Nice Aeon article on biological individuality

Siphonophores by Ernst Haeckel

By Ernst Haeckel – Kunstformen der Natur (1904), plate 17: Siphonophorae (see here, here and here), Public Domain, Link

Derek Skillings from University of Bordeaux/CNRS has a new article at Aeon about biological individuality:

For millennia, naturalists and philosophers have struggled to define the most fundamental units of living systems and to delimit the precise boundaries of the organisms that inhabit our planet. This difficulty is partly a product of the search for a singular theory that can be used to carve up all of the living world at its joints.

Skillings reviews the deep historical roots of the question, touching on the views of Charles Darwin and his grandfather, both Huxleys (T. H. and Julian), Herbert Spencer, and other 19th and early 20th century thinkers, as well as some more recent authors, including Daniel Janzen and Peter Godfrey Smith.

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Life cycles in major transitions, and some clueless critique

Jordi van Gestel and Corina Tarnita have published a ‘Perspective’ in PNAS, “On the origin of biological construction, with a focus on multicellularity“:

…we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions.

van Gestel 2017 Fig. 2

Figure 2 from van Gestel and Tarnita, 2017. Relationship between life stages in hypothesized life cycles of solitary ancestors and group formation in derived group life cycles. (Upper) Simplified depiction of hypothesized ancestral solitary life cycles of the green alga Volvox carteri, the cellular slime mold Dictyostelium discoideum, and the wasp Polistes metricus. Life cycles here consist of a life stage expressed under good conditions (black) and a life stage expressed under adverse conditions (green). For the latter life stage, we show an environmental signal that might trigger it and some phenotypic consequences. (Lower) Simplified depiction of group life cycles of: V. carteri, D. discoideum, and P. metricus. Developmental program underlying life stages in solitary ancestor is co-opted for group formation (shown in green): differentiation of somatic cells (V. carteri), fruiting body formation (D. discoideum), and appearance of foundress phenotype (P. metricus).

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MicroRNAs in Chlamydomonas

One of the biggest changes in evolutionary theory in the late 20th century was the growing appreciation for the central role of changes in gene expression in macroevolution. Developmental genes, especially Hox genes, turned out to be remarkably conserved across lineages that diverged over half a billion years ago. The subsequent huge changes in morphology were more often due to changes in when and where those genes were expressed than to changes in the coding sequences of the genes themselves.

Even more recently, an entire new class of regulatory mechanisms was discovered and found to be important in developmental processes. MicroRNAs (miRNAs) are short (21-24 nucleotides) sequences of RNA that reduce gene expression by promoting the breakdown of messenger RNAs (mRNAs) and by repressing translation of mRNAs into proteins. We have only known that microRNAs even existed since the early 1990’s, and their importance in gene regulation and development wasn’t appreciated until the 2000’s.

Although they are structurally similar, plant and animal microRNAs repress gene expression through very different mechanisms. A new paper by Betty Y-W. Chung and colleagues in Nature Plants shows that the regulatory mechanisms of Chlamydomonas microRNAs have both striking similarities and important differences with animal miRNAs:

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Another step toward understanding sex determination in Volvox

Volvox and its relatives are a great model system for understanding the evolution of multicellularity. Their simplicity (relative to most other multicellular groups) and the variety of ‘intermediate’ species (‘intermediate’ in terms of size and complexity) make them especially suitable for comparative studies of their morphology, development, genetics, genomics, and so on. David Kirk’s book on the topic thoroughly reviews the work done up through the late ’90s, and advances since then have only increased the pace of discovery.

But in the last ten years or so, I would argue that the volvocine algae have emerged as a leading model system for an entirely different set of questions related to the evolution of the sexes. Males and females are defined by the gametes they produce, and the sexes came into existence when their gametes diverged into two different types. The existence of different male and female gametes (sperm and eggs, in most cases) is called anisogamy, and the ancestral condition of similar gametes is isogamy.

In 2006, Hisayoshi Nozaki and colleagues reported that volvocine males evolved from the minus (isogamous) mating type. To the best of my knowledge, this is the only group for which we know this. Since then, more clues have been forthcoming, and these were competently reviewed last year by Takashi Hamaji and colleagues. A new paper in PLoS ONE, by Kayoko Yamamoto and colleagues, adds another piece to the puzzle.

Figure S2 from Yamamoto et al. 2017. Light microscopic images of Volvox africanus (homothallic, monoecious with males type) and V. reticuliferus (heterothallic, dioecious type). Scale bars = 50 μm. sp: sperm packet, e: egg. A-C. V. africanus strain 2013-0703-VO4. A. Asexual spheroid. B. Monoecious spheroid. C. Male spheroid. D, E. V. reticuliferus. D. Male spheroid in male strain VO123-F1-7. E. Female spheroid in female strain VO123-F1-6.

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A confused mess, part 1

I follow Uncommon Descent to keep up with what the cdesign proponentsists are up to, even though I’ve been banned from commentingUncommon Descent pushes out about three times as many articles as Evolution News & Views, and it’s clear that less than a third as much thought goes into each one. Worse, the articles’ authorship is rarely identified, robbing me of my second favorite sport after fly fishing, pointing out creationists’ self-contradictions. For both of these reasons, I don’t comment on their posts nearly as often. But if you read this blog at all, you must know that I can’t pass on a video that 1) claims to provide evidence against evolution and 2) has Volvox in it.

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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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Non-model model organisms

Jim Umen, the lead organizer of the upcoming Volvox meeting, has written a section for a new paper in BMC Biology, “Non-model model organisms.” Like all of the BMC journals, BMC Biology is open access, so you can check out the original.

The article surveys organisms that, while not among the traditional model systems, have been developed as model systems for studying particular biological questions. The paper has an unusual format, with a discrete section devoted to each species, each written by one or two of the authors. Aside from Volvox, there are sections on diatoms, the ciliates Stentor and Oxytricha, the amoeba Naeglaria, fission yeast, the filamentous fungus Ashbya, the moss Physcomitrella, the cnidarian Nematostella, tardigrades, axolotls, killifish, R bodies (a bacterial toxin delivery system), and cerebral organoids (a kind of lab-grown micro-brain).

Dr. Umen presents Volvox and its relatives as a model system for understand the evolution of traits related to the evolution of multicellularity:

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In their own words, part 2

Evolution News & Views

I previously pointed out that Casey Luskin’s “false, straw-man [version] of ID” bears a striking resemblance to intelligent design advocate Michael Behe’s actual definition:

Let me get this straight:

life is so complex, it could not have evolved” is a “false, straw-man version” of

Cells are simply too complex to have evolved.

I promised that I would get to the second part of Luskin’s “straw-man version,”

…therefore it was designed by a supernatural intelligence,

and that’s what I mean to address in this post. Maybe Luskin wasn’t claiming that ID critics mischaracterize the logic that leads ID advocates to reject evolution, but rather that they mistakenly (or deceitfully) portray ID advocates as inferring supernatural causation. If so, he’s not alone. Advocates of intelligent design frequently deny that their theory has anything to do with the supernatural, and they imply that efforts to portray it as such are deceitful or, at best, misinformed.

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Cells, colonies, and clones: individuality in the volvocine algae

Biological Individuality

As I mentioned previously, I have a chapter in the newly published book Biological Individuality, Integrating Scientific, Philosophical, and Historical Perspectives. The chapter was actually written nearly five years ago, but things move more slowly in the philosophy world than that of biology. Finally, though, both the print and electronic versions are now available; here is the electronic version of my chapter. The book currently has no reviews on Amazon, so if you want to give it a read, yours could be the first. If you’re interested in current and historical views on individuality, there is a lot of good stuff in here, including contributions by Scott Lidgard & Lynn Nyhart, Beckett Sterner, Andrew Reynolds, Snait Gissis, Olivier Rieppel, Michael Osborne, Hannah Landecker, Ingo Brigandt, James Elwick, Scott Gilbert, and Alan Love & Ingo Brigandt.

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Volvox 2017: David Kirk will be there

David Kirk

Dr. David Kirk, Professor Emeritus at Washington University in St. Louis.

I just found out from Jim Umen, who’s organizing the Fourth International Volvox Conference, that David Kirk is planning to attend. This is great news; we’ve been wanting Dr. Kirk to come since the first meeting in 2011, but it hasn’t previously worked out.

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