Tag Archives: bacteria

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:

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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:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003891

http://phys.org/news/2015-05-bacteria-cooperate-siblings.html

http://schaechter.asmblog.org/schaechter/2015/10/kiss-and-make-up-myxococcus-xanthus-demonstrates-bacterial-cooperation.html

Biology is The Song The Cosmos Sings

0060-CosmicSongThe behavioral characteristics of biological structures rhyme. From the relatively simple single celled organism, to the entire biosphere there is an echo of form and function on widening scales. Behavioral characteristics at one level in the structure ebb and flow in a wave pattern at other levels.

Each cell inside our body has a skin in the form of a semi porous selective membrane. The membrane is geared to sense, communicate and negotiate relationships with the internal and external environment. These relationships are aligned under such purposes as sensing and responding to the environment, communicating with neighboring cells, letting in nutrients, expelling waste and defending against pathogens that might disrupt the function of the cellular system. The larger organs in our body have these same principles of form and function embedded in them. The external parts of our body including everything from skin, eyes, ears, anus, hands follow the same principles of form and function expressed at the cellular and organ level. The structural ideas reflected at the core are echoed in a rhyming pattern throughout our biological system. We are, in effect, a song written in the fabric of space-time and matter-energy.

If we widen the lens, this same rhyming aspect of form and function echoes outward beyond a single organism. A species develops a skin. Human communication itself is largely based on abstract membranes we call words that form the effect of a skin around a concept. Tribalism is the description of a cultural body that is also an ideological, ritualistic and sometimes geographic or resource driven skin. Expansionism and assimilation is the same principle as eating and digesting external resources. Religion, government, business, and professions as well as academic disciplines also develop this same skin like attribute within their structure.

Of course skin is just one of the many form and function aspects of a biological system that are echoed on many scales. The point here is not to outline all of them, but to describe the rhyming process itself and use it as a platform to gain some insight into ourselves. If we turn our eye toward understanding our nature with any degree of accuracy we must concede that we are far more a reflection – an echo – of the form and function of nature. The more we understand the depths of that communication made to and through the cosmos, the more able we are to navigate with intention through the waters she defines.

Ectosymbiotic Theory

This article is intended mostly primarily for people with an evolution, biology or otherwise similar background. It is a proposed tool to understand the relationships that define coherent systems in general, but more specifically biology, with a little more clarity. It looks at biological life through a relational lens, rather than one based on genetics or membranes such as skin (in the traditional sense) and so on. The intention is to lay the foundation to be better prepared to make good choices about how to cultivate fruitful biological relationships in intentional directions. It is not a light read. Feedback is both welcomed and sought after; how to articulate the idea better, where to take it so it can be of most value, or identify the reasons it should be trashed as bunk, altered, etc. Although I tried somewhat to make it understandable to people familiar basic biology, to those who dive in and get caught in the quagmire of a  partially formed idea that is not articulated as well as it could be, I apologize in advance.

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We are not alone. Without the plants, animals and chemicals like H2O and O2 we could not survive. Many of the microbes that live in and on us are also essential to the coherent system of relationships that establishes and maintains our biological integrity. Without these relationships we would disintegrate. The same way our organs deliver nourishing value to each other, communicating through their semi porous membranes in a community fashion, we live in the context of a greater body of life – a vast web of relationships that collectively establish and defend their mutual integrity and continuation over time. This greater field of relationships, bound together by the mutualistic dependency they share for continuing existence in the context of a sometimes antagonistic environment is what is being proposed here as ectosymbiotic theory.

Ectosymbiosis establishes the boundaries of an organism by relationship and not by such things as a cell membrane, skin, the capacity to interbreed, or shared DNA. To understand this concept we can start with the fact that many of the organelles (tiny organs) inside eukaryotic cells (the kind we’re made of) were once separate prokaryotic creatures (with a single membrane) that came together to work as a single unit. This coming together of separate life forms as one inside a single membrane is called endosymbiosis. We humans are multicellular eukaryotic organisms. The same community of relationships that make up our cells is echoed in the way our organs relate to each other. The theory proposed here, ectosymbiosis,  suggests that organisms are also built on the same principle of community, working together as a single body even though they are separated by DNA, membranes and the like. The key binder is a mutual role in each other’s survival.

Ectosymbiotic organisms are defined here as any coherent collection of structures that as operate as an interdependent dynamic body of relationships with self-sustaining properties, that have relational systems that can perceive and respond to the environment, that can differentiate between relationships that contribute to or destroy the cooperative integrity it depends on, that actively acts to defend against antagonists while cultivating the relationships that contribute to the strength of the entire system and sustaining the collective community, that can extract, transform and use various forms of energy from the environment toward this collective end, that have the capacity for dynamic self-replication and self-assembly as part of the drive for self sustenance and to saturate the environment to is maximal point to carry the collective relationship field, that does this through a collection of functional structures with separate individual capacities, but collectively aligned on a unified purpose growing to the maximal carrying capacity of the environment while simultaneously sustaining the integrity of the system, that seeks out, establishes and integrates new relationships that contribute to these ends and does so with some apparent measure of awareness.

If we use this ectosymbiotic lens to look at the various biological relationship fields we see peppered throughout the Earth, we can see at the foundation the photosynthetic and chemosynthetic organisms, (autotrophs and chemoautotrophs) which organize and channel energy from the raw materials of the cosmos and translate these using an energy source from inorganic to organic. These organisms, in effect, translate raw cosmos to biology. Further into the collective field of relationships we see heterotrophic organisms that live off the nutritional “milk” supplied by the auto and chemoautotrophic organisms. We can trace the entire biological web to this basic relational dynamic beginning with the cosmos, crossing the biological divide with autotrophs, and culminating in heterotrophs. Biological integrity from an ectosymbiotic perspective is not based on one organism’s relationship with another, but on the value of the relationship field that is threaded through multiple organisms, that operate as a whole to dynamically establish and maintain the entire system from the non biological environment. This means parts and pieces of the systems of one organism can be part of much larger ectosymbiotic body.

In biological terms ectosymbiotic organisms are dominated by mutualistic and commensal relationship dynamics that are both necessary and sufficient to nourish and perpetuate the ectosymbiotic organism. In contrast to the typical method of biological cartography where organisms are defined along genetic or as contained within a singular membrane such as a skin, ectosymbiotic organisms are defined by the collection of functions that mutually serve the entire community and are a necessary element of that body of relationships to nourish and sustain the collective body over time.[1] In biological cartography terms, with ectosymbiosis as the axiom to establish geographic boundaries of an organism we would group all the relationship systems like biosynthesis, metabolic pathways, as well as carbon oxygen and nitrogen fixing as part of the same ectosymbiotic organism without respect to geno-specific lines or those between organic and inorganic.[2] An ectosymbiotic membrane may encompass only a subset of the relationship functions in a specific species and the rest of the functions associated with that same species might be part of a completely different ectosymbiotic organism. It can also mean that a species or set of functional outcomes in one location is part of an ectosymbiotic organism where in another location it is not. Another way to look at ectosymbiosis is to identify the essential biodiversity to the point where it functions as a singular self sustaining body.

The following chart categorizes the relationships present in biological systems by their effect within the system and assigns a number based on whether the relationship produces strength or weakness in the overall integrity of the system. This model is designed to serve as a crude lens to better understand the general workings of biological systems, not as a precise metric to understand systemic thresholds of integrity and the like. These systemic effects are meant as a means to characterize the nature of relationships within systems such as mechanical and biology:

RelationshipTypes

The positive and negative values associated with each effect in the chart are intended as a method to give an approximate measure the relative strength of a system. The idea being if the relationship dynamics within the system and the environment were plotted based on the type of relationships and the context of a system and its environment it would demonstrate strengths and weaknesses. The primary purpose of this matrix is serve as a lens through which systems can be assessed from a macro perspective. The weakness of this crude type of lens is that would not identify micro vulnerabilities that could exist that might be exploited using relatively minor negativistic effects at a specific critical points in the system.

The same way microscopic lenses inherently reveal micro scale structures while obscuring macro scale ones, and telescopic lenses do the opposite, this abstract relational lens is meant as a telescopic view of systems. The value would be attained by measuring the strength of the ectosymbiotic organism in the context of the other relational factors, including other ectosymbiotic organisms in relationship with each other.

Ectosymbiotic organisms include all relationships necessary to sustain a body of life, whether organic or not, therefore an ectosymbiotic body is not bounded by genetic lines, but is instead defined by functional lines. The outside membrane of an ectosymbiotic organism can be drawn where antagonistic, amensalistic and competitive relationship dynamics that threaten the function of the internal workings exist.[3] Any relational element, no matter whether organic, inorganic, energetic, spatial, temporal or otherwise that does not strengthen the relational field of an ectosymbiotic organism body is considered “other”. Any neutral relationships in contact with the ectosymbiotic organism either internally or externally are just that; neutral.

What is the value of categorizing relationships through an ectosymbiotic lens?

Here are a couple key elements that would be made visible using an ectosymbiotic lens: The same way understanding the physics of erosion led to contour farming and subsequently no till farming in agriculture, we would be better positioned to understand and cultivate strength in biological relational systems that provide strength to the nourishing foundations on which we both stand and depend. We would be better positioned to understand how tampering with segments in the chain can have a cascade effect on the entire system as well as what that cascade effect might be. This could lead to better planning and execution of strategies that cultivate growth. It would help differentiate what is a “botanical weed”[4] in the context of a given ectosymbiotic system vs. what is perhaps an unpleasant but necessary element in the ectosymbiotic body.

We would be able to identify the global properties that emerge at different layers of organization; i.e. cell, organ, body and ecosystem and understand the value of cultivating mutually beneficial relationships as the key to strengthening the overall integrity of the body of life. Traditionally ecosystems have been defined by what is there, not by what would happen if the ecosystem was specifically cultivated as part of the same interconnected system.

Predictions if the hypothetical model is true:

We would expect to see the same differentiated morphological profiles in ectosymbiotic body that we see in other biological entities with differing germ layer profiles. This means we would expect to see some ectosymbiotic bodies would be monoblastic in nature like sponges,[5] diploblastic in nature like jellyfish and triploblastic morphologies such as we see in placental mammals. Extremophiles would probably fit in the monoblastic ectosymbiotic profile because of their autotrophic nature at the edge of the biological membrane. We would see some forms of radial symmetry with a differentiated top to bottom in diploblastic ectosymbiotic organism groupings as well as top down differentiations. We would also expect to see bilateral symmetry, differentiated front to back and top and bottom in triploblastic ectosymbiotic organisms.[6]

Within the triploblastic ectosymbiotic organism we would expect to see the same systems we see in a singular speciated organism of a triploblastic morphology. This would include the following:

  • A nervous system – Enables communication to send, receive, and process nerve and sensory impulses.
    • This would include a central nervous system as in a brain and spinal cord
    • a peripheral nervous system that branches off of the brain and spinal cord model carrying signals to the muscle and gland portions of the ectosymbiotic organism
    • an autonomic nervous system to controls involuntary actions such as heartbeat and digestion, regulation of certain systems.
  • A circulatory system enabling systemic transport and deploy nutrition, and certain elements that need system wide transport such as immune components through structures that mimic the arteries, veins, and capillaries.
  • A respiratory system that brings breath into the system and releases waste back out. (There may be multiple systems)
  • A lymphatic system that filters out disease-causing organisms and helps to drain waste in and around tissues and plays a role in defense against infectious intruders.
  • An endocrine system producing hormones histamines and other chemical communicators to control or influence various body functions such as metabolism, growth, and reproduction.
  • A urinary system that enables the processing and excretion of waste fluids as well as a role in regulating the flow of hydration.
  • A muscular system that enables movement as a function of activities and adaptation including involuntary such as would control the stomach and intestine cardiac etc. and voluntary which could carry out acts of volition.
  • A digestive system to break down food and obtain energy. This would include any necessary non-organic as well as organic sources in the ectosymbiotic body.
  • An integumentary system or a membrane to protect the rest of the body from various kinds of damage, define the boundary of the body and to play roles in regulating internal systems, aid the immune system elimination of waste, play a role in regulating homeostasis etc.
  • An Immune system – The immune system protects against infection and disease.
  • A skeletal or support system to aid in internal and or external support such tubules, skeleton, exoskeleton or shell.

Since commensal and mutualistic symbiotic relationships are the synaptic connections in an ectosymbiotic body, we would expect pathogenic attacks on an ectosymbiotic body to be responded to by specific species or groups of species within that body that play the immune defense system roles. The idea being we would look for same types of relational dynamics we see in organs and systems in our bodies to be mirrored in an ectosymbiotic relational body. The same way organelles are part of cells, cells are part of organs and organs are part of a body, we would expect to see a species as an organ or tissue in an ectosymbiotic body performing a specific task in the context of a community.

The immune defense system in an ectosymbiotic organism might take the form of specific bacteria attacking a pathogenic organism that destructively feeds on its relational web, or perhaps the immune response would be carried out by developing a destructive mechanism such as a strand of viral RNA capsid and organelle mechanisms to work in concert to attack the offending pathogenic host as we see in the case of HIV. The idea being one ectosymbiotic body is immunologically responding to disrupt the commensal and mutualistic symbiotic relationships that characterize the attacking ectosymbiotic organism’s attempts at homeostasis. This might take the form of destroying a critical primary producer in the ectosymbiotic matrix, or a key element in the bio-relational chain that attempts to disrupt the dependencies on nourishing flows within the ectosymbiotic body of the pathogenic vector. The fact that humans destroy the host of certain bacteria that live in avian esophageal tracts may in fact be the reason we get the flu. A bacterium that has an ectosymbiotic relationship may be producing a viral strand of RNA as a defense mechanism of its ectosymbiotic body. Plants and bacteria may adapt methodologies from their normal biochemical behaviors such as transformation, transduction and bacterial conjugation as vectors for functions like breathing, vision and so on.

Organ elements such as vision and brain functions within an ectosymbiotic organism would not necessarily be apparent if we are too parochial in our view of organs and tissues. Conventional understanding of organs must be viewed through a relationship lens and not a morphological one in order for the organ and tissue functions of an ectosymbiotic organism to appear. Vision and cognitive functions might involve one species within the ectosymbiotic organism reading the histamine profile of another organism within its body as a signal that necessitates an adaptive or homeostatic behavioral expression. In essence this is the method for stimulus response mechanisms within the ectosymbiotic organism as well as cognition. We would expect to see a hierarchy of concentric awareness the same as we do in triploblastic organisms. In other words; the same way our body functions as an organ or a cell we would expect to see this concentric representation on the ectosymbiotic organism level.

We must not limit ourselves to expecting nonporous membranes in ectosymbiotic organisms. There would be a biodiversity of ectosymbiotic organisms the same as we see it on a species level.

Since this is a relational lens and not a genetic one, we would not necessarily want to limit our lens to genetic similarity either. Male and female splitting would be an expression of ectosymbiotic nature within a species. Differentiated tasks aligned around a singular purpose is the relational axiom. The male female aspect of many organisms is just such an expression. We would be able to trace male female aspect this back to the split that happened after autotrophic organisms almost drown in their own feces (O2) that forged that first ectosymbiotic split in the form of heterotrophs. This ectosymbiotic organism lens could further clarify everything from evolution to current bio-relational dynamics.

A Venn diagram model might be best to visualize these morphological connections in ectosymbiotic bodies. Were an ectosymbiotic organism or web to be drawn out it would look like a rhizomatic Venn diagram – a network of intertwined symbiotic relationships. It may also be that a singular self-correcting ectosymbiotic body exists and parasitic and predatory mechanisms within it are methodologies for self-correction.

Should the ectosymbiotic organism hypothesis prove true its usefulness would become apparent in terms of tracing the vectors of pathology between organisms to manipulate, leverage and or cut off vector pathways – the same way antiseptics or probiotics can cut off vector pathways or facilitate health of certain pathogens in human relational environments.

Hint: We might see primary producer organisms as part of the lung digestive function in ectosymbiotic organisms. A profound possibility might be that discover there is a fully functioning cognitive creature or creatures woven into the body of life that we have been missing because our focus is on reductive abstractions instead of a system biased rhizomatic lens. The same way we see a much more revealing image of the cosmos using radio telescopes and the like, using an ectosymbiotic organism lens may help us see our own nature with more depth and understanding.

[1] It should be noted that “nourish” is used here in the sense of developing to saturate an environment to the fullest extent and “sustain” is used in a broad sense to include behaviors such as renewal in the form of reproduction when this is a necessary means of sustaining the system.

[2] One example of this would be how lightning and atmospheric nitrogen participate in nitrogen fixing which is necessary for plant metabolism.

[3] This is not to imply that ectosymbiotic bodies do not have to deal with negative relational aspects, just that these negative relationship aspects are not part of the ectosymbiotic body. (There may be necessary exceptions to this)

[4] A botanical weed is defined here as any life form seated in the context of an ectosymbiotic body that exhibits antagonistic, amensalistic or competitive relational dynamic.

[5] porifera

[6] It would not be unusual to see these same characteristic groupings mirrored in social bodies, linguistics, behavior profiles, thinking capacities, personality profiles etc. For instance a person exposed to extreme stresses might have a monoblastic personality profile, unable to connect with mutual beneficial lines across a pluralistic social landscape.

Who Is Mother Nature Really?

English: A freshwater aquatic and terrestrial ...

English: A freshwater aquatic and terrestrial food-web. (Photo credit: Wikipedia)

A biological food chain[1] is an abstract model used to look at the relationships between biological life forms. The food chain outlines the nutritional relationships between biological organisms in linear form from “primary producer” to the “top” of the food chain. Primary producers organize specific atoms, molecules and energy sources like sunlight or heat into what we know as biology. Photosynthetic organisms like plants algae and phytoplankton are examples of primary producers in a food chain.[2] These primary life forms then support many other species in the “food chain” either directly or indirectly through a series of feeding relationships.[3] Food chains are constructed with links from primary producers through primary consumers secondary consumers and so on to what is called the “top” of the food chain. At the top of the chain is a species that has no other species that feeds on it.[4] Terms like “King of the Jungle” are used to describe such a top feeder on the food chain. In a lake environment, a fish might take the top tier of the food chain.

Like most models, the “food chain” is useful, but it has limitations at illustrating the whole image of the relationships that define biology. Even though primary producers act as a clear bridge from non-biological processes to biological ones,[5] the total biological economy can be more accurately represented using a nonlinear web as the model rather than a linear chain. This is because there are many tangled and cross referenced relationships in a food web.[6] A web could have more than one primary producer and these can be cross linked in numerous ways throughout the interdependent system. Even with a sole primary producer, interdependent biological systems (called a biomes or ecosystems) are not a strict linear route from bottom to top as a “food chain” model implies.

So let’s listen to what this web of biological relationships says; a primary producer species is an umbilical cord that feeds on the broader womb of non-biological reality. It translates a non-biological system into a biological one. The same way the letters and phrases that compose this communication are based on a certain order of relationships to each other that gives rise to meaning, primary producers channel matter and energy into the complex organized interdependent relationship systems we know as biology. The term organism is fitting for biological systems of all types because of this fact.

While there are so many things communicated through the fantastic relationship dynamic that gives rise to biology, one statement that stands out is the fact that reality is the womb from which we are formed and draw our nourishment. Have you hugged your Reality today?


[1] The idea was introduced by the African-Arab scientist and philosopher Al-Jahiz in the 9th century ACE.

[2] In addition to photosynthetic organisms there are also chemosynthetic primary producer organisms that use heat and chemicals as the basis of conversion of inorganic to organic biomass.

[3] Non-feeding relationships also exist between biological organisms. These can be broadly categorized as cooperative and/or competitive.

[4] Predators can be infected with such things as parasites and destructive viruses, so the notion that the top is undisputed top is a bit of a misnomer.

[5] Non-biological sometimes called abiotic and biological called biotic structure in ecosystems.

[6] There are three feeding type relationships typically defined in biology. These are the food chain, the food web, and trophic levels.