4 responses to “Questions from Jeremy Fox about the LTEE, part 2

  1. Pingback: Questions for Rich Lenski about his amazing Long Term Evolution Experiment (UPDATEDx4) | Dynamic Ecology

  2. Thanks for this Rich. Particularly because this was the worst question on my list and it would’ve been fair enough to tell me to get off my lazy butt and go read the first papers to come out of the LTEE. 🙂

    I like your distinction between broad motivating questions and more specific, testable hypotheses. I probably should’ve been clearer in my question that I knew you had the former, but wasn’t sure if you had the latter. So no, I didn’t think you were swimming completely naked! I guess I was wondering more if you were swimming in a Speedo, or in one of those Victorian-era fully-body swimming costumes. 🙂

    Your answer here hints at the answer to another of my questions: why not have two or more treatments in the LTEE? Since your hypotheses were hypotheses about how evolution by natural selection should *always* work–fitness increases should always decelerate, the early phase of all adaptive walks should be step-like–you didn’t need multiple treatments.

    Interesting to hear that for some motivating questions, you also had specific hypotheses that you knew how to test initially, while for other motivating questions you didn’t. I wonder, if you hadn’t had specific hypotheses for *any* of your motivating questions, would the LTEE still have seemed like a good idea? I can imagine that it would have. I think there’s an important role for experiments that are out ahead of theory and hypothesis development. That give theory a “target to shoot at”, something to explain. In my own field, that’s how I think of early biodiversity-ecosystem function experiments like Naeem et al. 1994 and McGrady-Steed et al. 1997. (Aside: yes, those early BDEF experiments were pitched as having “hypotheses”. But honestly, those “hypotheses” were such loosely-defined verbal models, or such phenomenological descriptive statements like “function will increase with diversity”, that they didn’t really add much in my view.) Although while those early BDEF experiments may have lacked hypotheses, the investigators did know how to collect data addressing the broad motivating question. Which as you say is a contrast to having a broad motivating question but no idea how to actually answer it.

    Which leads to your comment at the end, where you’ve partially answered another of my questions, regarding the role of external factors like technological advances in the LTEE.

    • Great points and follow-up questions, Jeremy! On the whole, I feel we’re thinking along similar lines here.

      I also think you’ve started to anticipate my answer to your question “Is the LTEE actually an experiment?” I’m looking forward to writing some of my thoughts and ideas on that, and I hope the issue comes up in the Q&A in Calgary next week.

  3. Pingback: The LTEE as meta-experiment: Questions from Jeremy Fox about the LTEE, part 3 | Telliamed Revisited