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In case you missed it on the home page, here is the latest writing about Code World and the genetic code, as of 7-19-2014

1. The Meaning of Code World

2. Code World Model of the Origin and Operation of Life

3. Crystal Concept of Genetic Information

4. Description of a new branch of mathematics based on Code World

The rest of the following stuff is much older, but nonetheless still valid.

 

The genetic code dogma has utterly failed.

Introducing: The Perfect Code Theory

The first step toward properly understanding the genetic code is to realize that nobody actually understands it.

The second step is to realize that the genetic code is a dodecahedral molecular language.

The third step is to realize that the genetic code is so complex that it will take decades of good work to build a proper platform for actually understanding it. It will alwaysl be difficult for even the most intelligent humans to grasp the nature of this molecular language. It is not simple; it is extremely hard. It should take years not minutes to properly learn or teach the genetic code. The simple idea that the codon table is the genetic code is now nothing but a hoax. Huge mistakes have been made, and they will be difficult to correct.

• What is the ideal form of a DNA molecule? It is a double helix.
• What is the ideal form of the double helix? It is a dodecahedron.
• What is the ideal form of the genetic code? It is also a dodecahedron.

As important as the double helix was toward understanding DNA, the dodecahedron is equally important toward understanding the genetic code. Perhaps more so.

The difference is that DNA is relatively easy to understand and the genetic code is not. A bigger difference is that the men of science deperately wanted to know the shape of DNA but they refuse to believe that the genetic code actually has a shape as well. Sometimes science behaves badly. This is merely one of those times.

Perhaps the best way to begin to understand the many concepts behind the perfect code theory is to make side-by-side comparisons with the standard model of the genetic code. At the end of the day, one must chose one or the other as the proper way of knowing the genetic code.

The Standard Dogma

The Perfect Code Theory

Cipher

Language

Simple

Complex

One-dimensional

Multi-dimensional

Linear

Non-linear

Unidirectional

Bidirectional

Disproportionateness

Symmetry

Arbitrary

Highly optimized

Universal

Wide spectrum of variation

Frozen

Hotly evolving

Sequence

Structure

Time independent

Time dependent

Molecular information equals sequence

Molecular information involves structure through time.

Two codons mean two amino acids think two neurons.

Two codons mean the relationship between two amino acids think one synapse.

Excludes tRNA and anticodons

Includes tRNA and anticodons

No spatial molecular information

Includes spatial molecular information

Relates codons to amino acids

Relates nucleic acids to amino acids

Genetic code = Codon table

Genetic code = relationship between nucleotides and proteins

Cube

Dodecahedron

Uninformed by shape

Informed by shape

Ignores basic principles of crystallography

Consistent with basic principles of crystallography

Stores uncompressed information and compresses it during translation.

Stores compressed information and decompresses it during translation.

Information loss - entropy

Information gain - negentropy

Inconsistent with larger patterns of evolution.

Consistent with larger patterns of evolution.

Creates intractable Darwinian paradox

Fully integrated with concept of natural selection.

Top down organization

Bottom up self-organization

Build protein

Search and build protein and DNA

Mid 20th century computer metaphor

21st century computer metaphor

Depends on flawed central dogma

Corrects central dogma

Molecules invent a spreadsheet

Molecules performing mathematics

Codons

Symmetrical relationships between nucleotides

Amino acids

Symmetrical relationships between proteins

Easy to understand

Difficult to conceptualize

Fully understood

Partially understood

Dogma

Reason

Homunculus

Self-organization

Unsupported by empiric evidence

Consistent with all empiric evidence

Universally accepted

Heresy

Religion

Science

Precludes questions

Invites further investigation

I have been contacted by people from all over the world, and my ideas have already been taught in one form or another in high school, undergrad and at graduate levels. Unfortunately, there currently is no easy way to grasp and communicate the concept of a complex, non-linear, multi-dimensional genetic code. Conversely, it is all-too-easy to teach the flawed linear model.

Once one is ready to accept the fact that we do not know or understand the genetic code, one must search for ways to better understand it. Perhaps the biggest of all ironies is that the codon table provides the best insight. I believe that I have invented the "best possible codon table." Here is my explanation of the codons and codon tables: The G-Ball, A New Icon For Codon Symmetry and the Genetic Code. If you intend to read one thing posted here, I think I would read that. It was originally a chapter from Book #4, but I greatly expanded it and posted it to an online science archive.

A group of like-minded academics from around the country got together and published an article in Cell Biochemistry and Biophysics, Volume 55, Issue 2, pp 107-116: The Genetic Code - More Than Just a Table

I don't think anybody really wants to or needs to read all this stuff, but I'm keeping it all up here and available in case somebody might find something useful or entertaining.

Over the years I have written many books, papers, emails, web pages, etc. You can find the books here: Rafiki Books

We have a serious problem when it comes to the task of understanding the genetic code. The biggest part of the problem is in convincing people that the genetic code is entirely misunderstood. So, the first step toward solving the problem is to realize that there is a problem. I argue that the dogma regarding the genetic code is: The Worst Idea in the History of Science. This is a chapter from Book #4.

People always ask me what use there is for my ideas. I will answer with a famous question put forward by Ben Franklin: What use is a newborn baby? Apparently most people see no inherent value in being right. One of the things that strikes me most is the difference in the questions that are asked by the standard model versus a new paradigm entirely, so I wrote this: Please Judge Me First by the Questions I Ask.

Here is a paper that first describes the nature of the problem with the standard dogma, and then it takes some tenative steps toward building a platform to correct it. One must first realize how entrenched the failed dogma has become not only in our thoughts but also our language. It is going to take decades to rip out the failed ideology and install a healthy new one: Four Laws of Biology Used to Locate the Genetic Code.

Once one realizes that we don't know the genetic code. A dodecahedron goes a long way toward building a platform to actually understand it. This paper , I think, helps quite a bit in that regard: What is a Dodecahedron?

I was contacted by the daughter of a Russian who had similar ideas. She sent me one of his papers, unfortunately it is in Russian, but you can clearly see the similarities.

Here is a paper that reviews the basic problems of understanding the genetic code and offers a few simple solutions: What is a Protein?

The next step is trying to figure out what it would mean to actually know the genetic code. Here are two papers that address that:

Everybody Knows the Genetic Code: An ornery myth of science

The Genetic Code: A Good Example of Bad Science and Why it Needs to Get Much Better. This is a chapter from Book #4

In a similar vein, here is a brief paper about the basic logic organizing the genetic code: Why Three?

Here's a brief one arguing for a new approach: The Math of Life.

One of the biggest problems that I have run into again and again is that the current language used to describe the genetic code is so disfunctional that it prohibits any real understanding of the real genetic code. I got involved in a dispute with a professor trying to teach my stuff to some students, and he objected to my casual use of the words "peptide bond." Specifically, he said that I was using the term inappropriately and that I needed a new word for what I actually meant. I responded to him with this: Nomenclature. This led me to the conclusion that the whole language needed to change, and I described an idea about how to change it: Biocalc.

Several of the other papers above were derived from this. Here are some other random writings: Bio-Information, and The Problem With Language. Here is one that tries to frame the genetic code within the general context of basic language: The Language of All Languages.

Under Construction!

This effort is a work in progress, and progress has temporarily come to a halt while I go play golf. I am going to leave the following links up for amusement, but they are dated and probably not very helpful. Peruse them at your peril.

Introduction
This should be controversial
What can Rafiki contribute?
What is Information?
What is the Genetic Code?
How much genetic information gets into proteins?
The role of stereochemistry and tRNA
A new method of mapping Genetic Information
Maximum symmetry in the Genetic Code - The Rafiki Map
Seeing Codons
The role of symmetry in expanding the paradigm
Folding a Rainbow
Current Dogma as the Antithesis to Chaos and Complexity

 

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