Tag Archives: Systems biology

A Few Thoughts on Evolution

 

A few thoughts on evolution as a whole:

It is sometimes thought that evolution by way of natural selection happens due to happenstance mutations in genes that happen to offer some adaptive advantage, and are therefore more likely to be passed on to the next generation, thus preserving them through the generations. While this passive collection of traits is part of the evolutionary change process, natural selection is a much larger umbrella of influences, both passive and active, that have the capacity to shape the traits that contribute to an organism’s or ecosystem’s adaptive profile. The various behaviors and structures that ultimately remain coherent within an organism or ecosystem over time are those that enable the local biological field to negotiate the dynamic demands of the environment that they are continuously baptized in while also satisfying the structural hungers that must also be attended to in order to remain coherent. The relational environment contains both nourishing and antagonistic agents and is composed of both organic and inorganic influences that must be dynamically negotiated. This is no small task.

Biology is not just a relationship between organism and environment, it is also a relationship between and among organisms. It is also not solely a passive capture of traits by way of happenstance alone. Once an adaptive trait is “discovered” and embodied by various means, biology also develops various active means to pass the trait along. Biology also arguably searches out these traits and passing them along as well. Our human trait of being explorers in search of opportunity might be one of the ways this active search is facilitated. One illustration of this non genetic kind of trait is the way an animal can develop what are called “Fixed Action Patterns. A squirrel does not have to be told how to store nuts to negotiate the winter. That behavioral repertoire is embodied within the species and passed along through the generations. It was captured and stored at some level which may involve genes, but probably also entails other factors such as epigenetics as well.

Another important distinction to remember in order to see the larger landscape of biological evolution is that evolution is not a process that happens in the context of a species alone. Ecosystems also evolve as a whole body of life and there is a dynamic connection between the organisms within a species in that context. This relationship between organisms also means that organisms convey adaptive traits one to another through various means, both by way of the meaningful structured transmission of information and by way of happenstantial relational communications that confer adaptive traits. These information sources get captured at an organism or ecosystem level and actively spread the same way that the environmental trigger of a mutation in a sperm or egg that confers an advantage is more likely to get passed on.

Organisms exist in the context of many other organisms and this relational environment between organisms adds to the influential factors that shape the evolutionary process as a whole. It is this crucible that includes the deliberate transmission of traits as well as the acquisition of accidental occurrences that leads to the acquisition of adaptive traits that collectively drive the evolutionary process – this process that builds a hedge of coherency against the chaotic forces that would otherwise consume and disintegrate the body of relationships we call an organism, or ecosystem.

There are a number of ways that biological systems communicate adaptive traits one to another. This communication process that enables the passing along of adaptive traits can take the form of cooperative behaviors for instance. When we think about the wealth of adaptive capacities within our species we must consider the debt of gratitude we owe to our ability to share and cooperate. Not one of the words that are being used to communicate this idea for instance, would be understood if it were not for their structure and meaning having been shared with us at some point in time. This cooperative sharing platform has enabled humans to form our civilization.

Words are not the only way traits are transmitted between organisms. Our ability to capture and accumulate knowledge in a verbal net and transmit that knowledge one to another is synonymous with the way nature passes along of meaningful structural traits such as DNA and epigenetic information as well. Among these meaningful structural traits are sounds and behaviors such as postures or ritual sequences of behavior that convey meaning, as well as the passing of influential structures that serve as information one to another. This meaningful structural type of communication can take the form of molecules that we produce and perceive as scents, some of which, like hormones can meaningfully trigger massive behavioral shifts within and between organisms that serve various purposes like reproduction, establishment of adaptive hierarchies of social status, or the avoidance of danger etc. Still other forms of structural communication include the transmission of genetic information within and between organisms. This can happen by way of sexual reproduction, but in some cases can also occur through such methods as viruses, which can stitch genetic segments into already established DNA strands that can subsequently alter the organism in significant ways, some of which offer adaptive advantage.

Here is an article that takes a look at how viruses swap genes with a variety of cellular organisms and become part of that dynamic relational community that produced the fruit of adaptation in some cases.. In other words, viruses are also “agents of [adaptive] diversity” in certain cases:

https://dailyaccord.com/viruses-share-genes-organisms-across-tree-life/

Advertisements

The Nature of Biological Systems

The basic nature expressed through biological systems all the way from the atoms and molecules that flit about in our cellular cytoplasm, through the organelles that serve as the institutional expressions of stability, producing and installing the various proteins we need, through the organs which have different capabilities that are dovetailed with each other, to the way we fit as species in the context of an ecosystem which we are part of and depend on for life must operate by the principle of nourishing and defending the continuing coherency of that entire system in order to remain coherent over time.

Whenever we focus at any level in a coherent biological system, we see the principle of the nourishment and the defense of coherency in the context of an environment with both nourishing and antagonistic agents at work. The coherent community of relationships of which we are composed dynamically differentiates friend from foe, and uses that perception to either call to service that which nourishes or defends itself against antagonists to remain coherent as a system over time.

Out of this fantastically complex blend of relationships, biology brings order to relative chaos. As biological creatures we are destined to engage in this process of nourishing and defending the coherency we depend on to continue. In this relational community we see the emergence of an implied purpose etched into all biological systems, whether or not these systems are at odds with each other. We call this global purpose expressed through biology by many names like survival instinct, nature, and so on, but the overarching unified purpose is that of nourishing and maintaining coherency over time. As byproducts of this theme we see acts of kindness, fruitful relationships as well as sacrifice in the mix. These various characters are the agents of balance and growth we depend on to realize our potential.

One of the prime necessary defenders in a local biological system like our own are the immune cells called “killer cells”. These cells target bacteria that are perceived as a threat and eradicate them so that they do not destroy the cooperative nourishing bonds that we depend on to remain coherent as a biological entity. Here is a closer look at how these soldiers of coherency that work and sacrifice on our behalf do their part in the tapestry of characters in this biological community that works to nourish and defend itself over time.

Microbial murder mystery solved

From the article: “…for the first time, researchers have caught killer cells red-handed in the act of microbial murder, observing them as they systematically killed three strains of microbes: E. coli and the bacteria responsible for causing Listeria infection and tuberculosis. The process inflicts bacterial cell death regardless of whether the environment contains oxygen or not… [The] findings… reveal that killer cells act methodically, shooting deadly enzymes into bacteria to “program” a complete internal breakdown and cell death.”

https://phys.org/news/2017-11-microbial-mystery.html

In-Groups and Out-Groups: A Biological Perspective

There is a certain fungus that is able to control certain ants to serve as a vehicle to further its own reproductive ends. The ant, in this case, dies in service of reproducing the fungus. There is also the case of the bacterial parasite T. Gondii which edits rodent brains to be attracted to felines so they get eaten, which helps the bacteria to enter its spawning grounds, which is in a feline gut. (it also edits other mammal brains in different ways) There are numerous cases of parasites and viruses that have the capacity to influence other organisms in service of their specific ends. It could be said that this is the norm in nature – competing influences that ultimately result in emergent behaviors that we typically identify as belonging to “an organism” but are in fact based on the collective property of many organisms.

When we consider that we are also a collection of various organisms that are influenced by each other, each with various agendas and various means of carrying that agenda out, we can begin to see that what we call our choices, and what we think of as our identity, may in fact be a byproduct of the parliamentary constellation of influences that rises from the pool of biological organisms that define us. We may be a reflection of the relationship field from which we are composed which extends beyond human genetics.

A recognition of this, at least from the parasitic sense, there is a now “theory” on the block called ; “The parasite-stress theory” which sees our personal and cultural identities through the lens of the parasitic creatures that influence us to service their various needs. In some real respects, it posits that our cultures in large part are an emergent property of the parasitic microbes that influence our behaviors.

The evidence for this idea is the strong correlation between the strength of parasites in the relationship field of the people in a given culture and their relative state of peace or conflict in addition to whether or not the culture is conformist or individualistic etc. In other words, what we see as culture may be a mirror effect of the relationship field between organisms.

According to this video; the parasite-stress theory may be a general theory of culture and sociality. In a nutshell it acknowledges the fact that the various strategies organisms have to influence other organisms to serve its purposes do have a role in defining this thing we call us. My thought is that it would be a more accurate lens if it looked at the full spectrum of organisms, some of which are on the mutually beneficial range of influence – commensal organisms having a stake in the success of the community it depends on – and doing what they can to offer benefits such as stability, defense, long life and so on. In other words, I think this theory is on to something, but is not yet complete. If we factored in the full spectrum of influences, (rather than just the parasitic segment) we would be able to understand that our opportunity for cultivating an intentional experience of life, rather than riding ignorantly on the winds of biological chance, is rooted in whether or not we intentionally tend the biological relationship field of which we are, on which we depend and that defines this thing we call “us” to be inclined toward the commensal, mutually beneficial segment of the spectrum of relationships.

The Biological Community Defines Our Experience of Life

If we unpack the implications of the fact that a single celled parasite like Toxoplasma gondii can develop a strategy to modify mammalian neurophysiology and behaviors to suit its own biological ends, we can begin to appreciate the fact that the community of friends and foes in our local biological relationship field set the tone for what we experience as life.

There is a full spectrum of relationships that is possible in any given biological community that can span the spectrum from obligate (necessary) mutualism to parasitic and predatory relationship dynamics where seizing the fruit produced by other organisms is the core behavioral property of the organism.

Depending on the biological community’s bias toward cooperation involving mutual nourishment and common defense, or toward parasitic and predatory relational dynamics, the organism based community will tend toward homeostasis (balance), or instability. This makes whether or not we learn about, and act to appropriately tend the many organisms from which our local biology is composed is a key factor in whether balance or imbalance (health or disease) will happen. It also plays a key role in defining our identity and shaping experience of life. This makes understanding and cultivating the biological relational system we are part of a critical factor in effectively steering our experience of life.

Here is an article outlining how a number of parasitic and predatory organisms press their agenda within the larger biological community. It is important to remember that there is a full spectrum of relationship possibilities, some of which bring nourishment, strength and health or defense of the integrity of the system against disruptive agents.

http://www.the-scientist.com/?articles.view/articleNo/31536/title/Animal-Mind-Control/

Nature Echoes Nourish and Defend Behaviors on Many Scales

When our immune system sees a pathogen, something it perceives as harmful, it establishes ways to effectively neutralize or destroy that destructive agent. In doing this, it uses weapons (destructive agents), and vectors (vehicles) to carry the weapons it uses in defend to their appropriate location.

On a broader scale, this same defense of integrity through an “immune response strategy” may be what is going on at a larger scale in biological ecosystems. Since nature establishes defenses (things which destroy perceived pathogens) by establishing defensive weapons and looking for vectors to carry these destructive agents to their appropriate location in order to effect the “immune response”, why would we not expect to see this happening on different scales, from cell to body, to larger bodies of life?

The only difference in this relational dynamic that happens in a cell or single multicellular organisms that also may be happening in ecosystems may be the scale. This “immune response” may be also happening between larger bodies of life – bodies of life which transcend single organisms, and are constructed of networked metabolic structures that are stitched together through a vast array of species and subsystems within species – bodies of life that, although composed of many kinds of organisms, have a need to nourish itself, as well as protective skins and other defenses to protect itself, in addition to porous biological boundaries, the same way an individual cell or a larger organism does.

These larger bodies of life, which sometimes clash as a result of the existential debt nature demands for any coherent biological body – to nourish and protect itself, and to mount defenses against antagonists to that coherency. This may be the legend of the map that defines relationship landscape we see in biological ecosystems. It may also explain why, when there is less need for these defensive weapons to be carried to and fro to perceived pathogens in these larger bodies of life, that we also see these vectors less populated with these transgenic weapons, as we see in the case of mosquitoes in the rain forest, which tend to be less populated with the weapons of defense. Just a thought…

Disease-carrying mosquitoes rare in undisturbed tropical forests

From the article: “We found that fewer mosquito species known to carry disease-causing pathogens live in forested areas compared to disturbed ones… Mosquito species from altered forest sites are more likely to transmit disease than mosquitoes native to an area of mature tropical forest.”

Read more at: https://phys.org/news/2017-08-disease-carrying-mosquitoes-rare-undisturbed-tropical.html

Biology Reveals Insights into Human Culture

This is an excellent documentary that illustrates how biological ecosystems find an equilibrium that is a suitable adaptive response to the environment. This means all the organisms that express nourishing and defense behaviors in a given ecosystem become specifically suited to the environment and each other. Islands are one of the places this biological balance is illustrated clearly; where the particulars of the environment along with the baseline biological ecosystem that inherited the island come to express a behavioral economy that is adaptive in that specific context. Islands with no large land predators may bring about flightless birds for instance because of the lack of need to fly away.

Christmas Island is an excellent illustration of how that biological equilibrium can be dramatically disrupted by a newcomer to the biological social economy. This disruption can expose weaknesses that are present because there was no need to build defenses against the strategies of the imported invader prior to its arrival. This is what drives biology’s own evolutionary expression of a “Game of Thrones” and may also be a good insight into the way the various human cultures evolved throughout the world – a reflection of populations finding equilibrium with the environment, reflecting its nature, coupled with the periodic need to adapt to “invaders” as we began to cross pollinate as a result of things like trade, climate shifts and so on, leading to the human version of “Game of Thrones”.

Powerful Influence from Small Changes

While this article is on *Brain Inflammation and Obesity* specifically, there seems to be a number of deeper implications if we apply a wide angle lens to the fact that certain infections, or microbiome populations, or traumas, etc. in the context of our complex biological system can shift behavioral expressions on more than physical scales. This influence on our relational landscape has a powerful influence on our experience of life. Extrapolated further we might begin to get a glimpse of how our evolution, history, culture and sense of identity might all be far more nebulous and arbitrary than we are used to believing.

https://www.labroots.com/trending/neuroscience/6586/brain-inflammation-obesity

How Smell Shapes Our Lives

There is no thing that we do on a macro scale that does not exist on a micro scale. Recurring echoes of self similarity with a blend of melodic dissonance is what makes up the magnificent symphony of structure we call biology. Smell is no exception:

The Strategy Employed by Nature to get Things Done

When it comes to accomplishing tasks in the face of various forms of adversity and an environment that would need to be cultivated or persuaded to move toward a specific goal, one way of breaking down the various strategies that are possible to do this is a concept called destinationist. A destinationist strategy accepts that the current state of affairs is not desirable and that change is necessary, but rather than being a determinist, where the strategy appears to be “all or none”, where arms are flapped or folded folded and scowls are formed and baying at the moon over the current circumstances – how wrong everybody is and how the world is not right is the de facto strategy, the destinationist uses a strategy which accepts the reality of the current landscape, and attempts to move in the correct direction using realistic doable steps, perhaps not knowing if full success is possible or warranted. Nature appears to have this destinationist philosophy as it attempts to do things to move in a certain direction, even though the current solution may not be perfect. One example it the following: “while having diarrhoea might be a nightmare, not having it could be an even worse fate.”

Here is an article detailing how the body uses a destinationist strategy to deal with stomach issues that comes with some pain, but is best given the overall picture.

http://www.sciencealert.com/scientists-just-realised-the-purpose-of-diarrhoea-is-way-more-complicated-than-we-thought

The Battlefront between Order and Chaos

The level of depth perception coupled with the predatory behavioral inclination of cancer produces a number of intricate strategies to advance its agenda to make itself the center and overtake the carrying capacity of the community of cells in which it lives, destroying the community (and itself) in the process. Cancer is like a seditious saboteur bent on destroying a nourishing sustainable system of relationships. This predatory antagonistic bias toward the relational harmony an organism depends on and the concerted effort of that community of harmonic relationships to defend against these destructive agents is a clear illustration of the battlefront between order and chaos we see expressed throughout nature.

One of the more intricate destructive strategies employed by cancer is to cause a kind of black flag type operation, where it tricks healthy cells into producing false viral signals so that they look like they are the problem to the immune system. This diverts the healthy system’s immune response resources toward a false problem redirecting energy that might otherwise be directed at the cancer, enabling it to carry on its work of seizing more resources for itself at the expense of the larger biological community.

Here is an article detailing this process:

Researchers Now Know How Cancers Force Other Cells to Make Fake Viruses

http://www.sciencealert.com/researchers-now-know-how-cancers-force-other-cells-to-make-fake-viruses