LifeOS: exploring the system that executes DNA

September 17, 2007

Code Driven Systems

Filed under: Ch 03 Code Driven Systems, LifeOS:the Manuscript — insomniac @ 10:28 am

DNA and Computer Code

The big difference is that our computers run on mathematical operations on binary code while the biocomputer operates on holographic principles in living cells. But that difference may not account for much. One of the first things you learn in Computer Science is that the concepts expressed in code are independent of the platform, language or media involved, much like a story is independent of the media used to tell it.

We find that algorithms represent abstract concepts that can easily be translated from one coded language to another. Although the platform and/or operating systems may be different, the underlying capabilities of the computer to perform mathematical functions on binary code are identical.

Just as an algorithm is independent of the platform, language or media involved, so is the conceptual structure developed for the computer industry. It doesn’t make any difference what kind of switches one uses to store binary data, the conceptual structure is the same. The network structure developed to support the internet has evolved into a robust communications system by adapting to the realities of network accountability and responsibility. It has involved billions upon billions of man-hours by some of the smartest people ever to walk the earth. The result is a global communications system that allows any user to communicate with any other user.

Many of the concepts that make that possible would also apply to a global biological communications network. And so a holographic operating system would follow a similar structure, built upon its unique platform. The concept of a code driven system should follow a similar structure regardless of the system of memory, processing or output.

Common Attributes

 

DNA has both a physical and a data structure. The physical structure is the double helix. The data structure is the arrangement of organizational elements that give DNA code its meaning. Although computer code is binary, 1s and Os, and DNA code is made up of four base pairs, both strings of code represent meaning in similar ways.

Base 2(binary) has only two states, represented by the symbols, zero and one. Base 4(DNA) has four states represented by the letters, A, C, G and T. Which stand for the four compounds, called bases, that make up the rungs in the DNA ladder. The names of these bases aren’t really important to us, the abbreviations will do. A and T will bond with each other, as will C and G. That gives us only four possible combinations. A-T, T-A, C-G and G-C.

Since each base will only pair with one other, when the DNA splits down the middle, each half is a copy of the original sequential pattern. This happens every time a cell divides and during reproduction. Both the cells then reassemble their half into a new complete DNA molecule. During the manufacture of proteins, the DNA molecule does another split. This time it only splits in a specific section. This time, an RNA molecule forms on one side of the split. It is just like DNA except the T base is replaced by U. U is the same as T, in that it will only hook up with A. So you have a copy of the original sequence, but it can’t be mistaken for the original. Then this copy moves into the production area where it is used as a template to assemble amino acids.

8 Bits

 

In computer language, each character is represented by a string of 8 binary bits. In other words, the computer reads its code in chunks of 8 bits at a time. Eight bits, with two states equals 256 possible combinations.

At the very basic level, a computer can do nothing, but perform a very limited number of functions to that 8 bit chunk of data. It can perform some mathematical functions or send the code to memory or display or print what the code means. Where the computer excels is that it can perform billions of such operations in a very short time, without making mistakes. By using abstract concepts, we can use strings of binary code to represent almost anything. It makes for a very powerful tool.

The code can be content, like a text file or be instructions on how to display the information or internal machine code used only for processing other data. As text…For example: in ascii code,

01010101=U

01000001=A

00110000=0(zero)

00110001=1

With this set of 256 characters, punctuation marks and other symbols used as abstract tools, the user can write almost anything imaginable.

3 Bits

 

In DNA language, it reads the code in groups of three base pairs. This gives us 64 possible combinations. Three base pairs form what is called a codon, which represents a specific amino acid. There are twenty amino acids, so they are analogous to characters in an alphabet.

Using the letters, A, C, G and T, to represent the four base pairs, each amino acid is represented by at least one of these codons. For example, TGG is the codon that means tryptophan in DNA code and CAC translates to Histidine.

In RNA code, with the T replaced by U, TGG and UGG both equal tryptophan. Tryptophan is a fairly large and complex molecule. This code is clearly an abstract representation of an amino acid. These three linear code elements represent a highly complex 3D object.

In biological systems, the basic level consists of the manufacture of proteins by assembling amino acids into polypeptide chains. Just as in the computer, these basic processes are repeated many, many times, producing highly complex output.

This is pretty clever stuff.

Computers and Cells

 

In both computers and cells, the basic activities that produce such complex results are very precise in nature. Mistakes in the process are to be avoided at all cost. In computer systems we have error correction routines, virus scans and a host of security measures to insure the integrity of the results. This is analogous to the immune system in biological systems, which routinely eliminates damaged cells.

Three Codons

 

“Three of the codons, UAA, UAG, and UGA, do not code for any amino acid. They act as signals for the release of the polypeptide from the ribosome, thus stopping the process of making that polypeptide.” –world book

These guys are like an “end of file” marker.

These three codons are a different kind of code from the ones that identify which amino acid goes next. In computer code, we would say that the codon for a specific amino acid is content, while the these three codons would be part of the protocols of the operating system or the program being run. It is information that is not represented in the output, but only used internally by the system to identify the end of a protein sequence.

This is our first evidence that there exists a universal biological operating system.

These three codons have no counterpart in the physical world, no place for environmental pressures nor natural selection to get a foothold.

It is analogous to a Word document where the user may change the content with ease, but can’t change the internal code that the word processing program uses to signify the end of the document. That part of the code is part of the internal language of the program and out of reach of the user. In this case the three “end of sequence” codons are out of the reach of evolution and part of the DNA code that cannot change without disrupting the entire biological system.

Clever Stuff

 

Within this code we find levels of abstraction much like those of computer code. At the lower levels, the protocols become standardized and seldom change. They are the common “agreed upon” meaning that makes the language work. Like these three “end of sequence” codons. Since every cell has to produce more than one protein, these elements within the DNA language had to be in place before cells could function at all. Something had to start and stop the production of protein in the first cell. Something had to recognize the first code as instructions and know to execute them.

What came first, the chicken or the egg? Before we can have a chicken or an egg, we need DNA instructions on how to build it. Before the code can function, we need something to read it. The language, specific code to produce the first cell and operating system must have all become functional at the same time in order for any cellular activity to have occurred. None of the three are likely to have occurred at all without intelligent intervention.

Like i said, this is very clever stuff. If we were to find code this sophisticated carved in stone or streaming in from outer space, we would conclude that it came from an extremely advanced civilization. This stuff reeks of intelligence.

Cheers,

jim

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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

September 13, 2007

Setting Our Goals

Filed under: Ch 01 Setting Our Goals — insomniac @ 8:08 am

Our Mission

 

Once you start to look at biological systems as being information processing systems first, with protein production being secondary output, a very different picture emerges of their structure and organization.

It is our mission to explore that structure and discover its rules of organization.

Alternative View

 

What i am proposing is a clear alternative to the models of reality given us by religion, science and the occult. It is the systems approach to understanding the reality underlying all world views.

One of the things that makes computer programs so powerful is that they allow us to look at things in different ways. It is the ability to take many different views of the same data. In animation and 3D programs, the artist can view his work from many different angles and well as in different modes. The power of spread sheets is the many ways one can look at the information. Computer models used in predicting weather are a good example of programs with the ability to look at data in different ways.

LifeOS is just another view we can use to look at biological systems. It can compliment the many other views currently in use.

Advantages of the Model

This model has been constructed by the computer science community, using the behavior of biological systems as a starting point(Information Theory and cybernetics), but independent of the constraints of growth and reproduction. Its sole criteria was the ability to function as an information processing system, whose output is simply data, rather than living tissue.

In other words, the information processing system developed by the field of Information Technologies was developed solely for its functionality and not in any attempt to mirror biological systems. However, biological information processing systems evolved to the same criteria, functionality. So it should be no surprise that the systems are so similar.

This model of network functionality is universally accepted across language and cultural barriers, everywhere computer networks exist. So, the concepts necessary to understand LifeOS are well established in our world culture. Consequently, there is lots of agreement on what it takes to make such a network operate.

Just how well does this model really fit with biological reality? Of course, this is yet to be established. That’s what we are doing here.

The Journey

 

At first glance this may seem like a simple task, to explore the similarities between biological and computer systems, but it involves passage through some potentially dangerous territory. The ground we must cover is rife with barriers and pitfalls.

Of those obstacles, the most formidable might be our own ego. Current models of reality used by both religion and science place human beings very high in the hierarchy of animal species. Religion places mankind directly descendent from god, well above all other creatures, while science does away with god altogether and places mankind squarely in the top spot.

Unfortunately, this new model has no top spot at all. There is no superior position for human beings. The ego might not be content with the loss of status.

A related obstacle we face is the entrenched dogma and superstition that will try to divert our attention from our goal. We find these two pitfalls no matter what the territory, religious or scientific. Our beliefs are built from a combination of sources and don’t necessarily fit into a comprehensive whole. By looking at the whole, we will be able to spot those flaws in our model. That can be another hit for the ego.

Then there is the fact that computer systems are intimidating to some people and the mere suggestion that we are anything like computers is summarily rejected.

However, discovery is our goal, and we will overcome all obstacles to attain it, including our own trepidation.

Cheers,

jim

September 11, 2007

Biological Operating System

Filed under: An Introduction — Tags: , , , , , — insomniac @ 8:47 am

All creatures alive today, plus the remains of all living things that have gone before, all the organic compounds, all fossils, all fossil fuels, all the biomass accumulated by this planet over billions of years, exists because, information coded into DNA was accessed, read and acted upon by a cell. Before any one of those cells could grow, before any living tissue could be manufactured, before any polypeptide chains could be assembled, before anything could happen in ANY cell, DNA information had to be processed. Information processing is the very first act of Life.

Why is this an important distinction? Because information processing involves a set of concepts that are independent of the processing method being used. For one, there must exist a consistent set of rules or protocols that govern information processing within the system. This is called an operating system, or OS.

All living organisms follow the same rules for accessing and reading DNA code. These universal rules infer the existence of a biological operating system. I call it LifeOS.

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