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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
Virgil Cain:
AGAIN- we use science to show that Intelligent Design exists. Obviously if it exists it is possible.
Obviously, if biological ID is impossible, it doesn't exist. Show the world of biology that biological ID is possible.
Carpathian: How else could he make his modifications to an organism that is already in an ecosystem? Virgil Cain: Why would he have to?
1) Unless he's infallible, he would have to fix any mistakes he or his team have made. 2) If an organism cannot "evolve" new functionality, he would have to add it. 3) If his organisms can produce new functionality on their own, then "Darwinism" works as stated.Carpathian
August 27, 2015
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AGAIN- we use science to show that Intelligent Design exists. Obviously if it exists it is possible.Virgil Cain
August 26, 2015
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Carpathian:
But you’re not showing that ID can account for any of these either.
That is the only thing that can.
Then we wouldn’t be discussing “Darwinism” if ID had proof/evidence of a designer.
We have to for the reasons provided- it exists and the way to the design inference is through it and all like it.
That’s exactly how I would expect an ID instructor to be like.
Explaining what ID is and what it isn't? That is what I would expect. I would also expect the students to be able to grasp the simple facts.
How else could he make his modifications to an organism that is already in an ecosystem?
Why would he have to?
We’re not talking “Darwinism” where a successful mutation propagates through a population.
Talk about oversimplification. What is "successful" is relative and changing.
We’re talking about a necessary modification from outside the organism.
What necessary modification?Virgil Cain
August 26, 2015
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Virgil Cain:
Carpathian: If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once? Virgil Cain: Why is that a requirement?
How else could he make his modifications to an organism that is already in an ecosystem? We're not talking "Darwinism" where a successful mutation propagates through a population. We're talking about a necessary modification from outside the organism.Carpathian
August 26, 2015
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Virgil Cain:
We don’t, moron. If the student is too stupid to grasp the fact that ID is about the DESIGN and not the designER then that student is in the wrong class.
That's exactly how I would expect an ID instructor to be like.Carpathian
August 26, 2015
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Virgil Cain:
AND if your position had something then we wouldn’t even be discussing ID, yet here we are watching you hump your strawmen.
Then we wouldn't be discussing "Darwinism" if ID had proof/evidence of a designer. Prove ID is possible . There is no such evidence from Dembski, Behe, or anyone else in the ID camp.Carpathian
August 26, 2015
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Virgil Cain:
The laws that govern the universe; living organisms; ATP synthase; bacterial flagella; cilia; the genetic code- if you could show that materialistic processes can account for any of those then ID would be in deep trouble.
But you're not showing that ID can account for any of these either. Show me that ID has an answer. Don't say something to the effect of; the guy who painted my house must have been called Bob because you can't prove his name is Steve. Prove there was an intelligent designer. You also haven't even attempted to answer how you would roll out a change into a billion organisms spread out over the world. If you attempt to answer it, you'll find out it can't be done.Carpathian
August 26, 2015
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Carpathian:
Not even trying to examine the designer or his mechanisms would convince me you don’t believe in the science of ID yourself.
Umm, the science of ID is in the detection and study of intelligent design. We can't study the designers of Stonehenge. We use the existence of Stonehenge to posit the designers also existed. AND if your position had something then we wouldn't even be discussing ID, yet here we are watching you hump your strawmen.Virgil Cain
August 26, 2015
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Carpathian:
If the intelligent designer created life that could respond to changes in the environment, why bring up the intelligent designer at all?
We don't, moron. If the student is too stupid to grasp the fact that ID is about the DESIGN and not the designER then that student is in the wrong class. That said, only an intelligent designer can explain the intelligent design.
If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once?
Why is that a requirement?Virgil Cain
August 26, 2015
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Carpathian:
Detectives don’t stop at; “ Someone must have done it, case closed.”
Detectives aren't scientists. If there aren't any witnesses then all they have is what forensic science tells them. Then sure, they can pound on doors and harass people in the hope something will turn up.
Show me the evidence for an intelligent designer.
The laws that govern the universe; living organisms; ATP synthase; bacterial flagella; cilia; the genetic code- if you could show that materialistic processes can account for any of those then ID would be in deep trouble.Virgil Cain
August 26, 2015
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Virgil Cain:
Why not? There is plenty of evidence for an intelligent designer so obviously there was opportunity.
Cuz you say so? That’s not an argument. Show me the evidence for an intelligent designer. How do you make a change in billions of organisms spread out over the planet? How long would it take in years? How long would it take in generations? Is it done all at once like updating your browser over the internet? If so, how are organisms networked? If they're not networked, how do you get feedback from them in order to plan an update?Carpathian
August 26, 2015
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Virgil Cain:
Carpathian: When a detective investigates a case, he doesn’t just look at circumstantial evidence, but also looks into motive and opportunity. Virgil Cain: Detectives are not the forensic scientists. And they don’t always find out who did it. But the crime still exists.
That doesn't change the fact that they look into motive and opportunity. This is done to exclude some probable suspects from suspicion and also to exclude all the crackpots who call in to confess to famous crimes. The crime still exists but the active work of the detectives can lead to conclusions that might include suicide or accident instead of an assumption of murder, which would not have happened if they had closed their case without looking into motive and opportunity. Detectives don't stop at; " Someone must have done it, case closed."Carpathian
August 26, 2015
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Mapou:
Why do we continue to waste our time with this stupid troll? What is our motive?
Your motive is to get creationism in schools. The problem ID has is that it can't answer the questions an average student would ask. That's why you get frustrated with people like me. I ask questions, and you don't have answers. Here's a few questions students might ask. If the intelligent designer created life that could respond to changes in the environment, why bring up the intelligent designer at all? If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once?Carpathian
August 26, 2015
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Carpie:
There is no motive for an intelligent designer. There is no opportunity for an intelligent designer. That rules out an intelligent designer as a suspect.
Why do we continue to waste our time with this stupid troll? What is our motive?Mapou
August 25, 2015
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Carpathian:
When a detective investigates a case, he doesn’t just look at circumstantial evidence, but also looks into motive and opportunity.
Detectives are not the forensic scientists. And they don't always find out who did it. But the crime still exists.
There is no motive for an intelligent designer.
Cuz you say so? That's not an argument.
There is no opportunity for an intelligent designer.
Why not? There is plenty of evidence for an intelligent designer so obviously there was opportunity. OTOH your position still has nothing.Virgil Cain
August 25, 2015
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Virgil Cain:
That is a scientific requirement. Look, obviously you are just an ignorant troll. Why do you even bother posting seeing that you are so ignorant as to not understand anything?
When a detective investigates a case, he doesn't just look at circumstantial evidence, but also looks into motive and opportunity. Why doesn't ID? I can tell you. There is no motive for an intelligent designer. There is no opportunity for an intelligent designer. That rules out an intelligent designer as a suspect.Carpathian
August 25, 2015
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Carpathian:
If you really want to make headway, find the programmer.
That is a scientific requirement. Look, obviously you are just an ignorant troll. Why do you even bother posting seeing that you are so ignorant as to not understand anything?Virgil Cain
August 25, 2015
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Earth to Alicia Cartelli- Your position cannot explain biology. It cannot explain Drosha nor Pasha. So please buy a vowel.Virgil Cain
August 25, 2015
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bornagain77:
As to the fact that the cell is a sophisticated biological computer, programmed far above anything man has ever accomplished in his machines, do you disagree with that fact? If so you are more ignorant of biology than expected in spite of how hard you toot your own horn.
The dispute between evos and IDists is exactly whether the cell has been programmed by an intelligent agent or not. What you have implicitly said is, "We are right since we are obviously right" That's not a very scientific argument. If you really want to make headway, find the programmer. Find how designs are updated across millions of population members distributed across continents. It shouldn't be difficult since you have his/her/their designs. That would convince people. Not even trying to examine the designer or his mechanisms would convince me you don't believe in the science of ID yourself.Carpathian
August 25, 2015
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You guys are funnyyyy! I mean really, the people that actually study quantum dynamics barely understand it. And I'm supposed to believe that the keyboard warriors here have enough of a grip on it to apply it in a conversation about biology? Please. You guys have a lousy understanding of biology and yet love to talk about its complexities, and it shows. I can only imagine how a conversation with both molecular biology and quantum mechanics intertwined would go. When someone wants to talk about BIOLOGY and not the far-flung field of "quantum biology" that apparently exists, I will be here.Alicia Cartelli
August 25, 2015
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SA, “We’re smarter than you, so evolution wins” yes exactly. :) Moreover, this whole “We’re smarter than you, so evolution wins” argument has been around for a very long time. In fact, Paul describes their “We’re smarter than you, so evolution wins” strategy all the way back in Romans 1:22-23
Romans 1:22-23 Professing themselves to be wise, they became fools, And changed the glory of the uncorruptible God into an image made like to corruptible man, and to birds, and fourfooted beasts, and creeping things.
bornagain77
August 25, 2015
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BA77
Of course, wd400 beat you to that whole ‘shtick’ years earlier. i.e. ‘You just don’t understand evolution
That's the best. :-) "We're smarter than you, so evolution wins".Silver Asiatic
August 25, 2015
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BA77 @ 122 -- LOL. Some great arguments there. :-) I love this one:
"You brought up quantum dynamics and molecules carrying out computations. What you have said simply makes no sense to me, and is far removed from any actual biology."
Or, in translation: "It's not the linear sequence that Darwin proclaimed in the 19th century, so it's not real biology". Or a better translation: "The quantum dynamics in protein folds are irreducible to my primative materialistic worldview, so I don't want to talk about it". If she keeps working that shtick she might land a nice stand-up routine in the Catskills. Ba-da-bump.Silver Asiatic
August 25, 2015
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“Mystery at the heart of life” https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/ “The third way…” https://uncommondescent.com/evolution/a-third-way-of-evolution/bornagain77
August 25, 2015
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BA77 Please, would you mind to letting your 'nice' interlocutor know that there's plenty -over 1600 (combined) references to recent research papers- to talk about biology (the real deal) in the discussion threads (started by News) "Mystery at the heart of life" and "The third way...". Thank you.Dionisio
August 24, 2015
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Of supplemental note to protein folding. Protein folding is now found to belong to the world of quantum physics and not to the world of classical physics as is presupposed in the reductive materialism which undergirds neo-Darwinian thought:
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Today, Luo and Lo say these curves can be easily explained if the process of folding is a quantum affair. By conventional thinking, a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between. But Luo and Lo say that if this process were a quantum one, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
bornagain77
August 24, 2015
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Ahh, we were starting to like your 'shtick'. i.e. "Its junk I tell you because I am so much smarter than you!" :) Of course, wd400 beat you to that whole 'shtick' years earlier. i.e. 'You just don't understand evolution' LOL You guys really need to get a new routine!bornagain77
August 24, 2015
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And there you have it. Goodbye bornagain. Anybody who wants to talk about biology, I'll be checking in every once in awhile.Alicia Cartelli
August 24, 2015
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Alicia Cartelli, you did not answer my question, i.e. are you a true believer in neo-Darwinian evolution or are you among the growing number of heretics? Please clearly state your religious preference. :) I promise the beheading will be merciful :) Since you apparently hate 'cut and paste', (i.e. knowledge), Alicia, not to mention hating any empirical evidence that might hint at design, and I certainly don't want to hurt your love for your delusional atheistic religion, you can just ignore the rest of my post Alicia Cartelli as it will not be addressed to you. (and since you will ignore the relevant points of evidence anyway) ========= For onlookers, Alicia Cartelli displays her self imposed neo-Darwinian ignorance here:
"What you have said simply makes no sense to me, and is far removed from any actual biology."
Actually, despite her apparently self-imposed Darwinian ignorance of biology, 'quantum computation' is turning out to have everything to do with biology. From Protein folding to DNA repair, to who knows what else, quantum computation is strongly implicated to be essential in bio-molecular processes. For prime example, one of the most profound puzzles in molecular biology is the question of how does a protein find its final folded form so quickly. Specifically, it is now known that proteins do not find their final folded form by random search as would be expected in a neo-Darwinian view of things:
The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012 Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are. http://www.evolutionnews.org/2012/10/a_revolutionary065521.html Confronting Science’s Logical Limits – John L. Casti – 1996 Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard. http://www.cs.virginia.edu/~robins/Confronting_Sciences_Logical_Limits.pdf
Linking together a few hundred thousand computers has shortened the time to a few weeks
A Few Hundred Thousand Computers vs. (The Folding Of) A Single Protein Molecule – video https://www.youtube.com/watch?v=lHqi3ih0GrI
The reason why finding the final form of a folded protein is so hard for supercomputers is that it is like the ‘traveling salesman’ puzzle, which are ‘Just about the meanest problems you can set a computer (on) ‘.
DNA computer helps traveling salesman - Philip Ball - 2000 Excerpt: Just about the meanest problems you can set a computer belong to the class called 'NP-complete'. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the 'travelling salesman' puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,, Solving the traveling-salesman problem is a little like finding the most stable folded shape of a protein's chain-like molecular structure -- in which the number of 'cities' can run to hundreds or even thousands. http://www.nature.com/news/2000/000113/full/news000113-10.html
And protein folding is indeed found to be a 'NP-complete' problem
Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results – 2009 Excerpt: Protein Folding: Computational Complexity 4.1 NP-completeness: from 10^300 to 2 Amino Acid Types 4.2 NP-completeness: Protein Folding in Ad-Hoc Models 4.3 NP-completeness: Protein Folding in the HP-Model http://www.cs.brown.edu/~sorin/pdfs/pfoldingsurvey.pdf
Yet it is exactly this type of ‘traveling salesman problem’, i.e. NP complete problem, that quantum computers excel at:
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013 Excerpt: quantum computing is, "in some cases, really, really fast." McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "travelling salesperson" problem that's been a foundation of theoretical computing for decades.,,, "This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory." per Science Daily Scientists achieve critical steps to building first practical quantum computer - April 30, 2015 Excerpt: If a quantum computer could be built with just 50 quantum bits (qubits), no combination of today's TOP500 supercomputers could successfully outperform it (for certain tasks). http://phys.org/news/2015-04-scientists-critical-quantum.html
That proteins have the inherent ability to perform quantum computation, and thus provide an adequate solution to the protein folding enigma, is established by the fact that proteins are now found to have quantum information embedded within them:
Classical and Quantum Information Channels in Protein Chain - Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija - 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural - amino acids and peptide planes, (2) energy - classical and quantum state, and (3) information - classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491
And Quantum information is indeed the 'physical resource' by which quantum computation is accomplished:
Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/
supplemental note on quantum information in DNA:
Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it) https://youtu.be/2nqHOnVTxJE?t=1176
bornagain77
August 24, 2015
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I also said I would entertain anything that was "biologically relevant." You brought up quantum dynamics and molecules carrying out computations. What you have said simply makes no sense to me, and is far removed from any actual biology. I fear that "the sequences have...some type of computational purpose, perhaps quantum...molecular information is expressed ...to allow an appropriate computation to take place," is just you trying to work in your typical copy/paste quantum dynamics-post nonsense. You either need to explain yourself better, give an example, or admit that you actually have no idea what you are talking about when it comes to biology (and quantum dynamics while were at it). Cue the "spooky actions at a distance" and the other usual nonsense copy/paste job...Alicia Cartelli
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