Introduction to Rafiki's quest to break the genetic code.

Quotes to set the rebel tone

Although I am fully convinced of the truth of the views given in this volume…, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed during a long course of years, from a point of view directly opposite mine. …(B)ut I look with confidence to the future – to young and rising naturalists, who will be able to view both sides of the question with impartiality.

Charles Darwin
Origin of Species

… how an individual invents a new way of giving order to data now all assembled must here remain inscrutable and may be permanently so… Almost always the men who achieve these fundamental inventions of new paradigm have either been very young or very new to the field whose paradigm they change… (they) are particularly likely to see that those rules no longer define a playable game and to conceive another set that can replace them.

Thomas Kuhn
The Structure of Scientific Revolutions

The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...’

Isaac Asimov

The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man.

George Bernard Shaw

If we were still listening to scientists we’d still be on the ground.

The Wright Brothers

One might imagine from these quotes that Rafiki intends to champion new ideas, and indeed this is the case.

To be frank, our mission started simply enough: we wanted to sell toys. Mea Culpa. The idea that a geometric puzzle could be useful in the study of genetic translation was pure marketing - just this side of a hoax. Then the Rafiki map was discovered and the attitude quickly changed. Rafiki became intensely determined, obsessed if you will, with the task of learning the fundamentals, and then the gestalt of the genetic code.

Science is today without a viable paradigm to explain the origin, meaning and general function of genetic information. Our view of genetic information and translation has become little more than faith-based philosophical doctrine. The perplexities and counter-instances to the cherished dogma are multiplying like Fibonacci's famous rabbits. Therefore, this is an area of science desperately in need of a paradigm shift. Come hell or high water, Rafiki intends to see that shift take place.

Rafiki has come full circle. Instead of using the genetic code to sell toys, We intend to use toys to sell a new paradigm of the genetic code.

Hundreds of pages of text and twice as many illustrations have been generated in a determined effort to explore and communicate these eccentric, heretical ideas. I have no illusions about my abilities as a writer, scientist or persuader of scientific paradigms. In fact, I know that I am marginal in all of these areas. My language is a tragically imprecise hodge-podge of non-scientific colloquialisms. Much of my thinking is under-developed and confused, and some of the writing , especially the earliest writing, veers dangerously toward gibberish, but there's got to be a pony in here somewhere. Besides, all of it is just good, clean fun, and making it available might provide someone somewhere the insightful spark they need to pick up the ball and run.

The bottom line: the dogma doesn't make any sense to me, and I've yet to find any evidence to confirm the cherished and ritualistically protected dogma. What started as a lark is picking up momentum and credibility, and it is on its way toward full-scale scientific jihad. The Rafiki notions, although blatantly heretical, make good sense from most angles, but these ideas consistently draw immediate disdain. Granted, a big part of this reaction is due to the eccentricities of the messenger as well as the outrageousness of the message, but the evidence just isn't there to reject these wacky ideas out-of-hand. In fact, existing evidence appears to support the heresy. So the beatings will continue until morale improves, and the crusade will march forward until the empiric death knell is sounded. Science is being put on notice: the dogma is being put back into play. Definitive empiric evidence is now finally being requested.

This is a quest, a search rather than a destination. It's a search worth making, and it's time that somebody formally recognize the need to make it. The genetic code is an unsolved puzzle and a puzzle worth solving. It's fascinating and fun to boot!

I am an inventor. I am finding out that Inventors and scientists are two different kinds of animal. They typically are at odds - understandably - but they each depend on the other. Inventors piggyback on the good work of scientists, and scientists advance through the fruits of invention. There is a dichotomy to the standard mindsets however. To paraphrase a popular phrase, inventors are from mars and scientists are from venus. Scientists spend entire careers adroitly learning the nuances of dogma, and then they struggle in the good fight to cleverly apply the existing dogma for outstanding problems - primarily in an attempt to bolster the dogma. In short, they are believers. (This view of workaday scientists is more deftly espoused by Thomas Kuhn.) Inventors, on the hand, never met a dogma they didn't hate. What happens when a cherished scientific dogma fails?

The dogma behind the genetic code has failed.

In the words of Thomas Kuhn, the theory is in crisis, or should be, and we must look forward to the next scientific revolution. The empiric evidence is greatly at odds with the paradigm, and this humble ;-) inventor intends to contribute his two cents to the new paradigm. Here are the broad strokes. The devil, as always, is in the details.

• Genetic information has more than one degree of freedom in translation from nucleotides to proteins. The function that translates genetic information and converts primary sequences into proteins is not linear or one-dimensional. Codons are inherently ambiguous with anticodons, and this is informative during translation. In other words, there is more to making a protein than just sequencing amino acids. In short, synonymous codons aren't entirely synonymous.

• Any complete view of genetic translation must include the information added to the process by tRNA.

• Just as molecules and molecular information assume an ideal form, so too do the rules of molecular translation. Information has structure, and the translation of information has structure as well. The ideal form of genetic translation is a dodecahedron.

• Life must constantly find new and diverse sets of protein morphologies on the landscape of all possible protein morphologies. The genetic code serves as a search engine in that task. The search cannot become stuck in isolated regions of the protein landscape, so it is optimized to perform a robust and efficient search for new protein forms. Genomes and the genetic code are both full of symmetries. These symmetries are co-adapted, like hand-in-glove, to execute an optimized search of protein morphologies.

• Symmetry lays the foundation for all of life. It is the starting point for all molecular processes, and organic molecules are no different. Symmetry lays the foundation, but it is symmetry breaking that actually defines organic information.

These web pages are evolving along with the ideas. But originally they were mostly cut and pasted together from the thinking, investigating and writing that has been done since openning Pandora's box on the genetic code. I intend to continue editting and adding to these pages through time, but I especially look forward to posting the continuing contributions of others. The original Rafiki goal was to publish a general interest book to help circulate the eccentric ideas about genetic information and the processes of life. On that score I have so far failed. Writing in general is really time-consuming, hard work, and this project continues to expand and evolve, so web publishing is the best option at this time. Two books were actually written and illustrated, but they are woefully uneditted, and no serious steps toward printing were taken. Rather than rotting in the digital ether of a single computer, they have been made available for completeness, entertainment and as a historical documentation of this fascinating journey - a peek inside the creative process, so to speak. Why not? The web makes anything possible.

The first book carries the cryptic working title of 'Rafiki - At the Edge.' The second one was given the working title 'Organic Computers and Genetic Information - the Rafiki Code.' The first one was done in color, and is quite colorful, but the second was done more soberly and cost consciously in anticipation of self-publication. It is tastefully done in black and white, and formatted for printing in 6' x 9'. Perhaps I will return to the book project at a later time, but for now a 'real book' is still a part of the twisted Rafiki dream.

At some point after writing the first book, I started writing shorter pieces in an effort to get some ideas published in an academic journal. Some of these pieces will surely be posted, but in general the idea of scientific publication is a rat hole for my time. Again, I failed. As I admitted earlier, I am no scientist, and there seemed to be no place for Rafiki in big-league science today. Rafiki is the science of tomorrow, I suppose. I think it was Hunter Thompson that said, 'when the going gets weird, the weird turn pro.'

Some spit and vinegar (another typical internet rant of the heretic): I am frustrated by the institutional arrogance that I routinely encounter, the lack of curiosity or sense of adventure, and mostly by my inability to pick a good fight. Clearly, these folks are too busy chasing grants and making a living to spend any time on their own ideas, let alone the ideas of cyberspace heretics. Their disdain is comprehendable; however, the close-mindedness is stunning. 'Not my area' is the scientific euphemism for 'piss-off, piker'. I was actually told by one of the big boys at the get-go, "you're wrong, and so what if you're right?" Can't really argue with that, but it does remain quite vivid in my memory nonetheless.

Here is my rebel yell:

Proteins are not functionally or logically equivalent to sequences of amino acids, and the path to understanding this must pass through a dodecahedron!

The rally cry: Symmetry!

Much of the earlier hard work as a writer was cut apart, recombined and augmented in these web pages. I have made the originals available free of charge in the books section of this site, but they represent dated material. They are useful, colorful and entertaining, but they are not being updated as Rafiki learns and grows.

If you have wandered into the Rafiki circus as an unwitting novice, attracted by the glitz and pretty lights, please do not be frightened away just because you might not have a rudimentary familiarity with cell biology, biopolymers, DNA and proteins. There are many good web sites for these basics. Here are some links.

Great intro to proteins
Folding@Home
North Harris College
Genetic Science Learning Center
Freeland Lab
DNA Sciences
Hypermedia Glossary Of Genetic Terms
The Dictionary of Cell Biology
The Human Genome Project
Unraveling the Mystery of Protein Folding

The basics are not that hard, and it doesn't take too long to get up to speed - not as long as you might think. A contemporary textbook in 9th grade biology is all you should need to get started and join our search for a better understanding of genetic information and translation, the gestalt of life's processes. In fact, the less indoctrination the better. Smart folks with computer, math, art, cryptology or just puzzle-solver backgrounds will thrive in this area.

Whatever you do, don't drink the cool aid. Look at the situation with fresh eyes, and make your own critical assessment. Don't accept the 'everybody knows' argument from authority without being shown the goods.

The thrust in these pages is slightly more abstract than any biology text treatment of the subject. That is the nature of the beast, and the preferred realm of this author. I do not intend at this time to create primer pages for the basics, but you never know. Please share with us some of the web pages that you find particularly good or useful in these areas. We are interested in views and studies that either confirm or contradict the ideas put forth here, and we are just getting started.

Enjoy.

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