Second, separate language found in DNA code

_{Denyse O'Leary

December 13, 2013

Genetics, News}

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Yikes, even the Dead Tree News Wire (UPI) has now noticed:

SCIENTISTS FIND SECOND, ‘HIDDEN’ LANGUAGE IN HUMAN GENETIC CODE

UPI 12/12/2013 11:12:42 PM

SEATTLE, Dec. 12 (UPI) — U.S. geneticists say a second code hiding within DNA changes how scientists read its instructions and interpret mutations to make sense of health and disease.

Since the genetic code was deciphered in the 1960s, scientists have assumed it was used exclusively to write information about proteins, but University of Washington scientists say they’ve discovered genomes use the genetic code to write two separate “languages.”

One, long understood, describes how proteins are made, while the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long, a university release said Thursday.

So we are now expected to believe that not only can a language get started by natural selection acting on purely random mutation, with no intelligence, but that a second language (somewhat like a hidden code) inside the first language can also get started the same way with no intelligence. All purely by chance.

Commenters at one news site:

why oh why do people still think there is no intelligent design behind things is beyond me…

Because, you know, languages just ‘appear’ via evolution.

Then Darwin’s mob arrives and drags the discussion south, demanding that we “define” “language.”

Comments

Who said anything about blind and undirected forces? Is there a third or fourth? The theory of evolution not being able to explain something only means more research needs to be done.AVS_{December 14, 2013
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Now in your post above, can you give me an example of one of the meta-meta-codes within a cell?
I don't have to identify anything. I merely extrapolated from the hypothesis that the genome is organized hierarchically. If there are multiple levels in the hierarchy, it follows that there must be multiple meta codes. It's not rocket science; it's simple. So go find them yourself, you lazy asteroid. A Nobel Prize is waiting for the discoverer of the meta-meta-code, I'm sure. I never claimed to be a biologist.Mapou_{December 14, 2013
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AVS: There’s the protein coding sequence of DNA and there’s a regulation code that controls gene expression.
Obviously, you believe that those two codes can be explained by blind and undirected forces. But how about 3 codes? Or 4? At what number do you say: 'this cannot be explained by naturalism'?Box_{December 14, 2013
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Here we go scordova, citing the same "12 codes" guy again. Where on earth did you get that number from? This guy is just taking the different characteristics of the genome and calling them a "code." Just like in your other half-assed example where alternative splicing is an example of a code somehow...no it's not. There's the protein coding sequence of DNA and there's a regulation code that controls gene expression.AVS_{December 14, 2013
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Good for you Mr. poo. Now in your post above, can you give me an example of one of the meta-meta-codes within a cell?AVS_{December 14, 2013
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AVS, Thorton is a freaking moron. Maybe you are Thorton in disguise, eh? I love cheetos and beer. I also love weed and wine. :-DMapou_{December 14, 2013
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On the subject of the number of genetic codes, it's obvious that every level of the genomic hierarchy will have a different type of code. At the bottom you'll find the protein-coding sequences and above that you find a layer of regulatory sequences which are themselves regulated by the layer above them. It's all about codes and meta-codes and meta-meta-codes, etc.Mapou_{December 14, 2013
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So you're the computer simulation guy that does what the biologists tell him to do? Right. You must be really good at arguing the whale/bat echolocation issue since you've been doing it (and losing )for years now Louis SavainMay 8, 2012 at 10:33 PM I predict that huge complex sequences of DNA responsible for echolocation will be found to be identical in both bats and echolocating whales. This will bring an end to the theory of evolution because common descent, the main prediction of the TOE, will have been falsified. When that happens, and it will, ID will be triumphant. Darwin will spin like a top in his grave and evolutionists everywhere will cower in shame. Reply Replies ThortonMay 9, 2012 at 5:19 PM Louis Savain I predict that huge complex sequences of DNA responsible for echolocation will be found to be identical in both bats and echolocating whales. That's already been falsified, as the means for generating the transmitted signals are completely different in bats and whales. We covered this exact topic a few months ago, remember? Louis SavainMay 9, 2012 at 8:30 PM Thorton: That's already been falsified, as the means for generating the transmitted signals are completely different in bats and whales. So what? That's still a tiny fraction of echolocation. There is a hugely sophisticated program used to precisely time the outgoing signals and interpret the bounced signals so as to create a 3-D representation of the detected objects. Get a clue. ThortonMay 9, 2012 at 8:54 PM Louis Savain Thorton: That's already been falsified, as the means for generating the transmitted signals are completely different in bats and whales. So what? That's still a tiny fraction of echolocation. Having ay least 50% of the process be entirely different isn't a "tiny fraction". What happened to "Designers don't reinvent the wheel"? There is a hugely sophisticated program used to precisely time the outgoing signals and interpret the bounced signals so as to create a 3-D representation of the detected objects. Get a clue. So? All mammalian brains have the capability to locate objects from echoes to a degree, even humans. Ever walk across a darkened gymnasium with a hardwood floor while wearing hard soled shoes? You can tell when you're getting near the wall by the relative strength and timing of the echoes. Since you have two ears you can also determine the direction of objects by sounds, just like binocular vision gives you depth perception. Bats and whales have just highly refined the inherent signal processing available to all mammals. Can you at least change your go to "cheetos and beer" quote, it's getting old.AVS_{December 14, 2013
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AVS said: Your are bullshitting like always. There are two codes within DNA sequences, the code for protein and the code for regulation of gene expression. That is it. Scientists says:
Ann N Y Acad Sci. 2012 Sep;1267:35-8. doi: 10.1111/j.1749-6632.2012.06589.x. Multiple levels of meaning in DNA sequences, and one more. Trifonov EN, Volkovich Z, Frenkel ZM. Source Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel. trifonov@research.haifa.ac.il Abstract If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code.
and http://www.technologyreview.com/view/426330/biophysicists-discover-four-new-rules-of-dna-grammar/
For 60 years, biologists have known of only two grammar-like rules that govern the language of DNA. Now they’ve found four more ... But in the 60 years since Chargaff discovered his invariant patterns, no others have emerged. Until now. Today, Michel Yamagishi at the Applied Bioinformatics Laboratory in Brazil and Roberto Herai at Unicamp in Sao Paulo, say they’ve discovered several new patterns that significantly broaden the grammar of DNA. Their approach is straightforward. These guys use set theory to show that Chargaff’s existing rules imply the existence of other, higher order patterns. Here’s how. One way to think about the patterns in DNA is to divide up a DNA sequence into words of specific length, k. Chargaff’s rules apply to words where k=1, in other words, to single nucleotides. But what of words with k=2 (eg AA, AC, AG, AT and so on) or k=3 (AAA, AAG, AAC, AAT and so on)? Biochemists call these words oligonucleotides. Set theory implies that the entire sets of these k-words must also obey certain fractal-like patterns. Yamagishi and Herai distil them into four equations. Of course, it’s only possible to see these patterns in huge DNA datasets. Sure enough, Yamagishi and Herai have number-crunched the DNA sequences of 32 species looking for these new fractal patterns. And they’ve found them. They say the patterns show up with great precision in 30 of these species, including humans, e coli and the plant arabidopsis. Only human immunodeficiency virus (HIV) and Xylella fastidiosa 9a5c, a bug that attacks peaches, do not conform. “These new rules show for the first time that oligonucleotide frequencies do have invariant properties across a large set of genomes,” they say. That could turn out to be extremely useful for assessing the performance of new technologies for sequencing entire genomes at high speed. One problem with these techniques is knowing how accurately they work. Yamagishi and Herai suggest that a simple test would be to check whether the newly sequenced genomes contain these invariant patterns. If not, then that’s a sign the technology may be introducing some kind of bias. This is a bit like a checksum test for spotting accidental errors in blocks of data and a neat piece of science to boot.
A grammar rule is an encoding rule, and that counts as code.
scordova_{December 14, 2013
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Querius, LOL. I have no credentials. I am a crackpot and a lunatic. That's what's going to make it all the more enjoyable.Mapou_{December 14, 2013
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C'mon, AVS. You're not going to let Mapou score are you? Maybe you could challenge Mapou on his credentials. Better yet, call him names. Do something! ;-) Got room on your couch, Mapou? I'll bring extra beer. And chips. -QQuerius_{December 14, 2013
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Don't thank me. You'll be shaking in your boots, alright. Computational genetics has already shown the lie of common descent: multiple identical and highly complex genetic sequences have been found to have "evolved" independently in two species (echolocating bats and whales), millions of years after they hopped onto different branches of the tree of life. Imagine that, hundreds of identical code sequences miraculously evolved twice via random mutations and natural selection. Darwinian magic is powerful indeed. Not. More surprises are in the works. And yes, I do have an excellent familiarity with computational neuroscience and AI. I write pulsed neural network computer simulations in my research. This is why I have such a high confidence about it and why I can predict that upcoming new developments in the field will astound many.Mapou_{December 14, 2013
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Thanks for the warning Mapou, I'm really shaking in my boots here. I'm sure you are extremely familiar with all the fields of computational genetics, physics and computational neuroscience/AI, as well as evolutionary biology...not.AVS_{December 14, 2013
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Ah yes you both say there's "about 12." And yet the best evidence you can provide is a webpage from the panda's thumb which gives a brief overview of alternative splicing...and that's it. The paper BA cited gives three types of "codes" one of them having to do with more than just the DNA sequence, and the other having to do with RNA (which is not DNA last I checked. Your are bullshitting like always. There are two codes within DNA sequences, the code for protein and the code for regulation of gene expression. That is it.AVS_{December 14, 2013
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AVS @30, LOL. Don't say I did not warn you but soon, new developments in computational genetics, physics and computational neuroscience/AI will send panic in the ranks of the Darwinists. There shall be much weeping and gnashing of teeth. I'll be watching the whole thing unfold with a grin on my face, a bag of cheetos in one hand and a beer in the other. :-DMapou_{December 14, 2013
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How bout those 12 languages of DNA, scordova?
For starters in 2007: http://www.pandasthumb.org/archives/2007/10/konstantin-b-ze.html and then as BA77 noted:
Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. http://link.springer.com/artic.....0081#close
Whether you agree or not AVS is up to you, but don't say it wasn't advocated by someone in peer reviewed literature.scordova_{December 14, 2013
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Of course you think it's a perfectly sensible argument. "I'm too stupid to understand its so why bother trying...god did it...and the peasants rejoiced...yayyyy...." You wouldn't know a sensible argument if it slapped you across the face.AVS_{December 14, 2013
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Oh yes! They used the word "design," therefore they must be talking about god's intelligent design of life! The stupidity on here knows no bounds.AVS_{December 14, 2013
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AVS:
Oh yeah, that guy is good… “cells are complex, therefore god made them.”
As much as you want to make it appear otherwise, I think it is a perfectly sensible and powerful argument. Darwinists hate it and jump up every time it is used because it has the same effect on them as holy water on a vampire. It hits them where it hurts. LOL.Mapou_{December 14, 2013
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Dr. Robert Carter apparently. He's a funny guy.AVS_{December 14, 2013
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Boragain77, http://www.ncbi.nlm.nih.gov/pubmed/20439753 I like the pubmed link because it corroborates what I've been saying about the hierarchical organization of the genome. Here's the abstract (emphasis added):
Abstract The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers' continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.
Isn't it funny how the authors see no contradiction in using "evolution via random mutations and selection" and "design principles" in the same abstract? It boggles the mind. But at least, they acknowledge that evolution via fine tuning can also be the result of intelligent design.Mapou_{December 14, 2013
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Oh yeah, that guy is good… “cells are complex, therefore god made them.” Nice
To whom are you referring?TSErik_{December 14, 2013
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Oh yeah, that guy is good... "cells are complex, therefore god made them." NiceAVS_{December 14, 2013
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What Is The Genome? It’s Certainly Not Junk! – Dr. Robert Carter – video – (Notes in video description) http://www.metacafe.com/w/8905583 Comparing genomes to computer operating systems – Van – May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753bornagain77_{December 14, 2013
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boarnagain77 @21, Most of the quotes and references you provided above are really evidence that the genome is organized hierarchically like a tree. The genome is really an extreme form of data compression, not unlike what would result from a computer compression algorithm. Low level sequences are simply reused over and over by high level control codes. For example, after compressing a string of text, a single substring such as "the", "about" or "and" needs to appear only once in the genome. With the use of single pointers, a code can be reused in many different high level phrases and sentences without having to be repeated in every sentence. Needless to say, a mutation occurring high in the hierarchy can result in catastrophic consequences. As an aside, I believe this is the real tree of life that is metaphorically referred to in the book of Genesis. A thorough understanding of the tree of life will reveal the secret of physical immortality. After all, it's just a code. Humans are once more on the verge of eating the fruit of the forbidden tree of life. Brave new world.Mapou_{December 14, 2013
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@ post 4
Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. http://link.springer.com/article/10.1007%2FBF02460081#close 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. Apart from the classical RNA-protein translation code, the genomic DNA sequences carry many other, nontriplet codes of different nature. Those of them which are at least partly deciphered are discussed in this review in the order of their estimated occupancy in the eukaryotic genome. Each of the codes is degenerate, like the triplet code. This is the basis for their coexistence in one and the same sequence, so that the same base often (if not always) belongs to several different overlapping sequence patterns. The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages. Codes of biosequences - E. N. Trifonov - 2007 http://is.muni.cz/el/1431/jaro2007/Bi_IB8/Codes_of_biosequences.pdf Multiple levels of meaning in DNA sequences, and one more. Trifonov EN, Volkovich Z, Frenkel ZM. - 2012 Abstract: If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code. Nucleosomes preferentially are located at the ends of exons, thus protecting splice junctions, with the N9 positions of guanines of the GT and AG junctions oriented toward the histones. Analysis of protein-coding sequences reveals numerous traces of tandem repeats, apparently formed by triplet expansion, which in effect is a genome inflation ``code''. Our data are consistent with the hypothesis that expansion of simple tandem repetition of certain aggressive triplets has been a characteristic of life from its emergence. Such expanding triplets appear to be the major factor underlying observed codon usage biases. http://www.ncbi.nlm.nih.gov/pubmed/22954214 DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011 Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code, http://www.sciencedaily.com/releases/2011/01/110128104244.htm Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011 Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer." per ENV The genetic code is nearly optimal for allowing additional information within protein-coding sequences Shalev Itzkovitz and Uri Alon Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. http://genome.cshlp.org/content/17/4/405.full DNA as Poetry: Multiple Messages in a Single Sequence - James Shapiro - 2012 Excerpt: Another question is harder to answer: How do multiple messages come to be inscribed in a single sequence in the course of evolution? This is an evolutionary mystery, especially when the second message has a complex structure. My own particular intellectual headache comes from structures called "shufflons" found in some bacteria that use them to diversify extracellular protein structures. Variability in surface proteins is advantageous in extending the range of specific cell-cell attachments for transfer of DNA and other macromolecules. In a shufflon, the coding sequence contains two or more copies of the intricate signals required for a DNA rearrangement process known as "site-specific recombination." When a coding region carrying two or more recombination sites undergoes an inversion, the protein sequence changes because there is now a new string of triplet codons between the recombining sites. Some shufflons have up to seven different recombination sites embedded in the coding sequence. These structures are theoretically capable of generating over 100 different protein-coding DNA sequences (33 of which have actually been isolated from one shufflon). Such remarkable protein diversifying systems in bacterial genomes pose a mystery. How do the recombination sites evolve within sequences encoding functional proteins? It does not make sense to argue that each one evolved by selection operating a few nucleotides at a time; there is no benefit until at least two complete recombination signals are present. Moreover, known mechanisms for duplicating and inserting copies of a complex DNA signal at multiple locations generally disrupt coding capacity. Further, as in mammalian dual-coding regions, we do not understand how both strands evolve simultaneously to encode functional protein segments. At a time when we pride ourselves for being able to read DNA sequences with increasing speed, it is salutary to keep in mind that we are still far from knowing how to interpret the complex overlapping meanings contained in the genomic texts we store in our databases. DNA, like poetry, often has to be read in several ways. http://www.huffingtonpost.com/james-a-shapiro/dna-as-poetry-multiple-me_b_1229190.html "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010
Besides multiple layers of 'classical information' embedded in overlapping layers throughout the DNA, as astonishing as that is, there has now been discovered another layer of 'quantum information' embedded throughout the DNA "holding the DNA together":
Quantum Information In DNA - short video http://www.metacafe.com/watch/5936605/
Of related note:
DNA: The Ultimate Hard Drive - Science Magazine, August-16-2012 Excerpt: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare." http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. per Science Daily
bornagain77_{December 14, 2013
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How bout those 12 languages of DNA, scordova?AVS_{December 14, 2013
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Wow, 12 languages for DNA? What are they? I've never heard of stuff like that.AVS_{December 14, 2013
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The fact that UPI now apparently knows it makes it doubly known. I was just surprised to see something like that moving down a conventional news wire along with the news from Mandela’s funeral and the Christmas shopping frenzy. O’Leary for News
I suspect because elements of the media are beginning to become sympathetic to ID. That's not to say there will be wholescale turning, but like CNBC and FoxNews emerging, there will be dissension from the party line. But what is bad is there are already 12 or so known languages for DNA. This only 1 more. Why wasn't the media around to report on those other languages?scordova_{December 14, 2013
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Scientists go deeper into DNA (Video report) (Junk No More) - Sept. 2012 http://bcove.me/26vjjl5a Quote from preceding video: “It's just been an incredible surprise for me. You say, ‘I bet it's going to be complicated', and then you are faced with it and you are like 'My God, that is mind blowing.'” Ewan Birney - senior scientist - ENCODEbornagain77_{December 14, 2013
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