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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