Tuesday, July 26, 2016

The Japanese Microbiome Calls: 共生生物どうぞう!(Welcome, Symbionts!)

  T   he Japanese microbiome must be vastly different from the Western one.

Contrary to popular Western beliefs, the Japanese don't dine on sushi for breakfast, have sukiyaki for lunch and then grill a nice Steak Teriyaki for dinner, all accompanied by their sticky rice.

What they actually eat is so vastly different from us (but catching up, no doubt about that!) that I can't even describe it to you. It involves lots of vegetables you've never heard of and treats that would make you puke.  And yes, there is lots of rice.

The thing is, they do eat rice often, but not in large quantities. Their microbiomes love the extra sugars and carbohydrates, but they're extremely complex carbohydrates with multiple compounds that benefit the microbiome in ways vastly different than our slice of all-dressed pizza.

But yes, I'm going to make my two-week stay in Japan yet another experiment—because I live to be a guinea pig. (Moru-motto in Japanese—their fucked-up interpretation of the word "Marmot." They use this to talk about all lab animals, irrespective of species.)

I will take a sample the day before I leave—conveniently on a Sunday again—and then eat my "Japanese" diet while I'm there for two weeks. The day I come home I'll take another sample.

Regrettably, I won't be eating sushi and ramen every day. Because the area around my hotel, in downtown Nara, is populated by Italian and hot dog places.

This chain café is everywhere in Japan and serves great hot dogs. I won't be eating them, but my son, Tai-chan, loves them. I might ask HIM to take a sample. Now that might be interesting! I think I'll take a kit with me to Japan . . .
There are no places that serve the so-called Japanese food that everyone is familiar with. There is no steak teriyaki—there is something called teppan-yaki (鉄板焼き) but it's frequented by high rollers and you'd better be ready to flash a wad before entering. Sushi places are also for high rollers. The average Japanese go to places like robata-yakis which are fairly cheap and you can drink like a fish.

I will not be drinking like a fish. In fact, I will not be drinking at all—and my biome cheers.

But back to my biome, and my test results. It's all very curious—and unsettling.

Let me explain: I did my first test at the second week of the grand experiment—for two weeks I had been eating my regular diet, allowing all sorts of things like whipped cream and cake and Clamato, all sorts of other things I don't consume any more. It was meant as a control—in other words, went my thinking, this will be the bad test, the one which will show how fucked up my diet really is.

So when I went to do the sample, I actually used two test "kits," which actually are small vials containing some sort of preservative clear liquid. The idea is, you swab a small tissue (provided) with your "contribution sample," and then swish the tip of the swab in the vial containing the liquid. You screw back on the top, shake it up, and voilà. It's ready to ship.

Thing is, they provide a "spare" vial—I guess just in case you screw up the first sample.

Well, I didn't screw up the first sample, but I contributed to the "spare" vial, with a swab from the same sample on the tissue that I had used for Sample One. So if you're following, the Spare vial should have contained roughly exactly the same quantities and kinds of bacteria that the Main vial contained.

Except it didn't.

When I got the results of my first test, I kind of ignored the fact that they'd done a complete test on my Spare sample as well—when I finally came to the realisation that I actually had two sets of results from the same test, I was naturally expecting the results to be identical. I mean, the swabs had come from the exact same sample on the tissue. How different could the results be?

Well, take a look. I'm not sure which one is the Main sample and which is the Spare, but it doesn't really matter. What matters is how different they are from each other. (Right-click to open the images in a new window; then magnify.)

For example, look at the "Diversity percentile." It differs by an incredible 8%. If that is the case there, how much should I trust the figures on all the other pages?

Then, I got the results from my second test. When I did the second test, it was three weeks after the first test, to the day. The first of those three weeks, I had radically eliminated everything from my diet. No sugar—at all. No dairy, at all, No gluten, at all. I was truly deprived, for a week.

The second and third weeks before Test #2, after the week of the Great Purge, I started with the pre-and probiotics—Prebiotin powder in kefir for breakfast, with a probiotic pill containing 50 billion bacteria, and the rest of the day with very careful and measured reintroduction of only the healthiest comestibles that I could come up with. Viz. lots of broccoli, lots of fruits and nuts and no added-sugar anything. At the end of those three weeks I did Test #2, in exactly the same manner I had done the first test.

So I was expecting radically different results.

What I got, however, was just a puzzle . . . (remember, the dates on these tests are not the dates I took the samples—they're about a month delayed).

Notice how my "Diversity percentile" has plummeted—exactly the opposite of what I thought would occur. Even my "Wellness match" is disturbingly reduced.

How can this be?

But don't take my word for it—take a look for yourself (link and password in my mass email of this post. (Email me here if you want the link and password).

I took Test #3 a couple of weeks ago and am waiting for the results. But it takes a keen eye and a head for figures to analyze the results—a degree in microbiology wouldn't hurt, either.

But the Japan trip opens up a new realm of possibilities. Can I really radically reshape my microbiome just by being in another country?

Results at juu-ichi-ji!

Tuesday, July 19, 2016

We're Surrounded

  I   t's always puzzled me: these scientists on this rabid quest to find life on other planets. What are you gonna do, guys, when you find the life? You're gonna fuck it like you've fucked the life we have.

And we have so much life! We have life on every square millimetre of this planet—and all the way to the edge of space and to the bottom of Earth's crust, there is life. In fact, you could say that Earth is just one huge organism, which it is—in the Great Oxygenation Crisis cyanobacteria came along and produced oxygen, which killed 99% of the life that was living at the time, because they were all anaerobic. In other words, the bacteria destroyed the lungs of the planet and changed them into oxygen-loving lungs.

And then, the life adapted. The huge amounts of oxygen in the air enabled giant life forms to evolve; giant dragonflies the size of small eagles.

So why don't the scientists turn their attention to the enormous amount of life we have right before our very eyes—in fact, ALL OVER our very eyes.

I was cleaning some cilantro just now and thinking about what I was holding in my hands: a magnificent edible plant with its own unique character that evolved over millions of years to be this way, to taste this way. And only this plant tastes like this; for reasons that no one can possibly know.

And what will they find on Mars? They won't even find the smallest protein or amino acid, and they surely won't find a bacterium. But why do they care? Why not study Earth and all its magnificent progeny?

All life came from bacteria, billions of years ago—and viruses.

People, even knowledgeable people, seem to get very confused when confronted with bacteria and viruses. They really don't seem to know the difference, so they ask for antibiotics when they get a cold. This is ridiculous, as is the notion that if you're wet in the cold, you'll catch a chill. The cold does't give you a cold; viruses give you a cold.

So what is the difference? If I had to qualify bacteria and viruses, I'd have to say that bacteria are tiny animals with no brain that are simply surviving for one purpose: to reproduce. Collectively, they form a brain, like a vast beehive. They're aggressive, but careful. They want only to live, to reproduce.

Viruses, on the other hand, are simply brainless bundles of proteins that are wrapped in bad news. There are actually disputes as to whether or not they can even qualify as being alive. Perhaps they're more like vitamins, or minerals. Non-living but reproducing nonetheless.

But they aren't too concerned about protecting their hosts; they don't care if their host dies; they just want to reproduce until they can't reproduce any more.

Bacteria and viruses survive side by side, but they're like the Irish and the Italians in 1920s Chicago. They agree to disagree, but they divide up their turf peaceably, because it's business.If they went around just killing each other, they'd all starve.

I've just received the results from my second biome test, and they're extremely puzzling. They're not at all what I expected.

But that's for next time. Do the study on the difference between bacteria and viruses, and remember: you are literally swimming in an ocean of invisible life. Don't worry about aliens.

They'e already here.

Tuesday, July 12, 2016

Deadly New Virus Warning

Asparagus Syndrome victim
  I    rarely comment on things that are not biome related, but I feel the need to point out a dangerous new virus that seems to have originated in Japan.

It goes under various names, among them "TinyHead virus" and "Head-shrinking virus" but with a bit of sleuthing, I have identified the true culprit to be a cellular-phone virus originating from something called "PokemonGo v.1.0."

I have, for the sake of pronounceability, renamed the virus "Asparagus Syndrome."

Asparagus Syndrome is characterized by the rapid fashion in which victims are overwhelmed with spontaneous microcephaly (shrinking of the head) and an  overpowering urge to keep a cellular communication device six inches from their face at all times.

The main risks from Asparagus Syndrome are not caused by the disease itself but rather by injuries sustained from walking into stationary illumination installations (SIIs), more commonly known as lamp-posts.

If you suspect you have had any recent contact with a Japanese person, Japanese people or products originating in Japan, the CDC recommends either avoiding the usage of all cellular communications products, or as a last resort an emergency head transplant, available at most witch doctors' nationwide.

Monday, July 11, 2016

What Osama Bin Laden Taught Me About My Microbiome

  O  nce, a long long time ago, I had a Great Job.

I'd get up mornings and shuffle from bed into the living room and over to my computer.

I'd drink my coffee (or a beer—I wasn't choosy at the time) and play with my mouse all day, putting pretty pictures on the screen, writing giggly things and then digitally crumpling them up.

Then, occasionally, I would summon The File, and carefully erase the figures entered in it with new figures, save it as a PDF and then send it off in an email.

There. I might have just sent off an invoice for $12,764.54.

No, really. Happened all the time.

Maybe not $12,764.54, every time—maybe just $453.21, or $76.87, or $5572.83—you get the picture.

I usually just made up the figures out of thin air. How much aggravation should I bill them for this time? And then I'd type out what looked to be a very carefully calculated number—except that it wasn't. I'd just make it up, right there, right then. The only calculation I did was how many jackets, or stereos, or TVs, or cameras, or restaurant dinners I'd buy with my winnings.

I was, from 1996 to 2001, the sole graphic designer for the entire company of Air Canada Cargo. Not Passenger, you understand—Cargo. But Cargo was pretty big. It occupied an entire floor at The Base, at Dorval Intl/YUL, or in the unmarked Air Canada building in Vendôme, where it moved later on.

I did all their ads, all their newsletters, all their posters. All their brochures, all their business cards, all their logos, all their calendars. And finally, I singlehandedly designed Air Canada Cargo's first-ever website.

All out of my home, in my slippered feet, with a beer or a coffee at hand, day or night, day in, day out, for five glorious years. And I raked it in. They had dumped the ad agency they had been dealing with before me in disgust, and I had somehow stumbled onto the job because a friend was the son of one of the top managers there.

It was a great partnership—I dealt with a tiny group of Air Canada Cargo people and they told me roughly what they wanted and I made it happen.

I was having the time of my life, making more money than I'd ever seen before, looking forward to a rosy, $$$-filled future.

And then Osama Bin Laden brought it all crashing down.

Air Canada's recent run of profitability—one could say profligate profitability, since they seemed not to care too much whether I charged $8,762 for a calendar or $12,987—ceased right then and there on September 11, 2001.

The towers fell on Tuesday, and I was out of a job by Friday. "You understand," my boss said regretfully, "there's no way we can continue to spend like this now. We're going to bring all this in-house."

So what was the problem? Get another job!

Not so fast! During the time I had spent with Air Canada I has scrupulously avoided moonlighting—I hadn't wanted anything to get in the way of The Job. I didn't even want rumors of my having other interests to reach their ears—I created montrealfood.com in complete secrecy while I was working for them.

So my job diversity had been limited to one, and now that was gone.

And what, you might ask, does that have to do with my microbiome? Diversity, diversity, diversity.

This article points out, rightfully, the perils of removing whole categories of foods from your repertoire.

Remove gluten, for example, and the bacteria that prefer gluten—bifidobacter, for example—might diminish and let other bacteria, say, prevotella, move in.

Since the jury is still lunching at McDonald's about all of this, we have no idea what a gluten-deficient diet will actually do to your microbiome, especially if your normal state has always been glutenous.

It's been reconized that a healthy microbiome is a diverse microbiome, and that makes sense. In lean times, when a particular food, say, sugar, was off the menu for the hunter-gatherer dudes that the Paleo Diet so wants to emulate, the diversity of their repertoire swallowed the gap quickly and with little overall effect. When the honey suddenly became available again, the population adjusted quickly, as a smaller segment had to be moved around; the prevotellas didn't particularly mind being reduced from 1.75 trillion to 1.24 trillion.

And one notable characteristic of the Western diet compared to more primitive diets like the Hadza tribe, is a severely curtailed repertoire of bacterial diversity.

So if your microbiome's diversity is small to begin with, as is the case with most of our western diets, then the removal of a whole food group—gluten, say, or fats—will have far more signifcant consequences on the population as a whole.

Looking back now, I was a fool to put all my cards into the Air Canada pot. I had nothing to fall back on, and no alternatives waiting in the wings. It would take years for me to regain my earnings levels—years that continue to this day.

The lesson I learned, in work as well as diet, is keep a lot of options open. The more cards you have on the table at a time, the less you're going to miss it when a few—or all—are removed from the equation.