Tag Archives: Systems biology

Where does Intelligence Reside?

The one on the left is a wasp, the one on the right is a moth. The question is; Where, how and on what level does the intelligence by which this mimicry takes place reside?

 

If we define intelligence as the ability to acquire and apply knowledge and skills, examples of mimicry like the example detailed in this story (linked below) have always left me wondering how a biological organism would be able to perceive and respond, at whatever level it takes, to recognize and assemble this cloak of deception without some capacity to sense “other minds” as well as a capacity to carry out a morphological change in response to that recognition of what’s going on in the mind of the other species…

For this moth to drape itself in the cloak of a wasp is a remarkable event, which we seem to be able to adequately describe, but our descriptions are certainly not explanations. In terms of explaining the event, what we typically call out, (adaptation, which is a description, not really an explanation) seems inadequate on its own without some kind of recognition of a sophisticated capacity for conceptualization and response embedded in the biological framework going on at some level that produces this sophisticated expression of adaptation. Just thinking out loud here.

https://phys.org/news/2017-02-biologists-years-textbook-wisdom-explanation.html

The Power Law and The Nature of Systems

Zipf’s law, also known as the power law identifies the uncanny consistency of the frequency of behaviors in natural systems, including complex organized adaptive systems like biology. For instance; the frequency of the most used word in any language no matter where it originates will occur approximately twice as often as the second most frequent word, three times as often as the third most frequent word, and so on.

Ziph’s law goes by other names, such as the power law, but the orderly distribution of relative frequency is remarkably consistent across many systems, these include physical, biological, and social systems. City populations follow this distribution. So do the sizes of craters on the moon, the strength of solar flares, the frequency of behavior patterns such as sex or foraging in various animal species as well as the sizes of activity patterns of neuronal populations, volcanic eruptions, and so on. It is also true of social systems.

This information on Ziph’s law has a lot of implications if it is fully unpacked. If we extract the value from what it means we might consider the fruitless waste of time it is doing things like angrily baying at the moon over the 1%, or whatever name is given to primary social influencers. Changing Ziph’s law seems fairly unlikely to succeed no matter how loudly we squeal. It is perhaps a more effective strategy to focus instead on the fact that we are all responsible for the tone of the relationship climate we all live in and contribute to.

Based on the fact that natural systems arrange around this law, including social systems, a more effective thing would be to build a social economy based on how much we can give to each other, rather than how much we can get from each other. In this way those who, in the future, will assume the inevitable mantle of having the most influence might also be inclined to behave with these same values. Even if this took a couple generations to take root and bear fruit, it would be worthwhile. A quote attributed Gandhi, perhaps falsely, but good advice no matter where it came from comes to mind; “Be The Change You Want To See In The World”

 

 

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.

Cancer Is a Biological Outlaw

0152-Monopoly Win

Cancer is a biological outlaw. It begins its career as a cell triggered by a set of circumstances that cause it to diverge from participating in a contributory role in the community it draws nourishment from. Instead of a vested stake in the biological community that sustains it, cancer turns to a life characterized by parasitic behaviors that turn predatory over time.

Cancer turns against the cooperative unity on which biological systems depend and becomes an expression of destructive greed and consumption without a community aligned purpose. Its implied purpose narrows to its own interests, to the immediate gratification, to right now, to more and more, to domination over cultivation – to itself at the expense of the community. Through its behaviors, cancer becomes a biological outlaw.

If cancer was assigned the attributes of a self aware being, it would be defined as either failing to recognize its detrimental behavior toward its own future, or identified as someone that doesn’t care. Either way, it’s devoid of participating in the implied social contract that all sustainable living systems depend on; that of working in the limited context of the environment and contributing nourishing value back to the biological community it depends on for life, so that community is stronger than it ever could be as isolated parts.

There are many kinds of cancer with many different causes, but the common thread is a lack of regard to translate the taking from the community with corresponding activities to give back something of value to it. In the case of Pancreatic cancer, once the cancer takes root and steals the resources it needs to establish a foothold, it begins to use that theft to hijack the production machinery of nearby cells to feed itself even more. It uses this fuel to grow stronger and demand more. With increased strength, it now causes the enslaved cells working at a frenzied pace to serve its demands to sacrifice their lives in order to make more room for it, and for it to selectively feed on the dying remains to strengthen the cancerous process still more…

Cancer can enjoy a burst of extravagant artificial wealth by predatorily consuming great quantities of the genuine wealth produced by the nourishing relational acts of the biological community from which it feeds. As it increasingly consumes without regard for renewal, it crosses a terminal threshold where its demands exceed the capacity of the system to compensate for the collective theft, murder and interference of nourishing biological commerce. It is at this point where the biological system cancer depends on to fuel its excesses collapses in on itself.

Why does cancer behave this way? Why does this myopic collection of predatory behaviors consume without an eye for the sustainability of the system on which it depends? Cancer dominates, but if its strategy is successful, it becomes a victim of its own success. It ends up dominating itself out of existence. It is destroyed itself in a bonfire of its own greed and ignorance.

Upon seeing this cancerous behavioral agenda clearly exposed we might recognize that cancer comes in many forms. We might be inclined to see the parallels between cellular cancer and social behavioral cancer on other scales. Upon seeing this parallel and coupling it with some of the behavioral dynamics coursing through our human behavioral veins, we might be compelled to wonder if there is such a thing as “Mancreatic Cancer”. We might also ask whether we ourselves are engaged in aligning our individual and collective activities toward cultivating that which sustains us – that which we need.

When it comes to the micro decisions that lead to the macro effects of our life, not only reflected back on itself, but echoing outward to the community at large, we may want to be careful to define success before we engage in it, because in our frenzy to accomplish a false success, we could find out too late that as soon as somebody wins at monopoly, the game is over for everyone.

For more information about the way Pancreatic Cancer works: Click Here

Is Farming Evolution’s First Step toward Complex Organisms?

0001-Is Farming Evolutions Forst Step

There are certain ants that farm aphids for the food they produce, protecting and defending them for the nourishing survival value they provide. Leafcutter ants farm leaves in order to grow a fungus. This relationship has endured so long that they now depend on each other for existence.

We see a gradient of relationships in biology that go from optional beneficial value such as a food source or protection etc. these relationships can develop into a mutual dependency and perhaps grow all the way to an obligate relationship where one cannot live without the other. In effect, the once separate organisms that farmed each other may merge into an inseparable dance, becoming in effect, one body – each depending on the other for survival.

The various organs in our body follow this mutually dependent relational scheme, but so do some relationships in nature that transcend species lines like that of leafcutter ants and the fungus they farm. We may be witnessing a gradient of relationships that move along a spectrum from useful to necessary and in some cases result in once separate organisms becoming a singular organism over time.

This process of merging may begin with what could be termed “farming” or relationships built on mutual benefit, that over time merge into a single body of mutually nourishing entities. Eukaryotic cells are thought to have emerged over 2 billion years ago may have been one such merger that began as “farming”.

Creatures and or biological bits of information such as proteins and RNA etc. that provide adaptive value may have become so dependent on each other that they merged into a singular body. This in fact may be the backbone of evolution.

Of course this is speculation, but it may be that farming is the start of the process for more complex life forms, but where did farming begin? Perhaps it began long before eukaryotic creatures arose on earth and may have been a precursor to that merger known as endosymbiosis that led to eukaryotic cells.

The article linked below illustrates a farming relationship between a bacteria and amoeba where the bacteria turn the amoeba into farmers. This is one piece of evidence that may indicate that farming may have begun before the emergence of eukaryotes and may indeed be the first step toward the sort of biological convergence we know of as complex organisms.

For the article on the relationship between the bacteria and amoeba that appeared in National Geographic in 2015: Click Here

 

To see more on Ants Farming Aphids:

For more on leafcutter ants:

 

 

 

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:

Developing Sustainable Cycles in Farming

Developing sustainable cycles in farming is important. Although we have come a long way in terms of production capacity, this is not the same as developing a sustainable model. Capturing the principles of sustainability is of great value because it leans us toward a future that is not peppered with boom and bust cycles because we did not tend to our long game. Here is one such person, who may happen to have a crappy job, but is leading the charge for the future.

Ant Colonies have Group-Level Personalities

Antz1

This glimpse at ant life may help give us some insight into human group dynamics. As it turns out, ants have group-level personalities as well. The same way human cultures are shaped by environmental circumstances that powerfully influence their characteristics, ants and other social creatures may be influenced by these same factors.

From the article: “Colonies of funnel ants show group personality, which affects their success at collecting food and competing with other colonies… Some colonies are full of adventurous risk-takers, whereas others are less aggressive about foraging for food and exploring the great outdoors… these group “personality types” are linked to food-collecting strategies, and they could alter our understanding of how social insects behave.

For the full article Click here: