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