Life cycles in major transitions, and some clueless critique

Jordi van Gestel and Corina Tarnita have published a ‘Perspective’ in PNAS, “On the origin of biological construction, with a focus on multicellularity“:

…we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions.

van Gestel 2017 Fig. 2

Figure 2 from van Gestel and Tarnita, 2017. Relationship between life stages in hypothesized life cycles of solitary ancestors and group formation in derived group life cycles. (Upper) Simplified depiction of hypothesized ancestral solitary life cycles of the green alga Volvox carteri, the cellular slime mold Dictyostelium discoideum, and the wasp Polistes metricus. Life cycles here consist of a life stage expressed under good conditions (black) and a life stage expressed under adverse conditions (green). For the latter life stage, we show an environmental signal that might trigger it and some phenotypic consequences. (Lower) Simplified depiction of group life cycles of: V. carteri, D. discoideum, and P. metricus. Developmental program underlying life stages in solitary ancestor is co-opted for group formation (shown in green): differentiation of somatic cells (V. carteri), fruiting body formation (D. discoideum), and appearance of foundress phenotype (P. metricus).

[Read more…]

What do all these quotes have in common?

Trump may be setting the US on the path to World War III. —Sen. Bob Corker 2017-10-08

Congress must govern with a president who has no experience of public office, is often poorly informed and can be impulsive in his speech and conduct.” — Sen. John McCain 2017-08-31

Fucking moron. — Secretary of State Rex Tillerson (alleged)

[Read more…]

MicroRNAs in Chlamydomonas

One of the biggest changes in evolutionary theory in the late 20th century was the growing appreciation for the central role of changes in gene expression in macroevolution. Developmental genes, especially Hox genes, turned out to be remarkably conserved across lineages that diverged over half a billion years ago. The subsequent huge changes in morphology were more often due to changes in when and where those genes were expressed than to changes in the coding sequences of the genes themselves.

Even more recently, an entire new class of regulatory mechanisms was discovered and found to be important in developmental processes. MicroRNAs (miRNAs) are short (21-24 nucleotides) sequences of RNA that reduce gene expression by promoting the breakdown of messenger RNAs (mRNAs) and by repressing translation of mRNAs into proteins. We have only known that microRNAs even existed since the early 1990’s, and their importance in gene regulation and development wasn’t appreciated until the 2000’s.

Although they are structurally similar, plant and animal microRNAs repress gene expression through very different mechanisms. A new paper by Betty Y-W. Chung and colleagues in Nature Plants shows that the regulatory mechanisms of Chlamydomonas microRNAs have both striking similarities and important differences with animal miRNAs:

[Read more…]

A valid point

A reader commented by email about my criticism of the PLoS ONE article that inferred a multigene phylogeny of eukaryotes, with Chlamydomonas reinhardtii as the outgroup (“A cautionary tale on reading phylogenetic trees“).

Although you are of course correct to complain about nearly everything in the paper (esp. re “basal” and node rotations), and I am sure the tree is wrong in more ways than it is right, I think you might reconsider or put in context complaints about the “provides a link between”. My thought is simply that if one has a long branch between two nodes in a tree, if you add a taxon group that branches off in the middle of this long branch, then it does, in a sense, provide a “link” between these two nodes. A more proper way to put it is that it provides information concerning the ancestral state at the two original nodes (i.e., may substantially modify the posterior probability of the states at the two nodes). I doubt that the authors mean it in this sense, but in the general context of teaching people about trees, I would want students to understand this.

[Read more…]

No means, no motive, and no suspect

I don’t want this to become the ‘Cuba’s sonic weapons are bullshit’ blog, and I apologize for my readers who are just here for the Volvox. But there is a massive failure on the part of major news organizations to apply the most rudimentary skepticism to outlandish claims of mysterious weapons, and there’s every reason to think that it’s affecting United States foreign policy toward Cuba.

The story is starting to change as news organizations acknowledge what their experts have been telling them from the start, namely that sonic or acoustic weapons are not a plausible explanation for the reported symptoms of U.S. embassy personnel in Cuba. CBS, one of the least skeptical sources right from the start, is desperately clinging to the magic sound gun narrative:

Investigators are now probing whether the attacks were caused by something more than just mysterious sonic devices after U.S. government personnel complained about hearing loud, bizarre and unexplained grinding and insect-sounding noises in homes and hotels, sources tell CBS News.

“My own multiple sources are saying that some of the evidence, medical evidence, being shown by the patients that have been affected could not all be related to sonic waves,” said Dr. Andy Gomez, interim director of the University of Miami’s Institute for Cuban and Cuban-American Studies. “What other measures did whoever the perpetrator was committing these acts do to cause these health issues with our U.S. personnel in Havana?”

[Read more…]

Cuba’s “magical sci-fi sound gun”

Finally, a major news source is applying some skepticism to the claims of acoustic attacks on U.S. embassy personnel in Cuba. A new article in Wired by Adam Rogers acknowledges that acoustic or sonic weapons are not a plausible explanation for the reported symptoms:

Most of the reporting on this story so far has talked about some kind of a “sonic weapon” or “sonic attack,” maybe a side-effect of a surveillance technology. The problem is, physicists and acousticians don’t know how ultrasound (high frequency) or infrasound (low frequency) could do what the State Department says happened to its people. That leaves two possibilities: a new, sci-fi sound gun or something else.

[Read more…]

More acoustic credulity

Last week, I said that the State Department was ‘flirting with’ making decisions about United States foreign policy toward Cuba based on pseudoscience. They’re done flirting.

From BBC News:

The US has expelled 15 Cuban diplomats, saying Havana failed to protect US diplomats from mysterious acoustic attacks.

[Read more…]

A trio of algal biophysics talks

APS logo

The 70th Annual Meeting of the American Physical Society Division of Fluid Dynamics, November 19–21, 2017 in Denver, Colorado, will include a few talks about Volvox and Chlamydomonas motility. Timothy Pedley from Cambridge will present “An improved squirmer model for Volvox locomotion“:

[Read more…]

ZX81

I can usually one-up most anybody when it comes to my first computer (anybody except my mom, that is…more on that later). Around 1981 or 1982, I got a Sinclair ZX81, probably for Christmas or my 11th or 12th birthday. My dad says that ‘we’ assembled it from a kit, which undoubtedly means he assembled it from a kit and I watched as long as my 11-year-old attention span allowed.

The ZX81 rocked a Zilog Z80 8-bit CPU at 3.25 MHz. For those of you who grew up in the 90’s and never saw an ‘M’ in front of the ‘Hz’, that’s three and a quarter megahertz, just about 1⁄1000 the speed of today’s PCs (if a cycle got the same amount of work done, which it certainly didn’t). The operating system was BASIC, and programming was accomplished using the pressure-sensitive membrane keyboard (sort of like the pin pad of an ATM or gas pump). The keyboard was only about six inches wide, so typing was strictly a hunt-and-peck affair; even my 11-year-old fingers wouldn’t fit on ASDF JKL;.

Sinclair ZX81 with 16 kb RAM pack and thermal printer. By Carlos Pérez Ruiz – Flickr: ZX81 + rampack + ZX Printer, CC BY-SA 2.0, Link

[Read more…]