The Discovery Institute is SO proud that they’ve managed to accumulate over 1000 signatures in nearly 20 years from people who doubt “Darwinism”, I thought I’d see what other petitions have over 1000 signatures:
Registration for the Fifth International Volvox Conference (July 26-29, 2019) will open next month, but meanwhile there are several opportunities for students and postdocs to apply for financial help. The newest of these (and the one with the nearest deadline) is a set of five travel awards from the Kato Memorial Bioscience Foundation:
Funding from the Kato Memorial Bioscience Foundation https://www.katokinen.or.jp/ for five travel awards for overseas (i.e. non-Japanese) students (PhD, Masters, undergraduates) and postdocs for Volvox 2019, 26-29 July, Tokyo is now available. Travel awards are 50,000 yen per person (~$500 US) and will be distributed at the Volvox 2019 registration desk by the local organizers, on 26 July 2019.
Applicants are required to submit a pdf file of the completed application form (download here) to Volvox2019 Office (E-mail: volvox2019 (at) gmail.com) by February 20, 2019. Five awardees will be chosen based on their abstract and need for financial support. The successful applicants will be informed by March 1, 2019. Travel receipts must be submitted to the local organizers at the conference to be eligible for reimbursement.
Developmental biologist John Tyler Bonner has passed away. Bonner was a giant, as far as I’m concerned, and his writings have had a big influence on me. I won’t attempt to eulogize him, since I’m sure there will be others closer to him who will do a better job than I could. As I’ve written previously,
Among many other contributions, Bonner was a pioneer in the development of the social amoeba (or cellular slime mold) Dictyostelium discoideum as a model system for multicellular development and cell-cell signaling. A member of the National Academy of Sciences and a fellow of the American Association for the Advancement of Science, he has published over twenty books and mountains of peer-reviewed papers.
Imagine you’re swimming in nice, warm water, happily making your own food without a care in the world (other than zooplankton). You just need to store up enough starch before nightfall to hold you through the night so you can quit swimming, absorb your flagella, and wait for the sun’s return. You see a green light below, and you swim toward it. You can’t help yourself; your phototactic machinery is hardwired to respond.
Next thing you know, you’re captured by a giant, tentacled polyp. You look for a way out, but there is none. You’re stuck there for the rest of your life, forced to work and have the food you produce stolen by your coral overlord. Resigned to your fate, you absorb your flagella and get down to photosynthesizing.
My postdoc makes fun of me for having a lousy memory. Not long ago she showed me a paper about microRNAs, and I said I hadn’t read it. She responded, “Yes you have; you blogged about it!” The other day we were discussing the use of antibiotics to prevent bacterial contamination, and I said I thought I might have done that at one time. She told me I had, it was ampicillin, and the concentration.
I’ve been blogging for nearly four years now, and I’ve published well over 400 posts. So I’ve learned that before I sink a bunch of time into writing a new blog post, it’s worth a quick search to make sure I’m not going to repeat myself. When a new paper from Takashi Nakada and colleagues popped up in my Google Scholar alerts, I didn’t immediately realize that I had already written about it. That post was mainly about a new analysis by Thomas Pröschold and colleagues, with the Nakada trees serving as a point of comparison. The new paper is worth its own post, though.
A group of researchers from Keio University have published a new analysis of evolutionary relationships among green algae in the order Volvocales. Takashi Nakada, Yudai Tsuchida, and Masaru Tomita inferred relationships using one nuclear gene and five chloroplast genes.
Previously, I focused on the monophyly of the multicellular volvocine algae, i.e. the Tetrabaenaceae, Goniaceae, and Volvocaceae (TGV). The multigene analysis shown above supports monophyly, although the support values for the critical node are not shown (meaning that the Bayesian posterior probability is <0.90 and the bootstrap proportions are <50%). Similarly, the new phylogeny doesn’t do much to resolve the backbone relationships within the Volvocaceae. There are differences from previous analyses that would be important if true, specifically in the positions of Volvox globator (the sole representative of Volvox section Volvox) and of Yamagishiella (which appears as part of an isogamous clade rather than sister to the anisogamous/oogamous Eudorina/Pleodorina/(most) Volvox clade). Neither of these differences is well supported, though, which is typical; most published phylogenies provide poor support for these relationships.
The main point of the new paper, though, is the close relationship between the multicellular volvocine algae and Chlamydomonas pila. The critical node for this relationship is is supported by a high Bayesian posterior probability (1.00) but crappy bootstrap values (55% for maximum likelihood and <50% for neighbor joining). The authors did do some analyses with fewer taxa to test this relationship, and those trees did have better support, but they also changed other relationships.
Correctly identifying the closest unicellular relative of the multicellular volvocine algae is critical for reconstructing the first steps in the transition to multicellular life. This is far from the first time that other species of Chlamydomonas and some of Vitreochlamys have been implicated. I’m not aware of any previous phylogeny that includes Chlamydomonas pila, but Chlamydomonas debaryana (for example) is usually closer when it is included.
I wouldn’t say that the evolutionary relationships in this group are fully settled at this point; the particulars vary among authors, depending on the gene(s) analyzed, and even depending on the method of phylogenetic inference. Even the monophyly of the multicellular species has been called into question, though I think it’s definitely too early to be confident in that conclusion. Right now it seems that Chlamydomonas pila is the best contender for the sister species to the multicellular clade, and almost certainly a closer relative to Volvox and co. than Chlamydomonas reinhardtii. As the authors point out, this makes C. pila a good candidate for whole-genome sequencing. The closer a relative to the multicellular group we can find, the better we can resolve which changes are specific to the multicellular clade.
Nakada, T., Tsuchida, Y. & Tomita, M. 2019. Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae). Mol. Phylogenet. Evol. 130, 1–8. doi: 10.1016/j.ympev.2018.09.013
“The Diamond Lens” is a short story published by the Irish writer Fitz-James O’Brien in 1858. It describes the quest of an obsessed amateur microscopist for ever greater degrees of magnification, a goal for which he is willing to go to exceptional lengths. O’Brien was apparently known for mixing scientific themes with mysticism, and “The Diamond Lens” certainly fits this description. I won’t spoil it any further; interested readers can download the story for free (in several formats) from The Gutenberg Project.
As the narrator and protagonist becomes a proficient microscopist, he encounters Volvox:
Last year I wrote a series of posts on convergent evolution and misrepresentations of the history of the concept by proponents of intelligent design including Günter Bechly, Lee M. Spetner, Granville Sewell, and others. I didn’t intend for there to be a two-month gap before the final installment (nor am I sure this is the final installment), but here we are.
The Discovery Institute is producing a revisionist history. To hear them tell it, convergence is something that evolutionary biologists have either barely heard of or that they “invented” or “made up” to hide problems with the tree of life. Convergence “destroys the tree of life,” it “contradict[s] the [modern synthesis],” and it is “quite unexpected” to evolutionary biologists. All of that is a big, stinking pile of wrong. In reality, biologists since Darwin, and including Darwin, have always appreciated the importance of convergence, have written thousands of papers about it, and have included it in every evolutionary biology textbook I’m aware of.
I explained why the argument that convergence is evidence against common descent is daft, and I gave a spectacular example of convergent (or parallel) recruitment of life cycle genes in plants and brown algae. I also promised that I would write about convergent evolution in Volvox, which I have so far failed to do.
For those of you who don’t use a feed reader, I have set up a Facebook page for Fierce Roller: facebook.com/FierceRoller. If this works the way I think it should, all you have to do is go there and hit the “Like” button, and you’ll get an alert each time I publish a blog post. If you do use a feed reader, you can follow the blog by adding freethoughtblogs.com/fierceroller/?feed=rss2.
The Thompson lab at University College London is looking for a postdoctoral researcher to study the evolution of multicellularity:
The Thompson lab, based at University College London, is seeking a Research Fellow to work on understanding how gene network heterogeneity affects the evolution of multicellular development.
Recently, we found that cell-cell variation in cell cycle position facilitates symmetry breaking during development, as it primes cells to respond to different differentiation cues (Gruenheit et al, Developmental Cell, 2018).