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Cell Requires Hundreds of Kilobases for Mature Micro-RNA

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Here’s todays headscratcher from Phys.Org.

It appears that to contrive a “mature” micro-RNA (mi-RNA), involved in gene regulation, the cell requires hundreds of kilobases of sequence. How odd. “Mature” mi-RNA’s are ~22 bases in length, and hundreds of thousand of nucleotide bases are needed (of primary-mi-RNA) to effect this ~22-nucleotide regulatory element?

Here’s what they say:

MicroRNAs are short noncoding RNAs that play critical roles in regulating gene expression in normal physiology and disease. . . .

Although mature miRNAs are only ~22 nucleotides, their transcripts are up to hundreds of kilobases long. Primary miRNA transcripts, or pri-miRNAs, are quickly processed into mature miRNAs from hairpin structures located in the exons or introns of pri-miRNA transcripts.

One remarkable feature of primary miRNAs is their extreme length, even in cases where they function only to produce a single ~22 nucleotide miRNA,” said Joshua Mendell, corresponding author of the study. “Although it seems wasteful to produce such long RNAs, most of which will be immediately degraded, this organization may have arisen to allow complex mechanisms of regulation of the encoded miRNA.

As usual, they’re “surprised” about their findings (very likely they are ‘surprised’ because they weren’t expecting things to turn out so complex). And, as usual, the pro forma reaching out to “evolution” as the explanatory mechanism, when, in fact, no explanation is given at all: . . . this organization may have arisen to allow complex mechanism of regulation of the encoded mi-RNA.”

It may have; but, it may have not. Is this scientist willing to consider this other possibility, or is it simply an article of faith that “evolution-did-it”? One wonders.

Comments
It must suck to be a Moran.Mapou
August 23, 2015
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Larry "Junk DNA Disproves Intelligent Design Creationism" Moran are you reading this?Box
August 23, 2015
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Folks, Money shot clip from JDD's link:
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003569 Much of the human genome is composed of intergenic sequence, the regions between genes. Intergenic sequence was once thought to be transcriptionally silent “junk DNA,” but it has recently become apparent that intergenic regions can be transcribed. However, the scope, nature, and identity of this intergenic transcription remain unknown. Here, by analyzing a large set of RNA-seq data, we found that >85% of the genome is transcribed, allowing us to generate a comprehensive catalog of an important class of intergenic transcripts: long intergenic noncoding RNAs (lincRNAs). We found that the genome encodes far more lincRNAs than previously known. A key question in the field is whether these intergenic transcripts are functional or transcriptional noise. We found that the lincRNAs we identified have many characteristics that are inconsistent with noise, including specific regulation of their expression, the presence of conserved sequence and evidence for regulated processing. Furthermore, these lincRNAs are strongly enriched with intergenic sequences that were previously known to be functional in human traits and diseases. This study provides an essential framework from which the functional elements in intergenic regions can be identified and characterized, facilitating future efforts toward understanding the roles of intergenic transcription in human health and disease.
Translation, Darwinist expectations of abundant junk DNA were real, and are now dead. This is a new world. One in which the obvious candidate is that a lot of DNA is carrying out programmed control of cell processes in ways we are just beginning to get hints of. Where, this is being directly tied to medical issues. FSCO/I is staring us in the face and is pointing to its only known, only credible explanation. Intelligently directed configuration. KFkairosfocus
August 23, 2015
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Dr JDD # 81 - Absolutely. It is a worldview issue, a matter of faith. It is absolutely impossible to prove anything to anyone unless they choose to hear. If it is more convenient to live in a world where there is no purpose, there's nothing one can do.EugeneS
August 23, 2015
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http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003569 Plenty more out there when people shake off their biased EVO mindset and actually ask "why is this here?" and "maybe this has a function" rather than "this is sloppy genomes from accidental evolution". Yet we will still here things like lincRNAs actually areonly a very small percentage of the genome as countering rebuttals...Dr JDD
August 23, 2015
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PaV:
The pressure keeps building; soon, I suspect, the ‘dam will burst.’
Yes. And it will happen sooner than most suspect and it will come from the one place that nobody would expect. In fact, it's almost at the door. And it won't be pretty either. But it will be spectacular and will shake the foundations of civilization. Wait for it. Just saying.Mapou
August 23, 2015
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Dr JDD: I always appreciate your comments on this board. As to the link, and "transcriptional noise," evolutionary biology is under tremendous pressure to change. The pressure keeps building; soon, I suspect, the 'dam will burst.'PaV
August 23, 2015
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http://www.nature.com/nrmicro/journal/v12/n9/full/nrmicro3316.html PaV - they will never admit they were wrong nor will they change their view because it is a necessity for their worldview. But keep writing as you are because it is helpful for those reading who are not committed to materialism yet and are seeking answers and truth to be exposed to their hypocrisy. The literature is full of examples where people (evos typically) have pushed a view of uselessness and lack of function to support their worldview, and then new evidence comes to light explaining functionality. Usually by those who are not in the evo field so have little to lose...Dr JDD
August 23, 2015
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What they describe is unexpected and peculiar. No reason, then, to extrapolate this as some byproduct of randomness. I can't explain this any better than that: the implications are there to be seen. I'm glad, though, that you're at least open to the possibility of function being found. Are you open, also, of said found function to make you look at the Darwinian narrative differently?PaV
August 23, 2015
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"there’s no reason to believe that this shouldn’t be happening all the time. But it isn’t. So why don’t we see this happening everywhere within the genome? Why just here?" You're not making sense anymore, Pav. And sure, ill wait and see if they find any function in the thousands of bases that are transcribed and then immediately chopped off and degraded. Won't hold my breath though.Alicia Cartelli
August 22, 2015
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What?wd400
August 22, 2015
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So, evolutionary biologists always knew there was some purpose for so-called "junk-DNA"; but, of course, there IS "junk-DNA," and ID is silly. Quite a trick.PaV
August 22, 2015
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But it isn’t. So why don’t we see this happening everywhere within the genome?
~20% of the human genome is intronic. Some introns have regulatory sequences, but they're mostly junk. And, as I said earlier, there are plenty aberrant transcripts in eukaryotic cells.wd400
August 22, 2015
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AC: My major area of study these days is in physics. What I work at is neither physics nor biology. Molecular biology has become incredibly more complex over the last 10 years. I don't have the time to become expert. And, I don't have the financial wherewithal to buy journals willy-nilly; nor do I work at a university where journals are avaiable online. So you'll have to excuse the fact that I haven't read the article. But, I don't think that's the issue here. My whole point is that the ID perspective, and the Darwinian perspective, are very different. We approach the same set of facts in different ways. You talk about "waste." I say, "No, it's not waste; there must be some kind of function." This contrast in views parallels the "junk-DNA" controversy. Whereas "junk-DNA" was, and still is, thrown in the face of IDers as proof of randomness, nowadays many, if not most, evol. biol. say, "Oh, we never thought it was 'junk'." So, this becomes a good exercise in trying to determine which scientific viewpoint has more explanatory power since we don't know where all of this is heading. You firmly take the position that all this is "waste," and you don't think anything will ever be found to change this story. Well, it may take years to finally determine what we're looking at here with all thee bases, but it offers a chance for "objectivity," a chance of testing the viewpoints. I've invited you to take advantage of this opportunity, but your mind is made up: "End of story." In writing the following, you seem to miss the obvious: My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes. Maybe a few miRNAs are alternatively spliced, meaning some more of the transcript is functional than I was aware of, but there are still a massive number of bases that are transcribed and then immediately degraded. End of story. Here's what you're missing: If you reach the conclusion that this is a "wasteful" process ("End of story"), then there's no reason to believe that this shouldn't be happening all the time. But it isn't. So why don't we see this happening everywhere within the genome? Why just here? This has all the hallmarks of a critical design where "margins of errors" are built into the design. Intuition suggests that "function" will be found. Time will tell. And we can all reevaluate our views when that time comes.PaV
August 22, 2015
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Alicia Cartelli, contrary to how confident you may be that it must be a huge waste of energy, you simply have no evidence to back up your claim other than your own self exalted opinion of your knowledge in these matters. In fact, you were shown empirical evidence directly contradicting your claim that the cell must be extremely inefficient in its energy usage. i.e. The 'horrendously complex' metabolic networks of the cell are found to be 'optimal'. That you still insist that it must be a huge waste of energy for the cell, in spite of being shown otherwise, thus does not, indeed can not, flow from the empirical evidence in hand but must flow from your faulty theological presupposition of 'God would not have done it that way because I would not have done it that way'. I'm not impressed. In fact, as was amply demonstrated with the junk DNA fiasco, your Darwinian theology is a science stopper! Considering the unfathomed complexity being dealt with in the cell, and considering the fact that unguided material processes have never been observed to create even a single protein of that unfathomed complexity, I suggest you swallow your arrogant pride and allow the possibility that God just may know how to design life a little better than you do. Now if you really want to impress me with your all your superior knowledge of biology, so that I start to respect your chest thumping opinion in these matters, I suggest you go create life in the lab first. Until then I consider you a arrogant blowhard, no better than a drunk bragging that he can defeat the heavyweight champion of the world.bornagain77
August 22, 2015
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Alicia:
Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy.
And your position cannot account for any of that-> the process nor the energy. And again there could be a valid reason that we don't grasp because of our ignorance due to the adherence to evolutionism.Virgil Cain
August 22, 2015
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Elizabeth:
Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy. You, like Pav it would seem, have no idea what you’re talking about.
Why do you kou keep repeating the same lame, blah-blah strawman? The design hypothesis predicts that, as soon as we get a better understanding of what is really going on, we will find out the reason for the observed mechanism. The argument against your position is that ID is correct and it was designed for a purpose by a highly advanced and knowledgeable group of designers. So given ID, there is a purpose that obviously escapes you and everyone else. Otherwise, you would not be here arguing about something that you are, after all is said and done, really ignorant about. Soon, you will be proven wrong because we continue to learn and we have powerful computers to do it with. And one more thing. You don't own science. Science is nobody's dog. In fact, true science is the Darwinist's worst enemy.Mapou
August 22, 2015
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Bornagain, I think you have me confused with someone else. But anyways, it is not an unsupportable claim in the slightest. Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy. You, like Pav it would seem, have no idea what you’re talking about.Alicia Cartelli
August 22, 2015
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BA77 don't you crush Alicia's dreams of sweet purposelessness. Let us be kind. Her good heart makes a little jump on those extremely rare occasions that something in biology doesn't strike us as sublimely designed.Box
August 22, 2015
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Alicia:
My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs.
And natural selection and drift explain that, how, exactly?Virgil Cain
August 22, 2015
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Also of related interest: Here is, according to a Darwinist, a ‘horrendously complex’ metabolic pathway chart:
ExPASy - Biochemical Pathways - interactive schematic http://biochemical-pathways.com/#/map/1 Map Of Major Metabolic Pathways In A Cell – Picture http://2.bp.blogspot.com/-AKkRRa65sIo/TlltZupczfI/AAAAAAAAE1s/nVSv_5HRpZg/s1600/pathway-1b.png
And remember, Darwinists have yet to demonstrate how a single protein of that 'horrendously complex' metabolic pathway came about (Axe; Gauger). Moreover, as if that were not ‘horrendously’ bad enough for Darwinists, metabolic pathways are found to operate on ‘Quarter Power Scaling’ parameters. i.e. Metabolic Pathways operate as if they were ‘four-dimensional’ not as if they were 3-dimensional as would be expected if the processes had been 'cobbled together' by natural selection:
Kleiber’s law Excerpt: Kleiber’s law,[1] named after Max Kleiber’s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the 3/4 power of the animal’s mass. http://en.wikipedia.org/wiki/Kleiber%27s_law 4-Dimensional 'Quarter Power Scaling' In Biology – video http://www.metacafe.com/w/5964041/ The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf
Jerry Fodor and Massimo Piatelli-Palmarini put the insurmountable problem that Quarter Power Scaling presents to Darwinism this way:
Post-Darwinist - Denyse O'Leary - Dec. 2010 Excerpt: They quote West et al. (1999), “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection." They comment, "In the words of these authors, natural selection has exploited variations on this fractal theme to produce the incredible variety of biological form and function', but there were severe geometric and physical constraints on metabolic processes." "The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection. It's inconceivable that so many different organisms, spanning different kingdoms and phyla, may have blindly 'tried' all sorts of power laws and that only those that have by chance 'discovered' the one-quarter power law reproduced and thrived." Quotations from Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79.
The primary reason why ’4-Dimensional’ metabolic pathways are impossible for Darwinism to explain is that Natural Selection operates on the 3-Dimensional phenotypes of an organism. ’4-Dimensional’ metabolic pathways are simply ‘invisible’ to natural selection. The fact that 4-Dimensional things are completely invisible to 3-Dimensional things is best illustrated by ‘flatland’:
Dr Quantum - Flatland - video https://www.youtube.com/watch?v=BWyTxCsIXE4
In keeping with the preceding claim of the 'invisibility' of these 4-Dimensional processes to natural selection, such 100% efficiency and optimality being found metabolic processes is hard (impossible?) to explain on Darwinian terms given that selection rarely even 'sees' the fittest mutations:
Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration Excerpt: An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,, By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales. http://phys.org/news/2014-02-evolutionary-important-success.html
As should be needless to say Liddle, I find your theological claim that 'it's just junk therefore God would not have done it that way' to be, besides being grossly unscientific, to be without empirical merit.bornagain77
August 22, 2015
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Elizabeth Liddle I thought you had been banned for lying, lack of integrity, or something along that line? Anyways you state:
"My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes."
Aside from your arrogant 'I would not have done it that way therefore God would not have done it that way, therefore it must be junk' theologically laden science, I find your claim that a 'massive amount of energy is being wasted' to be a empirically unsupportable claim. I certainly don't claim to be as smart as you think you are in biology, (and in your Darwinian Theology for that matter), but from my scant understanding of the metabolic processes of the cell, the energy efficiency in the cell is found to be astonishingly optimal. Thus, although the RNAs being rapidly degraded may not suit you particular engineering druthers, for you to say there is absolutely no purpose for the process, especially considering the astonishing integrated complexity already found in the cell, is naive at best and most likely 'not even wrong' in its conclusion. Here are a few notes establishing the amazing energy efficiency of the metabolic processes of the cell:
Metabolism: A Cascade of Design - 2009 Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. http://www.reasons.org/metabolism-cascade-design Making the Case for Intelligent Design More Robust - 2010 Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites. http://www.reasons.org/making-case-intelligent-design-more-robust Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
Also of related interest to the 'optimal' energy efficiency of the cell, it is found that the integrated coding between the DNA, RNA and Proteins of the cell apparently seem to be ingeniously programmed along the very stringent guidelines laid out in Landauer’s principle, (by Charles Bennett from IBM of Quantum Teleportation fame), for ‘reversible computation’ in order to achieve such amazing energy/metabolic efficiency as it does.
Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20
The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day:
Reversible computing Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing Can reversible computing really dissipate absolutely zero energy? Of course not. Any non-equilibrium physical system (whether a computer or a rock) dissipates energy at some rate,,, Okay, then can reversible computing really make the energy dissipation of a computation be an arbitrarily small non-zero amount? Only insofar as the computer can be arbitrarily well isolated from unwanted interactions, errors, and energy leakage,,, But, despite all these caveats, it may yet be possible to set up reversible computations that dissipate such amazingly tiny amounts of energy that the dissipation is not a barrier to anything that we might wish to do with them - I call such computations ballistic. We are a long way from achieving ballistic computation, but we do not yet know of any fundamental reasons that forbid it from ever being technically possible. http://www.cise.ufl.edu/research/revcomp/faq.html#zeroenergy of note: I hold the computation in the cell being done for such things as protein folding and DNA repair to indeed be 'ballistic'
bornagain77
August 22, 2015
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Well if you had bothered to read the paper, Pav, you’d realize how much of a stretch “dramatically expanded” is. The major finding of the paper is the sequence information and predicted secondary structures of the pri-miRNAs. The secondary findings are the use of alternative promoters, clustered miRNAs, and alternative splicing of miRNAs. Notice that the first two are pre-transcription, so they do not help your argument. The only thing that helps your argument is a tiny paragraph near the end that corroborates the findings of another paper. They found that a few select miRNAs happen to have splice sites that could potentially alter their function. Notice that some variation of the word “potential” is sprinkled throughout the parts of the paper that talk about regulatory mechanisms as well. Much of what you are trying to use as evidence for your argument is largely speculation on the researcher's part. I'll let it slide though. My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes. Maybe a few miRNAs are alternatively spliced, meaning some more of the transcript is functional than I was aware of, but there are still a massive number of bases that are transcribed and then immediately degraded. End of story. Don’t confuse pre- and post-transcriptional regulatory mechanisms. We are talking about post-transcriptional regulation. And for the last time, you are using the word “primer” wrong. The original transcript is the 10,000-100,000nt pri-miRNA, it is cleaved to 70nt pre-miRNA, and then processed to ~20nt miRNA. I have never seen “primer” used in the way you are trying to use it. Also, you accuse my knowledge of being out of date, but the only thing out of date here is the wiki article you cite. The abstract you, yourself copy/pasted says “the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10’s to 100’s of kilobases in length.” So when wiki says its ~80nts, you should have realized the mistake. Like I said, wiki does not replace an education in biology. It is obvious you are no expert.Alicia Cartelli
August 22, 2015
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PaV @64, Thanks for that revealing and devastating comment. Elizabeth is such a good little Darwinist soldier that she took it upon herself to start on a new trail that leads to more ridicule being piled on top of Darwinism. The whole edifice of Darwinism is crumbling at an astonishing rate. It's painful to watch the demise of a once mighty religion.Mapou
August 22, 2015
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From the abstract of the Genome Research paper:
Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
I bothered to search for this abstract, AC, because you insist your understanding is replete. Their "understanding" has been "dramatically expand[ed]." Isn't it ironic that what they discovered---which was not mentioned specifically in the release from the OP---fits in almost exactly with what I said should be expected from an ID perspective?
And they are immediately cleaved to a few 70-nucleotide fragments based on the formation of secondary structure by the RNA.
We can all find this in Wikipedia. None of this has changed from before; but, we're talking about all that "waste." Well, it seems like it "interacts" and "regulates". Didn't I suggest this?
Goodluck finding a function in the thousands of extra transcribed bases, do you know of any possibilities?
Isn't a "regulatory mechanism" functional within the transcription process? As to "primer," the "primer" appears to be the original, non-coding transcript. Later, it is chopped down, and, from what Wikipedia seems to be saying, it then becomes "pre-miRNA." I'm not expert in molecular biology; not even close. Nevertheless, I will comment upon it when I think it's appropriate. As to "pre-miRNA": from Wikipedia:
miRNA genes are usually transcribed by RNA polymerase II (Pol II).[47][56] The polymerase often binds to a promoter found near the DNA sequence encoding what will become the hairpin loop of the pre-miRNA. The resulting transcript is capped with a specially modified nucleotide at the 5’ end, polyadenylated with multiple adenosines (a poly(A) tail),[47][51] and spliced. Animal miRNAs are initially transcribed as part of one arm of an ?80 nucleotide RNA stem-loop that in turn forms part of a several hundred nucleotides long miRNA precursor termed a primary miRNA (pri-miRNA)s.[47][51] When a stem-loop precursor is found in the 3' UTR, a transcript may serve as a pri-miRNA and a mRNA.
It doesn't appear that I'm confused at all about what the length of "primer miRNA" was thought to be. The prevalence of Drosha made finding it difficult, that's all. Now they know a way around the problem.PaV
August 22, 2015
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wd400:
And if you want examples of wasted transcription just check out eukaryote protein synthesis. There’s a whole system dedicated to cleaning up the mess that makes.
And another system that neither natural selection nor drift can explain.Virgil Cain
August 22, 2015
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Alicia:
I highly doubt all three of those statements, Virg.
So what? You have nothing to offer.
And so you believe that organisms were once much more efficient and since then have only “devolved?”
If natural selection and drift are the mechanisms then that is the only fate.
Interesting, the only problem is that your belief flies in the face of everything that people who actually understand biology have agreed upon.
LoL! Who cares what people agree upon? In science it only matters what people can demonstrate. And evolutionary biologists cannot demonstrate natural selection and drift actually producing something. Look your position cannot account for gene regulation. It cannot account for transcription factors. Yours is forced to start with all of the stuff that requires an explanation. Yours cannot account for molecular biology.Virgil Cain
August 22, 2015
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Yes, much longer. The original transcripts are ~10,000-100,000 bases long. And they are immediately cleaved to a few 70-nucleotide fragments based on the formation of secondary structure by the RNA. Goodluck finding a function in the thousands of extra transcribed bases, do you know of any possibilities? You’re using the word “primer” wrong as well. It doesn’t mean what you think it does. What I know is not outdated. It is part of the RNA-induced silencing mechanism currently being taken advantage of by researchers and has been studied carefully for many years now. And I was not off by a factor of anything if that was what you were trying to say; wd400 has already straightened you out as far as that goes. Wiki does not replace an education in biology. I suggest you let this be an experiment in whether you should be talking about molecular biology in much detail. Hint, the answer is no. I’m plenty open minded. I’ve seen both sides and I understand the arguments of both sides.Alicia Cartelli
August 21, 2015
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If Darwinists run with this ball, it will turn out to be another junk-DNA type debacle. Just saying. LOLMapou
August 21, 2015
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FWIW, the ~70nt sequences are the pre-miRNAs, not the pri-miRNAs. And none of these sequences are primers. And if you want examples of wasted transcription just check out eukaryote protein synthesis. There's a whole system dedicated to cleaning up the mess that makes.wd400
August 21, 2015
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