African Volvox in Montana

Ninepipe Reservoir

Ninepipe Reservoir near Charlo, MT. Photo by Aeravi.

Last summer, I hosted Drs. Hisayoshi Nozaki, Noriko Ueki, Osami Misumi, and two graduate students from the University of Tokyo, Kayoko Yamamoto and Shota Yamashita, to collect volvocine algae from Montana lakes. To our surprise, we found a species of Volvox (V. capensis) that had previously only ever been found in South Africa! Dr. Nozaki’s team identified the algae collected in Ninepipe Reservoir based on their morphology and DNA sequencing. South Africa and Montana: this is about as disjunct as a distribution can be. Is Volvox capensis a master of long-distance dispersal? Is its distribution actually cosmopolitan, and if so, why hasn’t it ever been found anywhere else?

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Fierce Roller is under attack!

In the last 24 hours, 20 new users registered on the Fierce Roller blog (prior to yesterday, there were 15). Good news, right, expanding readership and all that? In the same 24 hours, there were 35 malicious login attempts, where the previous four weeks had seen 2. All  of the new registrants are from a or .website address, and none of them bothered with a real name. I’m not sure why someone would bother hacking a blog that’s lucky to hit 200 views in a week, but that’s what seems to be happening.

Some time today, I will purge all of these new registrants. If you are a legitimate reader and you get caught up in this, the solution is simple: just email me and tell me you’re a real person.

Chlamy song

Posts may be thin this week. I am preparing a talk for AbSciCon and a manuscript that’s due Monday. Saturday morning, I will board the Empire Builder in Whitefish for a 30-hour ride to Chicago (no doubt some of the manuscript will be written on the train).

Meanwhile, here’s a song about Chlamydomonas (skip to 1:05 if you don’t want to hear the intro).

Pierrick Bourrat responds

[I invited Pierrick Bourrat to respond to my two posts about his new paper and to comments to those posts. He kindly agreed, and he provided the following guest post, which I have edited only for formatting.]

First of all, I would like to thank Matthew Herron for his interest in my work and his invitation to respond to his posts. Also, I would like to thank Rick Michod and Deborah Shelton for their comments.

I will respond to several issues pointed out both in the posts and the comments.

About the usefulness of the export of fitness view of ETI: I agree that it is a useful way of thinking about it, as long as it is used as a heuristic. This means that I am not inclined to think that building models with the assumption that the fitness of a cell would have been 0 had it been in an environment with not social partners will be able to explain in some deep sense ETIs (and even more so the origin of fitness at some level). In his comment to Matthew’s first post, Rick Michod claims that I somehow confuse realized fitness from a more counterfactual notion of fitness.  Well, to be honest, I do not see how one could simulate (I do not mean ‘explain’) the evolution of a process if the variables in the model do not correspond to realized properties of the system. If I want to model a particular phenomenon, I ought to use variables and parameters that represent the target system and clearly, at least for me, this counterfactual notion of fitness does not represent any properties the cells have because they always have social partners. It is common to use expected rather than realized fitness in models, but this assumption is justified when we can assume that population are large and the environment is overall not fluctuating too much. With the counterfactual notion of fitness, aside from being useful for explaining the ETIs, I fail to see how it could be successfully integrated in models (by successfully, I mean how it could represent meaningfully the target system).

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Friday Golden Fleece: America [already] COMPETES

Rep. Lamar Smith

That’s right, he’s the Chairman of the House Committee on Science, Space, and Technology

Imagine (or remember): you’re a grad student; you’ve struggled through your first two years juggling classes, teaching and research; you managed to get your committee together so that you could contend with three weeks of written then three hours of oral comprehensive exams. You synthesized your dissertation proposal and your written comps into something coherent, passed a dozen drafts back and forth with your advisor, and finally managed to navigate the FastLane website to get it submitted to the NSF before the deadline. In all likelihood, it was rejected, so you tried again the following year. One day you’re working at your computer when the lab phone rings, and you’re stunned to find that it’s your program officer telling you that your Doctoral Dissertation Improvement Grant has been funded. $20,000 over two years to support your field work in Bolivia! Some time later, you learn that the Chairman of the U.S. House of Representatives Committee on Science, Space, and Technology is telling the world that your research in particular is a waste of taxpayer money.

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Expression and form: Arash Kianianmomeni on gene regulation

Figure 1 from Kianianmomeni 2015.

Figure 1 from Kianianmomeni 2015. Gene regulatory mechanisms behind the evolution of multicellularity. Model illustrating the role of gene regulatory mechanisms in the evolution of multicellular Volvox from a Chlamydomonas-like ancestor.

Arash Kianianmomeni’s latest paper in Communicative & Integrative Biology addresses the possible roles of gene regulation and alternative splicing in the evolution of multicellularity and cellular differentiation (Kianianmomeni, A. 2015. Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae. Commun. Integr. Biol., 37–41. doi 10.1080/19420889.2015.1017175). The article is an ‘Addendum’ to a 2014 study by Kianianmomeni and colleagues in BMC Genomics. Communicative & Integrative Biology often invites authors to write these addenda after they have published a (usually high impact) paper elsewhere, providing authors the opportunity to publish material that was not included in the original paper due to space limitations or because it was opinionated or speculative. I may address the BMC Genomics article in a future post, but right now there is more new volvocine research than I have time to write about (it should be an exciting Volvox meeting this summer!).

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Pierrick Bourrat on levels, time, and fitness, part 2: collective fitness

Last week, I posted some thoughts on Pierrick Bourrat’s new paper in Philosophy and Theory in Biology, focusing on his criticism of Rick Michod’s ‘export of fitness’ framework. This week, I’ll take a look at the second of Bourrat’s criticisms, regarding the transition from MLS1 to MLS2, as first defined by Damuth & Heisler, during a transition in individuality.
MLS1 and MLS2 refer to two different versions of MultiLevel Selection. As Bourrat describes it (and this is pretty much in line with other authors), fitness in MLS1 is defined in terms of the number of particles (or lower-level units, or cells) produced, while in MLS2 the fitnesses of the particles and collectives (or cells and multicellular organisms) are measured in different units. Cell-level fitness (for example) is defined in terms of the number of daughter cells, organism-level fitness is based on the number of daughter organisms. (As with last week’s post, I’ll generally stick to cells and organisms, though the principles apply equally to any two adjacent levels.

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Friday Golden Fleece: Wildflowers in a Ghost Town

Colorado wildflowers

Colorado wildflowers. Photo by Aeravi.

In response to the American Recovery and Reinvestment Act (a.k.a. the stimulus) Senators Tom Coburn and John McCain published a Stimulus Checkup in December, 2009. This pamphlet concludes that “…billions of dollars of stimulus funding have been wasted, mismanaged, or directed towards silly and shortsighted projects,” and, not surprisingly, many of the projects so identified are federally funded scientific studies. Number 35 in this list is an NSF grant to Dr. David Inouye and colleagues:

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Volvox, the…game?

The Steam Greenlight Community has announced the development of Volvox (warning: autoplay video), a puzzle game with the goal of building “the first pluricellular beings.” Written by three students and former students of Italy’s Politecnico di Milano, the game features triangular cells called Trimoebas that roll around under the player’s control and gain abilities as the game progresses. The team, which forms Neotenia, Ltd., won the Italian national competition and is a semifinalist for the 2015 Microsoft Imagine Cup. The first fifteen levels are available as a free Unity WebGL Demo (takes a while to load).
The game reminds me a bit of Lemmings or Lode Runner in its simplicity and focus on solving deceptively simple tasks. It looks good, with a sort of hand-drawn, colored pencil, pastel look. Each trimoeba has an eye that mostly follows the mouse pointer, although they get bored and start looking around if it doesn’t move for a few seconds. Powers (at least those that exist in the demo) are indicated by the affected side of the triangle being colored; for example, blue sides can’t be stuck in glue. The documentation is a little thin right now, and it took me a while to figure out what was expected on the second level.

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Pierrick Bourrat on levels, time, and fitness, part 1: zero fitness?

Pierrick Bourrat’s new paper in Philosophy and Theory in Biology criticizes aspects of the influential ‘export of fitness’ framework developed by Rick Michod and colleagues and extended by Samir Okasha (Bourrat, P. 2015. Levels, time and fitness in evolutionary transitions in individuality. Philos. Theory Biol., 7: e601. doi: 10.3998/ptb.6959004.0007.001). According to this view, an evolutionary transition in individuality, for example from unicellular to multicellular life, involves a transfer of fitness from the lower level units (e.g. cells) to the higher level unit (e.g. nascent multicellular organism). Fitness is defined as the product of viability and fecundity, and the emergence of a division of labor between reproductive (germ) and non-reproductive (somatic) units at the lower level exports fitness to the higher level. Full disclosure: Rick Michod was my Ph.D. co-advisor, and he has had a huge influence on my thinking about this topic.

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