PLoS ONE responds

PLoS ONE logo

PLoS ONE is a strange journal. Until recently, it was the largest journal in the world, publishing as many as 30,000 papers a year. It’s definitely the low end among the Public Library of Science (PLoS) stable of journals, but opinions of its quality vary over a wide spectrum. PLoS ONE‘s mission is explicitly different from most journals, as they say impact (i.e. significance) is not a consideration:

Often a journal’s decision not to publish a paper reflects an editor’s opinion about what is likely to have substantial impact in a given field. These subjective judgments can delay the publication of work that later proves to be of major significance. PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound. Judgments about the importance of any particular paper are then made after publication by the readership, who are the most qualified to determine what is of interest to them.

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“It may seem the stuff of sci-fi novels”

This Associate Press report is almost two weeks old, but it reinforces my impression that the alleged ‘sonic attacks’ on the U.S. embassy in Cuba are imaginary:

New details learned by The Associated Press indicate at least some of the incidents were confined to specific rooms or even parts of rooms with laser-like specificity, baffling U.S. officials who say the facts and the physics don’t add up.

“None of this has a reasonable explanation,” said Fulton Armstrong, a former CIA official who served in Havana long before America re-opened an embassy there. “It’s just mystery after mystery after mystery.”

As I said yesterday, sonic weapons are not a plausible explanation for the range of (often contradictory) reports and health complaints of the affected diplomats.

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Sonic stupidity

You and I may disagree about politics. It’s a near certainty that we disagree about at least some political issues. But I hope we can agree that United States foreign policy shouldn’t be based on pseudoscientific claims with no plausibility.

The Executive Branch is flirting with doing just that. Whether or not you think reversing Obama-era warming of relations with Cuba is a good idea, I hope you agree that we shouldn’t do it based on phantom attacks using a non-existent weapon. I’m talking about the so-called ‘sonic attacks’ that, until recently, were being touted as a reason to close the U.S. embassy in Cuba:

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A cautionary tale on reading phylogenetic trees

I have written before about the perils of naive interpretations of phylogenetic trees (“Extant taxa cannot be basal“). Others, notably Krell & Cranston and Crisp & Cook, have pointed out that this is not just a language issue; such misreadings can cause substantive problems in the way evolutionary history is understood.

A new paper in PLoS ONE, “A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species,” contains several instructive examples. PLoS ONE is open access, so you can read the original paper without an institutional subscription. A tweet by Frederik Leliaert got this paper on my radar, and it piqued my interest because of the startling observation that the inferred phylogeny shows Chlamydomonas as sister to all other eukaryotes.

It made me frown, too.

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Georgia Tech President responds to protests

Georgia Tech President G.P. “Bud” Peterson sent a message to the main GT listserv Tuesday. I’m not sure I buy the bit about ‘outside agitators’–one of the three people arrested was a Georgia Tech student–but all in all I think it’s a pretty evenhanded response. Here’s the whole message:

The events of the past few days have been incredibly difficult and challenging for the entire Georgia Tech community. Consistent with our traditions and values, it is especially important that during times like these we come together and support one another.

One of our student leaders, Scout Schultz, has died and we all bear the tremendous weight of that loss. I met Scout last year at the Lavender Graduation ceremony, and our entire Georgia Tech community is mourning the tragic loss of this smart and passionate young person. Losing a student, friend, colleague, and campus leader is one of the most difficult experiences that any of us will have to face.

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Mechanics of Volvox inversion

Variation is everywhere in biology. Structural variation is present at molecular, cellular, organismal, and population levels, and functional variation occurs in processes from metabolism to development to behavior. In spite of this, we often describe biology in typological terms, and this is often a source of confusion.

Some variation is crucial; for example, evolution is dependent on genetic variation, and behavioral variation within ant and bee colonies ensures that all the necessary jobs get done. Much variation, though, is simply biological noise, an unavoidable consequence of the mostly analogue nature of living systems. In extreme cases, variation of this sort can complicate and even derail development, but in general development is remarkably robust. A variety of regulatory mechanisms prevent small amounts of variation early in development from being amplified into large variations in adults.

Pierre Haas and colleagues have posted a preprint to arXiv describing variation in the developmental process of inversion in Volvox globator. Facultatively sexual organisms such as Volvox are great for studying non-genetic sources of variation, because it’s pretty simple to produce millions of genetically identical individuals. When they are raised in identical conditions, variation due to environmental differences is minimized, and most of the observed variation is stochastic.

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Not much information

GTENS alert

CNN has the story now, but no real details:

Georgia Tech police urged students to stay inside and lock their doors as violent protests erupted Monday on campus after the fatal shooting of a student by police over the weekend. There was a planned vigil for the slain student on Monday.

That’s really all there is that we didn’t already know.

By the way (in case my mom is reading) I’m at home, a mile from campus.