In defense of preprints

At the end of July, I criticized an opinion piece that Tom Sheldon published in Nature, “Preprints could promote confusion and distortion“:

While the article casts preprints, preprint servers, and scientists who post their work to preprint servers as potential sources of misinformation, its arguments better support the case that science reporters should act more responsibly…What irks me is that I can’t find any hint in the article that Sheldon thinks journalists share the blame when they sensationalize bad science.

The latest issue of Nature includes three more critical responses to Sheldon’s nonsense.

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Volvox inversion review

Alexey Desnitskiy from St. Petersburg State University has published a short review of the process of embryonic inversion in the genus Volvox. It is a translation, by the author, of his Russian-language paper in the journal Ontogenez (Desnitskiy, AG. 2018. Ontogenez 49:147-152). The article, in the Russian Journal of Developmental Biology, isn’t listed as open access, but it also doesn’t seem to be paywalled.

Inversion occurs during the development of all known species in the family Volvocaceae (Colemanosphaera, Eudorina, Pandorina, Platydorina, Pleodorina, Volvox, Volvulina, and Yamagishiella), where it serves to turn the embryo inside-out and get the flagella on the outer surface of the colony. The paper discusses the two distinct inversion processes found in different Volvox species:

…the inversion of “type A” and the inversion of “type B,” represented by the two species most thoroughly studied, respectively V. carteri f. nagariensis and V. globator (Hallmann, 2006; Höhn and Hallmann, 2011). The principal difference between these two types of inversion is that this process begins at the anterior pole of the embryo in the first case, while in its posterior hemisphere in the second case. Coordinated displacements of cells relative to the system of intercellular cytoplasmic bridges play, along with changes of the cell shape, an important role in the inversion process in embryos of both Volvox species. In V. globator, though, the spindle-shaped cells could be observed not in the entire embryo but only in the posterior hemisphere at the stage of its compression.

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One more test post

If you’re an email subscriber (Hi Mom), you may have noticed that the links in the emails that accompany new Fierce Roller posts have been linking to old Pharyngula posts for a while now. The problem was that the links were of the form https://freethoughtblogs.com/?p=4279 instead of https://freethoughtblogs.com/fierceroller/?p=4279. With some help from WordPress chat support, I believe that problem is now fixed. Hopefully the email accompanying this and future posts will include the right links.

What’s a DOI?

Whenever possible, I try to link to a publicly accessible version of any scientific article I report on. Sometimes this is on ResearchGate, sometimes on an author’s academic website, sometimes even a course website. The benefit is that anyone can download and read the article; the downside is that these links sometimes disappear. Publishers issue takedown notices, academics change institutions, and courses end.

For these reasons, I usually provide, in addition to a publicly accessible link, a link that I can count on to not disappear (these appear at the end of the post, under “Stable Links”). Almost always, these are DOIs. DOIs are Digital Object Identifiers, persistent handles that are permanently assigned to particular documents. Almost all academic journals assign DOIs to all of their articles (Evolutionary Ecology Research is one exception, much to my annoyance), as do the preprint servers arXiv and bioRxiv and the digital data archive Dryad.

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Jonathan Wells debunks something nobody believes

Black bear

Black bear, Glacier National Park, September 2014.

Charles Darwin speculated that whales might have evolved from bears. He was wrong, but then he didn’t have the benefit of molecular sequence data, detailed morphological comparisons, and sophisticated methods of phylogenetic inference. We’ve known for at least 50 years that cetaceans (whales, dolphins, and porpoises) are most closely related to ungulates, specifically even-toed ungulates (artiodactyls). The current consensus is that the closest living relatives of cetaceans are hippopotamuses. Not everyone agrees with this specific relationship, but no one really doubts that whales are closely related to ungulates.

You wouldn’t learn that from reading Discovery Institute Senior Fellow Jonathan Wells’ recent post, “From Bears to Whales: A Difficult Transition.”

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A is for Algae

I got my copy of Jillian Freese’s A is for Algae earlier this week. Freese, a Ph.D. candidate at the University of Rhode Island, says the book is “Part birthday gift. Part #scicomm. Part stress relief.” It’s full of watercolor paintings of algae, mostly seaweeds but with some phytoplankton as well. Each species (one for each letter of the alphabet) is presented with its scientific name, usually a common name, habitat and biogeographic information, and some interesting factoids.A is for Algae

Warning: spoilers below the fold.

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Postdoc opportunity studying Volvox!

If I were a graduate student nearing graduation, I would apply for this: an NSF-funded postdoc opportunity in the Umen lab at the Donald Danforth Plant Science Center in St. Louis.

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Everything Flows

Everything Flows cover

Process philosophy has really just recently come on my radar, and I’m not sure what to make of it. I have written before that I don’t have a particularly strong background in philosophy, and so I’m hesitant to judge what I may not understand. At least some of the descriptions I’ve seen strike me as quasi-mystical word salads:

In short, a becoming actual entity prehends, or “feels,” not only other, past actual entities (which may be seen as the metaphysical basis for causality wherein one entity becomes part of another entity’s formation process), but also eternal objects (i.e., “pure possibilities”), which introduces novelty into the process. –Lukasz Lamza in Nature Alive – Essays on the Emergence and Evolution of Living Agents

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