Bible Freedom ScienceCopyright © 2010, Charles Henry Johnsen, III

Black Box Reality

Introduction: Punctuated Continuum

We see…

This is about the human universe. By that term I mean all that we human beings are able, or will be able, to see or hear or calculate by native senses or instrumentation. We incorporate what we find into our universe by creating a name and a story for each discovery. Mathematics is such a device for creating names and stories.

Truth, as correspondence with reality, is the goal. People have worked toward this for all of history. Some systems came closer, others not. Apparently only those outside of a particular world view are able to see its flaws. This history of truth and error stands as a warning. I may know more than Aristotle but I am not smarter than Aristotle. Bold in questions and expressions, we must also be humble and listen.

The Continuum

From the smallest and fastest to the largest and slowest, from non living to living, from visible to invisible, the whole is continuous. Every effect is a cause and every cause is an effect. Every part is made of something else and some parts are what something else again is made of. There is nothing available to us prior to, above, beyond, or beside the universal network of cause and effect.

No object is contingent on causing another object but is contingent on other objects.

The Punctuation

There are coextensive layers of reality separated by discontinuities of structure. Simultaneous to the cause and effect events of one layer, another layer takes for its constituting atoms the stable associations of particles in the smaller layer. This changes the description of the cause and effect structures from one layer to the next. For example, we use quantum mechanical mathematics to describe subatomic particle cause and effect interactions but use valence when understanding the cause and effect interactions among the atoms built from these subatomic particles. Both quantum mechanics and valence are operational at the same time and place but, isolated by the traditional atom's stability, valence alone describes the layer of molecules and whole atoms.

Between every such subdivision of reality are stable associations of particles, a sort of condensation, that I call virtual atoms. The elements themselves, such as oxygen or silicon, are virtual atoms because they are not actually atomic but composed of smaller particles. Notice that virtual does not imply unreal but merely names the role the very real object plays in this view of reality. At each boundary between layers there is a similar atomization. For example, corporations, businesses, nations, churches, etc. have as their virtual atoms individual human beings. Obviously we are composed of parts and are not actually atomic, even mentally. But as far as such natural associations are concerned, to all intents and purposes, we are atomic, virtual atoms.

While there may have been a time when smaller virtual atoms existed before larger ones, right after the Big Bang, for example, in the normal world that we experience the various layers are simultaneous, not sequential. Causes and effects are here not events with a time scalar but instead stable (even when chaotic), networked relationships. Such events are on a time scalar when the virtual atoms interact between layers.

The Stiles and Fenestrations

Imagine a many–paned picture window. The panes have no glass but allow one to stick one's arm through the framed spaces into the real world beyond. Stiles, or thin strips of wood, separate the empty panels. These are the virtual atoms, or tesselae, of the next door panel or pane. Between stiles, and defined by them, is a framed area I call a fenestration, and opening to the outside world through which we observe and finally manipulate reality. While my many–paned picture window is two dimensional the real world it pictures is multidimensional and simultaneous, the panes come in different sizes and shapes, and some panes are totally contained within another.

Within each fenestration there is a set of nouns, verbs, and syntax that describes the particles and events that happen there. That structure of cause and effect relationships operates on the virtual atoms provided by the lower scale fenestration and provides the stability of the virtual atoms used by the next larger scale fenestration. In this way our science and wisdom is segmented and isolated so that we are able to comprehend, first the open panel, then the separating stiles, and then the universal whole. From hole to whole, so to speak. This way of analysis comes to me from the black box methods of electronic and software design and troubleshooting. It is likely that this nested method of handling information is native to our brain's ability to combine phrases into sentences and sentences into paragraphs.

You will read the word mediation in my writing. Others have complained that this word, with this usage, is confusing. So I have stopped using it but many references remain so I will explain it for you. The image is ink on paper as the medium for human language. I am not here pointing to the encoded characteristic of A's and B's but to the way the medium holds and carries the language from one set of eyes to another. A medium is a structure and rule set that provides an underlying structure that is able to implement, carry, or enable another structure. Everything is mediated. In other words, flowers need dirt. Dirt does not cause flowers but provides the conditions and situations that a flower needs to germinate, grow, bloom, and reproduce. Dirt is the medium of flowers. In a similar way, the subatomic particles are the medium for traditional atoms, traditional atoms are the medium for molecules, molecules are the medium for cells, cells are the medium for organisms, organisms are the medium…

The word environment is not useful for these purposes because it implies a flatness of a single scale that the universe does not have.

The Greatest Differences in the Universe

I do not see the categories of existing and non existing as very important. Existence seems to me to imply a non virtual atom without location in one fenestration. It is a word without an actual referent. And then, as dark matter, dark energy, and the vacuum flux warn us, there may be no nothing to offer a contrast to something. The most important shift is that between living and non living. One is unencoded, the other coded. One is all entropy, the other eutropy. One has no freedom of intent, the other is all choice, selection, and opportunity. Another important super category is the break that happens with language. Where life is encoded recipes for more life, language is all coded meaning and allows huge freedom of choice and action. The only other super category is the Last Frame, where the biblical God meets us.


I confess to motivations for my search toward these ideas. First, I grew weary of quantum mechanical astrology, or the idea that somehow so-called random quantum mechanical changes of particles in the atoms in the proteins of the cells of the brain explained human free will. I call it astrology because Jupiter has about as much effect on human choices as beta decay in a single atom of a single molecule of a single neuron. The scales of magnitude from Jupiter's distance to the human body are less than the size difference between the human body and a proton. The brain, like all biological systems, is far too redundant and corrective to allow any significant effect at a behavioral level. Second, I positively reject the death cult of Platonic dualism and positively embrace the repeated use of the word Good in the First Chapter of Genesis. Third, I find chain determinism repulsive. These are the ideas that reduce all events to the demonic idea that there is no freedom, no chaos, no contingency; that the universe is fixed in time by particle to particle, chain determinism from the first and smallest to the future and largest events. Fourth, I have grown tired of the monotheism of politics, the elitism of scientists, and the arrogance of churches. The repeatability of physical experiments as the test of truth has little use in deciding historical truth. Ancient texts that closely followed the best science of 1,500BC cannot trump reason and more recent observations. But most of all, truth and faith will only flourish together in freedom of inquiry and speech. Consensus, majority rule, and regulation damage freedom of religion, freedom of learning, freedom of inquiry, freedom to own and trade, and freedom of speech. Much of my motivation to find this view of the universe is to hedge about and fence in the totalitarian State.

That explains the why for all the fenestrations and virtual atoms but one. For the last frame there is a last motive.

Geshua, the Crucified, is my God, not by my choice, but by His choice of me, an unlikely preacher, full of error and deeply flawed. Nevertheless, He calls me to speak and say that He is the Living God. To that end I have attempted to remove all hints of pagan theology and philosophy from my system for understanding the world. You will read here some one who knows the mythology from 5,500 years ago and the mythology of 150 years ago. Frankly, I prefer the primitive tall tales of Shumer to the arrogant nonsense of Hegel. Many expressions and ideas of modern culture and language are left over from ancient mythological systems. Much of our culture and knowledge owe their beginnings to these people. I do not apologize for using words like Saturday or sunrise. Instead of ignoring them or blowing up their ruins, I will follow the example of Genesis and turn the myths on their heads as a parody or mock them as risible silliness. I save my sharpest remarks for Pythagoras, Plato, and the death cult of the Egyptians. For their god was impersonal, a sort of force of nature (Hegel again), and exercised no will or conscious thought at all in oozing out the material universe. Dualist systems rely on a god removed from human reality yet bound into their conceptual systems of existence. The polar opposite is the biblical God. This one of all gods is alive. He speaks and acts as He wills.

The system I present here decouples nature and the Living God except as He chooses to act among us. Thus He made the last and most important fenestration, where He is and where He allows us to speak with Him.

I do not expect many people to accept this last frame of reality. Actually, none, unless He speaks to each He chooses. But that still leaves a very useful set of ideas to combat dualism, determinism, reductionism, and mythology. This will take some explaining, which I promise to do, but I will present a system which allows an atheist of good will and a Christian or Jew of good will to agree, at least in part, with each other.

You will notice that I make no claims for His existence nor offer any proofs. The word exist is fairly useless in this context. So is proof. I cannot prove I exist and refuse to even use that word about the human experience. What I do claim is that He is alive in the same sense as a human personality is alive, only more so. And, while I do not offer any proof, I do offer the experience of myself and others of knowing His Presence and love for a very long time.

Changes to Come

This view of reality is very much a work in progress. First, I identified five frames. Then seven. Then eleven. So that I do not have to keep rewriting this introduction, the details are not included. Look here to see the current count and list. All are welcome to offer modifications to this list and to this way of dividing and unifying the universe. email me at