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

Man, use some of those neurons between your ears, will you?Weren't we talking about the organization of the genome? I meant there is no need to repeat A, B, C and D in a bunch of places within the genome. Once is enough, although twice might be a good idea for the purpose of redundancy and fault correction. PS. I'm getting tired of this discussion. I've said what I needed to say. I'm highly confident in the correctness of my prediction. Hopefully, UD will keep this thread in the archives for future reference. See ya.Mapou_{December 14, 2013
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Oh of course, you don't need any knowledge about cellular biology to make predictions about future discoveries in cellular biology. Makes perfect sense. That's really all I needed to hear from you. AS for your example, your lack of knowledge in the field of biology makes you a little hard to follow. Why is a "liver protein" being expressed in "many places?" There is no need to repeat A,B, and C everywhere? But that's exactly what happens. All the cells in your body have the same genome. Non-liver cells contain liver genes and they must be repressed. I think you should try a simpler example, and try using biology lingo correctly if you want to make sense.AVS_{December 14, 2013
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No one needs to know anything about sub-cellular biology to predict that the genome is organized using a deep hierarchy. A hierarchy is always a logical consequence of intelligent design principles applied to the management and control of huge amounts of complex data and code. Like I said, it's Intelligent Design 101. A simple example could be the code for a complex liver protein that is expressed in many places. There is no need to repeat the code everywhere. One only needs needs a high level code to control the expression of the liver protein in many places. But let's say this particular liver protein consists of proteins A, B and C. Again, there is no need to repeat A, B, C and D everywhere. A single code can represent all four. So, in another sense, the hierarchy is also a representational mechanism that eliminates unneeded duplications. You can use it to represent all sorts of protein combinations. It's not rocket science. It's common sense design. It is commonly used in engineering and data/code management/compression. I posit it as a hypothesis for genomic code management. Of course, when it is found, Darwinists will waste no time in claiming that it was invented by natural selection and random mutations. But it's still intelligent design though. :)Mapou_{December 14, 2013
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Do you have any evidence that suggests a "deep hierarchy?" Can you name any biological function that does not fit into the two levels that I mentioned? Do you know anything about sub-cellular biology? This is why I do not bother with scientific arguments on here.AVS_{December 14, 2013
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Did I mention that a Nobel Prize awaits the first biologist or geneticist who discovers this hierarchy? Did I mention also that it is based on well-known intelligent design principles? I guess I did, eh? Sorry, but it bears repeating.Mapou_{December 14, 2013
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OK. And in the DNA sequence there is two codes. One is the code for protein, the other is the code for the regulation of expression. They are both controlled by protein interactions from the first level. It’s not much of a hierarchy…
Of course, it's not. Otherwise I would not venture a hypothesis. The genetic story is unfolding and still has a long ways to go. I predict a deep hierarchy will be found in the genomes of most complex animals.Mapou_{December 14, 2013
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As much as I'd like run experimental trials on you BA, I'm sure you and your mommy would not approve.AVS_{December 14, 2013
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OK. And in the DNA sequence there is two codes. One is the code for protein, the other is the code for the regulation of expression. They are both controlled by protein interactions from the first level. It's not much of a hierarchy...AVS_{December 14, 2013
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Animal Testing Is Bad Science: Point/Counterpoint Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,, The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,, Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses. http://www.peta.org/issues/animals-used-for-experimentation/animal-testing-bad-science.aspx The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/ In fact, as to the somewhat minor extent evolutionary reasoning has influenced medical diagnostics, it has led to much ‘medical malpractice’ in the past: Evolution's "vestigial organ" argument debunked Excerpt: "The appendix, like the once 'vestigial' tonsils and adenoids, is a lymphoid organ (part of the body's immune system) which makes antibodies against infections in the digestive system. Believing it to be a useless evolutionary 'left over,' many surgeons once removed even the healthy appendix whenever they were in the abdominal cavity. Today, removal of a healthy appendix under most circumstances would be considered medical malpractice" (David Menton, Ph.D., "The Human Tail, and Other Tales of Evolution," St. Louis MetroVoice , January 1994, Vol. 4, No. 1). "Doctors once thought tonsils were simply useless evolutionary leftovers and took them out thinking that it could do no harm. Today there is considerable evidence that there are more troubles in the upper respiratory tract after tonsil removal than before, and doctors generally agree that simple enlargement of tonsils is hardly an indication for surgery" (J.D. Ratcliff, Your Body and How it Works, 1975, p. 137). The tailbone, properly known as the coccyx, is another supposed example of a vestigial structure that has been found to have a valuable function—especially regarding the ability to sit comfortably. Many people who have had this bone removed have great difficulty sitting. http://www.ucg.org/science/god-science-and-bible-evolutions-vestigial-organ-argument-debunked/ Darwinian Medicine and Proximate and Evolutionary Explanations - Michael Egnor - neurosurgeon - June 2011 http://www.evolutionnews.org/2011/06/darwinian_medicine_and_proxima047701.html Intelligent Design and Medical Research - video http://www.metacafe.com/w/7906908bornagain77_{December 14, 2013
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AVS:
And what are the different levels of your hierarchy?
It's a control hierarchy, of course. One level has code sequences that control a number of other code sequences in the lower level. Hierarchical control has to do with the activation timing and the precise location of various proteins so as to form various cells and complex organs in the body. That is all I hypothesize. You need a hierarchy in order to promote as much reuse of low level codes as possible and avoid runaway and wasteful repetitions. It's Intelligent Design 101. Let me add that hierarchical structures are rampant in nature. Knowledge in the neo-cortex is also organized like a tree. In fact, I happen to know that there are two knowledge trees in each hemisphere, one for concurrent patterns and one for pattern sequences.Mapou_{December 14, 2013
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Ah yes BA, another individual with no clue what they are talking about. Everytime I come on here you paste the exact same articles into our responses. You are my favorite. I'll keep this simple. Do some research on yeast studies and tetrahymena and learn about the SWI/SNF complex and Histone acetylation and deacetylation. Now look at the same processes in humans, the similarities in protein functions and how much cancer research has benefited from the study of these processes in yeast. Now, why can we study these processes in yeast, and apply them to studies in higher eukaryotes and eventually to cancer therapy drugs? Because all higher eukaryotes have evolved from the same ancestor as yeast. We all share a large amount of the basic functions that are disregulated in cancer. The more you know.AVS_{December 14, 2013
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bornagain77, Thanks for the references---a breath of fresh air! The overlapping codes reduce the possibility of viable random changes in a genome by many orders of magnitude! Amazing! -QQuerius_{December 14, 2013
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In fact Darwinism has no mathematical demarcation criteria so as to separate it from being a pseudo-science: “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote as stated in 1973 LSE Scientific Method Lecture Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. … http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/ “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003) Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013 Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? https://uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/ Whereas nobody can seem to come up with a rigid demarcation criteria for Darwinism, Intelligent Design (ID) does not suffer from such a lack of mathematical rigor: Evolutionary Informatics Lab – Main Publications http://evoinfo.org/publications/ ,, the empirical falsification criteria of ID is much easier to understand than the math is, and is as such: "Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved." - Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design – video http://www.youtube.com/watch?v=N8jXXJN4o_A Well, do neo-Darwinists have evidence of even one molecular machine arising by Darwinian processes?,,, I have yet to see a single novel protein arise by neo-Darwinian processes much less a entire molecular machine! Without such a demonstration and still their dogmatic insistence that Darwinism is true, then as far as I can tell, the actual demarcation threshold for believing neo-Darwinism is true is this: Darwinism Not Proved Impossible Therefore Its True – video http://www.metacafe.com/watch/10285716/ How Darwinists React to Improbability Arguments – video http://www.youtube.com/watch?v=-9IgLueodZAbornagain77_{December 14, 2013
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And what are the different levels of your hierarchy?AVS_{December 14, 2013
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as to: "You trying to tell biology that it doesn’t need evolution is like a kangaroo rat telling water it doesn’t need to be wet." Materialists like to claim evolution is indispensable to experimental biology and led the way to many breakthroughs in medicine, Yet in a article entitled "Evolutionary theory contributes little to experimental biology", this expert author begs to differ. "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.,,, In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology." Philip S. Skell - (the late) Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences. http://www.discovery.org/a/2816 "Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case. It is difficult enough to study what is happening now. To figure out exactly what happened in evolution is even more difficult. Thus evolutionary achievements can be used as hints to suggest possible lines of research, but it is highly dangerous to trust them too much. It is all too easy to make mistaken inferences unless the process involved is already very well understood." Francis Crick - What Mad Pursuit (1988) At the 7:00 minute mark of this following video, Dr. Behe gives an example of how positive evidence is falsely attributed to evolution by using the word 'evolution' as a sort of coda in peer-reviewed literature: Michael Behe - Life Reeks Of Design - video http://www.metacafe.com/watch/5066181/ Podcasts and Article of Dr. Skell http://www.evolutionnews.org/2010/11/giving_thanks_for_dr_philip_sk040981.html Evolution (Not) Crucial in Antibiotics Breakthrough: How Science is Actually Done - Cornelius Hunter - Sept. 2012 http://darwins-god.blogspot.com/2012/09/evolution-not-crucial-in-antibiotics.html Evolution Rarely the Basis of Research: Nature's "Evolutionary Gems" Just Narrative Gloss - podcast http://intelligentdesign.podomatic.com/entry/2012-07-20T17_33_56-07_00 Where are the Scientific Breakthroughs Due to Evolution? - video http://www.youtube.com/watch?v=hSYoWHaBIwI Science Owes Nothing To Darwinian Evolution - Jonathan Wells - video http://www.metacafe.com/watch/4028096bornagain77_{December 14, 2013
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AVS, all I'm claiming (as a hypothesis) is that the genome is organized hierarchically. I'm not making up anything. If you come here with a smarter-than-thou, high-priestly, condescending attitude, you're going to get spit in your face. That is all.Mapou_{December 14, 2013
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Ah yes, conspiracy theory poo is at it again. One last time, you have no idea what you are talking about. You trying to tell biology that it doesn't need evolution is like a kangaroo rat telling water it doesn't need to be wet. You're a joke to anyone with a basic knowledge of biology.AVS_{December 14, 2013
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Yep. Predictable ad hominem attacks. I especially liked this hilarious statement:
The theory of evolution not being able to explain something only means more research needs to be done.
The statement can of course be applied equally to any theory. As in - The theory of Phrenology not being able to explain something only means more research needs to be done. - The theory of Racial Superiority not being able to explain something only means more research needs to be done. - The theory of Geocentricity not being able to explain something only means more research needs to be done. I'm sure I'll be the next recipient of gratuitous vituperation. Wait for it . . . LOL -QQuerius_{December 14, 2013
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Of Note SCordova, he states '13 codes' in the audio lecturebornagain77_{December 14, 2013
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here is a mp3 audio: One spectacular case of code crowding - Edward N. Trifonov - 2010 http://bio.natur.cuni.cz/~flegr/ctvrtky/audio/2010Z_01a_Trifonov.mp3 http://bio.natur.cuni.cz/~flegr/ctvrtky/audio/2010Z_01b_Trifonov.mp3bornagain77_{December 14, 2013
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Look Poo, you're not starting to make sense anymore. I said I don't have a full understanding, then you say I'm an ignoramus for not having a full understanding, and then you say nobody has a full understanding. I realize how much we know and how much I know. I can assure you it is more than how much you now on the topic. I also realize we don't understand a lot, but that doesn't mean you get to just make up whatever you want and assume it's true based on what we don't know. That may be how science is done on the ID side, but not over here.AVS_{December 14, 2013
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You moron, you think biology needs Darwinian evolution? There are probably hundreds of productive biologists out there who spit on Darwinism. They keep quiet about it because of the fascist atmosphere in the science. You asteroid orifices don't have a monopoly on science. You just think you do. It's a delusion of grandeur.Mapou_{December 14, 2013
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Multiple genetic codes Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code. Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins: in DNA sequences chromatin code (Trifonov 1980) is a set of rules responsible for positioning of the nucleosomes. in RNA sequences RNA-to-protein translation code (triplet code) Every triplet in the RNA sequence corresponds (is translated) to a specific amino acid. splicing code is a code responsible for RNA splicing; still poorly identified. framing code (Trifonov 1987) The consensus sequence of the mRNA is (GCU)n which is complementary to (xxC)n in the ribosomes. It maintains the correct reading frame during mRNA translation. translation pausing code (Makhoul & Trifonov 2002) Clusters of rare codons are placed in the distance of 150 bp from each other. The translation time of these codons is longer than of their synonymous counterparts which slows down the translation process and thus provides time for the fresh-synthesized segment of a protein to fold properly. in protein sequences protein folding code (Berezovsky, Grosberg & Trifonov 2000) Proteins are composed of modules. The newly synthesized protein is folded a module by module, not as a whole. fast adaptation codes (Trifonov 1989) are present in all three types of biological sequences. They are represented by tandem repeats (AB...MN)n. The number of repetitions (n) can change in the cell genome as a response to stress which may (or may not) help the cell to adapt to the environmental pressure. codes of evolutionary past binary code (Trifonov 2006) The first ancient codons were GGC and GCC from which the other codons have been derived by series of point mutations. Nowadays, we can see it in modern genes as "mini-genes" containing a purine at the middle position in the codons alternating with segments having a pyrimidine in the middle nucleotides. genome segmentation code (Kolker & Trifonov 1995) Methionines tend to occur every 400 bps in the modern DNA sequences as a result of fusion of ancient independent sequences. The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered. http://en.wikipedia.org/wiki/Edward_Trifonov#Multiple_genetic_codes citations: http://en.wikipedia.org/wiki/Edward_Trifonov#Citations Seems some heavy hitters are citing this '12 code' guy as well, Zimmer, Koonin Szostak, etc..bornagain77_{December 14, 2013
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If you don't understand how the genome is organized, you are an ignoramus, period. Your pompous, know-it-all attitude is insufferable. It's a sure bet that biologists have no clue about 99.99999...% of how genes work together to create a simple cell let alone a complex system like a human being. IOW, no matter how much you think you know, you're still talking out of your asteroid orifice.Mapou_{December 14, 2013
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Intelligent design engineering? Wow. Now there's quite a phrase. Careful, before you know it you'll have your own group of religious nuts following you. ID can do whatever the hell it wants because it has no scientific basis. Hence why it's not science. ID picks and chooses what facts to look at and what not to look at and twists around anything that proves it wrong until no one can recognize it.AVS_{December 14, 2013
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Lies? For a someone who claims to do research, you have quite a bias against research. Or is that only against evolutionary biology? Ah yes, you're one of those science conspiracy theorists; the evolutionary biologists are out to get you and your religious friends! Yup. Schizophrenia is manageable in this day and age Louis. Actually it's manageable because of research.AVS_{December 14, 2013
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Never claimed to have a full understanding of it. But I am pretty well versed on the topic. Enough to know when people are yapping about something they know nothing about.AVS_{December 14, 2013
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AVS:
The theory of evolution not being able to explain something only means more research needs to be done.
LOL. IOW, if the theory is falsified, just add more lies to it. What a joke. There is nothing the theory of evolution thinks it can explain that cannot be easily and better explained by intelligent design engineering. ID can do much better than that and go beyond living organisms. It can also explain the evolution of human designs over decades, centuries and millenia.Mapou_{December 14, 2013
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AVS, I'm sure you have a full understanding of genomic organization, of course. Not. Another scientist talking out of his asteroid orifice.Mapou_{December 14, 2013
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Ha oh boy. You are funny Poo. Just talking out of your ass. I'm not really surprised I guess. No shit your not a biologist, you haven't the faintest clue what you are talking about. Just another computer geek who thinks he's a scientist.AVS_{December 14, 2013
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