15 November 2018


An heirloom variety called the Turkish Black (via).

More info at the World Carrot Museum.

How your gut bacteria may affect your weight and health

Two articles in recent weeks detailed some new and significant findings about the human gut microbiome.  First from NPR:
Moving to the U.S. can seriously mess with immigrants' microbiomes, according to a new study that tracked the digestive health of refugees coming to Minnesota from Southeast Asia. "We found that when people come to the U.S.A., they almost immediately begin losing some of their native microbes," says Dan Knights, a quantitative biologist at the University of Minnesota and the study's senior author. Some of the strains they lose are ones that help them break down and glean nutrients from fibers found in Southeast Asian staples like wild greens, coconut and tamarind...

Among that group of 19 refugees, researchers noticed that a Western bacteria strain called Bacteroides began to displace the non-Western strain Prevotella within their first six to nine months in the U.S. But they lost more microbes than they gained — "so the diversity in their microbial communities decreased," Knights says. "And some of the Prevotella bacteria they lost were the ones that helped them digest fiber from plants and greens."

Some of the bacteria in our guts feed, and survive, on particular fibers found in grains and greens — and die off when they don't get enough. But changes in diet didn't explain all — or even most — of the change in immigrants' microbiomes. "It could be that other factors, like exposure to different medications, especially antibiotics or changes in the quality of water they're drinking, are also affecting their microbiomes...

"In speaking with community members, we also realized that for them, the biggest concern was obesity," says Vangay. "Because they had observed in themselves and their relatives and friends that when they moved to the U.S., they gained a lot of weight. And in some cases, they hadn't really changed too much about their diet."
Fascinating.  Now this from Harvard Magazine:
A. Sloan Devlin, an assistant professor at Harvard Medical School, and her team have discovered that altering a single gene in a single type of bacteria can even change the metabolism of the host organism...

During the 32-day study, the mice that could not process bile, for instance, had more fat in the liver and gained weight much more slowly than the other group. They also used proportionately less fat and more carbohydrate for energy...

“It’s a bacterium,” she points out, “and a single enzyme in a bacterium, that’s causing a change in whether the host is using fats versus carbohydrates.”
Control of body weight used to be conceptually so simple: calories in minus calories expended.  Now it appears to be much more complex than that.

Related: Fecal transplant to treat C. difficile colitis.

Introducing the pyrosome

I've never heard of such a creature before.  This one filmed off the coast of New Zealand.  Via.
Pyrosomes, genus Pyrosoma, are free-floating colonial tunicates that live usually in the upper layers of the open ocean in warm seas, although some may be found at greater depths. Pyrosomes are cylindrical or cone-shaped colonies made up of hundreds to thousands of individuals, known as zooids. Colonies range in size from less than one centimeter to several metres in length. They are commonly called "sea pickles."

Pyrosomes are brightly bioluminescent, flashing a pale blue-green light that can be seen for many tens of metres. The name Pyrosoma comes from the Greek (pyro = "fire", soma = "body"). Pyrosomes are closely related to salps, and are sometimes called "fire salps". Sailors on the ocean occasionally observe calm seas containing many pyrosomes, all luminescing on a dark night.
You learn something every day.

14 November 2018

"They Shall Not Grow Old"

I generally do not enjoy war movies, but this one looks awesome.
They Shall Not Grow Old is a 2018 British documentary film directed and co-produced by Peter Jackson. The film was created using original footage of World War I from the Imperial War Museums' archives, most of it previously unseen, alongside audio from BBC and IWM interviews of British servicemen who fought in the conflict. Most of the footage has been colourised and transformed with modern production techniques, with the addition of sound effects and voice acting to be more evocative and feel closer to the soldiers' actual experiences.
And here's a "making of" interview with Peter Jackson:

Blue dot in a red state

Here's the county-by-county voting pattern in the Minnesota governor's race last week.  You wouldn't know from this image that the candidate who won was a Democrat (blue).  The explanation lies in the closeup of the Twin Cities area:

It's the same here in Wisconsin.  I live in Madison, which is one of several "blue dots" in a state whose counties are almost all "red."  You can find many other examples if you search Google Images for "blue dot" "red state."

This degree of polarity is not healthy.  It was discussed at length in an Atlantic article in 2012:
The new political divide is a stark division between cities and what remains of the countryside. Not just some cities and some rural areas, either -- virtually every major city (100,000-plus population) in the United States of America has a different outlook from the less populous areas that are closest to it...

The voting data suggest that people don't make cities liberal -- cities make people liberal...The gap is so stark that some of America's bluest cities are located in its reddest states. Every one of Texas' major cities -- Austin, Dallas, Houston, and San Antonio -- voted Democratic in 2012...

In due course, these populous bastions of urban liberalism have helped spur state legislation and court rulings to create new laws, such as those permitting same sex marriage, that are often in direct conflict with federal laws and with the majority of fellow state counties...

These state laws are the foundation for potential future federal laws, but the sudden, radical divergence between laws from state to state is leading to a dizzying decentralization...

A mass murderer speaks through Instagram

"... the gunman who killed 12 people at a country music bar, posted on social media during the deadly rampage, according to law enforcement officials.

The first call to law enforcement came in at 11:19 p.m. Wednesday, officials said. The authorities arrived at the Borderline Bar and Grill in Thousand Oaks, California, three minutes later. They entered the building at 11:25 p.m.

[redacted], 28, first posted on Instagram at 11:24 p.m: "It's too bad I won't get to see all the illogical and pathetic reasons people will put in my mouth as to why I did it," the military veteran said in the post. 

"Fact is I had no reason to do it, and I just thought.... life is boring so why not?" [redacted] posted, according to ABC News and Buzzfeed.

Three minutes later [he] posted, "I hope people call me insane (two smiley face emojiis) would that just be a big ball of irony? Yeah... I'm insane, but the only thing you people do after these shootings is 'hopes and prayers'...or 'keep you in my thoughts'."

He added, "Every time...and wonder why these keep happening... --(two smiley face emojis)."

"I'm alone. I'm scared."

There are countless tragedies arising from the California wildfires.  As I get older I have increasing empathy for senior citizens who not only lose all their possessions in floods and fires, but who also have no close family or established support group to fall back on.
Marilyn Pelletier got a knock on her door in Paradise as the Camp Fire raged and was told she had five minutes to leave. She grabbed her medicine bag and her small dog, and when she left "the whole sky was pink."

"You could see the fire coming," she said. "It was devastating. It's horrible. The worst thing I've ever experienced in my life. I was just — I'm grateful I got out with my life."

Pelletier moved to Paradise two years ago after her husband passed away, and bought a house in the town which was destroyed in the fire, she said.

"It’s a beautiful home — it was. It was real pretty,” Pelletier said. "I'm devastated. I'm heartbroken, I'm alone, I’m scared."
The screencap and quote come at the end of a two-minute video on this page.

12 November 2018

This is an interesting book

Jonathan Rauch is a highly-respected journalist (New York Times, Washington Post) and contributing editor of The Atlantic.  After enduring and overcoming a mid-life stressful period, he extensively researched the psychosocial and behavioral science literature on happiness, and summarized it in this book.  I had seen several favorable reviews, but wasn't expecting much new insight into an admittedly nebulous concept of happiness/unhappiness.  I was wrong; this was a good read.

The book begins with several introductory chapters exploring the definition of happiness and unhappiness, discussing the measurement tools and the strengths and weaknesses of survey data, and examining the effect of various life experiences.
"All the evidence says that on average people are no happier today than people were fifty years ago... Yet at the same time average incomes have more than doubled... how you feel about your life does not necessarily reflect how one might suppose you should feel, at least by the materialistic standards of homo economicus... People who are in very fast-growing economies are less happy than people in slower growing economies... Rapid change makes people very unhappy... the paradox of frustrated achievers and happy peasants."
The U-shaped curve featured on the book cover has been recognized for decades and reproduced in a multitude of studies.  The reason for that shape is less clear, and is the focus of Rauch's book.  If you are in a hurry with little time to read, I recommend skipping to chapter 6 - "The Paradox of Aging: Why getting old makes you happier."
"Stress declines after about age fifty... trying to explain what caused stress to decline so sharply, they adjusted for about twenty variables... The pattern didn't change.  In fact, it grew stronger, as if age itself were reducing stress... Emotional regulation improves... part of the reason emotional weather tends to settle down with age may be the accumulation of life experience... "I don't let that stuff bother me anymore"... Older people feel less regret... healthy aging helps people accept what they can't control..."
There's way more to discover in the book, which can be read in a couple evenings, but I think it is deserving of a more leisurely perusal, leaving oneself time for self-reflection.  If nothing else, just the knowledge that the axioms "this too shall pass" and "things will get better" have some statistical validity is rather reassuring.

Lest we forget


Riding full circle on a paternoster

"A paternoster or paternoster lift is a passenger elevator which consists of a chain of open compartments (each usually designed for two persons) that move slowly in a loop up and down inside a building without stopping. Passengers can step on or off at any floor they like. The much smaller belt manlift which consists of an endless belt with steps and rungs but no compartments is also sometimes called a paternoster.

The name paternoster ("Our Father", the first two words of the Lord's Prayer in Latin), was originally applied to the device because the elevator is in the form of a loop and is thus similar to rosary beads used as an aid in reciting prayers.

The construction of new paternosters was stopped in the mid-1970s due to safety concerns, but public sentiment has kept many of the remaining examples open. By far most remaining paternosters are in Europe, with 230 examples in Germany, and 68 in the Czech Republic. Only three have been identified outside Europe: one in Malaysia, one in CEB Sri Lanka and another in Peru."

10 November 2018

Performing a fecal transplant at home

Excerpts from an interesting case report:
I’d had intestinal distress before, but never like this. I was excreting not just waste, but blood and bits of my colon’s lining — up to 30 times per day. My abdominal pain hit deeper and felt less productive than the pain of giving birth, epidural-free, to my second child. Even shingles, which stung like a dental drill against my face, paled in comparison. Such was the agony of Clostridium difficile...

Things started innocently enough. In early 2013, my doctor diagnosed me with a bacterial infection and prescribed an antibiotic. I had lived antibiotic-free for nearly four decades — a streak I was not inclined to break. But my doctor insisted on antibiotics, and I reluctantly complied.

Soon after, my stomach turned against me. I went to an emergency room and was sent home with a prescription for vancomycin, an antibiotic reserved for serious bacterial infections. But the drug proved little match for the microbes that had bum-rushed my colon. My weight and fluid loss accelerated. My colon risked perforation.

Because C. diff. spores can live for months on bedrails, doorknobs, and linens and easily shrug off common detergents and sanitizers, my master bathroom became my biohazard containment unit. There, I alternated between sitting on the toilet and lying on the floor. My husband, Esteban, brought me supplies and emotional support...

So, when I called around about the possibility of treating my C. diff. with a fecal microbial transplant, a sensible doctor might have offered to refer me to one of those approved practitioners. Instead, everyone I talked to refused to even entertain the idea, seemingly out of disgust.

“Yuck, you don’t want that. Just stay on the vancomycin,” my first doctor told me. A second, a gastroenterologist, simply substituted “gross” for “yuck.” A third, more tactful, expressed relief that FDA policy absolved him from having to offer the procedure...

And so it happened that when my C. diff. roared back, worse than before, after the end of my 10-day vancomycin course, my doctor’s response was to simply prescribe more vancomycin. With each subsequent treatment, however, my likelihood of recovery dropped dramatically. I started the ordeal with an approximately 70 percent chance of recovery. After months of failed antibiotic treatments, my chances had sunk below 10 percent.

My last trip to the emergency room was a grim formality. The C. diff. battle now raged beyond my colon. “You may want to tell loved ones about your dire circumstances,” my gastroenterologist said. It dawned on me that my doctor would sooner let me die than discuss a fecal transplant. That’s when I decided to do the transplant myself...

A New England Journal of Medicine article offered some procedural clues. For instance, my ideal donor would have a microbiome that was untainted by antibiotics. That ruled out Esteban, who had recently been administered antibiotics during an eye surgery. Ultimately, I turned to my 11-year-old daughter.

She responded openly and inquisitively, asking more questions than any of my doctors had. “Is this like in Clash of Clans when you have no troops left in your clan castle and you need someone else to donate some?” she said, referring to a popular multi-player video game.

Yes, it’s exactly like that.

She agreed to do it, and at around 10 pm on a Tuesday, Esteban collected the sample. He dropped it into a blender, added saline, blended it, strained it, and poured the concoction into an enema bottle, as I lay depleted on the floor. My gut drank up the infusion as if it were dying of thirst. My colon, after five months of near-constant spasms, recovered in one transformative instant. Overnight, I went from having 30 bowel movements a day to having one. For breakfast the next morning, I ate a quesadilla loaded with black beans, cheese, salsa, lettuce, and guacamole. I’ve had no recurrence of C. diff. since. 
There's more at the link.

Watch Mr. Wizard

This is a half-hour television episode from 1954. You'd have to be 60 years old or more to have seen this segment live, but younger visitors may remember later episodes or the Canadian revival in the 70s, or the updated Mr. Wizard's World of the 1980s.

For many baby boomers, this was our introduction to "hard science" and the concept that science could be interesting (and comprehensible). I suppose it would be different now; the teacher probably wouldn't be allowed to place a hand on Johnny's shoulder, and they probably couldn't make something explode on live camera by aerosolizing lighter fluid and igniting it.

Reposted from 2008, because Mental Floss has just posted an excellent history of the program:
Watch Mr. Wizard, which aired on NBC from 1951 to 1965, featured host Don Herbert performing a series of science experiments using everyday objects—glass bottles, cans, aquariums, matches—to illustrate the amazing world of physics. Eggs were sucked into bottles; water was boiled using an ice cube. They were pseudo-magic tricks, but instead of obscuring his method, Herbert satisfied the audience’s curiosity by explaining how science made them all possible...

Don Herbert Kemske was born July 10, 1917 in Waconia, Minnesota. He developed an interest in science while in the Boy Scouts and later obtained a degree in English and general science from the University of Wisconsin–La Crosse (then known as La Crosse State Teachers College) in 1940. But Herbert didn’t pursue a teaching career. Instead, he followed his interest in drama and theater to New York City, where he worked as a pageboy for NBC, acted opposite future First Lady Nancy Reagan, and was cast in a Broadway show...

Like a lot of television of the era, it was live, not taped. The pace was leisurely, with Herbert walking through general principles over the course of a half-hour. Crucially, he refused to wear a lab coat or conduct his experiments in a laboratory setting. Instead, he wore short-sleeved shirts and used common household items while broadcasting from a garage or kitchen...

Within a few years, Watch Mr. Wizard was being carried in more than 100 markets and was reaching between 1 and 3 million weekly viewers... After viewing a pilot, Nickelodeon agreed to fund 26 half-hour episodes of Mr. Wizard’s World for a 1983 premiere.

Following Herbert's death at age 89 in 2007, a National Science Foundation official claimed that, more than anyone, Herbert may have been the person most responsible for getting people interested in science. In the 1960s and 1970s, applicants to The Rockefeller University—a science research center based in New York City—were asked what inspired them to get into science. In the space allotted for an answer, half of them wrote: "Mr. Wizard."
What I didn't know in the 1950s was that Don Herbert was related to one of my high-school classmates.  Posted for Steve, currently enjoying retirement in Santa Fe, New Mexico.

Train rides in Norway

With a tip of the blogging hat to reader Drabkikker.

Driving in California yesterday

World Championship magic performance

Via Neatorama. (best viewed fullscreen)
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