Another take on volvocine individuality

Dinah Davison & Erik Hanschen

Dinah Davison and Erik Hanschen.

A couple of weeks ago, I indulged in a little shameless self-promotion, writing about my new chapter on volvocine individuality in Biological Individuality, Integrating Scientific, Philosophical, and Historical Perspectives. Now two graduate students in the Michod lab at the University of Arizona, Erik Hanschen and Dinah Davison, have published their own take on volvocine individuality in Philosophy, Theory, and Practice in Biology (“Evolution of individuality: a case study in the volvocine green algae“). The article is open-access, and Hanschen and Davison are listed as equal contributors.

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Initiation of cell division in Chlamydomonas

Deborah Shelton and colleagues have published a new article arguing that the reigning model of cell division initiation in Chlamydomonas reinhardtii needs to be revised [full disclosure: Dr. Shelton and I were labmates in Rick Michod’s lab at the University of Arizona]. The evolution of multicellularity almost certainly involved changes in cell cycle regulation; for example, there is good evidence that changes to the cell cycle regulator retinoblastoma were involved in the initial transition to multicellular life in the volvocine algae. So understanding cell cycle regulation is vital for understanding the evolution of multicellularity.

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Relentless use of passive voice

Image from ragan.com.

Image from ragan.com.

I have had the phrase “relentless use of passive voice” in my head for years as a criticism of overly dry scientific writing. I thought I learned it from the excellent paper “How to write consistently boring scientific literature” by Kaj Sand-Jensen. Like Gould’s tennis stadium in “Muller Bros. Moving & Storage,” though, when I went back to look for it, it wasn’t where I thought it was. If anyone can tell me where the phrase actually originated, I would be grateful.

Wherever I first heard it, the phase has affected my scientific writing (or should I say ‘my scientific writing has been affected by the phrase’). I have the impression, supported by no hard data whatsoever, that the relentless use of passive voice has declined over the past few decades in scientific writing. It is now common to read about what “we” (the coauthors) did in the Methods and what “we” found in the Results. It’s not even that rare to see descriptions of what “I” did or found in a solo-authored paper (the horror!).

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Heads I win; tails you lose: Evolution News & Views on Gonium, part 2: Model systems and gene duplication

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Erik Hanschen, the lead author on the Gonium genome paper, is also an old friend of mine from when we were both in Michael Doebeli’s lab at the University of British Columbia. He kindly agreed to write a guest post responding to Evolution News and Views‘ misunderstandings of his paper. Everything below the fold was written by Erik:

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Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 2

One of the cool things about studying the so-called major transitions is that they are as interesting to philosophers of science as to biologists. So you really can’t help being exposed to the philosophy of science literature, and many (maybe most) biologists in the field cross the lines at least occasionally. I’ve been to both, and I’m here to tell you that philosophy conferences are more fun than biology conferences.

Last time, I briefly summarized the various forms of the major transitions framework and addressed one of O’Malley and Powell‘s criticisms, that the framework is progressivist. Now I’d like to look at their other two problems: lack of unity and missing events. By and large, I agree with these points, although there are some caveats I’d like to point out. Next time, I’ll consider their proposed solution, which I’m afraid I don’t find helpful.

Disunity is actually O’Malley and Powell’s first criticism, but it will be a bit more complicated than progressivism to address, and I was short on time on part 1. Essentially, they are arguing that the major transitions are not a natural kind, philosophese for groupings that belong together because of some fundamental commonality, as opposed to more arbitrary groupings whose members are only superficially similar. So what are the transitions? Here’s the list from the book:

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

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Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 1

The so-called ‘Major Transitions’ framework is an attempt to explain the hierarchical structure of life on Earth: genes within chromosomes, chromosomes within cells, cells within cells (eukaryotic cells), individuals within sexual partnerships, cells within multicellular organisms, and organisms within societies. The best-known attempt to unify the origins of these relationships is a book by John Maynard Smith* and Eörs Szathmáry, The Major Transitions in Evolution.

MajorTransitionsCover

First published in 1995, the book focused on the origins of these hierarchical levels, connecting them with the unifying theme that

…entities that were capable of independent replication before the transition can replicate only as part of a larger whole after it.

For example, after a transition from unicellular to multicellular organisms (there were several), cellular reproduction either contributes to the growth of the organism or to production of new multicellular organisms.

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Volvox 2015

Today is day one of the Third International Volvox Conference in Cambridge, U.K. I arrived yesterday via Chicago, Ottowa, and a bus from Heathrow. Apparently there is a direct flight from Chicago to Heathrow; why I didn’t take that is a mystery. The accommodations at Wychfield are quite comfortable, although many of us have had the usual troubles figuring out English plumbing.

Last night was a pub dinner with half or so of the attendees; I had some very good fish & chips (good, but not as good as Go Fish).

Pub dinner with Stephanie Höhn, one of the organizers, in the foreground.

Pub dinner with Stephanie Höhn, one of the organizers, in the foreground.

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An Ode to Unicellularity

Biosphere 2

Biosphere 2, the site of the First International Volvox Meeting in 2011.

This year’s Volvox meeting, as with the previous two, will feature an image/video/arts competition. Erik Hanschen, a graduate student in the Michod lab, has kindly granted me permission to post the winning entry in the poetry contest at the first Volvox meeting: a sonnet in honor of Chlamydomonas.

An Ode to Unicellularity – Erik Hanschen

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