Monday, September 24, 2018

Trigger Warning Week

Listening to the news today, I noticed that every broadcast on NPR and some on CBS had content warnings due to sexual content surrounding the Kavanaugh nomination. I kept thinking, “This is not normal. This is way beyond the Clarence Thomas shitshow.” This entire week needs a trigger warning.

I’m going to take a moment to address trigger warnings- a certain breed of asshole, typically male, uses the term as an insult. My take on it is that trigger warnings are for SURVIVORS, they are meant to protect people who have lived through traumatic incidents. I’d be willing to bet that the typical conserva-bro using the term in disparaging fashion would not be able to handle such trauma.

It’s been a rough week, and it’s only Monday. I know that some commentators at blogs I visit are having bad time with the misogyny on parade in the media. The news reports are carrying trigger warnings, it might not be a bad time to take a breather. We’re going to need all of our strength in the coming weeks.

Sunday, September 23, 2018

I'd Say that the Sexual Misconduct Is a Feature, Not a Bug

Last year, when the story of a fatal fraternity pledge incident dominated the local news, I posted about the code of bromertà- the omertà-like behavior of men who engage in violent, usually misogynistic behavior. A teenager who covers up sexual misconduct or the injury, even death, by misadventure of a peer will grow up to be a man who will cover up corporate, political, or sexual malfeasance.

That brings me to the Kavanaugh nomination- here's a guy with a growing litany of allegations of sexual misconduct. Add to that his sketchy financial history, and a picture of an easily compromised individual emerges. This is a guy who is vulnerable to blackmail at best, a serial criminal at worst.

The very idea that this creep, who makes Robert Bork look like a moderate jurist, would gain a lifetime position on the Supreme Court is utterly repugnant. Given the Republican Party's recent string of candidates with histories of sexual misconduct, it's utterly predictable.

Saturday, September 22, 2018

It's That Time of the Year Again

Once again, today is the day of the local street festival, which, because I live in the Tavern District of the City of Y______, involves a lot of beer drinking:




I have plans to meet up with some cousins for the festivities, and I know that my neighbors will be out in force. It's a sure bet that the craic is going to be fantastic, we denizens of the neighborhood wouldn't tolerate things otherwise.

Thursday, September 20, 2018

Secret Science Club Post Lecture Recap: Swarming Bacteria

Last night, I headed down to the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture featuring Dr João Xavier, computational biologist and director of Sloan Kettering's X-Lab. Dr Xavier's topic was experimental evolution and swarming bacteria.

Dr Xavier began his lecture with a quote from Richard Dawkins:


My eyes are constantly wide open to the extraordinary fact of existence. Not just human existence, but the existence of life and how this breathtakingly powerful process, which is natural selection, has managed to take the very simple facts of physics and chemistry and build them up to redwood trees and humans.


He followed this up with a beautiful tribute to biodiversity, first showcasing the human diversity of New York City's populace with pictures from the subway system, then showing pictures of animal biodiversity, then expanding his focus to include plants, fungi, and bacteria. Dr Xavier then took a brief digression to note that he entered into the field of biology relatively late- he was initially more interested in math and physics, but eventually felt the call to apply his knowledge of those fields to biology. He followed up this digression with a brief overview of Darwin's theory of evolution by means of natural selection: put succinctly, successful individuals will be 'selected' by natural processes to pass on their traits to their offspring, and this selection will drive the direction in which a species will evolve. The basic mechanism of biological inheritance was formulated by Gregor Mendel, who observed the passing of traits in plant lineages. The central dogma of molecular biology, as formulated by Crick et al. is that DNA is the molecular entity behind evolution. DNA encodes genes which make proteins. DNA can be transcribed- it is copied when a cell divides, and sometimes there are errors in the copying, known as mutations. Most mutations are harmful to an organism, but occasionally they may lead to better survival outcomes. Diversity emerges through mutations, and the fittest organisms tend to propagate.

Dr Xavier then noted that everyone alive today descends from a common ancestor, then he amended this statement to note that every living organism on Earth comes from a common ancestor. He noted that this is a hard-to-grasp concept, so some people refuse to believe it. This refusal to believe led to the creation of the 'Intelligent Design' movement, which posits a director/designer in the evolution of life. The bacterial flagellum was considered the icon of Intelligent Design creationism, but Dr Xavier noted that the proteins behind the flagellum are understood- complex structures look precisely adapted to their environment, they look designed, but their evolution in incremental steps is explainable.

This talk of flagella then segued into the real topic of the lecture- the bacterium Pseudomonas aeruginosa, a human pathogen. Dr Xavier uses Pseudomonas to investigate the fundamental facts about evolution and their direct implications in medicine. Bacterial evolution can be deadly- Dr Xavier recounted a case in which a patient needed a bone marrow transplant, which involved suppressing their immune system. Ten days before the transplant, while the patient's immune system was compromised, the patient developed a Pseudomonas infection which was resistant to most antibiotics. The patient was treated with aztreonam, but the bacteria evolved resistance to this antibiotic through a mutation, sepsis set in, and the patient died. Antibiotics select for resistance against themselves- they kill off non-resistant bacteria, then the small population of resistant bacteria propagates. The evolution of antibiotic resistance is fast, and it happens all the time.

Dr Xavier then followed this cheerful news with another quote from Richard Dawkins:


“We are going to die, and that makes us the lucky ones. Most people are never going to die because they are never going to be born. The potential people who could have been here in my place but who will in fact never see the light of day outnumber the sand grains of Arabia. Certainly those unborn ghosts include greater poets than Keats, scientists greater than Newton. We know this because the set of possible people allowed by our DNA so massively exceeds the set of actual people. In the teeth of these stupefying odds it is you and I, in our ordinariness, that are here.We privileged few, who won the lottery of birth against all odds, how dare we whine at our inevitable return to that prior state from which the vast majority have never stirred?”



Bacteria evolve quickly because they reproduce quickly. The Pseudomonas bacteria form a swarming collective, they have motility due to their flagella. Dr Xavier studies this swarming behavior in petri dishes. Separate bacterial swarms in a petri dish repel each other. The bacteria need flagella to swarm, and this is the natural condition of the wild type. A non-swarming, non-flagellated form, known as flgK was developed in the lab. Dr Xavier then showed us a series of videos comparing the spread of swarming wild-type bacteria to the spread of non-swarming mutants:





Parallel experiments were conducted in different petri dishes, and they demonstrated the heritable and stable tendency to evolve into hyperswarming bacteria with multiple flagella, a new feature that evolved in the laboratory. Genome sequencing revealed the precise mutations which caused hyperswarming. Some bacteria evolved an excess of flagella, and too many 'tails' prevented swarming... the right number of flagella was needed. Hyperswarmers, though they move more quickly to exploit new resources, grow more slowly than the ancestral type bacteria- multiple tails require more resources.

Dr Xavier likened the petri dishes with different bacterial strains as to 'fighting arenas' in which the strains were pitted against each other. Different strains were stained red or green, and hyperswarmers were pitted against ancestral types. The hyperswarmers expand quickly and find nutrients, while the non-hyperswarmers are stuck in regions in which nutrients are exhausted. Faster speeds can come with a trade-off, though. Dr Xavier cited the invasive cane toad as an example of such a trade-off... in areas in which the toads are expanding their range, they evolved longer legs which enabled a faster spread. Dr Xavier joked that there was an 'Olympic village of cane toads' down under. The trade-off is that the longer legs, while enabling faster movement, also resulted in more spinal injuries among the leggy toads. In the case of Pseudomonas, hyperswarmers are not found in natural environments or in hospitals- while they can move quickly, they are bad at forming biofilms. In the fighting arena of the petri dish, the slow bacteria will eventually take over- in nature, the fast bacteria don't do well. It's difficult to evolve a change in the structure of the flagellum, the icon of the Intelligent Design movement. Dr Xavier got another dig in at the ID crowd- when the New York Times ran the headline “Watching Bacteria Evolve, with Predictable Results”, a creationist publication describing itself as 'a great tool for countering pro-Darwin propaganda' countered with the rejoinder 'They're still bacteria.' CHECK AND MATE, POINDEXTERS!!!!

Dr Xavier then went on to discuss the use of swarming bacteria to study social behavior- how do social behaviors evolve? Social behaviors can have a different impact on actors and recipients. In mutualism, everyone benefits- actors and recipients. Altruism is costly to the actor and benefits the recipients. Selfishness benefits the actor and is costly to the recipients. In the case of spite, everyone loses. Game theory uses mathematics to analyze behavioral choices. Dr Xavier cited the example of the prisoner game to illustrate game theory:





Kin selection explains many altruistic behaviors- altruism is more likely among relatives. When asked if he would lay down his life to save his brother, biologist J.B.S. Haldane was quoted as saying that he wouldn't, but that he would for two brothers or eight cousins. Altruism makes sense when it results in evolutionary fitness benefits.

Among bacteria, the whole population benefits from swarming, but swarming involves sacrifice among individuals. Non-swarming bacteria tend to consume all available nutrients in their environment until they cannot grow their population. Resources are spent to propagate a swarm, and the tiny contributions of individual bacteria can add up to an impressive spread. Alone, on-swarming bacteria cannot spread, but they can hitchhike along with swarming bacteria. In this cooperative situation, the ratio of swarming to non-swarming bacteria remains stable. Cheating is hard due to metabolic prudence- bacteria cooperate when they have excess metabolic resources to devote to swarming. Dr Xavier ended his lecture by joking that metabolic regulation of good behavior is not only found among bacteria- citing a study of judicial records which suggested that judges at parole hearings tended to become less lenient as they got hungrier, but exhibited renewed leniency after lunch.

The lecture was followed by a Q&A session. Some bastard in the audience, thinking back to Dr Paul Turner's SSC lecture on phage therapy, asked if there had been experiments to use selective pressure to 'breed' less harmful versions of pathogenic bacteria by selecting and propagating less virulent individuals. Dr Xavier replied that this hasn't been attempted, but that it would be possible for less harmful bacteria to out-compete their dangerous relatives. There's no good model for this sort of study, but it could be evolved... of course, as in the example of the introduction of the cane toad to Australia, things could go awry, as organisms don't necessarily behave in the wild as they do in the lab. The Bastard missed a bunch of questions while taking a break to micturate, but when he returned to the main auditorium, the question regarded cancer- cancer cells have an initial propagation advantage over 'normal' cells, but are an evolutionary dead end as they kill their hosts... they are successful for a while, then they fail utterly. He also mentioned the transmissable cancer that is devastating Tasmanian devil populations as a particularly horrific example of this sort of thing.

Once again, the Secret Science Club served up a fantastic lecture. I am particularly struck by the sheer coolness of a Professor Xavier setting up clashes among mutants in a battle arena. The multiple videos of the petri dish battles were gorgeous:





Kudos to Dr Xavier, Margaret and Dorian, and the staff of the beautiful Bell House.

Wednesday, September 19, 2018

MTA Trolling?

The day being beautiful and temperate, I decided that I would leave my car parked near home, and would start my journey to the beautiful Bell House for tonight’s Secret Science Club on foot. I walked to the MTA Bx34 bus stop at Katonah Ave and 237th St and waited, and waited- the 4:55 bus was not in evidence.

At 5:06, the 34 bus arrived, with a second 34 bus close on its tail. At the intersection of Katonah and 233rd St, they were front to back, and they kicked for position the length of 233rd St. Transit, like comedy, is a matter of timing- in this case, I think the MTA was playing a prank on us. Thankfully, I made the transfer to the 4 Train with a minute to spare, so I can laugh at the joke this time.

Tuesday, September 18, 2018

Beto'd Ban Barbecue? Bah! But Beto'd Better Ban Booger-Binging

I don't expect much from Texas politics, but Ted Cruz has brought proceedings to a new nadir of stupidity- at a campaign stop, he made a remark, passed off as a joke, that Beto O'Rourke would ban barbecue:


"When I got here someone told me that even PETA was protesting and giving out barbecued tofu, so I got to say, they summed up the entire election: If Texas elects a Democrat, they're going to ban barbecue across the state of Texas."


This is a companion piece to his campaign's stupid assertion that Beto would bring tofu, silicon, and dyed hair to Texas, as if those things weren't already there:


"We are seeing tens of millions of dollars flooding into the state of Texas from liberals all over the country who desperately want to turn the state of Texas blue. They want us to be just like California, right down to tofu and silicon and dyed hair."


Weird, I'd bet actually folding money that Cruz himself dyes his hair, as does his wife, the vegetarian.

At any rate, Ted Cruz has nothing to worry about, because whatever the hell this thing is, it sure as hell isn't barbecue:





But whatever it is, I wouldn't mind a ban on eating it.

Monday, September 17, 2018

No Trip Like the Nostalgia Trip, by Which I Mean the Fantasy Trip

The Tor Books site has a fun post about the 1977 Television special presentation of the Rankin/Bass animated film of Tolkien's The Hobbit.

I recently watched the animated film< and I believe that it holds up well. The character design is inspired by the illustrations of Arthur Rackham, a personal favorite of mine. Here's the Rankin/Bass version of Thorin and Company:




They look similar to Rackham's depiction of Henry Hudson and his crew from Washington Irving's Rip Van Winkle:




The animation in the film was done by Japanese company Topcraft, a precursor to Miyazaki's Studio Ghibli. The voice acting, featuring such Bastard favorites as Paul Frees and Don Messick, was excellent, with a standout performance by 'stand up tragedist' Brother Theodore as Gollum:





Yeah, not to badmouth Andy Serkis, who did a credible job as this creepy junkie analogy, but this is the real deal. Also, Peter Jackson put WAAAAAAAYYYY too much of this character in his movies.

Veteran actor Richard Boone also did a bang-up job as Smaug, perfectly portraying the arrogant, jaded dragon as a bully and a braggart playing cat and mouse with an unknown intruder:





The film, released in 1977, was a watershed moment in nerd culture, as the Tor piece asserts. A good portion of the kids viewing it ended up picking up the celebrated 1977 Dungeons and Dragons Basic Set and fantastic literature crystalized into a sub-Tolkienian orthodoxy... though it must be said that, judging from his gloriously purple prose, Uncle Gary was more of an A. Merritt fan.

Now, speaking of both nostalgia trips and fantasy trips, this year is seeing the resurrection of role-playing game The Fantasy Trip, which author/designer Steve Jackson was able to regain control over after it was killed off by an unscrupulous publisher who let the IP languish rather than sell it back to Mr Jackson at a reasonable price. This game, based off of a couple of skirmish-simulation microgames, was a favorite to play during short school breaks due to its speed and simplicity. I played quite a bit of it at school, and became adept at finding the more outré character builds while everybody else was stuck in that mighty sword rut... you see, I was also a big A. Merritt fan.