Friday Flora Late edition

Late indeed:
This is the withered remains of one of many honey locust suckers that have been sprouting up in front of the house. There were at least three honey locust trees there, and though we cut them out, their roots have been sending up suckers like mad. Honey locust trees are something nice to have elsewhere: the perfume of the flowers of a grove of them, a quarter-mile up the road from us, sweetened the air at our house this spring. However, we don't really want big trees this close to the house, and these can be quite nasty: they have vicious thorns that love to dig in deep and break off inside of you. Worse, trying to dig up the suckers is an exercise for, well, suckers: the roots are just too deep.

So, I put down the shovel and shears and picked up my crossbow. Crossbow is a mix of 2,4-Dichlorooxyaceticacid (2,4-D):
and 2,4,5-Trichloro-2-pyridinyloxyacetic acid (Triclopyr):
both of which have some similarity to indole-acetic acid (IAA)

and Phenylacetic acid
These last two are examples of auxins, perhaps the most significant naturally occuring plant hormones. Deprive a plant of the ability to produce or respond to auxins, and everything goes wrong--stunted growth, no blooming, no apical dominance, no ripening, and worse. However, zap a plant with a huge overdose of auxin-analogs, like I just did...well, anyone who has gone through puberty knows how rough an overdose of hormones can be. This is a few orders of magnitude worse--the plant is overwhelmed, activates genetic programs for development and senescence at the same time, and keels over dead in short order. Interestingly, these synthetic auxins don't do much to monocots (grasses, lilies and their ilk)--once absorbed into the plant, they are chemically modified into an inactive form.

It was not without misgivings that I strapped on the backpack sprayer. Both 2,4-D and triclopyr are considered relatively benign, as herbicides go--they have been shown to decay with a half-life in the range of a month or so, and not to bioaccumulate significantly. However, they do persist enough that we are discouraged from using them wherever we're going to have lactating animals grazing for a year. This is an issue, since we want to have milch goats roaming around the property.

Worse, like political candidates who hung out with a bad crowd in their youth, both 2,4-D and triclopyr have a historical association with 2,4,5-T. 2,4,5-T was part of Agent Orange--and it turns out that it's basically impossible to synthesize 2,4,5-T without having some of it undergo a spontaneous reaction with itself. That reaction makes 2,3,7,8-tetrachlorodibenzodioxin, a deadly poison, a carcinogen in any dose, and a molecule that is essentially immortal in the environment--one of the more evil chemicals humans have made since we started mashing together carbon atoms in the lab. Like politicians who have done their best to expunge certain historical facts from their record, triclopyr even underwent a name change--if you stuck to IUPAC naming conventions, you could also abbreviate its name as 2,4,5-T.

Also, I would love to have this property be organic*, and the Real Doctor and I are working to that end. Right now, though (WARNING! self-justification alert!) we are facing several years' worth of neglect all at once. We are figuring that for the next year or two, we will be using some herbicides, when necessary. But, tree-huggers that we are, we're going to do as much as possible in other ways. Consider the effect of the "natural" herbicides "Painted Lady" and "Ash":
It's kind of amazing to watch them go after blackberry brambles. They'll eat every leaf they can reach, and the effect is not too different from Agent Orange. Here's a picnic table that we didn't even know existed a week earlier:
two days' of nibbling by the goats revealed it, and all that is left of the once-enveloping bramble is the stems.

*I know 2,4-D is organic. I mean in the colloquial, not chemical sense.

This is good, and you should try it

It's spring, and asparagus is here. Our asparagus patch is still a little young. The spears that came up this year are thinner than pencils, and now we're moving away. Whoever gets the house will get a nice crop next year. Fortunately, the Sacto delta is prime asparagus-growing territory, and it's abundant at the farmers' market now.

In the book "Coming into the Country," John McPhee described the result of successfully hunting a moose. Here's a list of consecutive dinners, courtesy of Google books:

Spaghetti with mooseburger
Moosesteak
Moosesteak
Moose roast
Moose stew
Moose meatloaf
Leftover Moose
Leftover Moose
Moose sandwiches
Spaghetti with mooseburger
Swiss moosesteak
Leftover Moose
Roast Moose
Moosesteak
Moose sandwiches and soup
Mooseburgers
Mooseburgers
Clam chowder
Fried Moose liver
Swiss moosesteak
Ground moose in Spanish rice

I could live on an asparagus farm, and happily eat just plain steamed asparagus every night. This just about happens during asparagus season, but once in a while I'll make something different. Asparagus pesto is really good, easy to make, and you should try it.

2-3 cloves garlic
about 2/3 c grated parmesan cheese
about 1/4 c roasted unsalted cashews
about 1/2 c good olive oil*
juice of 1/2 lemon
a pound of asparagus, steamed and cut up
a generous bunch parsley
S&P to taste

Put the first three in a food processor and frap it up. Put the rest of the ingredients in, and frap until it's the right consistency. Amounts are variable, to taste. Add more or less olive oil--more, it will be saucy and go on pasta, less, and it's dip. Either way, it's good, and you can make it in less time than it takes to boil the water for pasta.

What's buried in the garden

The Real Doctor and I are grappling with the frantic business of moving. So far this week, we have met with two realtors, a mover, three painters, and a general contractor. Monday, we meet with a pest inspector and a garden guy.

I’ve been spending some time every day trying to get some of the uglier weeds pulled out of our garden. At this point, it’s not terribly hard. Several years of persistent work have given us some very well established plants, so an hour’s toil makes a good patch of the yard look somewhat presentable. Of course, the garden is a work in progress. There are still plots that just haven’t gelled—something unsuitable got much too established, or something was established but just up and died, leaving a big dead spot. And of course, our neighbors still have vinca and St. Augustine grass, which requires unsleeping vigilance. A decade or so more would have made it perfect.

Leaving our garden will be one of the hardest things about leaving Sacramento. We have a loverly herb garden—just about every herb imaginable, six kinds of thyme, four kinds of oregano, winter savory, summer savory, rosemary, sage, chives, lemon grass, lemon balm, lemon verbena, lovage, horseradish, sorrel, and so on. It’s a joy to the nose, and not bad looking either. The plants are mature, forming nice mounds of deep green, yellow green, emerald green, olive green, gray green, and grass green. Elsewhere in the garden are fruit trees, asparagus, artichoke, the alstroemeria and irises (or irides) that my Mom gave me, and more. These replaced the wilderness of brambles and vinca that greeted us when we moved in.

All the philosophies that I use to console myself advise against attachment. This move is proving a mighty test of philosophical equanimity. Until now, I’ve never really understood attachment to a plot of land. After all, plants will grow in Oregon. But in my backyard here, there’s a bunch of time, a bunch of labor, a bunch of me and the Real Doctor. If you go out past the garage to that patch of lawn she liked to lie down on, and dig down about three feet, you’ll also find the decaying bones one of the best dogs I’ve ever known. So now, I kind of understand why patriots think that one particular bit of the earth’s surface is better than any other similarly endowed acreage.

But it could be worse, and it will get worse. My Mom’s garden is (as has been noted) better than yours, or mine, or pretty much anybody else’s. My parents are getting old and my Dad is infirm and fading into the fog of dementia. Their living situation gives them some hardship, and there are definitely mechanical aspects of their life that would be much improved by moving to an “assisted care facility” as the Real Doctor’s parents recently did. But I think it would destroy my Mom. Separating her from her house and garden—from the mature trees that she planted, from the exquisite collections of bulbs and aloes and succulents, from the landscape that she made—would be separating a body from its heart. Philosophers will counsel against attachment, and the intellect will nod sagely and agree. But reality and the heart can dissent loudly and painfully.

My inner philosopher compels me to note: I will not miss the leaky taps, the ill-fitting doors, the gentle breezes that one can feel indoors on a windy day, the unusable spaces in the kitchen, the three-quarters of the house that is uninsulated, the idiotic, outage-prone electrical system…

Alea jacta est!

The big deal in my life right now is that the Real Doctor and I (and Opal and as yet unnamed) will be moving this summer. I find moving traumatic, no matter how necessary it may be. I know enough of the Four Noble Truths to realize that the cause of this trauma is attachment, and that I need to let go of things, but it's still hard when those things have personality.

Last Sunday we said adieu to our yard chooks; they've gone to a new home with one of the Real Doctor's coworkers, and are busy finding their place in the existing pecking order. So, here's some last pictures of the girls, as they were bundled into a carrier and greener pastures. Goldie, the gold-laced wynadotte:
and Rosie the Rose comb Leghorn with Barbarella the Barred Rock:
I've already started missing them; I was ripping up some weeds in our overgrown backyard and found a big, fat, juicy, green caterpillar. I'd picked it up and started walking towards the coop before I realized that there would be nobody to fight over it.

Ave atque vale, birdies.

How they grow

A week after they last visited our yard, Mama turkey and her three chicks came by again. The chicks have been busy growing...
We wondered how they got in and out of our yard. We knew the adults could fly well, but the chicks?
No problem.

The secret garden, or Who's zoomin' who?

"All that is very well," answered Candide, "but let us cultivate our garden."--Voltaire.

It’s probably pretty evident that I like my garden. I spend a fair amount of time on it; I enrich the soil with chicken poop and organics and adjust our cranky old watering system to favor the plants that I like. I spend a lot of time weeding and mulching to eradicate the plants I don’t like. I will even resort to biological and chemical warfare—iron phosphate, BT, copper strips and savage chickens—to discourage snails. All this is to make conditions just right for the relatively few species that I desire, which feed me and enrich my senses.

My plants think I am a sucker. I think I’m cultivating them so that I can use them. But they, to turn over a new leaf, think that they have got me very well trained to ensure the survival of their genomes. Really, since the meaning of life from a biological point of view is to make sure that your genes make it to the next generation, I am a thrall to my plants. However, just as I work to cultivate my plants, they work to cultivate me. They use sun, air, and their considerable chemical skill to make the sugars and flavones and pigments I crave. By doing this, they guarantee their survival instead of the triumph of the weeds. This isn’t really a new perspective—Michael Pollan wrote a book about it called “The Botany of Desire,” and the idea predates him by a long time. My garden reminds me that it’s possible for each partner in a relationship to be utterly selfish, and yet both will win.

All of us, from nomadic herders to suburban gardeners to skyscraper-dwelling urbanites, cultivate a secret, inner garden, and our relationship with its flora is even more complicated, beneficial, and dominated by selfishness than my personal relationship with sugar snap peas. Our gardens are what physicians call the “intestinal flora,” the squillions of microbes that live in our gut. We’re just now beginning to appreciate some of the complexity of this relationship, but it’s clear that each of us—microbe and human—is cultivating the other for our own selfish ends.

The simplest aspect of this relationship is digestive. We feed the microbes in our gut lots of polysaccharides (complex chains of simple sugars) and other stuff. Every different polysaccharide requires a unique enzyme to break it down, and we simply don’t have a big enough toolbox of enzymes to cope with all that we eat. But the microbes in our gut have thousands more such enzymes, and they can trim pretty much any polysaccharide into simple sugars; they then ferment these sugars, and get enough energy to live. They win. But we win too—the end products of these fermentations are things like alcohol and acetic acid, stuff that our cells are really good at using for fuel. So, we win. Or, as Reuben Bolling has it:

When I cultivate my plants, I cause the plants that benefit me to grow more healthily, and reduce the fitness of those I don’t want. Specific bacteria also cultivate us; those individual mammals (the experiment has only been done on mice, for ethical reasons) who are not hospitable to certain bacteria are noticeably unhealthy. So, it could be argued that the Bacteria are cultivating—causing to grow more healthily—only those mammals that benefit them.

We are very picky about the types of microbes that we cultivate—not just any bug will do. The wrong bacteria in your gut (or not enough of the right bacteria), is far worse for your health than too many dandelions in the garden. Most of the trillions of Bacterial cells in our intestines are of a handful of types in a well-regulated ratio, and a recent study by Andrew Gerwitz at Emory University suggests a mechanism by which we cultivate the right Bacteria.

Humans are increasingly plagued by “diseases of affluence” such as metabolic syndrome. Metabolic syndrome is a constellation of woes including type II diabetes, obesity, colon inflammation, hyperglycemia, irritable bowel syndrome, and on and on. Some of this is obviously due to lifestyle. However, genetics plays a role, as it is possible to find mice that are genetically predisposed to something that looks an awful lot like metabolic syndrome. These unfortunate mice are obese, hyperglycemic, hypertensive, insulin-resistant, given to overeating, and prone to all manner of inflammatory diseases. Not to be gross, but they are really different looking inside. The one on the right, with visibly more fat and inflamed colon and liver, is the mutant mouse:

It is not certain that these mice have the exact same thing as human metabolic syndrome, but it has all the hallmarks. As with humans, you can even make them much healthier by putting them on a restricted diet.

All the differences visible in the picture there, plus hypertension, insulin resistance and more are due to a single genetic defect. They are missing one gene, called TLR 5. So, how can the loss of one gene cause such multifarious misery? The TLR 5 gene encodes a protein that sits on the surface of the cells that line our intestines. This protein is similar to a class of proteins that are receptors for specific bacterial proteins—that is, they grab onto these proteins (which are presumably attached to bacteria), and hold on to them tightly. It made sense, then, for Gerwitz’s co-workers to look for differences in the intestinal flora between mice that had the TLR 5 gene and those that lacked it.

Mice, like humans, are born with a clean slate as far as intestinal flora are concerned. We both are rapidly colonized by a diverse array of bacteria and other microbes off of our mothers’ skin (and all the other stuff any baby will put in its mouth. I once made the mistake of talking about this with the mother of a newborn. It was not something she wished to think about.). So, a lot of what defines the cast of characters in our intestinal flora is what is in our environment.

But genetics matters too. Gerwitz used an embryo transplantation to put both fetal mice with TLR 5 and fetal mice without TLR 5 in the same mama mouse. The normal and mutant mice were born and raised together, with the normal mice turning out normal and the mutant mice looking like the stereotypical ugly American. Comparison of the bacteria living in their guts showed that the main difference was not what types of bacteria were present, but that some were much more prevalent in one or the other. The obese mice were especially lacking in some of the Bacteroides, the same ones that are helping to save Billy Dare. What’s worse, Gerwitz found that he could mostly sterilize the intestines of a normal mouse with antibiotics, then re-colonize it with bacteria from one of the mutant mice (I won’t go into methods here, but if you’ve seen the movie Pink Flamingos, you’ll know how it was done). The genetically normal mice with the altered gut bacteria developed all the ills of their mutant littermates. So not only was there a correlation between altered intestinal flora and metabolic syndrome, there is pretty clear causation.

We still don’t know the exact mechanism by which the wrong intestinal flora leads to metabolic syndrome, or indeed whether exactly the same thing happens in humans with this disease. However, it is known that many of the “good” intestinal bacteria produce a variety of chemicals that, in effect, soothe a rowdy immune system. Without this check, our immune system can attack our own cells, causing inflammation in the gut and killing cells that should be responding to insulin—both features if metabolic syndrome. It appears that mice have the gene TLR 5 mainly so that they can keep the “good” intestinal bacteria around—in effect, cultivating the right cells in their intestinal flora, and suppressing autoimmune reactions. A mutation eliminating TLR 5 means that the “good” bacteria are eliminated, and others take their place. These bacteria can’t pacify the immune system, and autoimmune attacks lead to metabolic syndrome.

All animals evolved in a world dominated by microbes—they are, and always have been, as much a part of the environment as air and water. From an evolutionary point of view, it is impossible to say just who is cultivating whom, and this study makes it clear that the answer ultimately doesn’t really matter. We mammals go to the trouble of having and expressing specific genes such as TLR 5 so that we may cultivate certain species of Bacteria. We do this, because if we did not, we would be unhealthy. Conversely, Bacteroides goes to the trouble of having and expressing specific genes so that it may improve the health of its mammalian host. It does this, because if it did not, it would be kicked off the gravy train flowing through our gut. Like me and my heirloom purple pole beans, it’s a relationship in which we both win by being selfish.

Matam Vijay-Kumar, Jesse D. Aitken, Frederic A. Carvalho, Tyler C. Cullender, Simon Mwangi, Shanthi Srinivasan, Shanthi V. Sitaraman, Rob Knight, Ruth E. Ley, Andrew T. Gewirtz (2010). Metabolic Syndrome and AlteredGut Microbiota in Mice Lacking Toll-Like Receptor. Science 328, 228-231.

Only a day old...

And already thinking of murder.
(oxalis leaf = about 15 mm)

Eat Local part II

The latest from the garden.


Spuds are one of those ineradicable plants, like horseradish or asparagus. Once you've planted them, you will have them forever. We last planted potatoes three or four years ago, but every year a couple of small plants come up. They're the nutritional and horticultural opposite of spinach: piles of starch and calories but not much else, and amazing yield. This is from two very sickly, spindly, single-stemmed plants that were buried in a patch of weeds and almost completely destroyed by slugs.

I'm sure that I left one pea-sized little spudling down there, and I'm sure I'll have the same thing next year.

Eat Local

Here's about a third of our spinach crop.

This is from one eight-foot row from the garden in the far background. The other two thirds went into a fritatta that fed us for a couple of nights, and this is also about two meals worth. So, four meals. It is left as an exercise for the interested reader to figure out how many feet of spinach would need to be planted to end our household's dependence on imported spinach. (You can also figure in the chance of crop failure, as the row of lettuce right next to the spinach completely failed.) Chard's a much more productive crop in terms of meals per meter.

Spring (continued)

Almost mowed this.

There's a reason it's called robin's-egg blue. It's hard to believe that the obese worm-suckers bouncing around our lawn came out of such tiny packages. This one appears to have been the victim of predation; there's a hole on the other side that looks a bit small for a chick to get out of.

Bugs-by-mail

We just received our latest shipment of fly parasites in the mail.


If you've got yard chickens, you've got chicken poop. If you've got chicken poop, you get flies. In the past, we managed this problem with fly traps (which attract flies by smelling worse than chicken poop). Last year we started using biological control. There's a company that breeds parasitic wasps that lay their eggs in fly larvae. The eggs hatch in the fly pupa, and the wasps eat the developing fly from the inside. The fly dies, and wasps hatch out of the pupa.

So, what you get in the mail is an envelope of fly pupae that are just starting to produce zillions of teeny wasps (the guy in the photo is about 2mm; the big brown thing is a fly pupa). You dump these guys out where the chicken poop is, and they attack the flies. They work very well; we haven't had any fly problems at all.

As a microbiologist, I should write something about how the bacteria Wohlbachia manipulates the wasps' reproductive system. Instead, I'll quote Darwin:

I cannot persuade myself that a beneficent and omnipotent God would have designedly created parasitic wasps with the express intention of their feeding within the living bodies of Caterpillars.

And William Blake, who is a little too trippy for me:

Little Fly,
Thy summer's play
My thoughtless hand
Has brushed away.

Am not I
A fly like thee?
Or art not thou
A man like me?

For I dance
And drink, and sing,
Till some blind hand
Shall brush my wing.

If thought is life
And strength and breath
And the want
Of thought is death;

Then am I
A happy fly,
If I live,
Or if I die.