Tag Archives: Systems biology

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

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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 โ€œorganismโ€ and โ€œgeneticsโ€ 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.

๐—”๐—ป ๐—”๐—บ๐—ฎ๐˜‡๐—ถ๐—ป๐—ด ๐—ฅ๐—ฒ๐—ฎ๐—ฐ๐˜๐—ถ๐—ผ๐—ป ๐—›๐—ฎ๐—ฝ๐—ฝ๐—ฒ๐—ป๐˜€ ๐—ช๐—ต๐—ฒ๐—ป ๐—ฎ ๐—ฃ๐—น๐—ฎ๐—ป๐˜ ๐—š๐—ฒ๐˜๐˜€ ๐—›๐˜‚๐—ฟ๐˜, ๐— ๐—ฎ๐—ธ๐—ถ๐—ป๐—ด ๐—ง๐—ต๐—ฒ๐—บ ๐— ๐—ผ๐—ฟ๐—ฒ ๐—ฆ๐—ถ๐—บ๐—ถ๐—น๐—ฎ๐—ฟ ๐˜๐—ผ ๐—”๐—ป๐—ถ๐—บ๐—ฎ๐—น๐˜€

“…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

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 incentivise 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:

๐—›๐—ผ๐˜„ ๐˜๐—ต๐—ฒ ๐˜€๐—น๐—ถ๐—บ๐—ฒ ๐—บ๐—ผ๐—น๐—ฑ ๐—ด๐—ฒ๐˜๐˜€ ๐—ผ๐—ฟ๐—ด๐—ฎ๐—ป๐—ถ๐˜‡๐—ฒ๐—ฑ

“… 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, arenโ€™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 carry the torch for the larger body of life in many ways we do not 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 valueย  they contribute to 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 relationships from which we all spring.

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” โ€“ 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 โ€“ 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/

The Stories Life Depends On

Cells are sometimes called the basic unit of biological life. When working properly, they’re composed of a community of interdependent structures functioning as a coherent whole. Although the individual parts within a cell perform different tasks, they’re also interdependently connected to each other by way of a shared and unified purpose toward nourishing and or defending the whole cellular system as a coherent community.

This principle of coherent structures that involves differentiated tasks connected by way of a shared purpose for nourishment and defense in the context of a larger community does not stop at the boundary of individual cells. Organs and systems such as the immune system are also arranged as coherent entities with specialized capabilities that are connected by way of a mutually dependent unified purpose. We also see this same community principle in the shared relationships between many other biological life forms such as bacteria, plants and the environment as a whole body of life. Without this web of relationships, our biological form breaks down.

Like any social network, the cooperative bonds that form a coherent biological society rely on this story of differentiated roles bound together by mutual dependence – a story that is retold over and over on many levels. The stories involve the sacrificial heroes in that nobly put the needs of the community above their individual needs. Along with these “brave defenders” we also see inventors, and a host of other roles that might be considered more mundane, but are no less vital to the continuing coherence of the community at large.

Here is a closeup of one of these many stories; the story of a sacrificial hero, that works together with one of the more mundane players. The hero, a soldier called a neutrophil that works together sanitation engineer called a macrophage – each needing to play their vital roles in the context of the larger community to maintain the integrity of the biological system we depend on for life.