To Deal With Big Stuff, Sweat the Small Stuff

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.”

Microbiological “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?

Ome Integration

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.

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  1. 1. Is “optimal” health possible?

    What is the definition of optimal? A synonym of optimal is flawless. So what is flawless health? Since medical science is constantly seeking improvement, does this, by definition, mean that human life is flawed? And if so, by what standard shall such a flaw be measured?

    2. What is a healthy environment for all life?

    There is life at the bottom of the ocean around hydrothermal vents that would be extremely toxic to anything and everything at the surface. Healthy environment for them, deadly environment for us. What if their environment is necessary for our environment?

    What is a healthy co-existing environment?

    3. What does clean mean? Can you be too clean?

    How does the immune system work? Aside from adequate sanitation systems what is healthy bacteria? If we sterilize everything, do we rely on artificial immune system medications? How do we control superbugs created from such sterilized behavior?

    4. What should infants experience to become healthy, functional adults?

    Why do mothers favor breast feeding to build the child’s immunity yet sterilize the surrounding environment?

    5. Can any individual know what a healthy diet is for them, personally?

    First, what is food?

    6. For that matter, what is a human being?

    Humans are a part of nature and dependant on nature with one exception, power over all. Humans have one ability not found in any other life on this planet, we can ponder the existence of everything, including what is beyond our physical senses. Hence, power over all life.

    Why do we have a monetized transactional system tied to economic growth that ignores our dependency on nature?

    We know that we do not know the complexities of nature (including our own body), why then do we act upon our assumptions as known fact?

    If a human is dependant on nature and nature is the source of human food, would the primal definition of a human being be the question of what is food?

    • Good questions to ponder. Really good questions don’t arithmetically precise answers. Rather, they prompt more questions. Some of them we might actually act on.

      The questions are all of this woolly kind, so I can only respond to the first question, not answer it.

      What’s optimal health? Optimizing anything presumes that we know what we want to happen and have a degree of influence over the processes to attain it. In model speak, we can define an objective function. However, some of us want to go like hell, and if we flame out young, that’s OK. Others want to mince around trying to live to be 100.

      Then we have great variation in the influences on our health. In what climate do we live? What are we exposed to? What do we eat? What do we do? What kind of stresses do we experience? Do we want to be a prime athlete, a hermit, or an all-night party hound? Etc. That is, do we want to be in great health, or just see how much we can get away with? Mental state affects bodily health.

      We are much more likely to agree on what constitutes poor health. Few people want to be ill, much less chronically ill; hypochondriacs excepted. How do we avoid bad health? If we are willing to follow them, many diet and life habits are known to stave off ill health.

      • Poor health is a peg we can measure from, but from where? What associations do we have with modern life that directly impacts health into the category of poor health? For example, how does smoking impact health any worse than agricultural chemicals or industrial food consumption? How about the problems of smoking, drinking and all night womanizing compared to eating fast food every day?

        What about water quality for the people of Flint, Michigan? Or maybe sanitation problems for most of America when floods wash everything into the rivers and consequently the ground water? How does our current science deal with this within the confines of limited monetized government? Who pays for what and why?

        Maybe our real problem is the money and not ill health for Americans? What if our health industry growth model exceeds the majority who can pay, including insurance companies and government Medicare? This is a question of when more than “if” because this scenario is more than real, it is upon us right now.

        Many of my old friends at Worthington have hit this wall of health. Those on limited health insurance and those on Medicare had no idea what was before them. They go for treatment, follow the doctor’s orders then end up with out of pocket expenses of $30,000.00 to $100,000.00. Since most are in their early 60s, this has become a mortgage level that shall be unpaid. Lose everything because the healthcare system has sold their medical debt to the vulture collection agencies.

        Out of ignorance due to medical propaganda, what happens to these poor souls? Simple, whatever was left in their estate shall be confiscated upon death. Which begs the question, why should I even enter this type of healthcare if the end shall be worse than if I had died right now?

        Therefore if poor health can be pegged, within today’s economics, what is the purpose? Unless I have adequate money to compensate, my life becomes nothing more than economic consumption.

        Is this how we all wish to live? Think about this. Even the elite with money have been categorized into the same system. The winner shall be no one.

        How do we talk about this for action to make changes?

        • Health care is a prime example of expansionary business logic run amok. Most of the prescriptions to improve it look only at financing current practice, not at how to change basic health care. That’s best left to the professionals — the experts — but given the proscriptions of the system, few experts have much incentive to challenge the overall structure of the system, but there are a few.

          The severity of the mess was dramatized by Peter Orzag’s economic study 10 years ago that projected that by 2081, health care costs would be 100% of US GNP. That obviously can’t happen, and if anything like it did, we’d all be deathly sick, but we’d be rich — maybe. (Even the definition of GNP is inadequate for a changing economy, so this whole argument collapses in it’s own foolishness.)

          In health care as elsewhere, we must drastically change our perspective from which we address our problems — learn to live well while using much, much less to do it. That’s not a perspective that people in Worthington or elsewhere can readily take up because the system tells them that everything “making more money” is the best system that mankind can devise. I fear that the end of that system will not be peaceful or pretty before our mass disillusion becomes obvious to us.

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