Tag Archives: Developmental biology

How We Develop Our View Of The World

Our development environment has critical periods where we are imprinted with what the world looks like based on a snapshot of whatever is going on at that time. If that picture we receive during critical periods of development is distorted, we can then become trapped in a prison of living in the context of responding to that distortion for the rest of our lives, even though it may no longer bear any resemblance to our current reality – an echo chamber of trauma is one example of this phenomena.


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.

A Small Glimpse at the Memory Pathway in Our Immune System

Our immune system has to detect and effectively deal with a wide variety of destructive agents, known as pathogens. Many of these come in the form of invasive viruses and parasitic organisms. It must be able to tell the difference between pathogens and healthy tissue and this is sometimes be difficult. It must learn to effectively differentiate friend from foe.

Immune systems learn. Like human beings, immune systems have critical periods where they are particularly sensitive to learning. If they are not exposed to the typical environmental pathogens at these critical periods the immune system may not respond properly.

Asthma is less prominent among farm children because they are exposed to native pathogens during this critical period. Children brought up without exposure to these things can develop an overreaction. In addition to this supercharged learning capacity that lasts a short time, the immune system also has a less powerful, ongoing learning capacity to combat novel pathogens. This learning process involves what are called B Cells. These are a type of blood cell, part of the immune system, and secrete antibodies in response to perceived pathogens. These antibodies are in effect tattletales. They mark the invader as an enemy so that T-cells (Another type of immune cell) can deal with them. Thanks to way b cells can learn and remember, our body then gets a head start fighting repeat offender pathogens. This memory process is what makes vaccinations work.

This article in this link explains how “naive” immune cells transition into memory cells. Click Here

Here is a brief overview of both the innate and adaptive immune system:

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:

Biology Is Social All the Way to the Core


Social psychology studies social interactions, including their origins and their effects on the individual. It focuses on the relationship between the mental structures within the individual and the social structures which that individual encounters and interacts with, and how that shapes the individual and the wider social landscape. One of the keys to understanding this relationship dynamic is in looking at the multiple flows on influence back and forth that define the overall nature of the entire relationship system. This complex relational dance brings up the intersection of multiple influences from which our experience and behaviors emerge. This same principle is now beginning to be understood on a biological level as we see the influence of various organisms on each other over time can shape our experience, our individual developmental paths and our evolution. A long history of just such a relationship dynamic can be witnessed by examining certain gut microbes that are thought to have been around humans since before humans were humans. They currently play powerful roles in steering the early development of our intestines, in training our immune systems to negotiate the “shark” infested waters they will have to contend with over a lifetime, and possibly affecting our moods and behaviors, including social behaviors, in many other ways.

So tightly tied together is this biological social dance that there is now genetic evidence that certain bacteria split into distinct strains at about the same times as their hosts split into distinct species, demonstrating the influence of organisms on each other in the evolutionary development story.

From a certain perspective, what we think of as human is composed of a parliament of biological bodies that together form a relationship system that defines who and what we are as “individuals” through a vast and intertwined collection of interdependent influences, and what could be more social than that?

For a more refined glimpse at a segment of the social relationship between gut microbes and humans, click here. From the article:

“Some of the bacteria in our guts were passed down over millions of years, since before we were human, suggesting that evolution plays a larger role than previously known in people’s intestinal-microbe makeup… our gut microbes, which we could get from many sources in the environment, have actually been co-evolving inside us for such a long time…  scientists found genetic evidence that the bacteria split into distinct strains at about the same times as their hosts were splitting into distinct species… One… happened about 15.6 million years ago as the gorilla lineage diverged from the other hominids. The other… about 5.3 million years ago as the human lineage separated from the lineage leading to chimps and bonobos.

Again Read more on this at: http://phys.org/news/2016-07-bacteria-human-gut.html

Is our social behavior an Echo of Physics?


Every atom the functions as part of our biological system craves specific relationships with other atoms. There are systems that are geared to satisfy those hungers and other systems, like our immune system, that are geared to reject and expel any elements the “do not belong to the in-group” so to speak. It is this complex social dynamic between physical elements that forms and maintains our biological structure.

Like the relationship dynamic that happens on a micro scale, as a whole, our biological system has specific hungers that must be met as well. From a certain perspective, our own behavioral and social actions are, in essence, a reflection of that from which we are physically composed. This can be found clearly echoed in scientific disciplines such as sociology. The following is one example:

According to Social Identity Theory, comparison with an outgroup is the main engine by which positive ingroup distinctiveness is formed.

Experiments conducted by Henri Tajfel and others into the so-called Minimal Group Paradigm illustrate this point well.

In the experiments to see what the minimum was to establish an in-group, a number of assumptions, concepts, values or practices were accepted in order to better allow a view of the onset of human group formation and of the appearance of discriminatory behaviours toward out-group.

From the article:

“Intergroup behaviour was analyzed in a situation of “mere categorization” such as where people involved as subjects in this research were told that they were individually “overestimators” or “underestimators” of the number of dots in a display. It was found that even under very flimsy and apparently baseless assigned social categorisation into two distinct, and previously “unheard of” social categories, in-group favoritism and out-group derogation occurred in the distribution, by the research subjects, of “rewards for participation” in the study.”

This is more evidence that shows how hard wired we are to cling to a group and reject anything perceived as out-group.  For a more detailed look Click Here

Ant Colonies have Group-Level Personalities


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:

What if relationship, rather than genetics is the dividing line between organisms?


In the video below, Gershom Zajicek M.D speaks about certain viruses as necessary (obligate) symbionts; meaning we were once infected with a virus that is now in an inseparable relationship with us. The common idea is that viruses are infections, but he argues that they span the spectrum of relationships from destructive, to beneficial and in some cases, necessary for our survival.

Some of these vital viral strings, embedded in our genome provide services such as helping forge the relationship between the uterus and the early stage embryo, the formation of the placenta and so on. Because they offer adaptive advantage they have formed an obligate relationship over time and this is how they get to ride on the wave of relationships we currently call human. One example of the fruits of this relationship is the proto-oncogene which governs cell division. It helps our cells grow and divide in specific and limited ways to form and maintain such things as cells and tissues. In fact, when this process is broken we see cancer.

Among the things Dr. Zajicek proposes is that transposable elements (TEs) and Human Endogenous Retro Viruses (HERVs) are two names for the same phenomenon. Transposable elements are snippets of DNA coding that can communicate one cell to another, or across organisms or species, and changes the way an organism operates. This means they can actively modify biological functions during the lifetime of an organism. This method of evolution may need to be added to the currently understood mechanisms which include , descent, genetic variation, mutation, genetic drift, natural selection, and coevolution.

If HERV’s and TE’s are synonymous, this would have enormous implications not only to evolution, but to many other disciplines such as medicine, ecology and so on. TE’s, for instance, may be in some cases an immune response from one creature to defend against what it perceives to be a pathogen (from its perspective). We would receive this as a disease. There may be vectors, such as bacteria that mediate this process. If we look through this lens, we see the dynamic root of many of our own diseases in the way we relate in the context of the larger biological body of which we are part, and on which we depend for nourishment.

Of course, whether this vision is an ghost due to the lens or a clear image of what is really going on remains to be seen. If we expand the notion Dr. Zajicek proposes on to the larger biological relationship landscape, this would indicate there is an active dynamic and far less than random communication flow by way of meaningful structures, not only within species, but between them. It would mean that species may not be the level at which we should define organisms, but by relationship spanning from antagonistic to obligate. (Necessary). If we were to apply a ven diagram to the biological landscape, we would see many overlaps that violate what we have traditionally considered species. In other words, defining organisms by genetics alone may have blinded us to how the larger, more revealing biological relationship landscape works. 

While we have a long way to go to unravel this Gordian knot we call biology, if this proves true, it would explain quite a bit, have enormous predictive capacity, and if applied properly would have a huge impact on our understanding of evolution on many levels beyond the scope of Mendelian (inherited) genetics.