Biomes (6 minute video)
The Complexity of the ‘Omes’ [or To Deal With Big Stuff, Sweat the Small Stuff]
How do we deal with complexity? Surveying the omes reveals microbiological research communities struggling to pull together, much like those of us concerned with the complexity of the macro environment that we can see. The masses of micro-sized detail interrelate, terminology is not standard, and to the public, arcane. The complexity exceeds the bandwidth of human brains. Practically, human societies can only reduce micro-complexity to rules for living that we can make habitual. To illustrate this, let’s start with a bafflegab review of micro “omes.”
Twenty years ago, the only biological “ome” I’d ever heard of were the mega-biomes vaguely remembered from biology. Looking it up again, there are five types of biomes, or regions of distinct natural balance: desert, aquatic, forest, grassland, and tundra. These stereotypes fuzz into transition zones, like high desert and low, and regions modified by mankind. (I think I live in a transition zone – fits no classic picture.)
Human Microbiomes: Decoding genomes inspired naming many newly explored micro-organic colonies as “omes.” In the media, microbiome usually refers to human gut microbiomes. They’re plural; no microbiome is uniform all the way down. But we host many other unique colonies of bacteria, viruses, fungi, and other little wigglers. They cover our skin. They snuggle in every body cavity, unseen to the naked eye. Microbiomes are inseparable from us; we can’t live without them; they can’t live without us. Learning all we can about this hidden 90% of us provokes different concepts of what we are – of what life is. Can you imagine yourself saturated with microbiomes?
Animal Microbiomes: Every living animal also hosts microbiomes. Their functions are similar to those in humans, but they are not the same. However, animal microbiomes are easier to study, so they are used in microbiome research. Imagine your dog hosting multiple habitats for colonies of micro-critters, all much smaller than fleas.
Rhizospheric microbiomes are symbiotic with all plants. They surround the visible roots, which pros call rhizomes. They energize the soil chemistry that keeps a plant healthy – or not. Fertilizing a plant feeds its rhizospheric microbiome. (Hmm, does pulling weeds intervene in rhizospheric microbiomes for my benefit – or not?)
Endosomes exist within cells. When an endosome matures and becomes a vesicle (nano-sized sphere) it becomes an exosome, leaving one cell and travelling to another as a signal and as a medium delivering nutrient or disposing of waste. As a whole the behavior of exosomes appears to activate bodily micro defenses when they detect a micro attack, or are deceived that they do. Endosomes and exosomes are part of the great mystery of immune systems and their malfunctions.
Exposome, easily confused with exosome, but a measure of all the “toxic insults” experienced by any organism (including human) over a lifetime. Exposure is usually inferred from biomarker metabolites, chemicals that result from bodily processing of chemicals to which it has been exposed. Lead and mercury have long been known to accumulate as toxins because our microbiomes don’t nullify them or discharge them. However, most exposome research must identify metabolic breakdown intermediates, and those characterize an organism’s disease state. This becomes “complex” – lots of variables: were you exposed to a high dosage one time, or to a low dosage constantly for decades. Was it mix of toxins? At what age?
Inflammasome was recently coined to denote an immune system functioning as described by microbiomes, but deceived and running amok. For example, microglia cells in the brain contain the protein NLRP3. When it senses enough perturbations in other brain cells it activates a macromolecular complex inside the cell. That’s the inflammasome. It exudes pro-inflammatory molecules that spread the inflammation.
Placebome is the most controversial ome. It’s conjectured to be a microbiotic response to a placebo, a pseudo remedy that does not intervene biologically, but only in the mind of the person administered a placebo. But is that really true? Does mind and mood somehow affect the body? Nothing is proven to scientific satisfaction, but analyses show that persons with the highest response to a placebo are genetically similar.
This is not an idle question. In almost every clinical trial of a drug or procedure, the placebo effect is a confounding variable, but what is this effect? Right now scoffers issue “shades of alchemy” criticism, assuming that mind affecting physiology is not possible. A thorough search for micro-effects might be paradigm changing.
What Should Ome Complexity Mean to Us?
Even the definition of complexity is so complex that we can’t agree on one, but here’s a straw dog: A system whose independent components interact in multiple ways, no central instruction guides them, and the system is always changing. By contrast, if a complicated mechanical device exhibits replicable performance, it’s more predictable than a biological organism with “a mind of its own.” That is, the causal linkages of a mechanical device are deterministic. Organisms and microbiomes have more causal loops and more causal uncertainty. (If your lawnmower won’t start, you may doubt this, and bug-laden software is not reliably deterministic, so boundaries are fuzzy.)
Labeling a zone of complexity as an “ome” raises a conceptual umbrella over a mass of interaction that we can be aware of, but can’t mentally process in detail; that’s why all the mapping data. To take action, we have to reduce the complexity into rules for living or working, but perhaps recognition of omes will let us devise them more holistically. If all life is modulated by complex microbiomes, does this knowledge alter your fundamental assumptions addressing or formulating questions like:
Is “optimal” health possible?
What is a healthy environment for all life?
What does clean mean? Can you be too clean?
What should infants experience to become healthy, functional adults?
Can any individual know what a healthy diet is for them, personally?
For that matter, what is a human being?
If microbiomes are becoming the rage to describe tiny biological systems, how about macro omes to designate big complex systems of other kinds? What about a healthcare-ome? An agricultural-ome? A transactional ome? An econ-ome?
Ome signifies that the roots of all human systems in nature, analogous to a rhizospheric microbiome, mediating between soil and plant. Then we see a human system more like nature sees it.
That’s one step in integration, but not enough. How about a “humanome,” suggesting all the linkages between human systems and an imperfectly predictable nature? That concept would take a lot of fleshing out, but it’s a start toward dispelling concepts of human systems as independent entities independent from nature, and all too often, isolated from other human systems. Its logic would be a huge contrast with established commercial logic.