Epigenetic Fermaculture

"The living communities within our bodies are our first responders, and their fast adaptive capacity depends a great deal on the diversity of their epigenetic choices."

Yesterday Sandor Katz joined us to combine his knowledge of gastroenteric culture with ours of the soil-food-web to produce a 5-hour seminar we were billing as Fermaculture.

Sandor had many interesting things to say, but one of the more interesting to us was about how bacteria from food — the juicy benefactors we get from fermented wonderfoods — actually perform probiotic functions in our bodies.

We know that in sheer numbers, microbes and their genes vastly outnumber our own genetic material in what we like to think of as “our” bodies, Realistically, we are far more than our flesh (or even our astral energetic bodies or our vibratory quantum self). As Michael Pollan reminds us, “It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about 10 resident microbes — including commensals (generally harmless freeloaders) and mutualists (favor traders) and, in only a tiny number of cases, pathogens. To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this 'second genome,' as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.”

According to Sandor, when a foreign bacteria enters your body, it is not necessarily met with a friendly reception, a lot of buddy bacteria backslaps and a toast. More likely it is tracked, attacked, and generally made to feel most unwelcome. That’s because the available niches began being given away in utero, and your body assembled almost all its microbial ecosystem in the first 3 years of your childhood.

Catherine A. Lozupone, a microbiologist at the University of Colorado, Denver, observing that rural people spend a lot more time outside and have much more contact with plants and with soil, says its no surprise that confers a greater diversity of gut bacteria. Also, being raised in extended families and being passed hand-to-hand as an infant may provide a wider range of “host” bacteria and a stronger, more responsive, immune system as an adult.

The American Gut project, which is DNA sequencing the communities of tens of thousands of people, is trying to uncover patterns of correlation between people’s lifestyle, diet, health status and the makeup of their microbial community. Pollan observes:

“Your microbial community seems to stabilize by age 3, by which time most of the various niches in the gut ecosystem are occupied. That doesn’t mean it can’t change after that; it can, but not as readily. A change of diet or a course of antibiotics, for example, may bring shifts in the relative population of the various resident species, helping some kinds of bacteria to thrive and others to languish. Can new species be introduced? Yes, but probably only when a niche is opened after a significant disturbance, like an antibiotic storm. Just like any other mature ecosystem, the one in our gut tends to resist invasion by newcomers.”

Sandor Katz

So how, then, can probiotic fermented foods, like yogurt or pickled bean paste, improve your health? Sandor offered an epigenetic explanation. Rather than being interested in new bacteria taking up residency alongside the established community in your gut, your host bacteria, via the magic of viral gene transfer, are more interested in the new genes that are constantly coming through on parade.

When you were just a zygote – remember that? — totipotent stem cells become the various pluripotent cell lines that allowed you to evolve into an embryo, which evolved fully differentiated cells in much the same way. From a single fertilized egg cell, you developed into a semi-organized collection of neurons, muscle cells, epithelium, endothelium, blood vessels, etc. Switching on an off like the lights on a Christmas tree, your coding activated some genes while inhibiting others. The code did not change, but the gene expression, or replicative (RNA) behavior, did.

An "epigenome" is similar to the word "genome", but referring to the overall epigenetic state of a cell. Where is the switch positioned at this moment?

In general, proteins fold into discrete units that perform distinct cellular functions, but some proteins are also capable of forming an infectious conformational state known as a prion. Prions are infectious forms of proteins.  They are epigenetic change agents. They catalytically convert other native state versions of the same protein to an infectious conformational state. In the context of our immune response, infectiousness is not always a bad thing. It just means that cells switch gene coding to make new versions of cells that may be needed to perform some function. Some food components epigenetically increase the levels of DNA repair enzymes such as MGMT and MLH1 and p53. Other foods components can reduce DNA damage, such as soy isoflavones and bilberry anthocyanins.

Fungal prions are considered epigenetic because the infectious phenotype caused by the prion can be inherited without modification of the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971, are the two best studied of this type of prion. In PSI+ cells, the loss of the Sup35 protein (which is involved in termination of translation) causes ribosomes to have a higher rate of read-through of stop codons, an effect that results in suppression of nonsense mutations in other genes.  The ability of Sup35 to form prions may be a conserved trait. It could confer an adaptive advantage by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon mutations.

Another possibility is more intriguing. Sup35 might be produced by prions selecting its code from the available pool of genetic carriers, including foreign bacteria that just happen to be passing through your body, and find themselves in the right place at the right time. Their genes are transcribed, re-encoded, and switched on by your native cells to express just what the body needs at that moment.

The federal Centers for Disease Control is investigating an outbreak in eight states, affecting nearly 300 people, of a stomach illness caused by Cyclospora, the one-celled parasite that causes diarrhea, stomach cramps and other symptoms normally associated with a viral stomach bug. Ten people have been hospitalized this month. Indigenous to the tropics, it is rare that cyclospora would be found so far north, but it is yet one more portent of what we can expect from climate change and global weirding. Niches of some species will expand while niches of others will shrink. We may get pandemics of many new or exotic bugs, and there may be little our bloated, sclerotic, top-down, corporate-captured, financial-house-of-cards-addicted Big Pharma medical system can do to respond in a timely fashion.

The living communities within our bodies are, and always have been, our first responders, and their fast adaptive capacity depends a great deal on the diversity of their epigenetic choices. What gene codes do they have to draw from?

The abilities of our bodies to respond to future threats may come in large measure from our own lifestyle choices, such as a probiotic diet and rural living, and from good plant nutrition, which comes, ultimately, from healthy soil and its diverse soil-food-web biology.
 

Turning the Herd

"Salvaging hope has to do with finding some wayward lead animals who are running oblique to the cliff’s edge and trying to persuade other members of the herd to follow them, in hopes that collectively it may actually slow momentum or even reverse direction of the herd, or at worst, save a few animals from being swept over."

We are sitting in a bay window of a stone cabin staring at the sunny, windswept west coast of Ireland, Rossbeigh Beach on the Iveragh Peninsula, overlooking Dingle Bay near Killorglin. We began this trip with an utterly absorbing International Communal Societies meeting in Scotland, moved on to a climate farming design charrette at a Permaculture center in Norway, then a repeat performance on a biodynamic farm in Sweden, and now the annual Feasta (Foundation for the Economics of Sustainability) retreat week in the west of County Kerry where we are brewing cool coffee with our Biolite stove and charging this iPad.

We travelled by train from Dublin with Nicole Foss (Stoneleigh of The Automatic Earth) after spending the night at the home of David Korowicz, to a quaint summer retreat cottage on the beach purchased by London barrister John Jopling in 1960 as a stone ruin and still being very gradually restored. It will house the dozen or so international participants of our conversation the coming week.

Arriving in late afternoon, we sat here in this window and curled up with a book we picked off the shelf, Sharing for Survival: Restoring the Climate, the Commons and Society, a Feasta anthology edited by Brian Davey and published in 2012. Now completely entranced by Davey’s opening chapter, in this post we will try to describe what we liked about it.

The chapter is called What can be done if mainstream politics loses interest in climate change, which seems at first glance a dumb question, being a fait accompli, but it turns out to be a compendium of the world’s best thinking on how to turn sour lemons into mojitos.

The first thing Davey observes is that great changes seldom come from confrontation. Rather, they are approached obliquely, indirectly, because from the standpoint of the historical participant, what needs to happen is unclear. Actually, as to our present dilemma, Davey’s essay points clearly to what needs to happen and catalogs the challenges.

Policymakers and business leaders are a tight-knit class locked into a commitment to growth. Growth underpins our global economic system, if for no other reason than money is merely the issuance of debt obligations and when you add the requirement of (unlent) interest, as Margrit Kennedy observed 30 years ago, it sets up a Ponzi scheme that is utterly dependent on growth, and endlessly seeking new patsies. This system requires both the unscrupulous lender and the gullible victim, and the globalized education system is geared to produce both in large numbers.

Money, drug and energy addicts share a brain chemistry that gets reinforced by both Western diet and social networks of fellow addicts. Policy is largely formulated by officials dialoging with the predator class and their skilled lobbyists and public relations hires, creating a mainstream narrative drummed by media that drowns out all alternative narratives, even the ones being trumpeted by Mother Nature in the form of superstorms, net fossil energy decline and global weirding.

No-one likes to maintain stressful confrontational relationships over long times, so regulatory capture is followed by the capture of non-profit opposition groups, popular media, and large open public fora, such as we described in past narratives of Rio+20 and UN climate conferences. Davey says, given this context, the situation appears pretty hopeless. We are a herd species and our herd is galloping towards a cliff.

Salvaging hope has to do with finding some wayward lead animals who are running oblique to the cliff’s edge and trying to persuade other members of the herd to follow them, in hopes that collectively it may actually slow momentum or even reverse direction of the herd, or at worst, save a few animals from being swept over.

We might think of these as “seed” experiments — complimentary currencies, ecovillages, “cool” stoves, and non-violent methods of conflict transformation — as the fringe of society but they are actually the leading edge of our inevitable future, if we are to have one.

In Denmark we can point to Ross Jackson’s “breakaway” strategy — a reform of global governance led by democratically or economically advanced countries like Iceland and Bhutan. In Germany there is the “solidarity economy” that hopes to congeal cooperative networks of CSA’s, community energy companies, community gardens and similar grass roots enterprises into a political force. From Ireland and the UK we have the Transition movement that combines town-scale remodeling projects with personal reskilling to cope with energy descent and climate change. From Italy we have Slow Food evolving through slow money and slow living to slow everything, very useful to the herd-and-cliff metaphor. From France we get Decroissance, which personally we prefer over its English version (Degrowth), because the French sounds more like a flaky pastry than losing your job. Something similar is emerging in Bolivia and Ecuador with Buen Vivir.

From these seeds, with some sunlight, water and the luck of a green thumb, who knows? What we may see will not be a centralized, pre-conceived new system replacing the old like Bolshevism or the Campuchean Revolution, but a bottom-up, decentralized Sacred Unrest, to borrow Paul Hawken’s words.

As Davey says, though, “What is still not clear is how far governments are capable of contributing to the new future.” It is argued by Naomi Klein, among others, that nations are now functioning as brands, running sophisticated PR campaigns designed by their financial sectors for the purpose of gaining expanded markets, access to raw materials, and new populations of debt slaves. Alternative futures will have to compete with this for minds and hearts.

It is helpful that governments and their economic schemes are increasingly seen as corrupt and bankrupt. It is less helpful that they are erecting a neo-liberal security state to impose power and undercut their opposition by violent means. Nonetheless, truth will out. As Napolean said, “Never harass your enemy when he is in the process of destroying himself.” The herd is not slowing yet, but the outliers are gaining adherents.