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What can Rafiki contribute?

The most significant contribution from Rafiki is in recognizing the deficiencies in the current model, and then going on to doggedly make a stink about it. Rafiki is nothing if not irritatingly persistent, but the emperor is naked on this one, and Rafiki is child-like enough to point it out. We've all been told that the genetic code has been cracked, yet many important questions are unanswered - in fact some really important questions have remarkably never been asked. Consequently, the genetic code remains unbroken, and our gestalt of the fundamental organization of life's clever molecular sets is found wanting. In essence we have only partially solved the puzzle of how proteins are made from information in DNA, but it is clearly a puzzle worth solving.

Rafiki has contributed four basic ideas:

1. The genetic code is not one-dimensional. There are other dimensions of information, besides primary sequence, that are a part of the genetic code. Another way to put this is that the thermodynamic hypothesis of protein folding is false. Thermodynamics are important to folding, but it is not the only factor involved.

2. There are many ways to map the correlations between nucleic acids and amino acids, but the best way to map them is on the surface of a sphere.

3. The genetic code is optimized not just for making proteins, but for finding new proteins as well. The process and mechanisms of new morphology creation was given short shrift in past considerations of the genetic code. The symmetry of codon assignments combines with genomic symmetry to accelerate the search for new protein morphologies.

4. Our language, metaphors and conceptual tools for studying genetic information are outdated and woefully inadequate. In addition to pointing this out, Rafiki has proposed a few modifications.

I'm frequently asked what I'm going to do next. Well, you're looking at it.

What do you want me to do, build a biochemistry lab? All I can do is keep shouting, because I'm not going to become a biochemist. I've actually got a life. In the mean time Rafiki has provided some excellent tools to advance the cause.

Code World is a nifty contribution toward understanding the genetic code. Code World and the genetic code are not literally one and the same, but their informative structures are. In this regard it is a fabulous tool to help us think about the problem of genetic translation at its very core. In other words, it shows us how two shapes can communicate information. In this case, it shows how information stored in a dodecahedron can be communicated to a tetrahedron. Please think about these concepts in the simplest possible terms, because that is what it is ultimately going to take to eventually get the job done: What is information? what is language and communication? How could the molecules of life organize and execute a language and achieve such sublime communication of information? This is the appropriate starting point in understanding a molecular code for genetic translation. This is an organizing principle for molecular languages, and it is missing from the dogma today.

Information must have a structure. Molecules must have access to this structure in some form when they execute methods related to that information. On what structures could these methods be implemented? Molecular information is related to spatial relationships, because this is fundamentally how molecular behavior is determined. The Rafiki Map takes the process one step further and shows us how the actual code is perfectly arranged within a dodecahedron. It effectively demonstrates the context of each molecular set in the code. It provides the most compressed, symmetric and objective view of this vital data. It perfectly demonstrates nucleotide triplets within the overall framework of the code, and it emphasizes the importance of unordered triplets in the form and function of the code. The Rafiki map highlights how the symmetry and coordination of these triplets can work in concert with a genome loaded with the symmetry of sequence transformations to efficiently generate novel protein morphologies. Because of the dodecahedral arrangement, the information involved in the genetic code can finally take shape, and the spatial relationships help define the information.

The Rafiki map is simply a superior way to view the data.

In all likelihood, Rafiki will not break the genetic code alone (somebody really smart probably will). But by raising long overdue questions, and by providing useful tools - Code World and the Rafiki map - we are contributing to scientific advancement. Perhaps this website will become an icon and a forum for that advancement, or perhaps that forum will develop elsewhere. If you are like-minded, curious or even just amused, please link with us. The more the merrier.

The primary theme here is symmetry, and within that theme the dodecahedron takes center stage. The three basic areas where applications of the dodecahedron to life and the genetic code are:

Translation. What is the fundamental nature of genetic information; how much of it gets translated, and by what molecular mechanism? If codons are truly synonymous and mutations are truly silent, why do they empirically make an impact on all areas of translation? The Rafiki doctrine of 'symmetry first' when applied to actual genetic translation, is the most persistent and heretical position taken here, but it is also the most important one to resolve.

Teleology (The use of ultimate purpose or design as a means of explaining natural phenomena.) What is the origin, history and degree of adaptation in the genetic code, and how has symmetry played its role?

Geometric and numeric. Can there be an optimum form to the structure of a code such as the genetic code, and would the numbers involved actually have an impact on that code's optimized behavior? In this case, the basic numbers are 3, 4, 20 and 64, which suggests the introduction of a dodecahedron. Is this just numerology, or is the code actually a combinatorial optimization of molecular sets as suggested by the numbers?

All three of these areas will require efforts for years to come of biochemists, computer scientists, physicists, chemists, cryptographers, philosophers, mathematicians; in general - puzzle solvers. Let's have at it!

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Last updated September 13, 2005 8:33 AM