What’s the poop?

One of my favorite topics at the moment is the human microbiome. That’s the part of us that’s not human. Back in May, I wrote a post about it:

A human body has about 10 trillion cells in it. And that very same human body (yours, for example), is also home to 100 trillion bacteria. Your mouth, your nose, your armpits, your navel, your skin and especially your gut are teeming with thousands of different species of bacteria. If you could separate out all those bacteria from the rest of you, they’d weigh 2 kilos.”

I was suggesting (only partially in jest) that we’re actually being crowdsourced by a superior form of collective intelligence. Just last month, I wrote another post about how the gut microbiome plays an important role in mental health.

I was wrong on one count. I mentioned a study that had found that excessive use of antibiotics can permanently damage your gut flora. It turns out there’s hope after all. Here’s the story:

Antibiotic overuse can allow a particularly nasty (and appropriately named) microbe, Clostridium difficile, to set up shop in the gut. This critter makes you really miserable – recurrent bouts of  severe diarrhea, abdominal pain, nausea and vomiting. It stubbornly resists treatment – well, most treatments. There is one that works.

A fecal transplant.

It turns out that the gut flora from a healthy human donor can outcompete C. difficile, restoring gut health in no time flat. (Ce n’est pas si difficile…)

And where can this gut flora be found? Right. Someone else’s poop. Wait. Don’t go away. Bear with me for a minute, this is really interesting stuff (this is a picture of some E. coli, magnified 10,000 times, originally from the USDA).


gut bacteria

Dave brought it up this morning in our regular chat.

Dave: Apparently it works.

Me: works for what?

Dave: (sends a link) It cures gut infections caused by antibiotic therapy.  Gives new life to the phrase “eat shit”

Me: I see. repopulating the gut microbiome. I can write about that.

Dave: That’s why I instantly thought of you when I read about it. (That’s my story and I’m sticking to it)

Yes, indeed. The article he sent me describes the case of 75-year-old Pat Shoop, who had a nasty C. difficile  infection. Her husband valiantly offered to provide a batch of bacteria from his own, healthy gut.

… Bob was under pressure to produce a usable stool sample within 15 minutes of her scheduled appointment. […] He complied and the pair rushed to the clinic, where Dr. Rubin snaked a tube through Shoop’s nose and into her stomach. “It was 20 minutes,” she said. “He told me, ‘You’re not going to taste it, you’re not going to smell it.’”

Apart from the obvious question of what constitutes “usable” – consistency? size? – one wonders why Bob had to be under so much pressure. Couldn’t he just refrigerate his offering? Another thing not mentioned in the article was exactly how the sample was prepared. I had to go elsewhere to find that information:

An article in the Scientist describes how Australian gastroenterologist Thomas Borody did his first transplant (in the mid-1980s) :

…He collected stool from the woman’s brother, and after screening it for known pathogens, he stuck it in a blender, added some brine, and filtered it to get rid of any undigested material. The stool, now turned into slush, was administered to the patient — who had her gastrointestinal tract previously flushed — via two enemas over the course of two days.

In only days, the patient was cured. Her colitis never returned.

In fact, a recent study shows that fecal transplants (which often go under the more palatable monikers of fecal bacteriotherapy, intestinal microbiota transplantation or human probiotic infusion) successfully cure more than 90% of intractable C. difficile cases and many other cases of irritable bowel disease (IBD) and ulcerative colitis. The transplant is administered either via enema, or, as in Pat Shoop’s case, via a nasogastric tube.

Borody oversees 5-6 fecal transplants a week, mostly for patients with IBD. It’s catching on in the US, as well:

Currently, while most fecal transplants in the U.S. are performed exclusively to treat C. difficile, a growing list of doctors, […] are beginning to expand to other gut disorders such as inflammatory bowel diseases. Because stool is not yet a marketable biologic product, the procedure is not federally regulated.”

Note the use of the word “yet” in that last sentence. I sense an entrepreneurial opportunity here. If I weren’t so damn busy translating…

It’s considered a treatment of “last resort,” which is also a bit odd, seeing as it has been used in veterinary practice for ages to calm the bellies of ruminants. In fact, come to think of it, don’t animals regularly partake? Could it be they know something we don’t?

Lest you be tempted to get out the blender and take matters into your own hands, be aware that this is a job for professionals only. The wikipedia page on fecal bacteriotherapy says that “The best choice for donor is a close relative who has been tested for a wide array of bacterial and parasitic agents.The enemas are prepared and administered in a hospital environment to ensure all necessary precautions.” 

The page goes on to describe a new “safer, more effective, and easier to administer” form of fecal bacteriotherapy that’s being developed, which requires the patient to keep a refrigerated sample on hand. In the event that he/she develops a C difficile infection, the sample is extracted with saline, filtered, freeze dried and put into capsules. The patient can then repopulate her gut with her own microbiome just by popping a pill! Now that’s a win-win.

One obvious question arises, however: How many of us are paranoid enough to prepare ahead for a C. difficile infection?  

And another, given the current lack of federal regulation:  What’s the refrigerator shelf-life of a shit sample? 

You might be wondering what all this has to do with mental health.

In January 2011, an article appeared in NewScientist magazine, which you can’t read unless you have a subscription 🙁 , telling the story of an elderly Parkinson’s patient who came to her doctor with a horrible case of constipation and an infected colon. I think the doctor treated her with a fecal transplant from her son, but I don’t know for sure, since I’m not a subscriber. Anyhow, rumor has it her Parkinson’s symptoms miraculously disappeared along with her gut infection.

What I do know is that Borody is currently doing a clinical trial on 18 Parkinson’s patients using C. difficile antibiotics. It will be very interesting to see what happens. Could it really be as straightforward as swapping out our shit? Like I said in my earlier post, maybe it’s time we paid more attention to all those freeloaders in our bellies.

A moment in the sun

chillin'Due to visitors, huge quantities of work that have piled up, and my growing obsession with trolling useless websites, I haven’t posted anything on Gydle for almost a week.

I think I need to take a lesson from my cat.

One of the cardinal rules of blogging is that you’re never supposed to write anything about your cat. Ever. I know this because the websites I’ve been trolling lately are those that purport to tell me about how I should be blogging.

The other thing they all seem to find important is a blog’s ability to generate “traffic.”

I wonder, though. It’s kind of like the question about the tree falling in the forest. If it falls, and there’s no one around to hear it, does it still make a sound?

I was a philosophy major in college, and so I spent a lot of time pondering this question, with and without the aid of alcohol. I came to the conclusion that it really doesn’t matter. Not to the tree, not to the person who didn’t hear it, not even to the little worm who got squished when the tree hit the ground. I’m pretty sure I wrote an essay on it at one point,  judged by an Oxford don as “Interesting…” (Note: when an Oxford don says something is interesting it means they think it’s completely worthless.)

Just because a blog has a lot of traffic doesn’t mean it’s worth reading. After putting some thought into it, I realize I’m not willing to do what it takes to get people to flock to Gydle. I could probably spend the time and do the cybergymnastics required, but I won’t. Because in the end, it doesn’t really matter if anybody in the vast cyberforest of the internet hears my particular tree falling. This blog is my moment in the sun. And that’s enough for me.

Does it look like Smokey over there cares if you’re looking at him or not?  He knows he’s handsome. Get a life, he says. And next time, clear all this crap off the chair before you leave the room.

Smokey has it right. Life’s too short to worry about whether you’re doing things right. Just enjoy the sunshine and don’t squish anyone.

Stay tuned, because once I’m caught up with my work, I’m planning to write about some exciting topics, including a manifesto on cognitive biases and another on units of measure. I might write about nutraceuticals, too, because I think they’re a huge scam. (I’m living in Nestle-land, after all.) As usual, I welcome your ideas and suggestions. I might really rock the boat and write a post about Smokey. He’s not an ordinary cat.

Here’s a link to a hilarious geeky gadget blog. I love its tone. It reminds me of my cat, who doesn’t care if I think he’s gorgeous or not. Thanks, Ellen, for showing it to me!


Linguistic commutivity

I got the e-mail on Thursday. A translation for a client, due Monday. It was short and non-scientific, which can sometimes be a nice break. It’s good to diversify! I had a bunch of other stuff to finish up on Friday, but I said I’d do it over the weekend.

Saturday at 7:15 am, I’m in the car with Luc, headed to his school for the PSAT.  We had discussed equipment the evening before.  Two pencils, an eraser. A calculator, just in case. A pencil sharpener.

Fifteen minutes into the drive, I think to double check. “Do you have your pencils?” check. “Eraser? Pencil sharpener? ID?” check. check. Check. “Calculator?” Umm. Oops.

What is it with my offspring and standardized testing? I utter a few choice expletives at high volume. At least this time, there’s no one else around to hear it. “I told you LAST NIGHT to get all this stuff ready!”

I pull off the freeway, looking at the clock. There isn’t time to go home, get the calculator, and get to the test on time. And now I’ve wasted even more time pulling off the freeway! More words exit my mouth. Luckily I have my phone, and he calls a friend and solves his own problem. All that excitement for nothing.

I’m also in a hurry because I have to hightail it home and take Brendan to the train station. He and two of Marc’s students are heading off to Africa to dig holes way the hell out in some godforsaken village in the bush, studying erosion. Marc isn’t joining them until a week later. I’m just a little anxious about all those malaria-carrying mosquitoes that want to feast on my firstborn’s innocent, unsuspecting eighteen-year-old flesh. I make sure we double-check: passport, Yellow Fever vaccination certification, mosquito net, insect repellent, headlamp. (No electricity.) “Remember to only drink bottled water,” I remind him for the five-thousandth time.

Sunday rolls around and I open the file. It’s two short interviews, one with an Irishman and one with a Brit, along with a short introduction. The title for each piece is a quote taken from the interview.

Now we translators may not be the brightest bulbs on the tree, but I know that these interviews were not conducted in French.

They were done in English, translated into French, and now I’m being asked to translate them back into English.

Here’s the thing: The commutative law of arithmetic doesn’t apply to language. You can’t assume A+B-B=A, where A= a bunch of words in English and B=those words translated into French.

I’m stymied. What, is this some sort of quality control test? Are they trying to see how close I come to the original English to see if I’m any good as a translator? 

I fire off an e-mail, asking for a copy of the original interviews. But it’s Sunday in Switzerland, which is sacred. Only Americans like me who don’t have any extended family in the vicinity can get away with working on Sunday. And since tomorrow first thing I’m heading to Zurich to hang out with my visitor Susan and my Dutch friend Mieke, it has to get done now. So I bite back my compunctions, translate the French back into English, and send it off.

Monday evening, in Zurich, I check my e-mail on Mieke’s computer. I have a message, with the original English interviews attached. “But please base your translation on the French translation,” it says.

Okay, I understand, we need to make sure the sentences are grammar-error-free and the whole thing hangs together logically. I’ve conducted plenty of interviews myself, and I know about cleaning things up. Talking is different than writing, and adjustments sometimes have to be made.

This said, I still feel very strongly about staying true to the words that come out of someone’s mouth.  People who translate or write for a living know that there are many ways to spin a story. In an interview, the person who was talking spun the story in a particular way, choosing a particular set of words. When I pulled off the freeway Saturday morning, I used specific words. I didn’t say, “Gosh darn shucks, Luc, that wasn’t too bright!”  It just doesn’t ring true, now, does it?

You see, doing a re-translation-of-a-translation violates the whole interview ethic. When you’re quoting someone, you’re sharing the words they used. Period. When I translate back from the French translation, I run the risk of using slightly different words, because English is a wonderfully rich language, chock full of synonyms. And if the French translation was less than optimal, that risk skyrockets. Without the original, I have no way of knowing how good the French translation was.

So, obviously, I was very relieved to get the original interviews.

I fixed them up and sent off the new version. In fact, the French translation had been good, and so my translation of the translation had been pretty close to the mark. I had warm fuzzies on two counts – number one, I wasn’t going to be involved in misquoting anyone, and number two, I don’t completely suck as a translator.

Back home Tuesday night, I opened my e-mail to a message saying that I had accidentally left a double sentence in one of the interview answers. I’d pasted from the original, but neglected to cut out my original translation. A mistake!!

“I’d appreciate it if you would pay closer attention in the future 😉 ”  he wrote (in French, “Merci de faire bien attention pour la suite 😉.”

That was it. No “Thanks for fixing it up at short notice!” or “Great translation!” But that’s okay, I knew it was a good translation. I don’t absolutely need positive feedback. Of course, a good word would have made the likelihood of my taking the next little job from this source about 100% greater…

Still, there was a wink there, and so in the spirit of the thing, I lobbed it back (in English):

“Sorry! Next time, please send the original English interview as well, so we can avoid the whole issue!!”

Pet oddities

Last week, an article in the local paper caught my eye:

143 Mexican redknees looking for good homes.

Whoa. That’s a lot of tarantulas. But believe it or not, that was only the tip of the iceberg.

In late August, someone tried to enter Switzerland with a suitcase containing 260 live Mexican redknee tarantulas loosely packed in plastic bags. Authorities confiscated the tarantulas and split them up between three zoos in Switzerland, one of which was the Vivarium in Lausanne. The picture accompanying the article showed a pile of McDonald’s salad containers, each of which presumably contained a tarantula. Whoops, that’s not my salad! Continue reading

Moment of beauty I

new mexico snow october

Not long ago, I did a guest post on the Running and Rambling blog. One of the best things about that blog is a series of entries called “Random Shots of Beauty” – pictures that Donald has taken out on his runs. I’ve decided to do a similar thing here.

This first entry is a picture shot by my brother Rob last week, i.e. early October, near Santa Fe, New Mexico. It took my breath away.

It should dispel the picture that many people mistakenly have of New Mexico as a hot, cactus-studded desert wasteland.  In fact, Santa Fe in winter is colder than where I live now, outside Lausanne, Switzerland. It’s higher in altitude, at nearly 7,000 feet (2,200 m). And in the summer, it’s appreciably cooler, drier and more comfortable than Baltimore, where we lived for seven years before moving here.

It rivals Switzerland and Nova Scotia as one of the most beautifully livable places on the planet, in my humble opinion. (Shhh. Don’t tell anyone. There are already too many residents of a certain shall-not-be-named neighboring state buying expensive summer homes and trying to ski on our slopes. But they’re probably not reading this blog, anyway…)

Greater expectations

The passing of Steve Jobs has rocked the world.  Tributes and retrospectives, quotes and video clips, comments and thoughts are inundating the Internet –  on Facebook, Twitter, Google+, on blogs, e-mails and news platforms. It’s sobering to realize that very few of us inhabited these places even just a decade ago. Now, largely thanks to Steve Jobs, we’re comfortably ensconced in this connected, vibrant community. And our lives are so much richer for it.

I was thinking today about expectations. I wondered how Steve Jobs’ parents felt about him not graduating from Reed College.  Maybe it wasn’t that big a deal to them. Maybe they didn’t have an image of him as college-educated, so he wasn’t letting them down. But then again, maybe he was.

At one point in his career, when he was leaving Apple, he said to a small group of employees, “I don’t wear the right kind of pants to run this company.” (He was wearing jeans – and barefoot!)  Another time, when asked what market research went into the iPad, he replied: “None. It’s not the consumers’ job to know what they want.”

I’m no Steve Jobs expert, but it seems to me that he did a remarkable job of freeing himself to follow his intuition and passion. When crunch time came and he had to make a decision, he chose to take his own path. He didn’t make any compromises. He knew.

Here’s to the crazy ones. The misfits. The rebels. The troublemakers. The round pegs in the square holes. The ones who see things differently. They’re not fond of rules. And they have no respect for the status quo. You can quote them, disagree with them, glorify or vilify them. About the only thing you can’t do is ignore them. Because they change things. They push the human race forward. And while some may see them as the crazy ones, we see genius. Because the people who are crazy enough to think they can change the world, are the ones who do. – Steve Jobs.

Most of us spend our lives working hard, striving, trying to do our best. We all want to make a difference, to leave this world a little better off because we were in it. But let’s face it, we’re most of us square pegs in square holes. We’re not the crazy ones. We’re the ones who feed the crazy ones, listen to their crazy ideas, do their crazy laundry, pay their crazy bills, teach their crazy kids. We’re the ones maintaining the boats that the crazy ones come along to rock.

But here’s the news flash: everyone, deep down, has a piece of that craziness in them. And sometimes it rears up its head and wants its day in the sun.

Why should the misfits have all the fun, after all? They know that satisfying other people’s expectations is incompatible with who they need to be and no fun to boot, so they forge on, shocking, upsetting and amazing people – and changing the world. It might take us square pegs a little longer, but if we’re lucky, we get a glimpse of it, too. That “divine cockeyed genius” that takes possession of you in order to express something larger than yourself is not something to be ignored, no matter when it appears in your life.

Steve Jobs was right. Here’s to the crazy ones. Set your own bar. Set it high.

image: Carl Blake

A bittersweet Nobel

It’s that time of year again – Nobel Prize season.  Today the physics prize was announced, and all over the twittosphere science writers were tweeting about one of the recipients – the first Nobel Prize winner with a non-professional twitter account! (@cosmicpinot) Would it, could it out-trend the iPhone 5 announcement? How many followers would he have by the end of the day? (It went from 350-1,230 by the end of the day in Switzerland….)

The physicist-tweeter, Brian Schmidt, is an amateur wine-maker from Australia; he also happens to be an astronomer who contributed to the stunning discovery that the universe is expanding at an accelerated pace. The mystery to it all is dark energy, which nobody understands yet. He shared the prize with Adam Riess from the Johns Hopkins University, who said, “The phone rang, it was 5:30 and it was some Swedish sounding people, and I knew they weren’t from IKEA…”

I know from personal experience that the IKEA in Baltimore doesn’t open until 10:00 sharp. No, that 5:30 phone call can only be one of two possibilities … either your teenage son is calling from the police station asking you to bail him out, or you’ve won the Nobel Prize. And from his picture, Riess looks way too young to have a teenage son.

The third winner, Saul Permutter, is at Lawrence Berkeley Laboratory in California. If they all got the news at the same time, he would have been woken at 2:30 am. “Mom? Is that you? No? Inge? What? A Prize? Holy shit, honey, I won the Nobel Prize!”

Things didn’t go so well for the Medicine awardees. This year’s prize was to be split, like the physics prize, between three men, half going to Ralph Steinman (New York) for his work on the role dendritic cells play in immunity, and the other half shared between Jules Hoffman (France) and Bruce Beutler (California) for their work showing how the immune system recognizes an intruder. The committee deliberated, made their choice, and then tried, in vain, to contact the recipients on Monday morning.

But 68-year-old Steinman had died on Friday night, after a long battle with pancreatic cancer. His family had not yet contacted Rockefeller University. When they did, the University immediately told the Nobel Committee. But the committee had already made the official announcement.  Nobel Prizes are not awarded posthumously, unless the person dies between the annoucement of the prize and the awards ceremony. Technically, Steinman had died before the announcement. What would the Swedes do?

They did the right thing, and announced that Steinman’s prize stood; the money will go to his heirs. They made their decision in good faith that he was alive, and indeed, he fought valiantly to stay alive to receive the news. In addition to standard chemotherapy, he treated himself with a vaccine based on his own research, surviving for four years, which is no small feat in pancreatic cancer. Only 20% of pancreatic cancer victims survive more than a year after diagnosis. Only 4% make the five-year mark.

The news touched me deeply – all I could think about was his family. My dad died of pancreatic cancer, and he, too, was treated with technology he helped invent (radiation therapy), also ultimately in vain. The story brought all those emotions back in force. I cannot imagine the overwhelming experience this must be for his family, all this media attention on top of the horrible pain of the loss, and the wrenching regret that he had to miss out on this extraordinary life event.

My heart goes out to them. The research he did will one day save many lives, but this life, the one that mattered to them, has been snuffed out far too soon.

Sandal spotting

I just got back from running the Morat-Fribourg race – 17.17 km over bucolic Swiss countryside from the charming walled town of Morat (Murten in Swiss German) to Fribourg. The race has historical roots; it supposedly retraces the steps of a courier who was spreading the news that Charles the Bold had been defeated in a nearby battle. This was back in 1476. The runner carried a branch from a linden tree. Like so many runners to follow him, he collapsed on arrival. They planted a linden tree to mark the event.

I’m not going to get into Swiss history here because I would definitely be out of my depth. Who the heck was Charles the Bold and what was he doing in Switzerland? I’d just reveal my ignorance. (Wait, didn’t I just do that?) The race, however, is very popular. There are people who have run Morat-Fribourg every year without fail for most of their adult lives. This was number two for me.

The defining feature of this race is its altitude profile. (If you look at the link, notice all the first-aid stations…) It can be summed up in two words: bad-ass hills. The race finishes on a brutal uphill. This year I ran it in my New Balance minimalist trail shoes that have recently become my number-one preferred footwear. I was a little nervous about this because the race is run entirely on pavement. Up to now, most of my runs in the minimalist shoes have been at least partly on trails. (They’re trail shoes).

They were fine. Perfect. My feet feel great. My left calf muscle is a little sore, but it was 17.17 km, a lot of uphill. I suppose that’s to be expected. I’m sure a couple of beers and some chocolate will take care of it.

But that’s not the news. The news is that for the last 10k of the race, I ran alongside a woman who was wearing Tarahumara-style sandals!! Universes are truly aligning here. This cannot be a coincidence.

Let’s backtrack for a minute to the pre-race milling about in the starting area and the port-a-potty lines. I spent a lot of time looking at other people’s feet. NO ONE was wearing anything other than bonafide, cushioned, stablilized, run-of-the-mill running shoes. No one but me, that is. So imagine my surprise when a pair of huarache-type sandals edged into my peripheral vision on a hill at about 6 miles. WOW! She wasn’t wearing lycra, either. All of a sudden, the race got a lot more interesting.

We had the same basic pace, that is to say, strong on the ups and lame on the downs – without all that cushioning you don’t tend to overstride and slap your feet down so much doing downhill. Even though we were both running along in our own little zones, I loved every minute – I’d found a kindred spirit. Her form, which unfortunately I got a good look at as she pulled away from me on the last hill, was impeccable. I tried to imitate it, even as I was internally empathizing with the poor courier and his linden branch, and worrying about my own imminent collapse.

I didn’t collapse after all, and as I caught up with her in the finish chute I congratulated her on her footwear. She pointed mine out, too. She said she’d tried to find shoes like mine in Switzerland, unsuccessfully. I told her I’d gotten them in the US, and she raved about all the great possibilities in footwear that could be had across the pond. We basked for a moment in our mutual admiration. She asked me if I’d read Born to Run. Does the bear shit in the woods? Is the Pope Catholic? Then we went our separate ways.

The only other person I saw wearing anything alternative was a man walking barefoot across the finish line, way at the back of the pack. But he was carrying his shoes and his feet had some really nasty-looking blisters on them, so I don’t think the barefoot part had been planned ahead of time. He didn’t look too happy.

On a brief, last barefoot note – last week I walked barefoot all the way from the nasty gnarly trail I photographed for my barefoot blog post to our house the other day (maybe 2km). I just had a sudden desire to go barefoot. It was painful, but great. I like feeling the ground without an intermediary. One of the commenters on my Running and Rambling post obviously lives near me because he recommended a path that I know well. That’s my next step, to run/walk that trail barefoot. I’ve survived Morat-Fribourg, so I’ll do it next week and keep you posted!