New spam filter

Image from Wikimedia CommonsFierce Roller has been getting a lot of spam comments, hundreds of them. They’re all pretty obviously spam, with user names like “Nfl Jerseys 2015” and “cheap ray ban sunglasses.” None of them get through, because I set up the blog so that I have to approve a commenter’s first comment, but just sending them all to spam was getting to be a chore (I have to look at them all, since I don’t want to send legit comments to spam).

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Kirsty Wan and Ray Goldstein have posted a new paper to arXiv*: “Coordinated Beating of Algal Flagella is Mediated by Basal Coupling.” The paper examines in unprecedented detail the mechanics of intracellular flagellar coordination. That’s cool and all, but first: hexadecaflagellates!

Wan & Goldstein compared algal cells with 2, 4, 8, and, yes, 16 flagella. I never knew there was such a thing. Pyramimonas cyrtoptera has 16, and its relative P. octopus has…well, you can probably guess.

Fig. 7 from Wan and Goldstein 2015: Pyramimonas cyrtoptera.

Fig. 7 from Wan & Goldstein 2015: Pyramimonas cyrtoptera, with hella flagella.

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Magic in Nature

A new Nature column on alternative medicine is full of subtle misdirection and outright logical fallacies. “Consider all the evidence on alternative therapies” by Jo Marchant defends the view that therapies that fail clinical trials should nevertheless be supported because they provide a beneficial placebo effect. This badly argued and self-contradictory essay illuminates nothing except the author’s wholesale failure of logic.


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Pathways to pluralism: Beckett Sterner on biological individuality, part 1

In grad school I wound up hanging around with John Pepper (yeah, Dr. Pepper) a good bit. I think I disagreed with him more than I agreed with him, sometimes to the point of exasperation, but conversations with him were never boring.


One of John’s most annoying refrains was “is it an organism?” I was studying (and still study) a group of algae for which this question can be genuinely confusing. Most people would say a Chlamydomonas cell is a single-celled organism, and most would agree that Volvox is a multicellular organism, but what about the four-celled species Tetrabaena? A four-celled organism or a collection of four single-celled organisms? What about an undifferentiated colony of 32 cells, such as Eudorina? Or Pleodorina, which is around the same size but with two cell types? Somewhere between a unicellular ancestor and Volvox, a new kind of individual emerged. Among the extant species*, where do we draw the line between organisms and groups of organisms, or can we (or should we) draw a line at all?

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Pussyfooting around evolution


I have been lucky to work with some excellent science teachers here in Montana. The state’s science education in general, though, could be better. In 2012, the Thomas Fordham Institute released its report The State of State Science Standards, and Montana didn’t fare so well. With an overall rating of ‘F’, Montana’s science standards were described as

…a thin amalgam of wooly commands and vague expectations…permeated with vague if high-sounding generalities that are of little or no use in setting up a course of study.

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In a post on human evolution (“BBC asks, why we are only humans still alive?“), Uncommon Descent asks,

It is unclear that any of these groups [Neanderthals, Denisovans, ‘hobbits’] ever were separate species. Is that not just more Darwinspeak? The serious discussion of what “separate species” means never happens because no Darwin follower can afford it. [emphasis mine]

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Why don’t we revise volvocine taxonomy?

Volvocine taxonomy is in a sorry state. Most nominal genera, and some nominal species, are almost certainly polyphyletic. More than once, I’ve been asked during a talk, “Why is Volvox scattered all over the tree?”


Fig. 2A from Herron et al. 2010. The traits characteristic of the genus Volvox—asexual forms with >500 cells, only a few of which are reproductive, and oogamy in sexual reproduction—have arisen at least three times independently: once in the section Volvox (represented by V. globator, V. barberi, and V. rousseletii), once in V. gigas, and once or possibly twice in the remaining Volvox species. Branch shading indicates maximum-parsimony reconstruction (white = absent, black = present, dashed = ambiguous). Pie charts indicate Bayesian posterior probabilities at selected nodes. Numbers to the left of cladograms indicate log-Bayes factors at selected nodes: positive = support for trait presence, negative = support for trait absence. Interpretation of log-Bayes factors is based on Kass and Raftery’s (1995) modification of Jeffreys (1961, Theory of probability. 3rd edn. Oxford Univ. Press, Oxford, UK.): 0 to 2, barely worth mentioning; 2 to 6, positive; 6 to 10, strong; >10, very strong. Boldface numbers following species names indicate Volvox developmental programs following Desnitski (1995).

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Best rejection letter ever, or science urban legend?

Antonie van Leeuwenhoek by Jan Verkolje. Public domain image from Wikimedia Commons.

Antonie van Leeuwenhoek by Jan Verkolje. Public domain image from Wikimedia Commons.

Trying to find some background on Van Leeuwenhoek’s discovery of Volvox, I came across the following on Wikipedia:

Despite the initial success of Van Leeuwenhoek’s relationship with the Royal Society, this relationship was soon severely strained. In 1676, his credibility was questioned when he sent the Royal Society a copy of his first observations of microscopic single-celled organisms. Previously, the existence of single-celled organisms was entirely unknown. Thus, even with his established reputation with the Royal Society as a reliable observer, his observations of microscopic life were initially met with both skepticism and open ridicule.[12]

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In which I agree with Uncommon Descent


We’re both fans of Betul Kacar‘s research (see “AbSciCon day 3: the tape of life“). I know why I like it, but I can’t quite figure out why they do. Dr. Kacar’s research combines molecular paleontology with experimental evolution, inserting ancient versions of genes into modern bacteria and observing how they evolve in response. I’ve puzzled over Uncommon Descent’s fondness for Dr. Kacar’s research before (“Evolution is evidence against evolution (?)“), and I’m afraid their new post on the topic (“Roll dice twice, see what turns up“) doesn’t really clear things up.

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Martian paleontology

NAISeminarsAt AbSciCon, I wrote about Mars Icebreaker, a proposed NASA mission that would search for signs of past and present life (“AbSciCon day 4: Mars, life, and Mars life“). Before Icebreaker, though, a new rover is scheduled to launch in 2020, with instruments designed to detect past and present biosignatures. Among these is the Planetary Instrument for X-Ray Lithochemistry (PIXL). On Monday at 1:00 PDT, Abigail Allwood from NASA Jet Propulsion Laboratory will be presenting a webcast seminar as part of the NAI Director’s Seminar Series:

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