Fruit salad and theocracy

Charles Bethea interviewed Roy Moore’s former law school classmates and professors. Nobody seems to have liked him, one of the professors nicknamed him “Fruit Salad” because he was so confused and mixed up, and they’re uniformly astounded that he’s running for the senate. But they also think he’s going to win.

None of the classmates or professors whom I interviewed, including those who described themselves as Republicans, said that they were supporting Moore’s Senate candidacy. “I probably won’t vote,” Melton said. “That’s how bad it is. I don’t think this Doug Jones has a snowball’s chance in Hell,” he added. “He’s a Democrat and they gonna . . . ” Melton trailed off. “Hell, Moore will get sixty-five per cent of the vote. I don’t care what the polls say.” Melton referred to a recent poll showing that Jones and Moore were tied. “I know what the public is gonna get out and do,” he said, sighing. “I mean, we’re one of three states without a lottery. Southern Baptists control the damn state. And they’ll vote for Roy. It’ll be a landslide.”

And there’s the problem with America in a fruit cup.

This one is going to be a marketing challenge

There’s a new company with a dream: Fitbiomics. They aim to make a probiotics sports drink.

FitBiomics™ is a sports biotechnology company spinning out of the Wyss Institute for Biologically Inspired Engineering at Harvard University. We utilize next-generation sequencing to understand what makes elite athletes unique. In particular, we’re sequencing the microbiome of elite athletes to identify and isolate novel probiotic bacteria for applications in sports performance and recovery. We are purifying these novel probiotics and commercializing as ingredients to disrupt the sports nutrition market and cater to the next generation athlete.

Oooh. “Disrupt.” When the revolution comes and we truly disrupt the system, the people who use “disrupt” to describe peddling overpriced water are going to be among the first against the wall.

But hey, here’s a better translation from corporate-speak.

Certain bacteria show up more often in the poop of elite athletes than in the poop of sedentary people. So researchers theorized that a probiotic elixir containing components of elite athlete poop could help boost athletic performance and become the next hot sports drink.

Yeah. That’s going to be fun, selling Poopwater, the drink of champions.

Note, however, that they haven’t actually done any science to back up any claims of benefit. The guts of people who produce lots of lactate through exercise contain bacteria that thrive on lactate does not in any way imply that Dennis Kimetto’s performance is driven by his well-honed, skilled, disciplined poop.

Also, Fitbiomics looks rather dodgy. It doesn’t actually exist.

The Fitbiomics website lists Scheiman as CEO and Church, his mentor, as co-founder. To be more precise, Scheiman could become the CEO… if Fitbiomics gets funded. You see, Fitbiomics is not actually a company, at least not in the eyes of Harvard and the Wyss Institute. I stumbled on that surprise when I asked Mary Tolikas, Wyss Institute Director of Operations, why I couldn’t find any official disclosure of a financial interest on the part of Scheiman or Church (as distinct from their informal personal declarations).

“There is no company. There is no licensing agreement. There are no IP [intellectual property] assets or financial assets,” Tolikas said. She added that if they do seal a deal, they will move their work out of the Wyss Institute. Wyss Institute Administrative Director Ayis Antoniou also told me by email that faculty are required to disclose their financial interests and move their work out of the institute when they execute a licensing agreement with Harvard. “Prior to the financial interest being created, there is no conflict in the research activities under way, and thus no need for disclosures,” Antoniou wrote.

So it’s a placeholder website, with 10 employees, that has no scientific data backing up their premise, but this is apparently what the big name scientists are doing nowadays, corporatizing their results before they’ve got them.

Borrowing from evolution to create more efficient crops

Dang. I’m not a botanist, and I’m honestly a bit weak on all that plant stuff, but I have to give some background on plant anatomy and photosynthesis to give some context for this cool story. Fortunately I was explaining all this to students in cell biology last week, so I can manage!

First, you all know that plants make sugar from carbon dioxide and sunlight. They use photosynthesis in a set of light reactions to produce energy (in the form of reducing compounds and ATP) that are passed on to a pathway called the Calvin cycle, which fixes CO2 into carbon compounds. It does that by adding the carbon in CO2 to a 5-carbon sugar called ribulose bisphosphate, producing a 6-carbon molecule that is immediately split into two 3-carbon molecules, called 3-phosphoglycerate or 3PG. The enzyme that carries out this reaction is called rubisco, and it’s not particularly efficient. In fact, it’s kind of terrible — it works poorly in a low CO2 environment (like modern Earth!), and plants can lose 25% of their energy to a reaction with O2, rather than CO2. The Calvin cycle is thoroughly intertwined with all kinds of reactions in plant biochemistry, though, so it’s pretty much indispensible. There isn’t an alternative, more efficient reaction that can substitute for it.

Evolution has been creating workarounds, though! Some plants have evolved a kind of supercharger for CO2 — they use an alternative enzyme, PEP carboxylase, to fix CO2, adding the carbon to a 3-carbon intermediate, phosphoenol pyruvate, to produce a 4-carbon molecule, oxaloacetate, which is then passed along to other cells where the carbon is cleaved off to form CO2 again, which sounds kind of pointless, I know…except that what it does is create a CO2-rich environment in the destination cells, so rubisco can run much more efficiently. See? A turbocharger for plant sugar synthesis.

These plants also have a specific anatomical organization, called the Kranz (German for wreath) pattern. There is an outer ring of mesophyll cells that specialize in fixing carbon with PEP carboxylase, and they transport the 4-carbon intermediate into an inner ring of cells, the bundle sheath cells, where rubisco re-fixes the CO2 into a 3-carbon intermediate.

Not all plants have this ability. The plants that don’t, that rely entirely on just the bare bones Calvin cycle that produces a 3-carbon intermediate, are called C3 plants. Familiar C3 plants are wheat, rice, and barley. The plants that do have a supercharger and produce a 4-carbon intermediate are called C4 plants. Corn and sugar cane are well-known C4 crops. C4 is better at coping with environments poor in CO2, like everywhere. What if we could transplant that C4 metabolism in crop plants that lack it, like wheat and rice? We’d expect significant improvements in growth.

You might argue against that by noting that the Kranz anatomy is rather specific and detailed…but it turns out that Kranz anatomy is not essential for terrestrial C4 plant photosynthesis. Some plants have the C4 enzymes without the mesophyll/bundle sheath cell arrangement, and they benefit. It may also be feasible to engineer a proto-Kranz arrangement into C3 plants as a first step, and this is being done:

The C4 photosynthetic pathway accounts for ∼25% of primary productivity on the planet despite being used by only 3% of species. Because C4 plants are higher yielding than C3 plants, efforts are underway to introduce the C4 pathway into the C3 crop rice. This is an ambitious endeavor; however, the C4 pathway evolved from C3 on multiple independent occasions over the last 30 million years, and steps along the trajectory are evident in extant species. One approach toward engineering C4 rice is to recapitulate this trajectory, one of the first steps of which was a change in leaf anatomy. The transition from C3 to so-called “proto-Kranz” anatomy requires an increase in organelle volume in sheath cells surrounding leaf veins. Here we induced chloroplast and mitochondrial development in rice vascular sheath cells through constitutive expression of maize GOLDEN2-LIKE genes. Increased organelle volume was accompanied by the accumulation of photosynthetic enzymes and by increased intercellular connections. This suite of traits reflects that seen in “proto-Kranz” species, and, as such, a key step toward engineering C4 rice has been achieved.

Key things to note: they are recapitulating known evolutionary pathways to more rapidly ‘evolve’ a C3 plant to a C4 state. They’ve generated a line of rice with the first step in this pathway, the proto-Kranz condition. This does not, however, mean that they’ve produced a rice plant with higher yields — they have yet to introduce all the other steps in C4 metabolism. They do state that this transition, while not increasing efficiency yet, has also not reduced the yield of the rice plant, which suggests that the initial steps in the evolution of this pathway did not involve a cost to the plant, and also that the morphological changes, which I would have naively thought would be the biggest obstacle, may have been relatively trivial.

The complexity of the anatomical and biochemical changes needed for the C3-to-C4 transition appears seemingly incongruent with the multiple independent origins of the pathway. However, the results presented here suggest that one of the earliest steps in C4 evolution, the transition from C3 to protoKranz, could have resulted from modified activity of a single gene.

Now onward, to radically engineered biological organisms!

Voznesenskaya EV, Franceschi VR, Kiirats O, Freitag H, Edwards GE. (2001) Kranz anatomy is not essential for terrestrial C4 plant photosynthesis. Nature 414(6863):543-6.

Wang P, Khoshravesh R, Karki S, Tapia R, Balahadia CP, Bandyopadhyay A, Quick WP, Furbank R, Sage TL, Langdale JA (2017) Re-creation of a Key Step in the Evolutionary Switch from C3 to C4 Leaf Anatomy. Curr Biol. doi: 10.1016/j.cub.2017.09.040

I think this is clickbait

Asking this simple question out loud could boost your chances of speaking to the dead, say experts, according to the Manchester Evening News. I marveled at that headline. It’s very impressive. It stirs up so many questions that I had to actually read the article. Who are these “experts” at speaking to the dead? (It doesn’t name any.) Do the dead ever answer? (No.) And mostly, what is the magic question? I’ll spare you the need to waste a click on them.

They explained: “You might consider talking to the spirit world whilst you’re investigating, encouraging the ghost to reveal its presence.

“Try to ask questions such as, ‘What is your name?’, instead of saying, ‘Is there anyone there?’ A lot of people might make this mistake.

“By asking ‘What is your name?’ you’re acting as though you know the spirits are there and this will increase your chances of making contact.”

The “they” referenced above are not dead people — if they were I might consider them credible — but instead, are flacks for a TV channel called “Really” that is putting on a week of shows about the paranormal.

I’m not impressed with their choice of a question. I’ve found shouting, “Your fly is unzipped” is far more effective at getting the dead to react.

(via Ally Fogg)

Both sides

Ladies and gentlemen, behold our new Ambassador to Canada, Kelly Craft.

I think that both sides have their own results, from their studies, and I appreciate and I respect both sides of the science.

She is a “business consultant”, her husband is the CEO of a coal company, and they donated $2 million to the Trump campaign.

I wonder if she thinks her dodge was clever? Because it wasn’t.

Halloween carbs!

We have Cafe Scientifique on the last Tuesday of every month, which just happens to fall on Halloween this year. So we’re having appropriate content — come to the coffee shop, learn all about carbohydrates from Alyssa Pirinelli, and then go hand out carbs at home!

D&D never went away, but it’s coming back

The last time I played Dungeons & Dragons was around 1979, maybe 1980, with two old friends from high school, Steve and Steve. The network of friends was broken up by my need to travel around the country, chasing an education and a career, and I never got back into it. It’s just not the same without those face-to-face friends. I have great memories of those years in that small gaming group in the Pacific Northwest, though, and it was my primary outlet for social networking at that time. I should just get on a plane to Seattle and surprise the two Steves some Saturday night.

Anyway, I guess there’s been a bit of a renaissance in D&D’s popularity lately, which, as usual, I’m missing out on. It’s an old-new way to escape some of the faceless anomie we sometimes experience in our digital universe.

In 2017, gathering your friends in a room, setting your devices aside, and taking turns to contrive a story that exists largely in your head gives off a radical whiff for a completely different reason than it did in 1987. And the fear that a role-playing game might wound the psychologically fragile seems to have flipped on its head. Therapists use D. & D. to get troubled kids to talk about experiences that might otherwise embarrass them, and children with autism use the game to improve their social skills. Last year, researchers found that a group of a hundred and twenty-seven role players exhibited above-average levels of empathy, and a Brazilian study from 2013 showed that role-playing classes were an extremely effective way to teach cellular biology to medical undergraduates.

Hey, what? Teaching cell biology with role-playing games? That sounds interesting, and I had to look that one up.

In short, an RPG is a game in which a person (in this case, the teacher) tells a story that is enacted by the players who are given roles as the various pieces of background information. Challenges related to the story are then presented and must be addressed by all participants. Each player represents a character in the story and is attributed (quantitatively-defined) skills. These skills are tested during the game to decide if the character succeeds in his or her attempt to perform a task that solves the problem or overcomes the challenge. The skill is usually tested against some kind of quantifiable decision-making system, such as rolling dice. The dice introduce randomness into the game, create suspense and provoke playfulness among the players. This is the main difference between role-play, which refers to the playing of roles in a theatrical play, and RPG, that introduces clear rules according to which the players must decide how to act.

One of the most interesting and significant aspects of the RPG is that the whole team must win together: there are no losers in this kind of cooperative game, ensuring that nobody is excluded or feels excluded.

Unfortunately, all the details of how the game works are in appendices that I can’t find online! I can believe that adding a narrative to the biochemistry of the cell would help with student engagement, I would just wonder if the investment of student time in a game like this is effective enough.

Turns out there is a price paid for spraying venom onto the internet

Horrifying. Read about the day Lane Davis murdered his father. Davis was deeply involved with the far, far right, working as an unpaid intern for Milo Yiannopoulos, writing for the demented Ralph Retort web site, and he finally snapped.

Lane had spent that Friday morning as he did most mornings, on the internet. This day, like the others, Lane read and retweeted posts celebrating the Second Amendment, bemoaning diversity, and spreading conspiracy theories that alleged Hillary Clinton’s campaign chairman John Podesta was involved in a child sex ring and DNC staffer Seth Rich had been murdered. It was the end of a busy week during which he contributed to the Donald Trump subreddit, and over on The Ralph Retort, a fringe blog where he worked as a political editor, (unpaid, according to the site’s owner), he had celebrated the idea of a Kid Rock Senate run, claimed America was under threat of Sharia law, and wondered whether CNN was “literally ISIS.”

Lane’s parents, Catherine and Charles Davis—Charles was known as Chuck to his friends— were used to their 33-year-old son’s outbursts. They had become so frequent that Charles had started recording the tirades on his phone. But that afternoon, they were tired of Lane’s screaming, wanted him to leave, and told him as much. Instead, Lane chased his parents around their home, spitting in his father’s face while screaming that he wasn’t threatening to kill them, but “pedophiles who were taking over the country.”

Whoa. Your 33 year old son is still living in your house and spends his time literally screaming at the internet? I think maybe it’s time to hold an intervention. Unfortunately, it’s people like that who get the most attention on the internet.

This 911 call goes on with ever escalating behavior.

“We’re trying to but he’s chasing us around the house,” she replied. “He’s mad about something on the internet about leftist pedophiles and he thinks we’re leftist and he’s calling us pedophiles. And I don’t know what all.”

Catherine laughed. “He just lives on the internet and he gets really worked up about everything that’s going on. He needs an intervention of some kind here.”

Police were on their way, the dispatcher told Catherine, and she hung up. But Charles’s phone kept recording.

His mother laughed. She’d become so inured to her son’s rabidity that she had lost all sense of perspective. That’s tragic, because the recording includes her son taking a kitchen knife and stabs his 73 year old father to death.

Not all right-wingers are incipient father-stabbers, but jesus…you have to recognize that somebody who’s ranting about PizzaGate, thinks Hillary Clinton leads a pedophile ring, and listens to professional internet assholes like Alex Jones or the Ralph Retort, has got serious problems. These aren’t the cause of the problem, but are symptoms that ought to be seen as potentially diagnostic.

It’s a metaphor for America. Like Catherine Davis and her dangerously lunatic son, we’ve gotten used to the Republican party and Donald Trump.