Tag Archives: bacteria

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.


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

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.


The Nature of Nature

If we look with a wide angle lens at a topographical map of the whole of nature, we see a web of interconnected relational systems, each with some combination of self similarity and differentiation. Atoms are similar to other atoms, with some key differences. Cells are similar to other cells, yet with key differences. These elements of structure also relate to each other in a combination of self similar and differentiated ways. A reverberating echo of self similarity and differentiation that we could use to see the nature of the entire relationship landscape we call the cosmos.

Of course we could categorize the many systems we see in nature many ways, some more useful than others, but one of the more useful ways of looking at interconnected systems, at least as they relate to us, is to gauge their value based on how well or poorly they contribute to what we need as biological creatures to stay coherent… Let’s take a look:

Continuing with a wide angle lens approach to looking at nature, we might see the question begging through the whole structure: Why are there any coherent systems in nature at all? Even deeper: Why are there complex adaptive coherent systems such as we see expressed through our own biology and the larger tapestry of life into which we are woven? This question has tickled the minds of inquisitive people in some way shape or form ever since we’ve had occasion to turn our gaze toward understanding this cosmic womb we are both part of, and continuously bathed in.

To find the answer to this, we can begin by looking at the global properties on which all coherent structures stand; to see what is communicated through all of them, and use this as a foundation to understand all structure. Whenever we see systems that maintain some form of equilibrium such as an atom, a solar system or an organism, we also see that they behave in two key ways. They both nourish and defend the coherency of the system in the face of the whole of nature, which has a blend of both nourishing and antagonistic elements in relation to that system. With this in mind, it appears the complex tapestry of relationships in nature is inclined to accumulate those things which result in a sustained coherency. This coherency is established through nourishing behaviors and defensive behaviors against antagonists to that coherency.

Here’s a link to just one example of a relationship between cacao plants and microbes that protect its coherency, but examples of nourish and defend behaviors can be found as the foundation of every coherent field of relationships in nature that is sustained over time. In fact; it could be said that this is the nature of nature.


On Free Will, Awareness and the Nature of Being

Many of us think we have agency – the capacity as individuals to perceive a certain portion of the local landscape of reality and use that as the basis to act independently, making our own free will choices. It comes as a surprise to some of us to discover that while an element of that perception of reality and corresponding response using a component of agency may be a piece of the puzzle, it is a small piece, if a piece at all.

Most of what we perceive and experience can be more accurately characterized as being “along for the ride” on a wave of relationship dynamics that occur on many scales, including molecular scales which are driven by the trillions of microbial life forms that live in and on us. In other words, we do not experience things due to what’s going on solely in our head, we experience things that stem from any number of sources known and unknown for which we manufacture what is in our mind a plausible explanation for those experiences.

Our capacity to produce plausible explanations is the real talent of our brain – producing things that are useful, but not necessarily things that are accurate. These explanations are inaccurate at best and often miss the mark completely, yet they produce a convincing picture, leaving us embraced in the comforting delusional cocoon of beliefs that may serve us, but do not correspond to the reality of the situation. Here is a small glimpse at the real world we so rarely get a glimpse of with our minds:


Humans are Part of a Much Larger Biological Parliament of Relationships

We humans are part of a much larger biological parliament of relationships. It is this wide context of relationships that transcends “human” and includes the other life forms we live in the context of is what defines how we experience our life. It is the whole community, not any isolated part that defines what we call “us”. Injuries that impact this larger biological parliamentary body of relationships we are composed of can powerfully shape us over time. Minor injuries for instance can heal without any long term effects, but deeper kinds of injuries can echo for long periods. We commonly know that serious wounds to our physical body, or severe trauma experiences can reshape our brain structure and define how we respond to the world from that point forward,. What is not as commonly known is that injuries to the collection of microbes that live in and on us (called the microbiome) can also affect the way we see and respond to the world for a long time. In this case, research done in mice indicates that a mother under stress can result in injuries to the microbiome we depend on for many aspects of development. This can cause cognitive defects and anxiety in the child, and the effects of these injuries can persist all the way through adulthood.

Life is an interconnected tapestry of relationships that requires certain conditions to be cultivated in order to be able to realize it’s full potential. Recognizing these the widely dispersed cause and effect cues in this complex relationship field is the key to being able to shape them intentionally.

Click here to read further “Stress During Pregnancy Negatively Impacts Fetus, Microbiome may Explain Why

Phylosymbiosis: Cooperative Relationships as a Matter of Survival


It has become increasingly apparent that larger organisms like ourselves cannot live alone. A certain community of bacterial associates must live in, and on a host organism. This relationship is sometimes essential for the host’s well being as well as that of the the microorganisms. Different animals have a specific array of microorganisms that function in roles that offer adaptive advantage in the context of the environment. These roles include digestion, protection from destructive pathogens and so on. They have also been shown to play roles in reproduction and sociality among other things.

This relationship between host and microbial organisms should perhaps come as no surprise because complex organisms such as ourselves arose from cooperative ties between microorganisms and viral components. We are, from a certain perspective, a microbial community ourselves as we are composed of a community of like cells, differentiated slightly into various organ roles that operate as a community. This same principle applies to the more fluid, extended microbial community in the environment.

How this community of relationships forms and develops between a host and the microbiome has been the focus of recent studies on the cutting edge of evolutionary biology. It appears that the relationship between host an microbiome can and does shape the evolutionary path of this collective “community”. Each organism plays a role as a voice in a choir, and the persistent demands of the environment is the choirmaster. The fact that there are severe fitness disadvantages in hosts that don’t have an appropriate blend of microorganism companions is an indication of how crucial this cooperative communal role is to develop. Together, the host and all the corresponding microorganisms that live in together are called a metaorganism.

The host organism actively cultivates a climate to identify microbial friends from enemies. One of the things that emerged in terms of understanding how these communal relationships are forged is that the host’s is able to recognize phylogenic similarities between itself and the various microbial genomes. It does so using its immune system as the sensor to differentiate friend from foe. In other words; the host’s genotype is in part responsible for the composition of microbiota which the metaorganism consists of. The more distantly related species, the less preferred it is. Of particular note is the fact that self similarity in the collective genomes between host and microbe are tied to their inclination to service each other’s needs. Phylogenetic similarity is what appears to incline them to confer advantage toward each other. In other words, the more similar, the more likely their behaviors will center on cooperation.

The host’s immune system is the vehicle that cultivates specific relationships from the environmental microbiome. It is this recapitulation of host phylogeny by microbiota that is called phylosymbiotic relationship. Over time, this relationship field in the metaorganism inclines toward a host-bacterial homeostasis that collectively offers adaptive advantages and in some cases, obligate (necessary) relationships, without which the communal social system would break down.

For more on this, see Seth Bordenstein’s talk on the topic.

On Bacterial Intelligence And Sociality

Although Eshel-Ben Jacob Died in June of 2015, during his life he was a leader in the theory of self-organization and pattern formation in open systems. He extended this work to include adaptive complex systems and biocomplexity. He studed bacterial self-organization, through a lens that holds bacteria the key or seminal force that can lead to our understanding how larger biological systems work, incluging ourselves.

Microbes are often thought of as reactive participants in the scheme of life. Mindlessly chewing away on food they happen to stumble on without much in the way of insight about the future, how they fit in to the larger biological community, or any other kind of depth perception necessary to navigate with competency toward a more certain future in a sometimes antagonistic and ever changing world, but this is simply not so according discoveries made by Eshel-Ben Jacob. He discovered, among other things that they exhibit population control, have an understanding of the need for biological diversity in order to deal effectively with changing environments, in addition to a powerful range of adaptive tools to negotiate the environment. As it turns out, bacteria may not be simple in any respect, they may merely express their intelligence and social life in different ways, on different scales than we do. This thought provoking lecture, given at google, is well worth a listen.

Self Replicating Proteins May be a Clue to Life Origins

The proteins in our body must not only be the right configuration, but the right shape. Prions are misfolded proteins that are also self replicating which can cause biological systems to malfunction such as forming holes in the brain called spongiform encephalitis (Mad Cow disease or Crutchfield Jacobs disease in humans).

Prions can spread from one organism to another by mouth, blood or contaminated surfaces. Like infectious viruses, prions can also have variants, or strains, that produce different effects, not all of which are harmful. Unlike the rest of biologically active structures, prions don’t have information-storage molecules like DNA or RNA, yet they are able to copy and transmit biological information. This has strained the idea that all replication of proteins must come from an information coding system like DNA or RNA. While it does put some strain on the validity of our conventional interpretations of how things happen in evolution and biology (that proteins are “only” manufactured from DNA to RNA and then to final form as protein), it may also be a clue to our origins. (Note* retroviruses are also known to violate this rule, called the central dogma of molecular biology)

Some researchers have proposed that it may be possible, due to the ease with which amino acids and peptides can be produced by abiotic means; that the first protocells may have been proteins only encapsulated in lipid membranes. (For more information look up Fox’s protein microspheres). These microspheres may have only acquired nucleic acids as an adaptation later on as a means information storage related to reproduction.

In other words; it is thought that proteins may have reproduced themselves by some autocatalytic process at first, like that which we see in prions today. Evidence for this can be seen in the fact that there are still noncoded peptides in certain bacteria to this day (See Day, 1979, p. 369). Is it possible that proteins began working in mutually beneficial symbiotic relation to each other and some of which eventually specialized in information storage and protein synthesis” This type of relationship dynamic is known to have happened in the case of mitochondria and chloroplasts, Eukaryotes are thought to originated as symbiotic prokaryote organisms that fused into obligate (necessary-inseparable) form.

Is it possible that RNA and DNA were adaptive strategies in service of prions? Is the behavior of prions a clue to our origins? Time may tell.

Here’s more on Prions:

Bacteria Discover the Advantages of Community

Fun Fact: Some species of bacteria are social creatures. They act as a community in a number of ways and because of this community behavior, their lives and their chance of survivability in adverse conditions is improved. Myxococcus xanthus is one such bacteria. They, like us, require a population that works together to enhance survivability. Like us communities of M. xanthus act as a singular unit, especially when they sense adversity. For instance; they move together to find food. If food is scarce, they reorganize themselves to become a complex organism with specialized, differentiated organ structures that is much more adaptable. Like us, this division of labor and specialization in their collective body structure enhances survivability. Along with increased mobility, some of the bacteria specialize in making spores to ensure survival through extreme conditions. They also specialize their behaviors to survive environmental changes like temperature and radiation. When damage occurs to their outer membrane M. xanthus cells cooperate with each other to make repairs in a process called Outer Membrane Exchange (OME). These bacteria have discovered the power of community – that looking out for each other is a much better strategy than competing with each other. When it comes to survival. This community trait in bacteria is also a clue to understanding the evolutionary transition to multi-cellularity.

For more information read these: