CRISPRbiome or: How I learned to stop worrying and implant DNA altering, gene splicing, bacterial assassins in my gut

There’s been a slew of news lately, a news slew, regarding the microbiome and its role in our health. Most of the stories go something like this: While we know little about what precisely makes a healthy microbiome, these trillions of organisms living inside us seem to play an important role in our immune function and the incidence of disease.  

There’s an entire ecosystem of bacteria, viruses, archaea and fungi engaged in a war of resources in our digestive tract. It seems some of these creatures are our allies and some our enemies. Should the resource war get tipped in the favor of the enemies, our health suffers; but if fortune favors our allies, we thrive. That much seems clear, but these different organisms potentially outnumber the cells in our bodies, so science has struggled to precisely categorize each one as friend or foe.

We certainly don’t have a gold standard for what a healthy gut looks like. That would be a bit like having an exact model of what a healthy rainforest looks like -- we need this number of this particular species of tree, shrub, insect, whathaveyou. Oh and that particular vine, we can’t have that in a healthy rainforest, it’s crowding out this tree we need so badly. Those mosquitos sure are a nuisance and spread disease, let’s eradicate them altogether.

I’m not saying there isn’t an ecological true north, just that it is difficult for us humans to accurately pin it down considering the complexity of ecological interactions. John Muir summed it all up, “When we try to pick out anything by itself, we find it hitched to everything else in the Universe.”

So one species of bacteria or fungi in our gut, like say Candida, might be associated with disease. It might be a good idea to discourage it’s growth, to limit the resources it seems to like. But now imagine waging an all out war on Candida, wiping it entirely from the face of our gut, and we find it was hitched to everything else in the Universe. We find its existence and its use of resources to perpetuate that existence to be keeping some other, more hazardous organism from thriving in our bellies. We find we killed the devil we know and unleashed the devil we don’t.

That’s the type of worst-case scenario I imagine when I read stories like this one -- a Danish biotech company with $50 million in financing to develop CRISPR technology to target bad bugs in our guts.

You know CRISPR, the genetic scissors that allow scientists to switch certain genes on or off, and splice entirely new DNA sequences into an organism’s genome. The technology that scientists just learned can inadvertently eradicate large swaths of DNA or even initiate cancer. Yea, that one, weaponized and unleashed on the unimaginably complex ecosystem in your digestive tract.

Now I’m well aware that these technologies are in part motivated by a desire to help, it’s just the other part of the motivation is cash, and that cash might cloud our judgement. It might encourage a sort of reductionist greed where we overestimate our ability to foresee unintended consequences.

Living systems like our microbiota, like the soil, are unimaginably complex. Wendell Berry spoke about this in “The Unsettling of America” in one of my favorite passages of all time.

“Because the soil is alive, various, intricate, and because its processes yield more readily to imitation than to analysis, more readily to care than to coercion, agriculture can never be an exact science [. . .] By farming we enact our fundamental connection with energy and matter, light and darkness. In the cycles of farming, which carry the elemental energy again and again through the seasons and the bodies of living things, we recognize the only infinitude within reach of the imagination [. . .] by aligning with it here in our little time within the unimaginable time of the sun’s burning, we touch infinity.”

The soil is the digestive system of the earth. It metamorphosizes nutrients and energy and is made up of trillions upon trillions of organisms that, just like our microbiome, we know little about. And so to extend the metaphor, because our guts are alive, various, and intricate and yield more readily to care than coercion, gut health can never be an exact science. Our guts yield more readily to culture than technology. I’ll stick to sauerkraut and kimchi, you can keep CRISPR for yourself.