Tag Archives: Systems biology

What is our role in defining our experience and do we recognize and leverage it constructively?

The relationships that define functioning biological systems exist on a spectrum ranging from vital, mutually beneficial relationships at one end to parasitic and predatory ones at the other. Vital relationships are when the parts within a system are essential to each other such as the vital organs in our body. After vital relationships are those that produce adaptive value but are not vital, such as arms or legs. On the negative side of the spectrum are parasitic and predatory relationships that act to disrupt these cooperative networks. Overall, a certain threshold of cooperative, mutually nourishing and-or defensive relationships is essential for coherent biological systems to exist.

The fact that destructive agents exist requires coherent systems to devote a certain portion of energy to contend with antagonists. Our immune systems are an example of this expression. Adaptive value is measured relative to a particular system. For example; predators nourish themselves at the expense of prey. From the predator’s perspective, this is an adaptive trait. From the prey’s perspective, it is destructive. Getting away more effectively or otherwise defending against the predator is adaptive to the prey.

This spectrum of relationships is expressed on many scales; on small scales within and between organisms, on larger scales in local environments and ecosystems. Out of this “relationship economy” come living monuments to the necessities of being. Complex adaptive systems that nourish and or defend coherence are what we see embedded in biology’s perceptions and responses. Each organism is tuned to this purpose. System properties that more effectively contend with the necessities of being over time are “selected” over those that do not.


The environment is the primary influence in defining the relationship properties of the systems that exist within it. Desert ecosystems tend to express a more defensive posture than do lush tropical ecosystems. All ecosystems have relationship elements from across the spectrum but the local emphasis is influenced by the necessities dictated by the environment.

Once behaviors get established, they tend to have their own “nourish and defend” aspects to them. This means behaviors that were once relevant to survive in one environmental circumstance can be carried over and adaptively misapplied in other settings. Renegotiating environmental variables is a necessary part of navigating over time in a changing environment. The impact of organisms can become part of that change agency. Ultimately nature manifests signals experienced by organisms as pain or pleasure to communicate when behaviors lose or gain value but there is an “echo from the past” aspect to these signal patterns. Not everything that worked to get us here is relevant to take us forward. This means we have to undergo sacrificial “pain” to give up established patterns that are no longer adaptive.

The same spectrum of relationships in physical biological systems exists in our human social relationships. The emphasis we express is built on environmental influence factors. An individual raised in a climate characterized heavily by parasitic and predatory relationship behaviors will develop a more defensive profile. The same influence factors apply at cultural levels. How we relate has a certain momentum that tends to make what has already happened more likely to happen again. This is especially true of large or long practiced behaviors. This can make pulling out of maladaptive behavior cycles difficult.

Insights into our behaviors can be applied constructively or destructively. We can apply our understanding toward the vital mutually nourishing end of the spectrum that strengthens the community of relationships we live in and depend on or toward the parasitic and predatory destructive end that diminishes vitality. This application influences our experience.

Understanding and applying this information is the oar we have at our disposal to intentionally influence what we experience. In the absence of this applied understanding, we ride on the experiential whims of ignorance and happenstance. We are defined by the environmental womb that formed us, with no voice in the choir that determines our experience.
There are a variety of opportunities available to us. Some of those within our reach can lay untapped until they are employed. Others are lost unless cultivated during limited windows of opportunity. Seeds out of geographic place or out of season for example.

Social systems, like all coherent systems, require a certain threshold of vital and beneficial cooperative relationship opportunities to be realized to service the integrity of the social group. Beyond this minimum necessity are the opportunities we can cultivate to make our lives more vibrant. Parasitic and predatory behaviors within this cooperative “matrix of necessity” can create a local benefit but diminishes and-or destroys the fabric of necessary cooperative networks. If a system is taxed beyond the threshold of its ability to cope with destructive agents its integrity collapses.

Behaviors at the destructive end of the spectrum demand more devotion of energy to defense. More energy to defense shifts energy away from the cultivation of cooperative opportunities. When our immune system activates, for instance, it shuts down energy devoted to growth, maintenance, digestion processes, and so on. This is to redirect those energies to the negotiation of the perceived stress. This realignment of energy is true within our body but also within and between species, within and between cultures, and between our species and the environment. This is the relationship economy that defines our experience operates.

We can become agents of our poverty on the altar of short-sighted gains or we can nourish our potential depending on whether or not we cultivate our opportunities. Having said that; it is not an easy proposition to overcome the momentum of parasitic, predatory and-or maladaptive behaviors that may be embedded in our nature. These events influence our perception and response profile and shape our experience. This does not mean to suggest opening the floodgates of trust. Extending unwarranted trust to each other is a danger when destructive agents exist in the social economy. Finding the place where we can realize the maximum opportunities that can authentically move forward is the only way we can effectively make progress happen.

If this analysis is correct, or at least useful as a lens to more clearly understand the role we play in experience, what are some ideas on how would we begin disciplining ourselves to strengthen the bonds of integrity we depend on and improve our experience? What would this look like?

The Behavioral Theme of Biology is Nourishment and Defense

One of the major themes expressed through biological systems of all types on many scales is activity that lends itself to supporting coherence over time. The strategies are numerous, but pivot on the theme of coherence by way of “renewal” actions over time. In a variable environment with antagonistic agents that break down systems that need continual renewal to remain coherent, coherence sometimes means making sacrificial gestures that may not appear to serve from a short term perspective, but are necessary in when the perspective shifts to the long term. Here is one of those examples: *How a slime mold near death packs bacteria to feed the next generation* “…In the final frenzy of reproduction and death, social amoebas secrete proteins that help preserve a starter kit of food for its offspring.” https://www.sciencenews.org/article/how-slime-mold-near-death-packs-bacteria-feed-next-generation

Biological Influences on Identity Being and Personality

The influences that conspire to define what we experience as things like identity, being and personality type are built on a deep ocean of context based relationships which we have only begun to see with any real clarity, much less harness to our advantage. The currents of influence on which we ride have yet to be captured by the meager net of abstractions we feebly waggle into the depths in hopes of capturing something of value. Here’s a look at one tiny portion of this vast ocean of opportunity we have yet to discover and settle by way of leveraging our understanding toward progress.

An Ancient Virus Lurking in Our Genes Could Play an Important Role in Some Addictions

“…An unusual version of a retrovirus nestled between genes involved in brain chemistry is more common in individuals with a drug dependency than the rest of the population.*

https://www.sciencealert.com/endogenous-retrovirus-hk2-insertion-dopamine-gene-role-in-addiction

The Relationship Engine that Defines Biology

 

If we step out of our structural model of “organism” and “genetics” and look instead through a relational model that defines biology in general, we see a relationship climate in the biological landscape spectrum that spans from obligate (necessary) mutualism, through commensal relationships that benefit both parties, all the way to predatorily competitive where one benefits and the other is destroyed. Through this lens we begin to see the basis for the emergent intertwined systems we see in biology.

With this model a full spectrum of behaviors would happen in the context of a single organism for instance. Our own system has certain obligate mutualistic relationships such as that between our vital organs. We have commensal relationships with microbes that provide valuable services for the proper processing of food and get to flourish themselves as a result. We also have an immune system that predatorily looks for antagonists and seeks to destroy them.

Systems that align themselves around coherence through the acquisition and support of sustainable nourishment and defense of that coherence through the destruction, or compensation for antagonistic factors (pathogens) that are perceived to threaten that coherence. (Autoimmune diseases would be an example of a disproportionate response in this process)

This twofold relational axiom (Coherence and defense of coherence) is what defines adaptive biological systems. When we look through this coherence lens, the membrane that defines sustained coherence is not defined by genetics, or by the skin of any one organism, neither is it based on a singular organism. It is defined by an adaptive array of relationships across the spectrum that lend themselves to establishing and maintaining coherence. These various relationships are threaded through many organisms and sometimes only parts of other organisms which together define a single relational system.

A sustainable relational economy is one that is adapted to the environment with a proportional amount sampled from that full spectrum. In other words, nourishing coherence and defense of coherence is threaded through many creatures that form a collective body.

Here is an accidental discovery that happened to discover one of these defensive systems in plants which occurred when trying to study the effects of gravity on plants.

𝗔𝗻 𝗔𝗺𝗮𝘇𝗶𝗻𝗴 𝗥𝗲𝗮𝗰𝘁𝗶𝗼𝗻 𝗛𝗮𝗽𝗽𝗲𝗻𝘀 𝗪𝗵𝗲𝗻 𝗮 𝗣𝗹𝗮𝗻𝘁 𝗚𝗲𝘁𝘀 𝗛𝘂𝗿𝘁, 𝗠𝗮𝗸𝗶𝗻𝗴 𝗧𝗵𝗲𝗺 𝗠𝗼𝗿𝗲 𝗦𝗶𝗺𝗶𝗹𝗮𝗿 𝘁𝗼 𝗔𝗻𝗶𝗺𝗮𝗹𝘀

“…When plants are under attack… their defense systems are raised in other parts…. plants use the same signalling molecules that animals use in their nervous system… the signals as they travel in waves through plants in response to a stressor… there’s this systemic signalling system, and if you wound in one place the rest of the plant triggers its defense responses… if a plant gets wounded, an electrical charge fires, propagating across the plant. In animals, an excited nerve cell releases an amino acid called glutamate, which triggers a wave of electrically charged calcium ions that propagate to cells farther and farther away from the site… what happened to the plants is… Waves of light flow out from the source of the wound, spreading through the plant… once the wave hits, defensive hormones rise in that region of the plant.”

https://www.sciencealert.com/plant-damage-response-defence-calcium-ions-glutamate-fluorescent

Exploring the Origins of our Social Nature

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When we are in a stadium or a packed movie house experiencing something on the edge, do we feed on the mindset of the crowd? Do we lose our sense of individuality and become part of the group body? Can cultures incentivize the adoption of ideas; not because the ideas themselves are valid, but because they act as symbolic markers of inclusion? Do these ideas become the de facto currency of social inclusion, something we tend to adopt because we are biologically wired to seek inclusion as a primary drive?

Could this be how intense stress can act to spawn populist movements with fierce devotees that tend to act on more narrow and non nuanced principles? Could this natural tendency toward a desire for coherence make us convinced of an idea, not because of its validity, but because of our need to belong to a group for protection, especially under perceived stress? Is this what happens on differing scales of intensity as a function of our social nature?

Is this holding of ideas as a means of ritual expressions that cement social bonds something we may do without being consciously aware? Is it possible we are not in touch with because we’re lost in our own little words while actually being carried on biological currents that are far deeper and powerful?

This article might reveal a clue of the origins of this type of behavior we see at many levels:

𝗛𝗼𝘄 𝘁𝗵𝗲 𝘀𝗹𝗶𝗺𝗲 𝗺𝗼𝗹𝗱 𝗴𝗲𝘁𝘀 𝗼𝗿𝗴𝗮𝗻𝗶𝘇𝗲𝗱

“… a unicellular organism that may transition into a multicellular organism under stress, has just been found to have a tissue structure that was previously thought to exist only in more sophisticated animals. What’s more, two proteins that are needed by the slime mold to form this structure are similar to those that perform the same function in more sophistical animals.”

https://www.sciencedaily.com/releases/2011/03/110314172317.htm

The Art of Communication Has A Long Tradition

Collections of cells working together as a unified body, producing specialized behaviors that lend adaptive advantage on a group scale which include some sacrificial acts that benefit that larger community is not unique to complex multicellular organisms like ourselves. It is more of a relationship theme that that has been threaded into biology long before multicellularity as we know it emerged. It involves perceiving necessities, and communicating these necessities across a biological domain so that effective behavioral responses can take place. This community principle, complete with communication across a wide biological landscape has been present, and conserved throughout our biological history – a unified purpose among different biological entities that arose out of necessity long before multicellular (metazoic) creatures emerged. Here is an example of how this takes place among microbes:

How Microbes Communicate Over Long Distances

“…Percolation is familiar to anyone who brews coffee, and it helped researchers at the University of California San Diego understand how bacteria communicate with one another over long distances. Communities of bacteria, sometimes called biofilms, aren’t just a clump of bacterial cells. It seems they can send signals to one another with ion channels, promoting the survival of the community and protecting it from attacks. New findings on that communication have been reported in Cell Systems.”

 

Link to full article:

https://www.labroots.com/trending/microbiology/12216/microbes-communicate-distance

We’re in this Life Together

Like so much of the choreographed biological relational dance that defines our own being – this place in the cosmos that we have only just begun to capture in our meager abstract net of words – the monarch butterfly lives a life of connectivity to itself and nature that steps far beyond it’s own capacity to grasp. When we witness this spectacle of the monarch life cycles, we can only marvel on the sidelines and partly describe the processes as one of nature’s mundane acts of profound expression unfolds before us. Like us, the monarch butterfly cannot sufficiently explain the intricate depths of its own being, and yet it is somehow aware at some level how to navigate the environment that would swallow it if it did not press back proportionally with an effective strategy to negotiate the perils. The monarch cannot explain why it eats what it eats, why it is equipped the way it is, or breeds successive generations, each with specialized roles and specialized understanding, geared to migrate a partial leg of a journey that spans a number of monarch lifetimes and thousands of miles through a myriad of environmental variables and challenges. It cannot explain the depths of its own genius – to act as a singular cohesive unit in the face of variable challenges with a collective body that spans lifetimes and acts in unison to preserve the species as a whole.

The Monarch butterfly carves out its cycle of life in part through a 2500 mile journey every year over four specialized generations of travelers, each lifespan lasting 2 to 6 weeks, except for those that wait through the winter to make the journey again. Like the monarch, we also temporarily carry the torch for a larger body of life that continues beyond our individual lifespan; we play roles in this larger scheme that we may not completely understand. The degree to which we can make sense of this journey we are on is perhaps rooted in the theme that is expressed through all biological forms; that the mark we make, like ripples in this common pond in which we all swim, get carried forward in time depending on how much value they contribute to this common body of live from which we all spring and the extended journey we’re all on. While the significance of our lives exists mostly beyond our field of vision, we can see that what we are is seated on the continuing nourishment and protection of this delicate economy of mutually nourishing and protective relationships that define us as a coherent and continuing form.

An Incredible Journey: The Monarch Butterfly Migration

https://www.isfoundation.com/news/incredible-journey-monarch-butterfly-migration

Balance is the Key to Sustainable Systems

 

Balance is the key to sustainable systems. Even vital substances like water can become harmful when they are out of balance. Too much, or too little water, T too high or too low a temperature and so on is harmful. The correct range is key, and this range is determined by the environmental context. When it comes to complex biological systems like ourselves, many forms of balance come into play. How many and which type of cells, proteins and so on are part of the biological economy that has different players with different attributes, but all operate under the unified purpose of nourishing and defending the integrity of the whole system. This principle is echoed on many scales, for instance; we must seek our nourishment, but we must also defend against antagonists as a social community, as a species, and we must nourish and defend the planet if we are to continue. The point is, this nourish and defend in the context of the community principle is what defines a stable and sustainable system. But even these “nourish and defend” traits also must be in balance; proportional to the context of the environment, otherwise they too become harmful.

The same way we go into a highly reactive mode when stressed or faced with a perceived mortal threat – this fight or flight mode, where we try out behaviors that we would never consider in any other context goes into effect. It’s part of the innate systems embedded in our biological systems that go into effect as a means of defending against the loss of the integrity we depend on to remain coherent.

Our individual cells are equipped with these same defensive mechanisms on a smaller scale. When our cells are faced with stressors or mortal threats they also try out radical strategies in an attempt to hold on to integrity as well. These radical adaptive expressions that attempt to stem the tide of destruction can sometimes result in cancer, which produces a radical class of “survivalist” cells, highly focused on, and able to rapidly, adapt. Once they gain a foothold of fiercely adaptive cells in the context of our body, which requires a certain cooperative mutually nourishing relationship climate in order to function, it threatens the integrity we depend on at that larger biological community scale.

In other words, the cancer begins to exercise this highly adaptive “try any and everything adaptive strategy” as the cancerous cells begin to multiply. The cells begin operating as an adaptive agent in its own right, with dynamic adaptive aims that separate from the unified purpose of the body which spawned the cells. It is like a speciation within a single body. Rogue maundering raider cells pillaging the body to continue to exist, not recognizing that this tax will destroy the foundation on which they depend.

Because the hyper active highly adaptive capacity operates without regard to the integrity of the larger system in which the cells reside is why cancer cells, once they develop a communal relationship with one another, are so destructive, and why they are so difficult to eradicate once gain enough ground. Their capacity to adapt by developing radical strategies on the fly makes them a particularly foe to eradicate. In this case, lung cancer develops a digestive system.

Scientists Discover a Tiny Stomach Hidden Inside Lung Tumours, Because Cancer Is Changing

Cancer cells will do whatever it takes to survive.

https://www.sciencealert.com/scientists-discover-a-tiny-stomach-hidden-inside-lung-tumours-because-cancer-is-changing

Cultivating Adaptive Relationships: A Key to Survival

Relationships that can form between organisms that generate adaptive traits that would otherwise not exist, traits which are sometimes crucial in the context of the environmental conditions, can mean the difference between continuing forward through time and extinction. When these adaptive capabilities emerge in the context of environmental pressures, long term mutually beneficial relationships can then be conserved meaning maintained over time. This “forging of mutually beneficial relationships” that nourish or protect a local biological economy in the context of the environmental pressures is another form of what we call natural selection.

 

At one time these relationships formed by chance, and accumulated as a result of how they contributed to adaptation. Understanding how to cultivate these relationships, along with actively facilitating them where they can serve that adaptive purpose in the context of the larger body of life we live in and depend on in a constructive way is part of the technological lever we have as humans to influence our present and our future. Here is an example of this emerging application of evolution that may make a crucial difference in our continuing survival.

Biology is a Symphony of Variations Built on a Coherent Theme

 

Any coherent system in nature has some combination of self similarity with other systems as well as some unique points of differentiation. In other words; nature has themes, and variations on the theme. Biology is no exception to this rule. When we consider the mind boggling complexity with which the relationship economy we call biology is expressed on many scales, we can easily get lost in the complexity. In order to understand it with a maximally useful perspective we must be able to tell the difference between the self similar themes and the mind boggling variations on those themes.

With an understanding of the difference between theme and variation, we can then identify the key leverage points which influence various systems more intentionally and effectively. As we ferret out the principle axioms on which complex systems rely – the simple rules behind the complexity – the global properties threaded through the biological economy – we then have tools to more rapidly see the many variations on the theme, and with this clarified vision, we are also poised to more effectively influence the nature of the processes and by extension our experience of life.

The heartbeat of the integrity on which biological systems rely is a relationship economy built on a cultivated harmony of mutually nourishing relationships, along with a proportional attendance to defending that nourishing relationship field from antagonists. This two stroke relational engine is facilitated by various means of perception structures that are aimed at identifying nourishment from antagonist, as well as a repertoire of corresponding behaviors that relate appropriately with each type of perception.

Biological systems must acquire information and act appropriately on that information – information related to acquiring nourishment while avoiding and or destroying antagonists. Acquiring nourishment in service of the mutually nourishing relationship field that defines its continuing coherency, along with an immune system to protect that nourishing social economy is the theme. Acquiring and sharing information to this “nourish and protect” end, along with manufacturing structures that facilitate a proportional response, is how biological systems are “expressed”.

Biology can be viewed as a collection of structures that must perceive and share information across the network of mutually nourishing bodies, as well as structures that can act on these perceptions. We see this theme at the cellular level, between cells, at the organ level, between organs, and at the species level, and between species. The same way varied expressions of musical communication can be generated from a basic theme of 7 notes, the overarching theme of the biological economy is variously expressed by way of simple thematic foundations – variations on the theme.

This “perception and response” theme that facilitates the axiomatic core of “nourish and protect” behavior is itself the thematic nucleus of biology. If information needs to be shared, it is accomplished by way of structures purposed toward a specific “meaning” that fits into this thematic core. If a defense requirement is perceived by way of structure, it is also expressed behaviorally by way of structure. Structures in the context of biology convey meaning.

These meaningful structures from which biology is composed also have self similar themes. Many established structures are variations on the theme; “perceive and respond to nourish and protect” – established structures are frequently repurposed to accomplish many different things in service of the perceiving and communication engine in service of nourishing and protecting.

With all of this in mind, we can then see that the way communication is facilitated by way of certain structures in the brain may be an expression of an isomorphic theme – a representation of the way organisms communicate between each other in the form of viral “communications” in the brain may also be seen as the means of carrying out the functions of perceiving, nourishing and defending in the larger biological body of life. Bacteria share information by way of structures, and viruses are certainly worthy of being considered as a potential means by which perceiving, nourishing and defending goes on in an ecosystem. The reason this may be worth consideration is because “thoughts” in the form of viral like structures is the the physical form of the information economy within the brain. When we consider this pathway for information sharing, we might ponder how this same structural process might play out in the larger body of life, using viral like particles as the means of sharing information, nourishing and or protecting integrity.

Brain Cells Share Information With Virus-Like Capsules

https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-information-using-a-gene-that-came-from-viruses/550403/