From ResearchID.org

Decoding DNA is the process of identifying the multiple codes embedded into the genome. This begins with syntax (statistical properties) and steadily increases into higher levels of semantics and pragmatics. i.e., where the meaning of DNA "words," "sentences," "grammar," "language," and design "objectives" are discovered.

Contents 1 Information hierarchy 2 DNA Statistics 2.1 Shannon Entropy 3 DNA Syntax 3.1 Genetic Codes 3.1.1 "Silent Mutations" affect Protein Folding 3.2 Common Vertebrate or "Ultra-conserved" Elements 3.3 Coehesin binding 3.4 Nucleosome Codes 3.5 Pyknons 3.6 Fractal Genenomics 4 DNA Semantics 4.1 Common or "Ultra-conserved" elements 4.2 Nucleosome code 4.3 Fractal Genenomics 4.4 Genome analysis 4.4.1 GeneSys Project 4.4.2 Decoding text strings 4.4.3 Multiple DNA Codes 5 DNA Pragmatics 6 DNA Apobetics 7 Bibliography 7.1 Gitt Publications 8 References 9 See also... 10 External Links

Information hierarchy

Intelligent Design expects DNA to exhibit multiple levels of information, and predicts fruitful results in searching for such information components in DNA. e.g. Werner Gitt (1981, 1994) categorized information into a five level hierarchy:

• 1. Statistics: Symbol frequencies, channel capacity etc. See: Information Entropy, Shannon's Theory
• 2. Syntax: All structural properties of setting up information.
• 3. Semantics: Meaning of symbols.
• 4. Pragmatics: Actions required by recipient to achieve sender's purposes.
• 5. Apobetics: Sender's purposes.

DNA Statistics

Dr. Rosalind Franklin applied X-ray diffraction and discovered the helical pattern of DNA.

Shannon Entropy

DNA Syntax

DNA Syntax is the search for and study of the structural properties of the components used to set up DNA information.

Genetic Codes

• The Genetic Codes Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A.
• Codon Usage Database

"Silent Mutations" affect Protein Folding

"Silent mutations" thought to be equivalent codons may affect protein folding and function:

• Silent mutations speak up: Overlooked genetic changes could impact on disease Nature News 21 December 2006
• "Silent" mutations are not always silent
• Kimchi-Sarfaty C., et al. "A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity." Science, published online ahead of print Dec. 21, 2006. Science, doi:10.1126/science.1135308 (2006)
• Pagani F., et al. Proc. Natl Acad. Sci. USA, 102. 6368 - 6372 (2005)
• Purvis, I.J. et al. "The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis," J. Mol. Biol. 193: 413-7. January 20, 1987.

http://www.the-scientist.com/pubmed/3298659

• Krasheninnikov, I.A.; Komar, A.A.; Adzhubei, I.A. "Role of the rare codon clusters in defining the boundaries of polypeptide chain regions with identical secondary structures in the process of co-translational folding of proteins," Dokl. Akad. Nauk. SSSR 303: 995-9, 1988.

http://www.the-scientist.com/pubmed/3250842

Common Vertebrate or "Ultra-conserved" Elements

Scientists have discovered nearly 500 ultraconserved elements or elements common to humans and other vertebrates.^[1]

Coehesin binding

• Essential Cell Division "Zipper" Anchors To So-Called Junk DNA. Wistar Institute researchers identified a cohesin-containing bridging complex was discovered that reshapes chromatin to enable cohesins to bind to DNA. The cohesins were found to bind to the "Junk DNA" (sic) region. Nature, August 29, 2002

Bridging proteins called cohesins are essential reshaping chromatin to allow cohesins to bind to DNA.

Nucleosome Codes

Segal et al. discovered a Nucleosome code code superimposed on DNA associated with nucleosomes. ^[2]

Pyknons

Rigoutsos et al. of IBM have developed pattern recognition methods that identified a subset of subset of 127,998 patterns, termed pyknons, in the "non-coding" regions of DNA that were ALSO present in the coding regions and relate to biological processes. ^[3][1] i.e. in what evolutionists have been calling "junk DNA" (sic).

Fractal Genenomics

Fractal Genomics or the fractal analysis of DNA for higher order semantic structures, especially in the genome's non-coding region, is beginning to discover fractal properties in genomes. A. Pellionisz (2006)has used the FractoGene software to identify fractal properties of pyknons. These Pellionisz termed Fractnons.

DNA Semantics

Semantics: The study of meaning.

Common or "Ultra-conserved" elements

Vertebrate common or "Ultra-conserved" elements are shared at extraordinarily high fidelity among the available vertebrate genomes. Finding these in what had been designated as "junk DNA" has caused great surprise, but such functionality was predicted by Intelligent Design practioners. These sequences are under intense scrutiny to discover their function. Preliminary indications suggest that some may be involved in regulation of vertebrate development from embryo to adult. ^[1][4][5]

Nucleosome code

The Nucleosome code appears to control the positions where the DNA is wrapped around histones to form nucleosomes. This appears to be one of numerous components critical to DNA compaction [2]. This may prove to be involved with controlling gene expression.

Fractal Genenomics

Intelligent Design pedicts evaluation of Fractal Genomics and Fractnons should lead to Fractal Semantics, or meaningful use of fractal DNA structures to achieve desired design outcomes.

Genome analysis

Numerous groups are studying genomic data.

GeneSys Project

GeneSys Project:

The GeneSys project is a long-term research programme aimed at bringing together the disciplines of mathematics, medicine and computing, in particular, the application of powerful insights from mathematical and engineering fields such as information theory, digital signal processing, error control coding and cryptography to ab initio phenomenological discovery in the genome. These include:

• Linear and Non-Linear Spectral Analysis for the discovery of:

Structural, functional and regulatory regions

Reading frame alignment

Protein coding regions

Promoter sites

• 1/f Noise Colour Analysis for the discovery of:

Long range structure and correlation

Higher level grammars

• Coding Theory for the discovery of:

Statistical information measures such as rate, redundancy, etc.

Possible error correction mechanisms

Fameshift mutations (deletion)

• Cryptography for the discovery of:

Underlying genetic "language"

Relationships to the proteome

• Computational Linguistics for the discovery of:

High level structure

Grammar and syntax

• Machine Learning Algorithms for the discovery of:

Long distance relationships

Predictability of sequences

These objectives go beyond statistical analysis of Information Entropy (Shannon Entropy) and begin to address higher levels of Werner Gitt's five level Information Heirarchy and Gitt's Information Theorems.

Decoding text strings

Simon Shepherd, (Prof. Computational Mathematics, Univ. Bradford), in testing his decoding method, on a Jane Austen text, identified 80% of the words in the text and then separated them into sentences without prior knowledge of English vocabulary or syntax. Shepherd and others seek to apply such methods of identifying syntax to identifying the "words", "sentences" and "language" of DNA.

Shepherd is working with Clive Beggs (Prof. Medical Technology) and Sue Jones (Lecturer, Biomedical Science, Bradford Medical Biophysics Research Group) to develop computational methods to decode DNA. [3] This includes GeneScan and the "software tool called GeneParser which uses Formal Language Theory to parse a genome into "words"."

Multiple DNA Codes

Helen Pearson found multiple ways to read a stretch of DNA. Helen Pearson, Genetic information: Codes and enigmas, Nature. 2006 Nov 16;444(7117):259-61.

DNA Pragmatics

DNA pragmatics seeks for the higher design information level of the actions desired to achieve the intended design purpose(s) for DNA.

DNA Apobetics

The purpose for DNA:

Bibliography

Gitt Publications

• Gitt, W.; Information und Entropie als Bindeglieder diverser Wissenschaftszweige. PTB-Mitt. 91 (1981), pp 1-17
• Gitt, W.; "Kunstliche Intelligenz" - Moglichkeiten undGrenzen - PTB-Bericht TWD-34, 1989, 43 p.
• Gitt, W.; Information: The Third Fundamental Quantity, Siemens Review, Vol. 56, No. 6 Nov./Dec. 1989, pp. 2-7
• Gitt, W.; Information-A Fundamental Quantity in Natural and Technological Systems Second Conference on the Foundations of Information - The Quest for a Unified Theory of Information. Vienna University of Technology, 11-15 June 1996.
• Gitt, W.; Information, science and biology Technical Journal 10(2):181-187, 1996
• 1994 "Am Anfang war die Information" Hanssler, Neuhausen-Stuttgart, Germany
• 1997, 2000 In the Beginning was Information ISBN 3-89397-255-2

References

1. ↑ ^1.0 1.1

   G. Bejerano et al. "Ultraconserved Elements in the Human Genome". Science 304:1321-1325, May 2004. Discussed in "'Junk' DNA reveals vital role", Nature (2004).

2. ↑ Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J. A genomic code for nucleosome positioning. Nature. 2006 Aug 17;442(7104):772-8. Epub 2006 Jul 19.
3. ↑ "Short blocks from the non-coding parts of the human genome have instances within nearly all known genes and relate to biological processes" by Isidore Rigoutsos, Tien Huynh, Kevin Miranda, Aristotelis Tsirigos, Alice McHardy and Daniel Platt (T. J. Watson Research Center, IBM, Yorktown Heights, NY), April 24, 2006, 10.1073/pnas.0601688103
4. ↑ Template:Cite journal
5. ↑ Template:Cite journal

See also...

• DNA compaction
• Junk DNA
• Fractnons
• FractoGene
• Fractal Genomics
• Information Theory
• Information hierarchy
• Nucleosome code
• Pyknons

External Links

• Pyknon
• JunkDNA
• GeneSys Project
• Fractal & Non-fractal genomic analysis