The conceptual hurdle

Thus far, by distinguishing between the hardware and software elements of the computing processes it has been fairly easy to compare the processing operations in biological cells with those of a digital computer. Storing biological data in digital form and using this to specify the manufacture of proteins is very similar to the way in which all digital processes are carried out.

The analogy then appears then to break down because the information has changed from being represented in a two dimensional digital form to that of a three dimensional shape - a ball of amino acids. The information is transformed from digital to analog taking it outside of our normal abilities to comprehend.

The reason why we cannot easily comprehend the information carrying capacity of a three dimensional shape is that three dimensional shapes require much more complex processing than two dimensional binaries. This causes the information flow to become irreversible because it is easy to get from a two dimensional binary to a three dimensional analog but impossible to work out the binary specification from a three dimensional shape.

To understand this will give you an insight into the problems of genetic engineers, virologists, drug companies and the like who need to work backwards from proteins to try to get at the nucleotide sequences of the genes on the DNA which specified them.

Let's take another look at the process which transcribes the nucleotide sequences on the DNA into messenger RNA (mRNA). This is illustrated in figure 11s.13.

A protein molecule called RNA polymerase that moves along a stretch of DNA and manufactures the complementary strand of messenger RNA carries out the actual transcribing. The mechanics of this process we have already covered as it is simply a question of matching up the couplings of appropriate nucleotides. The trick question is "How does the RNA polymerase molecule know where on the three billion stretch of DNA sequences it has to start reading off the sequence to transcribe a specific gene?".

This is the question that stumps the molecular biologists because the address is in analog form as a surface shape together with a specific configuration of charges on that surface. It is like a shaped key that has to fit into a specific matching lock. Molecular biologists would love to be able to know how to create the particular molecular keys to switch genes on or off but they cannot do so because they cannot work backwards to calculate from the analog protein the digital sequence of the DNA.

To understand the nature of this problem you might think of an alien life form capturing a human computer that ran a multimedia production using an A-Life Avatar cell (multimedia player). Assuming the alien life form was familiar with binary notation it would have no trouble at all in working out how an eight bit binary sequence could be used to represent a particular letter of the alphabet. It would also be able to work out that the system was using this eight bit format to produce words. However, this information would be very little use if the alien had no idea how the words were used to program the computer.

For example, how would an alien be able to relate a message in an email document :

doSkill mary

to the on screen activity it generates?

From a bottom up view it is quite easy to see how the binary information forms programming words which are put into a particular syntax to initiate all the programming steps necessary to create an object which responds to the message doSkill.

To an alien this would be totally baffling because it would be asking itself how these words managed to make the correct connections in memory to pull out the correct sequence to make a picture on the screen. To the alien the number of different combinations which could be made with the 64 base information language would be astronomical. What then, would the alien make of a few thousand lines of high level programming instructions written in Lingo. Not knowing the relatively small subset of all possible combinations of letters being used for programming in Lingo, such a document would look every bit as unfathomable to the alien as a cell full of proteins might look to us.

In other words a document of text in a multimedia environment is directly analogous to a protein complex in a biological system. Just as we can put just a few hundred particular words into a specific order and context to program an A-Life avatar cell so a biological system can string together proteins and amino acid sequences to program the activity within a biological cell.

What the unfortunate molecular biologists have to do to elucidate the programming of a cell is to do the equivalent of what an alien might have to do to understand an A-Life avatar cell. Observing that the words "doSkill Mary" results in a picture being put onto the screen the alien would have no choice other than to work backwards through all the digital activity which occurs in the processor and in RAM when these words are used.

Quite obviously, the aliens would have a much harder task going backwards through this system to understand it than the original human programmers had in designing it. In a similar way the problems in unraveling the chemical sequences of biological systems are many orders of magnitude more difficult than nature's evolutionary bottom up design process.

A more direct comparison between biological cells and A-Life avatar cell can be seen from figure 11s.14.

Within the A-Life avatar cell, information is stored in the form of binary sequences which can represent messages and define behaviors. Objects can be formed in the digital environment of RAM space using this same language with its two letter binary alphabet. This same language can also be used to allow objects to send messages to each other and transfer information.

Humans can readily join in this A-Life avatar world because they invented the language being used by the A-Life avatar cell system. A vocabulary has been established and a rigid syntax imposed. Humans can send textual messages and instructions to A-Life avatar cells in a way that the cell understands. This allows humans to build logic engines, specify behaviors, invent new messages and design receptors for the messages.

Although the biological system is identical at an abstract level, it is not so easy for a human to participate in the world of the biological cell because we haven't yet learnt the main communication language which has an alphabet consisting of three dimensional shapes. We can create nonsense words and instructions by creating random sequences of amino acids but the affect of these would be unpredictable to say the least. The ultimate aim of all people working in the area of molecular biology is to try to work out the vocabulary and syntax of the words created out of three dimensional shapes. But this has to be approached in an empirical manner, which as mentioned above is an extremely laborious process.

Currently, there is a large scale project to map all the nucleotide sequences in human DNA. This will allow patterns of sequences to be isolated and tested but it will be many years before the full vocabulary and syntax can be worked out. You might compare this exercise again to that of an alien that has a computer and is trying to control the machine by first listing all the patterns of the magnetic fields on the hard disk. Then having to experiment with these patterns, to try to discover the vocabulary and syntax of C++.

In comparing biological and computer systems, the concept of an alphabet consisting of three dimensional shapes may be difficult to grasp at first. The way to look at this is to think of the comparison between ancient Egyptian writings in the form of hieroglyphics (two dimensional pictures) and our modern text using alphanumeric symbols. To the untrained eye, there seems to be no common ground. Yet, when archaeologists eventually deciphered the meanings, hieroglyphics turned out to be able to convey information, meanings and ideas just as effectively as our present day alphanumeric system (albeit suited only for the limited use of written information in those days).

Just as in hieroglyphics, where a pictorial shape may convey the meaning of several words in modern day text, the shapes on the surface of a protein may convey the essence of whole sets of instructions.

The interaction and combination of protein molecules can create some surprising results, particularly when the shapes and affinities complement each other to form membranes and bubbles. In these instances it is very difficult to disassociate from the physical shapes to realize that in essence the proteins are the equivalent of a message line in a computer language.

If we take the example from before of the message line:

doSkill Mary

In "amino acid speak" this instruction would take the form of specifying the sequence of amino acids which would:

1) Create a message protein with a characteristic shape on its exposed surface. This shape would allow it to couple with a complementary shape on a "Mary" protein.

2) Create another protein,which will attach to the message protein, to provide a coupling site for a"doSkill" protein.

3) Create a third protein which will give the messenger protein an affinity for a membrane building protein.

4) Create another protein to couple to the messenger which would act as a label to let other proteins in the cell know where the Mary protein is located so that they could assist in transportation.

The chemical reactions of these proteins would result in a bubble forming around the message protein and this bubble transporting the message to where the "Mary" protein" is located. The resulting chemical interactions of the proteins would then produce the required effect. This all sounds unbelievable, but, all these processes have been observed to take place and many of the chemical reactions and thermodynamic processes fairly well understood. In the March 1996 edition of Scientific American there was a lengthy article that explained in exact detail how such protein messenger transportation systems occur (Budding Vesicles in Living Cells by James E. Rothman and Lelio Orci). Figure 11s.15 illustrates this process.

About figure 11s.15

The human cell is divided into a number of departments enclosed by membranes (organelles). Each of these departments have a specific role to play. For instance, one department called the endoplasmic reticulum produces many of the cell's necessary proteins. These proteins are then sent to another department called the Golgi apparatus where they are modified and shipped to another department, or, sent outside to go on to a department in another cell somewhere else in the body.

A process known as budding vesicles arranges the transfer of the molecular messages. A protein associated with the message will attach itself to the membrane wall and cause that section of the wall to bulge. With the help of other molecules attracted by the messenger protein, the bulging increases until it forms a little bubble on the outside of the membrane, this bubble will enclose the messenger proteins which are to be dispatched.

The bubble (vesicle), with its enclosed messenger proteins, then nips itself off from the membrane, and transports its cargo of molecules to a target membrane. This attaches itself through the 'address' proteins that have risen to the bubble surface. When the vesicle sticks to the target surface, new proteins come into play, which open up the membrane between the interior of the target and the bubble to allow the molecular contents of the bubble to escape into the new department. There, their molecular messages cause them to be relayed to an appropriate destination.

To observe this system with a top down view would make it appear just too incredible for such a complex process to have ever evolved. To reverse engineer such a system of protein messenger transportation would be quite beyond present day capabilities. However, this system wasn't created as a top down designed plan it is a process which evolved as a result of a simple set of chemical reactions evolving increasing complexity over millions of years.