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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
AC: You write: The pri-miRNA is transcribed with thousands of extra bases, only a small fraction of which play an important role in the next steps. This is where ID and Darwinism part company. I would not make this simple statement. Here's part of the orginal press release on this topic: Because processing occurs very quickly, standard methods such as RT-PCR or RNA sequencing detect full-length pri-miRNAs with poor sensitivity. Many miRNA genes, therefore, lack annotated features such as a promoter or splice sites, hindering progress in understanding their transcriptional and post-transcriptional regulation. The whole point of the article is that the pri-mi-RNA is much, much longer (which they have demonstrated) than was thought before, and that the techniques used before--the very techniques that you rely on when you criticize my position---were simply not powerful enough to enable experimenters to fully understand how the primer processing was taking place. The authors report the techniques they employed will help future experimenters to properly elucidate this processing. Your answer to me was telling me how these primers are processed. The article is telling us that the information you think you know is now outdated. [Here, for example, is what Wikipedia says about primer length: A single pri-miRNA may contain from one to six miRNA precursors. These hairpin loop structures are composed of about 70 nucleotides each. Only off by a factor of a thousand.] And I'm suggesting that you let this be an experiment in whether the Darwinian point of view, of which you are guilty, is the correct one, or that of ID. Just be open-minded about these things.PaV
August 21, 2015
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I highly doubt all three of those statements, Virg. And so you believe that organisms were once much more efficient and since then have only “devolved?” Interesting, the only problem is that your belief flies in the face of everything that people who actually understand biology have agreed upon. You’re going to advise me that my view is completely wrong, Pav? That’s a good one. The production of miRNA certainly is carefully directed. And this is done by a host of transcription factors, just as the expression of protein coding genes is. The pri-miRNA is transcribed with thousands of extra bases, only a small fraction of which play an important role in the next steps. This small fraction of bases forms a hairpin loop which is immediately cleaved by Drosha, while the excess bases dissociate and are chewed up by the cell’s nucleases. There is no methodical paring, just one cut removes the thousands of extra bases and later in the cytoplasm the small loop of the hairpin is cut to get an inhibitory ssRNA molecule. It doesn’t suggest that miRNA will “turn out to have a crucial role.” It is already well known how important it is in regulation and I have no idea why you think this would make me “abandon my Darwinian viewpoint.” I’m sorry to say this, but your pseudoscientific drivel may pass with the average person, but you would be laughed at by anyone who actually understands biology.Alicia Cartelli
August 21, 2015
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Evolution entails energy efficiency. Except when it doesn't.Mung
August 21, 2015
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AC:
Transcribing thousands of extra bases, the vast majority of which will just be chopped up, seems like an “intelligent search or fault elimination process?” Search for what? What faults? And can this be done in another way, without this huge waste of energy?
While this might be your natural inclination, I would advise you that your view is, almost likely, completely wrong. From my personal viewpoint, consistent with ID thinking, it is much, much more likely that what we're seeing is the production of something (the miRNA) whose effects are so powerful that its production must be carefully directed ('engineered'). Hence, there must be some kind of interplay between the long stretch of primal-RNA and other proteins, regulatory RNA elements, and genetic engineering elements in the DNA, which methodically (step-by-step) pares down the long stretch of RNA bases to the critical length. Analogously, we're very careful how we store explosive compounds. Instead of a simple can or jar, exotic steps may need to be taken to store it properly. Again, from my personal ID perspective, what we see here suggests that these miRNA will turn out to have a very crucial and pivotal role in the overall regulation of protein production and cell homeostasis. If you want to be fair-minded, then think this through ahead of time. Tell yourself that if this doesn't prove to be the case, and that, instead, there has been wasteful excess nucleotide production in the manufacture of miRNA, then this proves Darwinism is on the right track. But, if it turns out that there is some precise mechanism at work, involving many kinds (levels of interplay (interactions), with miRNA turning out to be much more important in regulation than at first thought, then you will abandon your Darwinian viewpoint, and begin to think along the lines of ID.PaV
August 21, 2015
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eignestate:
But this is precisely what does NOT happen with evolutionary theory.
Really? Didn't Darwin tell us that if the fossil record did not extend way into the distant, distant past, that this would invalidate his theory? Yes, he did. But the fossil record does extend that far back. If the paucity of fossil intermediates did not increase, then, Darwin said, this would be a difficulty on his theory. Yes, we have a whole lot of new "fossils," claimed to be "intermediates," but, are they true intermediates. The famous "eohippus" intermediates was proven not be true, and that was one of the 'best' such attempts. Stephen J. Gould, himself, has written about this. Then there was Mendelian geneetics, which turned out not to be of the type that Darwin has foreviewed in his Origins. The laws of genetics pointed in the direction of a kind of stasis. Something "new" had to develop, lest genetics ran the risk of just shifting things around ad infinitum, with little change. Fisher's Fundamental Theory of Evolution, based on two differential equations expressing birth rates and death rates, seemed to help. But this would lead to the idea that though enough variation would slowly build up via evolution, NS would be needed to maintain the "selected" new variants. Associated with this 'maintenance'was Haldane's Dilemna of undue genetic load. Now, when proteins began to be analyzed, and it was found that there was a tremendous amount of variability within them, Haldane's calculations made RM+NS untenable. It lead to the Neutral Theory of Motoo Kimura. He thought some other kind of explanation was required to explain the discovered level of polymorphisms. Darwinism wouldn't do it. Darwinists, trying to defend their view, said that "junk-DNA" was the likely outcome for a process that involves random events. They said the genome was full of junk. When ENCODE shattered this myth, they did to that team what they did to others before: throw scorn at them and deride them. "Junk-DNA"--- or shall we say its absence---disproves Darwinism (Modern Synthesis) once again. These are facts. And they are facts just like those that drove the move from CM to QM. Now, if you want to pretend none of this happened . . . . . well, I guess you're free to believe in unknown, unseen, untestable multiverses. You're free to do this. But DON'T call it "science." \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ ppolish:
I’m an IDiot, but I wonder – can ID be falsified?
There's lots of ways of falsifying it. (1) Find fossils that show a gradual development of features. By "gradual," of course, this means an extremely long list of fossil intermediates with small gradations in form. Claims are made; but, one must be a "true believer" to accept the parse evidence given. (2) The slow build-up of genes, starting with the most primitive forms, and ending with the most recent. What is most commonly found, and commented on elsewhere, is what could be termed "front-loading," an example of which is that the 'gene' for forming digits in the vertebrate hand is already present in the sea anemone (or sea sponge?). (3) Some natural law, or principle---like "least action"---at work in extremely simple biological systems that has the potential of bringing about change in such a way as to efficiently arrive at useful solutions. This is NOT what we see happening. E.g., in "The Edge of Evolution," Michael Behe demonstrates that the malarial parasite must simply "crunch out" the right answer, taking around 10^20 replications for it to do so. There appears to be not 'short-cuts' to this raw 'crunching out' of solutions. This severely hampers and limits what Darwinian evolution can bring about, hence the "Edge." Darwinists, of course, denounce him as a charlatan, who knows nothing, whose numbers are all wrong and deceiving. But, as you know, belittling someone's work doesn't mean you've disproved it.PaV
August 21, 2015
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Elizabeth uses speculation as fact. Darwinists do that all the time. It's a favorite pastime.Mapou
August 21, 2015
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Alicia:
It’s not propaganda, it’s an explanation of how evolution works geared toward laymen like you.
LoL! I understand how evolution is supposed to work. However I also understand the way it is supposed to work is impotent and cannot be modeled. BTW I bet this layman understands evolution and biology at least as well as you do.
ID is goal oriented?
Yes.
Why is the designer’s goal to waste massive amounts of energy transcribing and then destroying long stretches of nucleotides? Does that make sense?
Did you miss this: Yes but the alleged waste we do see could be due to random effects on that once much more efficient design. And it could be that there is a valid purpose that we just don't understand.Virgil Cain
August 21, 2015
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All in a days' work, UB. Another day, another dollar. Imagine what evamolution could do if it ever got some grey cells!Axel
August 21, 2015
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Crazy. Blind chaos can unleash itself from local dynamics to create an IC representational code, complete with open-endedness, efficient copying, and error mitigation, that will last for billions of years. It can put hollow bones, flo-through lungs and wings on the same frame. It can create the eye. And yet, those darn microRNAs...Upright BiPed
August 21, 2015
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My understanding of what is actually going on is correct. A lot of research depends on using RNAi correctly. Transcribing thousands of extra bases, the vast majority of which will just be chopped up, seems like an “intelligent search or fault elimination process?” Search for what? What faults? And can this be done in another way, without this huge waste of energy? “I predict that future research will uncover a few surprises.” You don’t say. I certainly hope it does. Great prediction. It’s not propaganda, it’s an explanation of how evolution works geared toward laymen like you. ID is goal oriented? Why is the designer’s goal to waste massive amounts of energy transcribing and then destroying long stretches of nucleotides? Does that make sense?Alicia Cartelli
August 21, 2015
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Alicia:
The bottom line is that evolution works with what is already present and isn’t goal-oriented.
That's propaganda, not evidence. Intelligent design evolution is goal-oriented
There is no “intelligence” involved in evolution, just making things more suited to the environment or better at survival, little by little.
More propaganda. A process in which whatever is good enough survives and reproduces wouldn't do that.
A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no?
Yes but the alleged waste we do see could be due to random effects on that once much more efficient design.Virgil Cain
August 21, 2015
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Elizabeth:
A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no?
Only if your understanding of what is actually going on is correct. You're just speculating. It looks more like the actual process is some kind of intelligent search or a fault elimination process. I predict that further research will uncover a few surprises. It always does. We've seen the bad design argument many times before. Remember junk DNA? As soon as one gets knocked down, another takes its place. It's old. Give it a rest.Mapou
August 21, 2015
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Elizabeth:
The bottom line is that evolution works with what is already present and isn’t goal-oriented. There is no “intelligence” involved in evolution,
Which is why it's a stupid theory. The curse of dimensionality kills it dead before it can get out of the gate.Mapou
August 21, 2015
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We know a good amount about “what is really going on during that process,” actually. Feel free to read-up on RNA interference. The bottom line is that evolution works with what is already present and isn’t goal-oriented. There is no “intelligence” involved in evolution, just making things more suited to the environment or better at survival, little by little. A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no?Alicia Cartelli
August 21, 2015
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Well don't we have something interesting here! Evolution can produce complex highly efficient proteins essential for life. In distant species it can converge multiple times independently to find the same complex solution to a common problem under different selection pressures. It can form complex organisms with coordinated nervous, secretory, vascular, lymphatic...etc...systems that work together in utter synchronicity. Yet what it really CANNOT do is evolve a regulatory system of a very short genetic component of 22bp in length but is stuck and unable to get around the horribly inefficient process of a huge genetic section needed for this small regulatory sequence. But this fits exactly what the theory of evolution predicts - nothing. If anyone honestly doesn't find this somewhat conflicting then they really lack the ability of discernment.Dr JDD
August 21, 2015
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Alicia:
So ID is the “other possibility?” Sure.
Actually it is the only possibility. Unguided evolution, ie natural selection and drift, are impotent.
There is nothing intelligent about a massive waste of energy.
And yet here you are.Virgil Cain
August 21, 2015
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Daniel King:
You’ve been at this for a long time.
Not as long as evolutionary biologists have been at it and they still have nothing. Unguided evolution is useless as a research heuristic.
What plans have you come up with?
Synthesize the parts one at a time- Venter already did the DNA.
Any ideas about the nature of the missing ingredients?
Software, ie immaterial information.Virgil Cain
August 21, 2015
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That massive "waste of energy" eventually led to a discussion of massive "waste of energy". Oops, you're right - massive waste of energy:) But isn't there some law about the impossibility of wasting energy? Doesn't it just move around or something?ppolish
August 20, 2015
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I just love it with these dirt worshippers. They never address or even acknowledge the weaknesses of their little pseudoscientific cult that others point out. Instead, they continually send their interlocutors on a wild goose chase. Lizzie:
Now my next question is where is the “intelligence?” Why spend so much energy transcribing so many bases, the vast majority of which will just be chopped up? There is nothing intelligent about a massive waste of energy.
You very well know this is a lame strawman argument on your part since you have no clue as to what is really going on during that process. A newborn's brain similarly has a huge numbers of synaptic connections, most of which disappear by the time the infant is a few years old. Lizzie would ask, "why connect them in the first place?" and Lizzie would be showing her cluelessness. Why does Lizzie think she can get away with her stupid tricks here? She's not very bright, that's why. But then again, very few Darwinists/materialists are.Mapou
August 20, 2015
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So ID is the "other possibility?" Sure. Ok, so the "design" is that the thousands of extra bases that are transcribed are part of a regulatory mechanism for the miRNA. Now my next question is where is the "intelligence?" Why spend so much energy transcribing so many bases, the vast majority of which will just be chopped up? There is nothing intelligent about a massive waste of energy.Alicia Cartelli
August 20, 2015
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Daniel, most bio research today is looking at design.
Design by an unidentified intelligence? What does "looking at" mean?Daniel King
August 20, 2015
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Find the software of life. If ID is right then living organisms are more than just matter, energy and what emerges from their interactions. We just need to formulate plans to flesh out the missing ingredients.
You've been at this for a long time. What plans have you come up with? Any ideas about the nature of the missing ingredients?
Intelligent designers invariably use a hierarchical architecture to manage complexity and the timing of events. Computational genetics researchers should search for this hierarchical structure in every genome.
Do you have any suggestions to guide that search?Daniel King
August 20, 2015
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King:
What is your research program for further investigation of Design?
Intelligent designers invariably use a hierarchical architecture to manage complexity and the timing of events. Computational genetics researchers should search for this hierarchical structure in every genome. Once it is found, it will open up a deluge of previously hidden information. One man's opinion.Mapou
August 20, 2015
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Daniel King:
What is your research program for further investigation of Design?
Find the software of life. If ID is right then living organisms are more than just matter, energy and what emerges from their interactions. We just need to formulate plans to flesh out the missing ingredients.Virgil Cain
August 20, 2015
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Daniel, most bio research today is looking at design. Of course, there are a few bonehead studies like the "E.coli Long Term Evolution" part time experiment. That's a waste of $$, but not very much.ppolish
August 20, 2015
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There is plenty of benefit to attributing something to a designer. For one it eliminates entire classes of possible causes and for another is tells us how to conduct any further investigation.
That might save a lot of time and money. What is your research program for further investigation of Design? I'll bet there are people who will fund it.Daniel King
August 20, 2015
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ppolish @21:
ID.,,,putting the logical back into biological.
I like that.Mapou
August 20, 2015
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ID...putting the logical back into biological.ppolish
August 20, 2015
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All stochastic search algorithms (e.g., RM+NS) are killed dead by the combinatorial explosion. They are only good for very small search spaces and toy applications. This is the reason that logical people look for an alternative but logical candidate, one that is nonstochastic. It turns out that the best candidate is intelligent design. The worst is dirt-did-it. If you are in the dirt-did-it camp, you are an idiot or an effing a-hole, or both.Mapou
August 20, 2015
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Throwing around the word "design" is more useful scientifically than throwing around the word "evolution", Alicia. That's why you see it being thrown around more these days.ppolish
August 20, 2015
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