LifeOS: exploring the system that executes DNA

September 14, 2007

Structure of Information

Filed under: Ch 02 Structure of Information, LifeOS:the Manuscript — insomniac @ 8:32 am

Structure

I said our mission was to explore the structure of biological systems. What kind of structure am i talking about?

We usually think of structure as in buildings, bridges and towers, but besides physical structures we have conceptual structures that we use daily. It is the structure of a sentence that allows us to to make sense out of language. Sentence structure is governed by the rules of grammar just as surely bridge construction is governed by rules of engineering. So, we can say that a structure has rules.

The structure we are talking about is a combination of physical and conceptual structures that work as a unit. It is the arrangement of physical elements we call reality and their virtual counterpart, the rules, plans or blueprints that make it happen.

An edifice is the result of a plan. Even a tiny mud hut is the result of a conceptual plan occurring in the mind of a builder. Skyscrapers require a huge volume of blueprints, plans, lists and such, that are physical representations of concepts, but also are encoded information about the finished product. Besides being represented in the overall structure, all of these elements have an internal structure of their own, both physical and virtual. Structure ties it all together.

An American football game is an example of multiple structures in action. You have a physical structure represented by the field with its boundaries, yard markers and goals. There is a team structure, with specific positions assigned to each player. You have a time structure, a time limit divided into periods. The unit of action is the play, which involves a virtual plan for each team, including a starting formation, a specialized plan of action for each player, which in combination, become a strategy for accomplishing a specific goal.

Each play is an action cycle, starting at rest, progressing through a planned sequence and ending again at rest. When a play is put into motion, the various structural elements play out their virtual values and manifest a physical result in the real world. The referee signals the beginning and end of play and assess the gains and penalties.

What all of these structures have in common is that they are governed by a set of rules. These rules establish the boundaries or parameters for the game and all its elements. The rules give the structure meaning by identifying relationships, giving location to elements, defining team and individual capabilities and by limiting some possibilities for variation.

The rules allow us to play the game, but also give us the labels we need to talk about the game. During the game, the physical elements are visible to all, but the virtual structure exists only in the minds of the participants. The players think. It is this invisible component of the structure that clearly defines the result. The plans made by each team, executed against the plans and the will of the other, produce a measurable result.

A football game is a simulation of a war scenario sanitized and regulated for entertainment and maximum macho expression, but in its essence, also imitates life. We can find and identify many common elements between football and the game of Life.

I thought we were going to talk about computers, what has football got to do with it? We are just practicing the art of recognizing common structural patterns and elements. We are learning to spot the interaction between physical and conceptual structures. We are looking for the structural rules in common between specific actions and Life in general. We are alert for the role that information processing plays in Life.

Structure is governed by a set of rules that organizes information by giving location and context to items.

Data Structures

 

The Information Age has given us a whole new perspective on the very concept of structure.

The structuring of data makes computer networks possible. All computer data is linear, essentially a list of 1s and 0s. But that list has a very definite structure that shapes it into usable units. The smallest structural unit is the byte; eight binary characters.

Eight slots with two options gives us 256 characters with which to build languages. That is plenty of characters for an alphabet, punctuation and some left over to describe more complex data structures. Then the computer can switch from a language that describes text, to a language that describes graphics, like jpeg or gif, and show us pictures, which are highly structured color representations of the data.

So, data structures are really fundamental to data processing, just as sentence structure is essential for understanding human language.

Our basic data structure is a list. The list has a name that tells us something about all the entries. Reading List, laundry list, grocery list, etc. The list can further define the contents if we prioritize it by putting the most important things towards the top.

We can further organize our data by having sub-lists like an outline. An outline is an information structure made up of nested sub-lists. We use indentation to group our information into meaningful units. This allows us to group items by other criteria like, hardware and groceries, or add details. We can prioritize on one branch and alpha sort another one. Or we can list steps in the order that they are to be executed. Or any combination of these types used on different branches. Lists help us organize, prioritize and execute our plans.

The outline is a very powerful tool. Using this information structure is one feature of our western civilization that sets it apart from indigenous people.

Civilization is built on the ability to plan and execute large public works projects. Those projects are made possible by the ability to encode concepts in physical form, and pass them around to the many workers involved.

The building of physical structures requires the application of conceptual structures.

Dynamic Structures

 

Weather is the most obvious example of dynamic structure. Fluid dynamics is the study of the structure of fluids in motion.

A flock of birds or a school of fish form a dynamic structure. They do it by maintaining a consistent distance from all their neighbors. Each critter is operating under the same set of guidance protocols. The result is a dynamic structure that moves as one. Information passes through the flock like a wave. In fact the wave at a sports event is an example of flock action.

Usually when we consider events, we think of them as one single action. We label them as one for convenience, but in reality they involve more than a single event. Not only is an event made up of a string of events leading up to the climax, but each event in the string has width and depth, giving the thing we label as a single event, much more complexity.

For example, a tree falls in the forest. There was a string of events, from the first chop of the ax, leading up to the tree hitting the ground. The word tree is a label for a mass of wood, bark, leaves, maybe some fruit, a bird’s nest or two and a huge number of other organisms. So what we casually label as a single event, is more like a swarm of smaller events, much like a flock of birds. Just like the birds, the flock of events has structure or pattern.

The patterns created by the rotation of the Earth, it’s orbit around the Sun and the orbit of our moon, give a rhythmic structure to the passage of time. We see them as day and night, the tides, phases of the moon and the seasons. Natural systems rely on these repeated patterns to regulate their own growth cycles.

The point is that dynamic structure enhances meaning, by giving elements context and location in both time and space.

The Internet

A World Wide Network of Dynamic Data Structures.

The internet is a structure in itself. It has a physical structure of connections and a set of rules to govern relationships. It is structured on several levels. First it has a purely physical structure, but beyond that is a multilevel virtual structure, which is vastly different. What makes it all work is that everything has its own address. Each machine on the network has an address. Each file within that machine has its own address. Every byte of data stored on the machine has its own address on a storage device, which also has an address. Every domain has its own address. An address gives its elements location within the structure.

Say you browse a web site from your computer. You enter a URL, the address of the domain. That address goes to a machine called a nameserver that looks up the URL and relays the request to the physical machine that hosts the domain. That machine looks up the address of the index page for that domain and reads that file. That file may be nothing but a list of addresses, anywhere on the internet, or any other network connected to the host, that will be found by the same process. Every time a machine looks up an address, it has to also look up the address of the relevant data on a memory device, which also has an address. Just like in the real estate or business world, the three most important things are: location, location and location. In a network, location is everything, not that any location is better than another, but without a location in the system, one does not exist.

Cheers,

jim

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