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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
Alicia:
The word design is thrown around a lot by scientists, but they never mean ID because there is no benefit to just attributing something to some designer in the sky.
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. BTW Alicia, ID is not anti-evolution which means it isn't enough to say "evolution did it". You have to be more specific. You have to show how unguided evolution can produce regulatory networks. Good luck with that as no one has been able to do so- it cannot be modeled.Virgil Cain
August 20, 2015
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Alicia Cartelli: So no one is offering up some “other possibility?” What are you talking about? I listed quite a few. Mapou: Alicia @18, obviously you have a reading impediment. Well, my post in response came right after the post asking the question, so I understand how it could easily be overlooked.Mung
August 20, 2015
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Alicia aka Elizabeth Liddle:
there is no benefit to just attributing something to some designer in the sky.
There is, of course, plenty of benefit to just attributing it to dirt-did-it. You just got to love dirt worshippers.Mapou
August 20, 2015
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"Designer in the sky" is an atheist phrase lol. Why pay any credence to that? Just one more example of Atheism stunting the science:) The "Appearance of Design" contingent is also stunting science:(ppolish
August 20, 2015
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Science doesn't "stop at surprising," don't worry. The word design is thrown around a lot by scientists, but they never mean ID because there is no benefit to just attributing something to some designer in the sky. What I originally asked for, was the alternative. Instead of evolution giving rise to what seems like a massively inefficient process, maybe you can tell me about the possible intelligence and reasoning behind this "design."Alicia Cartelli
August 20, 2015
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Alicia, seems obvious to me the "other possibility" PaV suggests is ID. Made it pretty clear really. So Science should not stop at "surprising", but try to understand the ID. Can actually move Science ahead that way. Many modern scientists are so afraid to use the "D" word, and it is truly stunting science sigh.ppolish
August 20, 2015
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The “other” possibility is that “evolution” can’t explain this result. You DON’T have to have another model in place to know that there is a conflict between what a theory expects and what is actually found. That’s how science operates.
You'd have to be able to point to where there is a conflict between what the the theory entails and what is actual found. The theory of evolution is not in trouble if scientific consensus the first stone tools used by hominids occurred X mya, and next week we find evidence from archeologists that under thorough analysis indicates that the first stone tools were used 2 million years earlier than X. That would be unexpected (else the consensus would not be a consensus) but that is not a problem with the model, the theory. Evolutionary theory does not predict or entail X or X-2mya for stone tools. Denyse will be happy to ring in her fee for filling post quotas here with amusement that those know-it-all scientists were "surprised" by the finding, but there is not problem with the model from these kinds of "don't fits". If we were to find species and lineages that did not share morphologies, and did not have genetics that formed ancestral lineages in a nested hierarchy, THEN we'd a problem with the model. We don't have those kinds of problems in view, and evolutionary theory is conspicuously free of these potent problems.
Quantum mechanics arose because the experimental evidence they uncovered about atomic spectra did not fit into strictly classical mechanical analysis. But the QM mathematical structure would arise later, as a RESULT of the fact that there was a contradiction between CM and the raw data.
This is a very good example of the principle described above. This is "model-problematic", and its entailed clearly by the math. The model cannot accommodate our observations and makes entailed predictions that do not match our empirical input. But this is precisely what does NOT happen with evolutionary theory. We can go over the entailments, the hard commitments of the model, and our empirical data does fit, and is not problematic. It validates the model in an overwhelmingly robust way. A good example of misconception is the creationist suspicions about the Cambrian Explosion. Many believe, through apologetic patterning from Meyer and other or other reasons, that the Cambrian Explosion is problematic for evolutionary theory. It's not, not even a little. It's certainly an area where scientist do not have robust answers for why speciation and radiation happened at the rates the did versus the rates we infer from other periods, but the Cambrian, on its most narrowly compressed timeline, spans way enough millions of years to accommodate all the changes we see and a great deal more. The OP of this thread is yet another example of confusing "surprise" in the details and outcomes from a general framework with a problem in the framework itself. If you can show where the evolutionary model predicts a different outcome than we find, an outcome that is entailed and experimentally at odds with this, then you have a point. But there is not such entailment, no such prediction from the theory on the size of the transcripts must be from miRNAs. If I missed that feature of the model, you'll have to direct me to it. That doesn't mean scientists aren't regularly surprised and won't continue to be. They will and that that's a good thing. There are umpteem million details to discover about the various aspects of biology that are going to surprised, need revision, and perhaps be revised again (and yet again) as more data fills in the huge gaps on the particulars of all these subjects. But these discoveries are not at odds with what evolutionary theory entails in the model -- common descent, nested hierarchies in speciation, cumulative feedback loops driving population genetics, etc.
The fact is that ID can “explain” what we see happening in terms of an intelligent agent. This doesn’t “prove” that the ID explanation is true; but, at least it has the merit of being able to explain, if not predict, the experimental evidence.
Explaining in this is story-teller terms is trivial. We can explain anything with "Goddidit", literally anything, and that has been a "go-to" alternative for humans since time immemorial. What is challenging, but worthwhile in terms of epistemology and knowledge building is explaining with a model. This makes the explanation accountable and compatible with the rest of scientific knowledge if successful. QM models, like you referenced above, are a good example of this, and a stark contrast to what ID provides as explanation, which is "story-teller explanation". ID's story telling may be correct. But if so, it's not addressable as science. To explain what we have happening around us in terms of an intelligent agent AS part of a scientific model is a formidable task, no doubt. But that's how science operates. As it is, it all works out as it should. ID advocates are fine with story-telling models, from what I've seen and neither need nor particularly value the epistemic gains that would come from a scientific model that was centered around an intelligent designer, if such a model were to succeed when it came into contact with empirical tests.eigenstate
August 20, 2015
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Well, the author of the original paper proposed that the transcription of a massive nucleotide strand in order to ultimately produce just a ~22bp fragment allows for complex regulation of the miRNA. I am asking what the "other possibility" is, that was mentioned by the UD author.Alicia Cartelli
August 20, 2015
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Other than what, Alicia Cartelli? Other than the Modern Synthesis? How about EES or ID?ppolish
August 20, 2015
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Alicia @18, obviously you have a reading impediment.Mapou
August 20, 2015
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So no one is offering up some "other possibility?"Alicia Cartelli
August 20, 2015
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ppolish - it's interesting because self-organization is evidence for ID on one side and evidence for "just the way it is" on the other. But ID is more reasonable since it proposes a source for self-organizing powers. Ultimately, evolution and ID trace back to the same source for organization, function, purpose, the appearance of design, ordering principles and systems ... to whatever it was at the very beginning. The multiverse story could simply claim that self-organization of molecules to organisms to the earth's biosphere were already present at the big bang (and are the lucky result of one of an infinite number of universes). Or it's even easier just to say that the big bang possessed all those qualities just by virtue of being a thing that could go bang. Proposing that purpose and functional order have their origin in an ultimately purposeful source of order and design, is more parsimonious and philosophically coherent. It makes sense of much more than merely the organization of molecules -- namely, it makes sense of human cognition, self-awareness, purpose, moral judgement and religious sense that has always been present in every human culture. The multiverse gives a just-so story about origins, and everything that follows is "just the way our universe happened to be".Silver Asiatic
August 20, 2015
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"That’s how science operates. Exactly, PaV. A scientific theory can never be proven true - there is always a chance it can be falsified by experiment. I'm an IDiot, but I wonder - can ID be falsified? Like a Multiverse, ID can explain the the impossible complexity and fine tuning in Nature. But I'm not sure it can be falsified.. Although the evidence supporting ID is much stronger than the evidence supporting unguided purposeless oops. I mean it's the same evidence for both, but ID explains that evidence in a more scientific way. Evo Design better than Evo Oops. EES moving in that direction though. When the Extended Evolutionary Synthesis (EES) speaks of Evolution Design, I don't think they mean "appearance of design". They've move past that.,,ppolish
August 20, 2015
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eigenstate: The "other" possibility is that "evolution" can't explain this result. You DON'T have to have another model in place to know that there is a conflict between what a theory expects and what is actually found. That's how science operates. Quantum mechanics arose because the experimental evidence they uncovered about atomic spectra did not fit into strictly classical mechanical analysis. But the QM mathematical structure would arise later, as a RESULT of the fact that there was a contradiction between CM and the raw data. The fact is that ID can "explain" what we see happening in terms of an intelligent agent. This doesn't "prove" that the ID explanation is true; but, at least it has the merit of being able to explain, if not predict, the experimental evidence.PaV
August 20, 2015
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The question of design is a binary one. Either design is the case or it's not. "Who is the designer" is irrelevant to the question of design. I accept that "how x came to be" is not indicative one way or the other relative to this question. I also accept (IMHO) that the question while a binary one, can and should only be analyzed as a matter of probability. Even if blind-watchmaker evolutionary processes were the case they can easily be a false positive for non-design as science is limited in scope to what it can observe and measure collectively and beyond. So I conclude, that ID is a viable hypothesis and the design question cannot be limited to science (at least not the current version), but must incorporate all aspects of reality including our experiences which themselves should be weighed in as evidence as I feel since we're the product of this design that we should therefore understand it better than a rock.computerist
August 19, 2015
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eigenstate, A few points and I'm gone. 1. Your or anyone else's understanding of what Yahweh (or any other hypothetical designer) can or cannot do is irrelevant to the theory. 2. Your or anyone else's belief that there was or was not a designer is irrelevant to the theory. 3. The three items in the first list are not predictions. They are the hypotheses of the theory. 4. Hypotheses are assumptions. Predictions are claims that will falsify the hypotheses (hence the theory) if they don't pan out. That is all. I don't wish to discuss this anymore. Sorry.Mapou
August 19, 2015
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@Mapou, I guess i missed this part of your comment on the first pass:
So there you have it, 3 falsifiable predictions based on intelligent design. And guess what? Items 1 and 2 have already been corroborated by direct observation. Item 3 is in the process of being corroborated as we begin to use computers to unravel the secrets of the genome. One cannot be more Popperian than this.
Let's just focus on the first one in efforts to keep things simple. You gave us this generalization for #1:
1. They conduct fact finding or what-if experiments.
That's not a prediction of a model, but if I understand you, this would translate to a prediction like this: 1. The Designer has to conduct fact finding or what-if experiments or simulations to determine what some aspects or outcomes of a candidate design will be. That strikes me as way underspecified, but setting that aside for now, how would we test for falsification of this? That is, what test could we run that would show us this prediction is false, if it were indeed false?eigenstate
August 19, 2015
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@Mapou, Kudos for at least giving this a go, which is more than most everyone else on the pro-ID side is willing to venture.
Well, here goes. Intelligent design supposes the existence of intelligent designers. We know a lot about how intelligent human designers design things and we can use that knowledge to make a few predictions about how living organisms were designed. We know that intelligent designers do the following: 1. They conduct fact finding or what-if experiments. 2. They reuse existing designs as much as possible. 3. They organize complex systems hierarchically.
Ok, I think all these are reasonable as typical or practical tasks for intelligent designers we know of.
1. Multiple waves of species explosions followed by sudden extinctions should exist in the fossil record. Given the complexity of terrestrial ecology, these fact-finding experiments could conceivably last tens or even hundreds of millions of years. There are certain things that cannot be calculated in advance because the combinatorial explosion will not allow it. They must be allowed to run their course.
This does not follow. For some conceivable designer, perhaps. For every supposed Designer that qualifies, you can match it with a Designer that is not so bound, or so limited. Just to name a popular example, Yahweh as our putative Designer would not have any trouble with forward-looking calculations, no matter how complex or chaotic (he is an omni-god, after all doncha know). So right here, you'd have to start "giving shape" to your Designer in your model. That's good and well, but now you have a Designer than cannot probe or simulate far into the future.
2. Organisms should be classifiable in a mostly nested hierarchy.
Doesn't follow, is not entailed. If I'm imagining an extraterrestrial/alien style Designer, something like a (smarter human), this is plausible, but even then in no way is it entailed. More importantly though, nothing precludes a Designer that designs each species "from scratch", or maybe just starts anew with each "baramin". There are no rules or expectations to be had, and thus no predictions that can be deduced from the "imaginary space of Designer candidates" you are drawing from. Why not a Designer who eschewed all three of your "typicals"? Einstein didn't have that problem because his model was mathematical, and was ultimately fully entailment-rich by virtue of the math. It was just a matter of symbolic calculus, you or I could have calculated the same perihelion for Mercury as he did as a prediction of the model. Just offering that for stark contrast with the problem ID proponents have in this area.
3. The genome is organized within a strict control hierarchy.
We have NO Designer in view, even as a conjecture, to deduce this from. If there was a Designer, then I wouldn't be surprised to find that was "trait" of this Designer, simply because that's the pattern we observe in genetics. But this is the Texas Sharpshooter Fallacy redux: you're looking at what is -- 'where the bullet hit' -- and mapping human characteristics to an unspecified, abstract Designer -- 'painting a target around the bullet hole'. Scientific models go the other way, which is what grounds the epistemology. We conceive of a model we suppose might account for the phenomena, but which is not dependent on that phenomena, or beholden to it -- it's general. We can apply it to new and previously unconsidered scenarios and ask "what does the model predict", and then test it. With your anticipations here, none of them proceed from any model. We might just as well say that none of them apply or that a putative Designer maybe adopts (1) but not (2) or (3). And the evidence being what it is won't help you, because there's nothing in the model that compels it to be that way. blockquotes, spellingeigenstate
August 19, 2015
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eigenstate:
What novel predictions does this competitor model entail? How would those predictions be different than the current (hypothesized) model, and how would that be tested? It would be awesome to see something substantive proposed here, something that could be put through the same testing and evaluation regimen as the current (mainstream biological) model. So, let’s see the alternative model, already!
Well, here goes. Intelligent design supposes the existence of intelligent designers. We know a lot about how intelligent human designers design things and we can use that knowledge to make a few predictions about how living organisms were designed. We know that intelligent designers do the following: 1. They conduct fact finding or what-if experiments. 2. They reuse existing designs as much as possible. 3. They organize complex systems hierarchically. For each of the hypotheses listed above, we can make the following predictions: 1. Multiple waves of species explosions followed by sudden extinctions should exist in the fossil record. Given the complexity of terrestrial ecology, these fact-finding experiments could conceivably last tens or even hundreds of millions of years. There are certain things that cannot be calculated in advance because the combinatorial explosion will not allow it. They must be allowed to run their course. 2. Organisms should be classifiable in a mostly nested hierarchy. 3. The genome is organized within a strict control hierarchy. So there you have it, 3 falsifiable predictions based on intelligent design. And guess what? Items 1 and 2 have already been corroborated by direct observation. Item 3 is in the process of being corroborated as we begin to use computers to unravel the secrets of the genome. One cannot be more Popperian than this. Don't run from the evidence. Live with it.Mapou
August 19, 2015
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@ppolish,
The “Guided Evo Model” had fewer surprises than the “Unguided Evo Model”, Eigenstate.
Nah. Literally everything that happens in a guided evolution hypothesis is a surprise, unless you incorporate God or the Designer in as part of your model -- and that's never been done. The awesome thing about scientific models and the sucky thing about "guided" models is that the unguided models actually can make entailed predictions, predictions that proceed directly from the dynamics of the model. <blockquote) Instead of being surprised, the Guided Model says “hmmm…how did Nature do that?”. Good question. Good Science. Better than “oops – surprise!” It's not science at all, because "Nature" is not an actor. With a guided model -- which is just code words for "God did it" or "Designer did it", you are immediately at a dead end as soon as you ask the question. How would you determine an answer for "how did Nature do that?" All one can say is that "This is how the Designer/God wanted to do it". The Designer/God is not available to ask (we can't even get a point where we have a rational basis for believing such an entity exists in first place!), we can't test it, can't freeze some variable and see what the Designer/God would do with X free and other key variables isolated, controlled. It's just a dead end. All we can do is whistle in wonder at the impassable ineffable, completely opaque and utterly mysterious nature of the Designer/God. Which is to say, we abandon good science for religion.
Guided Evo Model….”Scientists were impressed to discover…” Unguided Evo Model…”Scientists were surprised to discover…” Impressed Scientists are better than Suprised Scientists. Smarter.
No. It's fine to have a sense of wonder, but what makes scientists better are working models, and the ideas and conjectures from their imagination that can either be falsified, or mechanized into formal, empirically tested and validate models -- theories. Being impressed by a god is a handicap. There are lots of religious scientists who are good scientists, but as good scientists they set their superstitions aside and become "methdological naturalists" to do their work.
Mr Spock was never surprised by a discovery. He would raise an eyebrow and say “Interesting” or if really cool discovery “Fascinating”. Good scientist right there. 1st Science Officer I believe.
You know that was a kitschy sci-fi TV show from the late 60s and early 70s, right? ;-) Gods and cosmic designers are only as interesting and useful to science as they are applicable in scientific models. That's why both are non-factors in science, they don't fit, they're superfluous, useless, ciphers. The door is wide open for anyone to come forward with a working model that incorporated such an entity. They'd be instantly world famous if they could contribute such a thing. But no one does and no one will, because if God/Cosmic Designer exists, all we can do as puzzle and muse about the black box, the impenetrable anti-model it represents in our universe.eigenstate
August 19, 2015
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Guided Evo Model….”Scientists were impressed to discover…” Unguided Evo Model…”Scientists were surprised to discover…”
You forgot one. Perhaps "Evo", meaning common descent, is not really necessary. The results Creation Model... "Scientists were left in awe of the Creator by the discovery of...."tjguy
August 19, 2015
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There IS an alien craft on Mars. Rover. Probably brought some alien microbes there too.ppolish
August 19, 2015
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Headline: ALIEN CRAFT FOUND ON MARS eigenstate: "That's not a testable model therefore the supposition of alien origins is unscientific." Which occurrence is the least likely?englishmaninistanbul
August 19, 2015
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What Computational Biology simulation/program would be more impressive; 1) Oops - a Weasel or 2) How to design a Weasel #2 of course. Why even waste your time on #1? Oh, I think we al know why:(ppolish
August 19, 2015
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The "Guided Evo Model" had fewer surprises than the "Unguided Evo Model", Eigenstate. Instead of being surprised, the Guided Model says "hmmm...how did Nature do that?". Good question. Good Science. Better than "oops - surprise!" Guided Evo Model...."Scientists were impressed to discover..." Unguided Evo Model..."Scientists were surprised to discover..." Impressed Scientists are better than Suprised Scientists. Smarter. Mr Spock was never surprised by a discovery. He would raise an eyebrow and say "Interesting" or if really cool discovery "Fascinating". Good scientist right there. 1st Science Officer I believe.ppolish
August 19, 2015
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Don't be coy then, throw out another model that should be considered as a competitor for the model being hypothesized in the article. What novel predictions does this competitor model entail? How would those predictions be different than the current (hypothesized) model, and how would that be tested? It would be awesome to see something substantive proposed here, something that could be put through the same testing and evaluation regimen as the current (mainstream biological) model. So, let's see the alternative model, already!eigenstate
August 19, 2015
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AC: What “other possibility” are you talking about exactly? Magic. Emergence. Poofery. Effervescent quality. Wishful thinking.Mung
August 19, 2015
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What "other possibility" are you talking about exactly?Alicia Cartelli
August 19, 2015
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