Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.
A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine, made the discovery. The findings are reported in the Dec. 13 issue of Science. The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for biological functions are stored in the human genome.
Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and 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.
"For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made," said Stamatoyannopoulos. "Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways."
The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.
The discovery of duons has major implications for how scientists and physicians interpret a patient's genome and will open new doors to the diagnosis and treatment of disease.
"The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously," said Stamatoyannopoulos.
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Zorlont3
1.6 / 5 (19) Dec 12, 2013We have evolution. Which describes what happened after all the nearly impossible stuff happened. Then we have some sorts of chemistry to describe what happened before any of the hard stuff happened.
Spend a few million years watching random bricks fall together, until they make a perfect square.
Close your eyes for a few billion years and when you open them, skyscraper!
Makes more sense to me that something stopped by and glued us together. lol
scottfos
3.5 / 5 (13) Dec 12, 2013back on topic, this is very cool. codons did a lot to explain why there is so much DNA similarity between humans, chimps, mice and canines; if this work on duons pans out it will open a lot of new opportunities.
11791
Dec 12, 2013AeroSR71
3.9 / 5 (7) Dec 12, 2013More on-topic, does anyone know why DNA has 64 letters? Or, said differently, why did evolution choose 4 base molecules (nucleotides)? Is there something about information that works best in bases of 2? There must be some underlying effect that makes symmetry appealing?
Whydening Gyre
1.8 / 5 (5) Dec 12, 2013CassusVas
5 / 5 (10) Dec 13, 2013DNA has 64 possible combinations per codon (4^3) because there are 21 normal/abundant amino acids. Basically, only 2 nucleotides per codon would only be able to code for 16 amino acids (4^2), so life went one further to 3 per codon to cover all the amino acids that are regularly used to make proteins/peptides. Also, the fact that there are 64 possible combinations used for only 21 normal amino acids allows for several different sequences/codons to be used for especially important amino acids (to give the system some flexibility/robustness against mutation, etc). Also, then some of these codons can be used for start and stop codons to signal to the cellular machinery what the start or stopping point of a peptide/protein is.
JVK
1 / 5 (3) Dec 13, 2013James V. Kohl
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.socioa...53/27989
JVK
1.6 / 5 (7) Dec 13, 2013Jaeherys
3.7 / 5 (3) Dec 13, 2013Although interesting, I find it not as important as snRNA reguation via RNAi or antisense snRNA mRNA interference. These snRNA can be found in noncoding regions of genes and DNA which shows multiple levels of regulation on a more genome wide scale and gene scale as specific miRNA are produced from introns from both 5p and 3p transcripts.
JVK
2.6 / 5 (5) Dec 13, 2013Torbjorn_Larsson_OM
4 / 5 (4) Dec 13, 2013The extension of such a "code" to transcription isn't surprising, nor the main mcehanism for regulation. As the perspective article says: "This "binding" code joins other "regulatory" codes that govern chromatin organization (3), enhancers (5, 6), mRNA structure (7), mRNA splicing (3), microRNA target sites (6, 8), translational efficiency (9), and cotranslational folding (10), all of which have been proposed to constrain codon choice, and thus protein evolution (see the figure)." [ http://www.scienc....summary ]
TheGhostofOtto1923
3.7 / 5 (6) Dec 13, 2013"8 Yet you, Lord, are our Father.
We are the clay, you are the potter;
we are all the work of your hand."
-So yea unto you, the hand of god is seen in the bowels of man once again. For written_it_is.
For yet more testimony see the outrageous crap posted by JVK.
JVK, there might be some god or other that is responsible for whatever it is you are talking about, but it is obviously not the god who said there was a flood (there wasnt), or an exodus (never happened), or a joshuan genocide (nope) or some great solomon/david kingdoms somewhere (uh uh) or a town called nazareth during the time of jesus (dirt in the desert).
THAT god is neither omnipotent nor omniscient nor honest nor good nor real. Amen.
Whydening Gyre
2 / 5 (4) Dec 13, 2013Whydening Gyre
2 / 5 (4) Dec 13, 2013Environmental change can drive nutrient change, which in turn would drive cell adaptation to a new set or ratio of nutrients). Surely those changes aren't spot on right in the beginning. A little trial and error (which nature/evolution does a lot of) - and the resulting biological species that survives is a result of "mutating" most propitiously.
Doesn't have to be a large change to be considered a mutation, does it?
JVK
1.8 / 5 (5) Dec 13, 2013If Climate change -> diet change -> ecological variation -> AGAIN, you get more adaptations (sans mutations)
What the study results reported here tell us is that transcription and gene expression are as flexible as they must be to allow for adaptations when climate change precipitates a dietary change due to the ecological variation that is responsible for adaptations via the de novo creation of olfactory receptor genes, de novo creation of species-specific blends of pheromones, and de novo creation of physical structures like teeth or eyes or whatever, which are all the result of alternative splicings and amino acid substitutions in all species.
The amino acid substitutions are not mutations and mutation-initiated natural selection defies the biophysical constraints that clearly facilitate ecological adaptations, not mutations.
Whydening Gyre
2 / 5 (4) Dec 13, 2013Jaeherys
3.9 / 5 (7) Dec 14, 2013Jaeherys
4.2 / 5 (5) Dec 14, 2013Jaeherys
4.2 / 5 (5) Dec 14, 2013JVK
2 / 5 (5) Dec 14, 2013What prevents you from recognizing that those changes are nutrient-dependent and pheromone-controlled? Is it possibly because you don't know the difference between a mutation and an adaptation? Are you, for example, Richard Lenski? If you're anyone else and don't change your definition of a mutation to include biophysical constraints on adaptations associated with evolution, biophysicists, chemists, and biologists will continue laughing at you -- if only behind your back. Is that why you participate anonymously here?
If I were you, I wouldn't want anyone to known that I had actually published anything on mutations theory that ignored the fact that mutations cannot cause adaptations, cannot be selected et al.
Jaeherys
3.7 / 5 (6) Dec 14, 2013Nutrient levels do affect mutation rates but as for pheromone-controlled, I'm not sure I follow. What is an example of a mechanism that directly leads to mutation and adaptation, and without pheromone involvement, cannot produce these results? I am genuinely interested as cell signalling is quite obviously vital in multicellular organisms and could quite possibly affect organismal fitness.
What I fail to conclude is that mutation and adaptation are not related. There is ample evidence showing that mutation may cause changes in phenotype that can manifest as an adaptation increasing fitness.
Is it not a bit presumptuous to assume that nutrients and pheromones are the only factors controlling the evolution of organisms? Especially considering the genetic changes that occur in constant nutrient environments in vitro when just left long enough on their own.
Jaeherys
3.4 / 5 (5) Dec 14, 2013I just don't see how pheromones and nutrients are the sole causes of adaptation. Why is it that some species remain predominantly constant over millions of years even in the presence of varying nutrient levels and pheromones? What I see is the environment not producing any selective pressure and deleterious mutations being selected against.
jxaxmxixn
3 / 5 (3) Dec 14, 2013Obviously you have not even the most fundamental clue on how chemistry works. You should probably try to learn how atoms are formed, and then how atoms connect together to form all of the simple to complex molecules that make up our planet universe.
The logic you've tried to use here (buildings building themselves, etc...) is NOT how evolution happens! Try reading a science book!
GuruShabu
5 / 5 (4) Dec 14, 2013JVK
1.7 / 5 (6) Dec 14, 2013Two H-bonds are critical for slow inactivation of Kv channels: one that confers stability within an individual subunit (the Trp434–Asp447 interaction), and a second that stabilizes the relative orientation of two adjacent subunits (the Tyr445–Thr439 interaction).
If this stability, which is probably important to the stability of life itself, results from randomness that somehow enables the thermodynamics of intercellular signalling, stochastic gene expression, and the amino acid substitutions that result in organism-level thermoregulation, which differentiates individuals and species from all other individuals and species via genetically predisposed differences in antigenic properties like those determined by a single amino acid substitution in the human influenza virus, the atheists are right and they could probably prove it.
Alternatively, the explanation is Creation, which atheists say Creationists can't prove. I believe that someone's bound to be embarrassed.
JVK
1.8 / 5 (5) Dec 14, 2013"I just don't see how pheromones and nutrients are the sole causes of adaptation."
Nutrients fuel the thermodynamics of intercellular signaling; species-specific pheromones control the physiology of reproduction in species from microbes to man.
What other causes of ecological adaptation might involve mutations? Is there a model of ecological, social, neurogenic, and socio-cognitive niche construction for that?
Jaeherys
4.3 / 5 (6) Dec 15, 2013JVK
2.3 / 5 (3) Dec 15, 2013Otherwise, you're going to keep thinking in terms of mutations instead of de novo creation of olfactory receptor genes, de novo creation of species-specific blends of pheromones and de novo creation of nutrient-dependent physical features like eyes or other morphological characteristics in cells from microbes to man.
Simply put, you will continue to think like an uninformed theorist who attributes the complexity of ecological, social, neurogenic, and socio-cognitive niche construction to mutations and natural selection instead of ecological variation and food choice.
Jaeherys
4.2 / 5 (5) Dec 15, 2013JVK
2 / 5 (4) Dec 15, 2013"We have shown here that the activity-dependent replacement of canonical H2B with H2BE, an olfactory-specific histone variant, has a direct impact on the gene expression and life span of olfactory sensory neurons. These findings uncover a novel mechanism by which the sensory experience of a neuron is recorded within its chromatin to affect its transcriptional program and longevity." http://elife.elif...1/e00070
Lots more evidence of cause and effect across species.
How do you account for your lack of knowledge in the context of ecological variation that obviously is linked from flies to amino acid substitutions in receptors in human olfactory receptor neurons as well? I think you may have been taught too much about theory, without asking if the theory was supported by experimental evidence. Thus like others, you think experimental evidence is a Creationist thing. To me, it's Science.
Jaeherys
4 / 5 (4) Dec 15, 2013Jaeherys
4 / 5 (4) Dec 15, 2013I mostly work in cell biology and gene regulation and not genetics or evolution, so i cant say either way if this is evidence for or against your theory. Also, considering how little change there is between the histone variants, dont you find that indicative of mutation? Such small genetic changes produce such a huge change in phenotype and ultimately the whole olfactory system!
And on a complete side note, my lab also studies cyclin G2 regulation and function in human ovarian cancer. Due to its unconventional nature, it appears to be a negative regulator of cell survival due to stress, DNA damage, etc. This H2BE-mediated reduction of MOE longevity is intriguing as glial cells seem to show CG2-mediated apoptosis. So I may have found another cell type to study in a more stable model system. So thanks for linking that paper!
JVK
2.3 / 5 (3) Dec 15, 2013I often wonder at how much different specialized areas of research contribute to the inability to see the forest for the trees. Most people are incapable of thinking in terms of modeling developmental changes across species. If they did, they couldn't possibly continue thinking in terms of mutation-driven evolution. They might never be capable of thinking in terms of
"Nutrient-dependent/pheromone-controlled adaptive evolution" http://www.socioa...53/27989
But if they weren't so specialized, at least they might start to think.
11791
Dec 16, 2013JinXer
3.4 / 5 (5) Dec 16, 2013JVK
3 / 5 (2) Dec 16, 2013If you have the source for that information, it might benefit others. I certainly would like to examine it, since I have never before heard that only the reproduction of one base pair was required to kick-start all the other types of storage. I'm reminded,however of an article by "Uncle Al Schwartz" about "The Power of Two" which might help to place the first base pairing in context.
SURFIN85
1 / 5 (1) Dec 17, 2013Whydening Gyre
1 / 5 (1) Dec 17, 2013JVK
1 / 5 (1) Dec 17, 2013Energy expenditure is controlled by the feedback of chemical signals that are typically called pheromones.
I'd love to see a followup to my comment here: http://comments.s....1243490 or to the summary of the four Science articles I posted to my domain: http://pheromones...s-redux/
JVK
not rated yet Dec 17, 2013"H2be may be subject to different post-translational modifications than canonical H2b. Indeed, Santoro and Dulac show that lysine 5 of H2be is not acetylated or methylated, unlike what happens with canonical H2b, and that the level of the these post-translational modifications in olfactory sensory neurons varies with H2be levels. Since these modifications have been positively correlated with transcription (Wang et al., 2008) it is intriguing to think that global transcription is less efficient in neurons with high H2be levels."
One of the authors of the piece I just quoted got my comments on it blocked and then they were removed. To me it was clear that I "nailed" the process of de novo creation of olfactory receptor genes via epigenetic effects of chemical signals from the bottom up that must result in organism-level thermoregulation, which is epigenetically controlled from the top down.
If I was wrong, discussion might have ensued.
Zephir_fan
Dec 17, 2013JVK
1 / 5 (1) Dec 17, 2013http://www.jbc.or...abstract
Kohen's group clearly links E. coli to Homo sapiens via amino acid substitutions that are conserved. They report that "…a four amino acid insertion (PEKN) was introduced early in the enzyme's evolution and is highly conserved in higher organisms." Conserved molecular mechanisms in species from microbes to man link amino acid substitutions that are conserved to other amino acid substitutions that differentiate cell types, individuals and species. It is not surprising to see a report on this research that states "At the molecular level, evolution reshaped some of the enzymes that help complete chemical processes — such as converting food into energy — in humans and all other life forms." The conversion of food into energy is a condition of life.
Mutations perturb the dynamic constraints of protein folding. They do not reshape enzymes to help convert food into energy that enables beneficial amino acid substitutions
JVK
1 / 5 (1) Dec 17, 2013Of course this suggests that the balance of transcription and gene expression must be finely tuned, which argues against mutation-driven evolution since mutations perturb intercellular signaling and stochastic gene expression.
A brief pulse of one transcription factor and you get an entirely different cell type without the magic of mutations that somehow cause differences in cell types in tissues of organs in organisms that must effectively thermoregulate their cell/body types to survive. How likely is it that a nutrient-dependent alternative splicing and amino acid substitution is involved?
arpotu
1 / 5 (1) Dec 18, 2013Jaeherys
5 / 5 (3) Dec 18, 2013The first article you posted did not and can not conclude de novo creation of anything as there was NO evidence of it. Your constant use the the phrase "amino acid substitution" separate from genetic mutation is just blatantly wrong. Perhaps more disturbing than your apparent disregard for the evidence going into the definition of the term, "amino acid substitution", is the fact that you don't seem to acknowledge the effects of billions of years of organisms that have lived and died in order to produce what we have today.
Mutation may be deleterious, have no effect, or be beneficial and this is EASILY proven. Not only from natural examples where small changes produce immediate and severe changes in function that can be selected for or against but through human manipulation of genes that change the function, with Tac polymerase being one of the best examples.
You seem quite intelligent yet you purposely bias evidence to fit your hypothesis and this is completely anti-science.
JVK
1 / 5 (1) Dec 18, 2013Asserting evidence that amino acid substitutions are due to mutations is theoretical nonsense and that nonsense has been revealed by what is currently known about the conserved molecular mechanisms of ecological adaptation in species from microbes to man.
The double meaning in the genetic code suggests that the millions of years time frame needs adjustment. However, it also attests to the obvious role that a balance of nutrient stress and social stress plays in enabling the conserved molecular mechanisms of ecological adaptations sans mutations.
The fact that you don't like the biological facts does not make them irrelevant -- except in the context of theory, in which the biological facts have never been considered.
Zephir_fan
Dec 18, 2013Whydening Gyre
5 / 5 (1) Dec 18, 2013Zephir_fan
Dec 18, 2013Whydening Gyre
5 / 5 (1) Dec 18, 2013Apology accepted...:-) And - you are correct in your observation....
Jaeherys
5 / 5 (2) Dec 18, 2013JVK
1 / 5 (1) Dec 19, 2013The circulatory system is not required, nor is anything else except ecological variation, which is why some people will understand how the biological functions that are stored in the genome must be epigenetically effected for cell type differentiation to occur in any species.
A SICB conference held in January was devoted to the topic of ecological epigenetics. That means there are many people who are well-informed about biologically based cause and effect. None of them participate here.
"...DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs..." What causes the DNA changes: ECOLOGICAL VARIATION.
Whydening Gyre
5 / 5 (1) Dec 19, 2013http://erikandrul...ing-dna/
Zephir_fan
Dec 19, 2013JVK
1 / 5 (1) Dec 19, 2013Old Guy in Stanton
1 / 5 (1) Dec 30, 2013Creator of the Universe or bored passerby messing with it's version of Legos at a rest stop. THAT is one heck of a choice there, Sparky! I gave you a five for throwing a full sized monkey wrench into the sandbox. (mixed metaphors, anyone?)
Seriously, Bored Passerby sounds just as probable and Universe Creator Yahweh. I'm starting The Church of the Bored Traveler.
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013You seem to know a lot about the open mindedness and thinking ability of Zor. Do you know him well? Or are you generalizing from your *own* preconceived confirmation bias?
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013That would depend, I would think, on what exactly that 2nd code says.
The best cutting edge cosmological theory of the creation of the universe sounds, to be frank, like the desperate pleadings of a voodoo ghost's High Priest who can't remember all the cons piled on cons. Weasel words? Check. Reader assault w/ jargon? Check. Ad hominem arguments? Check. Appeals to Authority? Check. Sounds religious to me.
(I'm essentially an atheist, but: (1) this current apparent dead end in cosmology, (2) the fact that I think I may have a mathematical proof that there *has* to be a God (but not like any vision of God ever imagined), and (3) a thought that absence of evidence is not evidence of absence, leads me to the conclusion that I have to allow for the possibility of a God (or a Bored Traveler).)
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013I read a "future documentary" about that. One of Asimov's, I think. A brilliant molecular biologist says to his friend (or someone - years since I read it) that our genetic code is actually a MESSAGE from an alien race that created it 4.3 billion years ago, meant for another race, today. A telegram, if you will.
The friend says, "So?"
The scientist says "There's every reason to believe that the telegram was delivered some time ago."
The implied question of course: What do you do with a telegram once you've read it?
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013>>>jxaxmxixn: "Obviously you have not even the most fundamental clue on how chemistry works. You should probably try to learn how atoms are formed, and then how atoms connect together to form all of the simple to complex molecules that make up our planet universe.
The logic you've tried to use here (buildings building themselves, etc...) is NOT how evolution happens! Try reading a science book!
Maybe it's just me, but I thought he was just waxing poetical, and stuff like atoms and molecules can get in the way of that. But I'm new here, so what do I know...
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013Serious request and serious question: Could you please restate the above in simpler language. Also why would this prove the atheists right? Thanks.
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013Good logic. And yet a Universe-creating "God" may in fact exist. In fact, if the probabilities I am thinking of check out, MUST exist. But IT would: (1) be like nothing we have ever imagined, (2) MAY in fact have created us by creating a specific Universe capable of supporting life, but (3) probably does not give a fig about us one way or the other. (4) OTOH he may have a use for us, once we have evolved enough.
JVK
1 / 5 (1) Dec 30, 2013That's obviously why Dobzhansky (1964) ridiculed anyone who based their opinions on what they could observe. In "Biology, molecular and organismic" he wrote: "...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!
Atheists need experimental evidence of something to support their claims! Otherwise they can't be serious.
JVK
1 / 5 (1) Dec 30, 2013