User:Helyxzion

HELYXZION THE LANGUAGE OF DNA HELYXZIONS "ANVIL" (ADVANCED NUCLEOTIDE VISUAL INTERPRETIVE LANGUAGE)

http://www.helyxzion.com http://www.helyxzion.org 

hidden language of DNA Comparison between the statistical properties of coding and non-coding DNA sequences has been interpreted as indicating a yet-undiscovered language in non-coding DNA.

This statement is decades old, there is a language in DNA and not just in non-coding regions of DNA. THERE IS NO SUCH THING AS “JUNK OR NON-CODING DNA”. the code The code, the text and the language of DNA Communication between scientists about their work is filled with images. This is inevitable when it comes to explaining complex ideas and concepts that are not directly observable, such as the subatomic particles that comprise a proton or an electron, or the processes inside a cell that lead to the correct formation of a protein. When new discoveries are made, the words to describe them are usually lacking and must be borrowed from the physical world or common speech: lipid rafts, chaperones, molecular markers. When scientists try to explain their findings to the public, or when the media try to make science more palatable to their readers or viewers, these metaphors become even more colorful: cells are factories, proteins carry zip codes, mitochondria are the power-house of the cell, and cells of the immune system go to school.

Explaining complex concepts is a creative process and it reveals how scientists think and how ideas about a world too small to grasp are represented in their mind. They accentuate certain aspects of the subject or process they are depicting, while neglecting others. Some-times they even awake associations not intended. When molecules suddenly acquire a personality of their own or are endowed with human goal-directed behavior—take, for example, a molecule that 'finds' a partner or a cell that takes a developmental 'decision', such as committing 'cell suicide'. Using molecular genetics as an example, I will try to follow some of biology's metaphors from their origin in scientific communication into the real world and analyze their impact on the public perception of science.Common language talks about DNA as 'information' or 'a code'. For a very long time, scientists suspected that something—some kind of plan, specificity or driving force—resided within the sperm and/or egg, such that a snake developed from a snake egg and humans created human offspring. But it was only in the late 1940s and 1950s, when cyberneticists, physicists and mathematicians entered the field of molecular biology, that scientists came to interpret this 'something' as information.

The complete pattern of the future development of an organism and its function when mature, is contained in the chromosomes in the form of a 'code'. The later discovery of the structure of DNA by Francis Crick and James Watson was a mile stone to the understanding of DNA as a code of some kind that allowed molecules in cells to carry information," in a paper on the implications of their DNA structure, they wrote that "it therefore seems likely that the precise sequence of the bases is the code that carries the genetic information." From today's perspective it seems rather inevitable that, when people started to think about the molecular basis of inheritance.

Today, it is hard for a geneticist to picture DNA as anything other than a code that transmits information.When H. Gobind Khorana, Marshall W. Nirenberg and other scientists revealed the trinucleotide code and the correlation between nucleic acids and proteins, this was referred to as 'decoding' or 'deciphering' the code. These metaphors have gained momentum and are now routinely used to describe the sequencing of the human genome. For the scientists involved, these references are clear by context—whether the issue is the DNA sequence itself or the relationship between DNA and protein. But news headlines such as "Decoding the book of life", "Cracking the code of life" or "Breaking the code of life", when referring to the sequencing of the human genome, imply that the decoded text can be read like a novel. In fact HELYXZIONS "ANVIL" (ADVANCED NUCLEOTIDE VISUAL INTERPRETIVE LANGUAGE) DOES JUST THAT!

No scientist would dispute that this is NOW the current state of the art. Understanding the message hidden in the 3 billion base pairs of the human genome would require a detailed translation of its sequence into physiological function. DNA itself is a "text with context", genes by themselves barely do anything. Genes just describe how to make proteins, or cease to make them, or regulate their production as directed by other proteins. Not even the basics of protein function at the level of protein folding can be deduced from the genes. It is in the introns that the real information of how intricate protein networks work, that constantly survey the environment outside the cell, monitor metabolic processes and integrate this information into physical function. Deciphering the text as laid down in the genome therefore predict how life works at the cellular and organism level.

Understanding the genome as a coded message, interpreting it as a text, book or language is not so far-fetched. These metaphors convey an important scientific principle: a sequence of a limited assortment of building blocks, like letters in a text, can carry a message. In his book The Language of Life, George Beadle wrote: "... the deciphering of the DNA code has revealed a language... as old as life itself, a language that is the most living language of all". More recently, when scientists celebrated the completion of the first draft of the human genome in 2000, the 'book' and 'language' metaphors were revived—not just reinvented by the press in the service of the public understanding of science, but used by high-ranking scientists involved in the genome project to describe their achievement.

On 26 June 2000, when Francis Collins, Director of the National Human Genome Research Institute, announced the completion of the first draft in a major media event at the White House, he said "Today, we celebrate the revelation of the first draft of the human book of life" and declared that this breakthrough lets humans for the first time read "our own instruction book." Today, Helyxzion is learning and reading the language DNA. We are also profoundly humbled by the privilege of turning the pages that describe the miracle of human life, written in the mysterious language of all the ages, the language of DNA.The real implications of "reading" the human genome sequence is just now being realized.

This could very well be the turning point in human evolution from a scientific point of view, it could change the role of science, because it introduces human will and intentions into the scientific exercise, after centuries of attempting to free science and research from the limits imposed by religious leaders. In the best case, it provokes sarcasm: In the worst case, it provokes public fear—the idea of the scientists 'playing God' is not too unbelievable. And the public does listen to what the scientists are saying—indeed, public attention to the genome project was unrivalled. In 2000, The New York Times alone published 108 articles related to the Human Genome Project. Was it this outburst in media attention that turned scientists into PR spokesmen and encouraged them to blow their speech out of proportion?

Thinking of genes as 'controlling' or 'programming' development dictates a certain view of these processes. "The Helyxzion "ANVIL" describe for us the exact content and structure, not only of each and every gene associated with a species, but also the intron information, that controls a particular gene. With the Helyxzion technology any one with a background knowledge of molecular biology will be able to grasp the sense of sequences easily.

Thinking of DNA as a language, information (encompassing both content and structure), a code a text and a chemical structure, all at the same time. The lay reader is overwhelmed with an impression of impact, meaning, prominence, significance and seriousness, but deprived of any means to understand what exactly has been said. Helyxzion allows practitioners to explain their work in simple and easily understandable terms.Moreover, Helyxzion eliminates confusion and misconceptions in Genetics. The potential of genetics is achieved by emphasizing the power of the language and also that of the scientist analyzing it. "Reading, from cover to cover, the first draft of this 'Book of Life'", is exactly what scientists are now capable of doing. Rather, then trying to infer some meaning from small individual chunks of text.

The powerful idea that the essence of life is a DNA sequence that scientists are about to read "from cover to cover", means that DNA can be analyzed and manipulated by the scientists, who are therefore taking part in human evolution. Use of this technology in various prenatal genetic diagnosis, gene patenting, the use of genomic markers to predict predisposition to disease, and the use of DNA to identify individuals. Scientists should not indiscriminately use this technology in an exaggerated way. As our parents used to tell us when we were children: "Watch your language!"

We argue that greater variance among nucleotide frequencies in ALL regions explains this assertion. DNA sequences are long strings composed of codons (four nucleotides A, C, G, and T). For a statistical analysis, these strings make “words” of fixed length n. Then the word frequencies, of non-Protein coding DNA was shown to be non-zero (as in natural languages) and significantly larger than that of protein coding DNA. however, this simply reflects that nucleotide frequencies are more unequal in non-protein coding than in protein coding DNA; R 1 increases as the variance of the p distribution increases.

The increase in R n as n increases is the same for all DNA and thus does not distinguish between them. Further more, it can be shown that correlations of finite range simply an increasing R n even for n. Which in short argue that a language simply must arise or DNA could not unfailingly impart any use information either from cell to cell or across generations of organisms? According to their frequencies, p, from most to least frequent, visible by a linear region in a double-logarithmic plot. The slope for non-protein coding DNA was found to be larger than that for protein coding DNA, and close to that of English text, as analyzed the Helyxzion “ANVIL” method and fixed word length was taken as further evidence that “all” regions are similar to natural languages.

Helyxzion ANVIL analysis shows that intron coding regions are not random strings of nucleotides, independently drawn according to the observed nucleotide frequencies. For equal frequencies, all n-codons have equal probability 4 2n. However, as the nucleotide frequencies become more uneven, increasingly distinct DNA appears for finite sequence length a random sequence of identical length and nucleotide frequencies. Considering the crudeness of the approximation, these curves are strikingly similar. Secondly, the most probable “DNA words” are not very different from those of natural languages. Like English, where the most common words are “the,” “of,” “and,” etc., in the present DNA example they are combinations of only the most probable letters—TTTTTT, AAAAAA, TTTTTA, etc. That these words occur more often than expected for uncorrelated random sequences, Can be readily explained by unequal crossing over, which preferentially occurs in regions of short repeats.

Thirdly, the linguistic approach has not been doubted for a long time: Even randomly generated “Text” (with words of different length) exhibits language behavior with an exponent close to that of natural Languages. We have thus shown all of the observations are simple consequences of nucleotide frequencies. Our explanation of the existence of a language in DNA would not be complete with out knowing that it is not base on guess work but well founded in the underlying “MATHMATICS DICOVERED IN DNA”.Helyxzion: The Language of DNA Helyxzion is the newest tool for personal identification. This technology will take all the mystery out of identification. Helyxzion DNA analysis, will convert the human genome into a digitally accrete picture of the person right down to their finger prints, making identification 100% correct. Biochemistry and molecular biology, has, from its origins, found itself in an unlikely arena, a court of law.

There is no question that the fundamental issues are complicated, but it is possible to present the bottom line conclusion in such a way that a Ph.D. is not necessary to understand its implications. The two most misunderstood buzzwords, which are apparently discussed at dinner tables and cocktail parties 'round the world, are statistics and the C-word, contamination. (I have had people come up to me on mountain tops and ask me to tell them about contamination!). By the end of this piece, you should at least be able to make better cocktail-party conversation.A Word about Terminology: Fingerprints Come From FingersUnreasonable expectations, as well as undeserved criticisms, have been visited upon the entire DNA identification technology of because of the unfortunate terminology, DNA fingerprinting, applied to the original typing method. In its current state, DNA typing is not directly comparable to fingerprints from fingers (dermatoglyphic fingerprints).

In dermatoglyphic fingerprints, it is possible to obtain all of the ridge detail information from all 10 finger pads; thus there are no missing pieces of information. Because only a small portion, perhaps 1 millionth, of the 3 billion units of human DNA are even available for examination by current methods, the result is better compared to a partial fingerprint. Similar to a partial print, however, it may not be necessary to have complete DNA information to be convinced of the individuality of a DNA profile.

Just as a certain number of points of comparison have been deemed necessary in order to declare that two fingerprints originated from the same finger, it has been suggested that a defined number of highly polymorphic (variable) DNA loci (chromosomal locations) may be sufficient in order to be convinced that two samples have originated from the same source. One more piece of not-so-trivial information: although identical twins have different fingerprints, in the absence of genetic mutation, the DNA profiles of identical twins are, in fact, identical. More about the DNA of related individuals later.Another Word about Terminology - Burn the "Match"Another word that should be banned from the language of DNA typing is the word match. Along with DNA fingerprinting, it misleads the hapless uninitiated into believing that any test called DNA will unequivocally associate a questioned sample with an exemplar.

Until all 3 billion of those genetic units can be easily and reliably analyzed, more appropriate expressions might be the same pattern as, concordant with or indistinguishable from, depending on the strength of the association. The fact that the English language does not provide an easy descriptor of statistical relationships should not detract from the potential power of DNA typing. When many highly variable DNA regions are analyzed, and even the most conservative statistical estimates indicate that not one other person with the same profile exists in the population of the Earth, indistinguishable from becomes one strong statement.The C word: Contamination Much of the opposition to the reliability of DNA evidence always seems to return to the now infamous catch-all term contamination.

Other than its negative connotation, what does it really mean? Does it only refer to inadvertently introduced material or might it also be applied to a legitimately mixed sample (e.g. blood from two victims). In fact there are a plethora of different types of contamination, and the final, if any, effect on evidence varies. Among the considerations in determining whether a second DNA type would even be detected is the type of testing involved. For instance, PCR-type testing, where the DNA in the sample is copied millions of times over, is inherently a more sensitive technique than RFLP, which also makes a PCR test more likely to detect traces of a second type, whatever the source. In addition, point of view comes into play - one person's contamination is another's mixed sample; it all depends on what you were expecting and for whom you are advocating.

Assuming that the criminalist collecting evidence at the scene isn't bleeding from an open wound, the greatest concern at the crime scene itself is from bacterial, not human, contamination. Crime scene samples, by definition, are in a fertile environment, and fluids like blood and semen provide a very acceptable growth medium for microorganisms.

The DNA of the microorganisms themselves is really not a problem - it won't show up in tests that are specific for human DNA. The major concern is degradation of the human DNA in the sample that the bugs are literally using as food. Even so, the DNA type will simply go away, as opposed to being magically converted into someone else's type. Partially degraded DNA must be interpreted carefully by a qualified analyst; if the sample is known to be of poor quality and there is a possibility that part of a pattern has been obscured, a conclusion of "inconclusive" may be the safest bet.Although great care should be taken as a matter of routine, it is really not that easy to interject extraneous human material into a sample.

Contrary to what some might have us believe, DNA does not float around randomly in the air, and cells that may be sloughed off or ejected out of a person are relatively few in number and may not contain any consequential DNA. This is not to suggest that precautions not be taken, but to put the matter in some perspective.Once the sample is dried, refrigerated and in the laboratory, the potential for contamination is mostly from other samples undergoing processing at the same time. This is where the training, qualifications of the analyst and quality control of the laboratory come into play. Safeguards are set up not only to guard against contamination from other lab samples, but just as importantly, to detect contaminated samples, should they occur.

By the way, the criminalist should remember to wear gloves and not spit in his samples.The biggest real concern that would actually result in an incorrect DNA type, as opposed to NO type, is a sample switch by the analyst. Until computers can process crime scenes, fully analyze samples and take the witness stand, education, and training and good laboratory practice are the best weapons against sample mix-ups.My Brother did it In some DNA typing techniques (not all) a statistical probability is used to estimate the rareness of any particular type - in other words, the possibility that two samples originating from different sources might show the same pattern by chance alone. This type of calculation is valid only with respect to random individuals in a population; it is not applicable to closely related individuals.

No two people share the same DNA type except for identical twins. However siblings potentially share more genetic material with each other than anyone else. This is because they inherit their genes from the same two people, Mom and Dad. This idea can be extended to more distant relationships such as children, grandchildren and cousins. In these relationships, some genetic material is shared, but the more distant the relationship, the fewer genes in common. For the highly variable DNA loci that are used in forensic testing, this means that even siblings are unlikely to test the same, especially when many highly variable markers are analyzed.

However, until alibis are established all around, your best DNA defense is still "my brother did it..."DNA in the Judicial SystemThe statistical interpretation of DNA typing results, specifically in the context of population genetics, has been the least understood (therefore by definition the most hotly debated) issue of recent admissibility hearings. The perceived incomprehensibility of the subject, fueled by the views of, what some feel, have been only a few outspoken individuals, has led to a recalcitrance of the judicial system to accept DNA typing. California, in particular, has become both a hotbed and testing ground for DNA admissibility issues. With some half-dozen conflicting appellate opinions, the California Supreme Court has recently moved to review three recent decisions, and come to a consensus as to whether DNA testing is generally accepted in the relevant community, and may be routinely admitted in criminal trials.