Welcome to the Rafiki home page,
Home of Code World,
and exploring the genetic code.
I have not been keeping this website very current, and I don't know if I will find the time to do so in the near future. I have now written five entire books and aborted several others, but only the first two are posted here. I don't know what I will do with them, so perhaps I will just put them all up here for people to enjoy. I would like to find a publisher for at least one of them, but even that has proven to be a royal pain in the ass.
My ideas have evolved since I stopped updating this website, but I doubt that I could parse through what's already up here and decide baby from bath water. On top of that I have invented another toy/game that is superior to Code World. Unfortunately, I don't seem to have what it takes to produce and sell them, so I am dithering about that as well. On the brighter side, I seem to be climbing on Google lists and I'm now getting lots of "interesting" feedback from all over the world.
Short of a perfect solution, I have written a preamble to my current project, which if I'm lucky will not become yet another book. After that I have a link to an article that I posted at an online science archive. Beyond that I will just keep the website as it was and let people pick through it for shiny pebbles and whatnot.
The Perfect Code Theory is a name I have given to a collection of ideas about molecular information to contrast them with the ideas that make up the conventional theory about the genetic code and its role in protein formation. The central premise of my theory is that a perfect code of spatial logic exists in the universe. The co-dependent processes of DNA and protein formation are consequences of that logic. Conversely, the narrow relationship between codons and amino acids - at first called the genetic code - reflects but a tiny portion of that logic. A proper understanding of protein formation will now require a complete rejection of the conventional theory. Furthermore, an enlightened view of the fundamental logic driving life on earth will require a proper understanding of the relationship between nucleotides and protein as it manifests a real molecular system of information based on a perfect code of spatial logic.
To be honest, articulation of my theory to date has mostly consisted of simply complaining that the old theory is completely wrong. I have a number of good reasons to believe this, but it has proven insufficient to merely call for the outright rejection of a universally accepted theory. So, I am now offering The Perfect Code Theory as a positive alternative rather than merely a negation of the universally accepted theory. I will put forth a number of hypotheses, arguments, explanations and proofs to support my general theory, and I will compare and contrast the implications of these with those of the conventional theory. Ultimately one must decide whether to keep or reject the conventional theory since it is mutually exclusive with the Perfect Code Theory.
A quick understanding of my theory can be gained by way of analogy with ordinary table salt, which is a sodium chloride crystal. There exists a perfect code of spatial logic in the universe that guides the formation of table salt. This logic can be completely described by a cube. Formation of the crystal is achieved by individual atoms of sodium and chloride organizing themselves according to the logic demonstrated by the vertices of dual tetrahedrons that form a cube. The “plan” for table salt is to make cubes from sodium tetrahedrons dual to chloride tetrahedrons. The only molecular machinery required is the molecular cube itself. The molecular information it generates and stores is trivial. In comparison, the Perfect Code Theory holds that a similar “plan” exists for protein and DNA. It is based not on a single form but on logical relationships between forms. The spatial logic is only slightly more complex, but the molecular manifestation of that logic is indeed profoundly complex, and the machinery required to translate the molecular information it generates encompasses a good part of known biochemistry. Life represents the function of time-dependent creation and accumulation of molecular information in this system of spatial logic. The general concept is deceptively simple, but the task of describing its actual operation will surely challenge the limits of human cognition.
The reason that I have chosen the name ‘the Perfect Code Theory’ is because it puts my theory in stark opposition to the conventional theory. It is currently an accepted idea that no spatial information is stored in DNA and translated into protein. This idea exists in numerous word forms, but it can be communicated by saying that the genetic code is one-dimensional. This means that the relationship between codons and amino acids exists only to translate sequences of nucleotides into sequences of amino acids. The one dimension of molecular information stored in DNA and translated into protein is manifest by a sequence of amino acids found in every protein. If this were true then no code of spatial logic – perfect or otherwise – is ever required to generate this system in nature or to describe this molecular system amongst man. However, this central idea has never actually been tested or empirically demonstrated to be true. In fact it is logically unappealing, conceptually devastating, and it has proven time and again to be empirically false. Therefore, only when we systematically explore the ramifications of the Perfect Code Theory will we finally realize the epistemic devastation that is wrought by the false central premise of the conventional theory. The contrast cannot be more stark: either protein formation is based on spatial logic or it is completely devoid of it. The choice is clear; the choice has been made, and the choice that was made is clearly wrong. It is time to consider alternative theories, and that is precisely what I am doing here.
Indeed this website is not very current, but it is an excellent digital museum of the early path that I took in arriving at my conclusions. Here is the most current and coherent explanation of the symmetry of the genetic code.
This website is a collection of fanciful ramblings about symmetry and the genetic code. We hope you enjoy it. There is a lot of material here, and perhaps it strays a bit more than it should, so to cut to the chase here are some stunning conclusions about the genetic code.
Although seemingly heretical, these statements are all logically true or have been experimentally proven true. Anyone who would like to dispute any of these claims should contact me at the above link, and I will post your argument and your evidence here.
It appears that life is doing math with molecules. There is a striking similarity to life on earth and the history of mathematics, where the development of our complex and various branches of mathematics parallel that of a living system of molecules interacting to exchange molecular information. Unfortunately, our accepted model of this system is flawed and entirely inadequate. We have no formal system for defining key components of the system and therefore have no hope of understanding the relationships between these components. The language and icons that we currently use are wholly inadequate. Therefore, all of biology will benefit by adopting the basic tools and techniques used for centuries by mathematicians to build a logical and coherent system of thought and communication. I believe that set theory will provide a foundation of logic and the essential tools for defining key components of biological systems and the informative relationships between them. I believe that symmetry and groups will be a key component of quantifying molecular information and achieving a better understanding of its translation.
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Last updated January 22, 2008 7:05 PM