Choanoflagellates with inversion

Salpingoeca rosetta

Figure 1A from Dayel et al. 2011. Spherical colony of Salpingoeca rosetta. Scale bar = 5 μm.

The closest (known) living relatives of animals are a group of unicellular or colonial filter-feeders known as choanoflagellates. Much of what we know about the evolution of multicellularity in animals comes from comparisons with choanoflagellates. For example, many of the gene families involved in multicellular development in animals, and previously thought to be unique to animals, have turned out to be present in choanoflagellates as well, suggesting that these gene families were present in animal ancestors before they evolved multicellularity. Some multicellular choanoflagellates have even been shown to have differentiated cell types (Laundon et al. 2019):

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Why I quit Mendeley

Mendeley log

I have used most of the major reference management platforms at one time or another: EndNote, RefMan, Zotero, and Mendeley. Most of my time in grad school, I used what my advisor used to make collaborating easier: EndNote at UCF and RefMan at Arizona. During my Ph.D. I played around with Zotero but found it clunky. Back in those days, Zotero only worked with Firefox, and it didn’t sync files, so I had to have a separate way of organizing my PDFs.

I was an early adopter of Mendeley, and I loved it from the start. It integrated citation management with PDF organization, synced across platforms, and had an interface that was about as intuitive as you could ask for. Importing PDF metadata didn’t always work, but that was fine with me. It was also free, for a limited (but pretty generous) amount of storage. It became such a vital part of my workflow that, when I had filled up the free storage, I was happy to pay for more. I’ve been paying Mendeley $54.99/year since 2011.

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A series of fortunate events

Salomé and Merchant 2019 Fig. 1

Figure 1 from Salomé and Merchant 2019. Taxonomic Basis of Chlamydomonas and Volvox. Ehrenberg’s drawings of Chlamydomonas and Volvox cells, published in 1838. Cells that belong to the same species are indicated by Roman numerals in the right panel. I, Gonium pectorale; II, Gonium punctatum; III, Gonium tranquillum; IV, Gonium hyalinum; V, Gonium glaucum; VI, Eudorina elegans; VII, Syncrypta volvox; VIII, Sphaerosira volvox; IX, Synura uvella; X, Chlamidomonas pulvisculus; XI, Uroglena volvox. The species was identified as Chlamidomonas pulvisculus but renamed Chlamydomonas reinhardtii in 1888.

In a new(-ish) article in The Plant Cell, Patrice Salomé and Sabeeha Merchant review the history and utility of the green alga Chlamydomonas reinhardtii as a model organism. The article discusses the advantages of Chlamy as a model organism, the scientific questions it has been used to explore, the history of Chlamy research, the characteristics of the species, the existing resources and databases, and genetic and genomic techniques. It’s a good introduction to Chlamy research in a more easily-digestible form than the massive, three-volume Chlamydomonas Sourcebook.

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Volvox rousseletii in Japan

A few years back, I invited Dr. Hisayoshi Nozaki to visit the University of Montana, and to my surprise, he came. In fact, five Japanese researchers came to Missoula for the better part of a week: Dr. Nozaki, Dr. Noriko Ueki, Dr. Osami Misumi, and two undergraduate researchers. We found a speciesVolvox capensis, which had previously only ever been found in South Africa, in Ninepipe Reservoir (about an hour north of Missoula).

Now Ryosuke Kimbara and colleagues have reported another apparent long-distance traveller. In a new paper in PLoS One, they report finding Volvox rousseletii, previously reported only in Africa, in Lake Sagami in Japan. Volvox rousseletii is a member of the group of species known as Volvox section Volvox (also sometimes referred to as Euvolvox), which includes the largest species (in terms of cell number) and evolved independently of the other species in the genus Volvox.

Kimbara Fig. 1

Figure 1 from Kimbara et al. 2019. Light microscopic features of asexual spheroids in culture of Volvox rousseletii strain v-sgm-17 from Lake Sagami, Japan. (A) Mature spheroid showing daughter spheroids (d). (B-D) Part of spheroids. (B) Top view of individual sheaths (asterisks) of somatic cells stained with methylene blue. (C) Top view of somatic cells with thick cytoplasmic bridges (b). (D) Side view of elongate-ellipsoidal, anterior somatic cell with stigma (s) and pyrenoid (p) in the chloroplast. (E) Developing embryo just after inversion, showing gonidia (g) of the next generation.

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Such is the history of it.

Mark Twain

Mark Twain by Unknown – This image is available from the United States Library of Congress‘s Prints and Photographs division under the digital ID cph.3a08820. Public Domain, Link

Tipped off by Dan McShea and Carl Simpson, I went and checked out Mark Twain’s brilliant dismembering of Alfred Russel Wallace’s version of the fine-tuning hypothesis, “Was The World Made For Man?“. Wallace is popular among intelligent design advocates because, after independently conceiving of a theory of evolution by natural selection, he became enamored of some ideas that resonate with them, such as that the universe has purpose and that material causes can’t explain human intelligence.

In his 1903 book, Man’s Place in the Universe, Wallace argued that the purpose of Earth, and indeed the universe, was the evolution and continued existence of humanity:

All nature tells us the same strange, mysterious story, of the exuberance of life, of endless variety, of unimaginable quantity. All this life upon our earth has led up to and culminated in that of man. It has been, I believe, a common and not unpopular idea that during the whole process of the rise and growth and extinction of past forms, the earth has been preparing for the ultimate–Man. Much of the wealth and luxuriance of living things, the infinite variety of form and structure, the exquisite grace and beauty in bird and insect, in foliage and flower, may have been mere by-products of the grand mechanism we call nature–the one and only method of developing humanity.

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David Kirk obituary

David Kirk

Dr. Kirk delivering the final talk at the 2007 Volvox Symposium at Washington University, an event that celebrated his retirement and his many contributions to the study of Volvox. The symposium was attended by representatives from every active Volvox lab at the time. During the symposium, Dr. Hisayoshi Nozaki announced the discovery of a new species of Volvox, Volvox kirkiorum, that he named in honor of the Kirks.

Rüdiger Schmitt and Stephen Miller have published an ‘in memoriam’ on David Kirk in the latest Phycological Society of America newsletter.

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Beautiful irony

Uncommon Descent astrologyFrom Denyse O’Leary:

I mean, if you leave out the crackpots, the idea that the stars, which are much more significant in size than Earth, rule our destiny makes sense. It’s beautiful and it was just what court intellectual needed, centuries ago. It doesn’t happen to be true.

The idea that natural selection acting on random mutation could fill the world with exquisitely complex life forms makes sense to fashionable intellectuals today and it doesn’t happen to be true.

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Upcoming talks, and some system maintenance

Chlamydomonas colonies from the predation experiment.

Chlamydomonas colonies from the predation experiment.

I’ll be giving a couple of talks on experimental evolution of multicellularity in the next couple of weeks:

  1. University of Georgia Department of Cellular Biology, Tuesday, September 11, 11:00 a.m. in Biological Sciences 404A
  2. Donald Danforth Plant Science Center, Friday, September 20, time and place TBD

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Honorary authorship is fraud.

Authorship on peer-reviewed papers is a big deal in academia. If you’re a grad student looking for a postdoc, the very first thing your prospective advisor is going to want to know is what you’ve published (this is arguably true at every level, though funded grants become important, too). Customs vary among fields, but in mine (ecology and evolutionary biology), the first author is typically the person who carried out the experiment and wrote at least a first draft of the paper, and the last author is typically the head of the lab group, who is presumed to have played a role in planning the research, advising the first author along the way, and writing and revising the resulting paper. In between (if there are more than two authors) are people who have made some other contributions, which can cover a wide range of activities.

Sometimes, though, people who haven’t made any significant contribution at all are listed as authors. This happens for a variety of reasons, but the one I want to talk about today is so-called ‘honorary’ or ‘gift’ authorship. This is something I have long had a strong opinion about: in my mind, honorary authorship is unethical. It is an abuse of the system. It is academic misconduct. [Read more…]