Saturday, March 2, 2013

Circular RNAs: A Hidden, Parallel Universe

When Are These Surprises Going to Stop?

Remember when microRNA burst onto the scene a few years back and revolutionized our knowledge of cellular regulatory processes? Evolutionists had to scramble because, after all, when you say your theory explains something and it turns out you don’t really understand that something, well it looks like you don’t know what you’re talking about. It wasn’t much of a scramble though, because evolutionists can pretty much say anything they want, at any time, about their theory. So when microRNA burst onto the scene, evolutionists said “oh, evolution did that.” Well now it is happening all over again, but this time with long RNA which often interacts with microRNA, and this week it was with long RNA that is circular.

Evolutionists once dismissed these long, circular RNA macromolecules—which can be thousands of nucleotides long—as rare genetic accidents or experimental artefacts. Now circular RNA appears to be, err, an abundant and crucial part of genetic regulation. There are thousands of them, probably fulfilling a multitude of functional roles in what one evolutionist admitted is “a hidden, parallel universe” in the molecular world.

And amazingly the genes encoding these RNA macromolecules often overlap with protein-coding genes. Recall that protein-coding genes, in addition to coding for an incredible protein machine, may also contain several more layers of information encoding signals for the transcript (mRNA) stability, mRNA editing, DNA copy error correction, the speed of translation, the protein’s three-dimensional protein structure, the stability of that structure, the multiple functions of the protein, interactions of the protein with other proteins, instructions for transport, avoiding an amyloid state, any other genes that overlap with the gene, and controlling tRNA selection which can help to respond to different environmental conditions.

That is a tall order and now we have yet another layer of information for which genes much encode: circular RNA macromolecules which just happen to interact with microRNA and which just happen to be expressed at the right time, because if they are expressed at the wrong time you don’t have a normal brain. And amazingly, in protein-coding genes, circular RNA macromolecules may be encoded both in the antisense strand and in the sense strand. In fact numerous circular RNAs form by head-to-tail splicing of exons.

Not surprisingly, beyond “oh, evolution did that,” evolutionists have no scientific explanation for how circular RNAs could have evolved. As one evolutionist admitted, “You just wonder when these surprises are going to stop.”

71 comments:

  1. Come on, Cornelius, come up with a original act. This shtick is getting old.

    In the midst of the 20th century physicists were baffled by the cornucopia of new particles they were discovering in experiments. Reacting to the discovery of the muon, I. I. Rabi asked "Who ordered that?" It was an embarrassment of the riches. I wonder what the likes of Hunter would say in those days. "Dem physicists, looks like they don't know what they're talkin' about."

    Stop being such a sourpuss, Cornelius. Hail new experimental discoveries. Enjoy life.

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    1. I've read throguh a few articles and was wondering

      DO you and thornton just kind of sit around all day waiting for Cornelius to post and haven't you figured out that most of the time he just ignores you?

      He is hailing new discoveries and enjoying them btw. You just don't like how much he is enjoying them is all.

      Delete
  2. Another interesting thing about microRNA is that it heavily conflicts with conventional phylogeny of higher taxa like mammalia.

    "Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree."
    http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

    Would be interesting to see some comparisons with long RNA as well.

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    1. Good point. I mentioned the microRNA incongruence here:

      http://darwins-god.blogspot.com/2012/06/evolution-professor-tree-is-all-wrong.html

      Delete
  3. 'And amazingly the genes encoding these RNA macromolecules often overlap with protein-coding genes. Recall that protein-coding genes, in addition to coding for an incredible protein machine, may also contain several more layers of information encoding signals for the transcript (mRNA) stability, mRNA editing, DNA copy error correction, the speed of translation, the protein’s three-dimensional protein structure, the stability of that structure, the multiple functions of the protein, interactions of the protein with other proteins, instructions for transport, avoiding an amyloid state, any other genes that overlap with the gene, and controlling tRNA selection which can help to respond to different environmental conditions.

    That is a tall order and now we have yet another layer of information for which genes much encode: circular RNA macromolecules which just happen to interact with microRNA and which just happen to be expressed at the right time, because if they are expressed at the wrong time you don’t have a normal brain. And amazingly, in protein-coding genes, circular RNA macromolecules may be encoded both in the antisense strand and in the sense strand. In fact numerous circular RNAs form by head-to-tail splicing of exons.'

    So, you're saying they're intelligently designed? Any fool could have thought that up.

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  4. Just another of Cornelius' 'it's too complex to have evolved' posts.

    Cornelius, why aren't you working in a lab and/or in the field helping to find the answers to scientific questions? You and your ID comrades bash evolution, evolutionists, Darwin, etc., but what have you discovered and produced that actually moves science forward?

    It has been said a million times that even if you could prove that the ToE is all wrong, it still wouldn't prove that a designer-god, and especially your chosen designer-god yhwh-jesus-holy-spirit, actually exists and that it designed-created the universe or anything else.

    Are you ever going to present your 'ID' hypothesis that will provide scientists with avenues of research that have not been thought of or tried already? Are you ever going to provide positive evidence for 'ID', and especially positive evidence that you ID pushers discover on your own? Are you just going to waste your life bashing evolution and looking for gaps (whether real or imagined) in scientific discoveries and explanations in the vain hope that doing so will prove that yhwh-jesus-holy-spirit is the one (or three) and only designer-creator-god?

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    1. truthy:

      It has been said a million times that even if you could prove that the ToE is all wrong, it still wouldn't prove that a designer-god, and especially your chosen designer-god yhwh-jesus-holy-spirit, actually exists and that it designed-created the universe or anything else.

      That has nothing to do with the fact that the theory of evolution has already been falsified. Heck it does not even get out of the gate because it is a logically inconsistent theory. But I agree that a falsified theory of evolution does not prove that Yahweh created life on earth. Something much stronger is needed. Your prayers will be answered soon enough, though. Wait for it.

      Are you ever going to present your 'ID' hypothesis that will provide scientists with avenues of research that have not been thought of or tried already?

      LOL. How lame. Others are afraid to touch this topic but I have no such fear. Intelligent Design theory (Big ID) predicts that living organisms are classifiable within a hierarchical structure, i.e., a tree of life. A design hierarchy unfolds automatically whenever intelligent design occurs over a long period and previous designs are reused in newer ones. Big ID predicts a non-nested, super-efficient tree of life. By non-nested, I mean that an organism can inherit traits from multiple ancestors that reside in distant branches of the tree of life. In other words, the main falsifiable prediction of Big ID is this: many organisms will be found to share complex genetic material that could not have been obtained via common descent alone.

      By the way, did you know that the tree of life is a Biblical concept? ahahaha... So is the tree of knowledge. That's right. You bozos did not invent hierarchies. Surprise! ahahaha... AHAHAHA...

      Delete
    2. truthy:

      Just another of Cornelius' 'it's too complex to have evolved' posts.

      It bothers you because complexity actually kills evolution dead. You can't stand it. ahahaha...

      Delete
    3. louis said:

      "Big ID predicts a non-nested, super-efficient tree of life."

      "Big ID"? What does little and medium ID predict?

      And would you please explain how extinctions, deformities, diseases, suffering, and death fit into a designed "super-efficient tree of life"?

      "Something much stronger is needed. Your prayers will be answered soon enough, though. Wait for it."

      In other words: Repent now, the end is near! (LMAO)


      Delete
    4. I wrote you a nice reply but, apparently, Cornelius censored it. You're lucky. LOL.

      Delete
    5. The Whole Truth:

      Since you guys are all about mechanisms and processes and such, maybe you could explain how circular RNA evolved. Y'know, what were the mechanisms and processes? I would like some details, like possible functional intermediates. And if you would be so kind as to quantify things, I would really appreciate it. Y'see, I just hoping that you will give me the stuff you demand from ID proponents.

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    6. crickets chirping as they always do? Whats new?

      Delete
    7. Yes, truthy wants infotainment. Otherwise, it's not science. Truths get boring. Especially, when you're pestered to respond to them.

      By the way, my earlier post was intended as sarcasm.

      Delete
  5. The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Landscape of transcription in human cells – Sept. 6, 2012
    Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
    http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html

    Time to Redefine the Concept of a Gene? - Sept. 10, 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance.
    http://networkedblogs.com/BYdo8

    Of note: RNA’s are far more difficult to align into presupposed evolutionary relationships than Genes were:

    micro-RNA and Non-Falsifiable Phylogenetic Trees - (Excellently Researched) video
    http://www.youtube.com/watch?v=qv-i4pY6_MU

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  6. I don't see the problem. It's precisely this sort of unexpected discovery that makes science fun.

    As for it being a surprise, since nobody knew they were there in such numbers before, that's as true for EID/creationists as it is for evolutionists.

    This research also raises awkward questions for the paranoids who believe that evolution is just the corpse of a defunct theory being propped up by a worldwide conspiracy of evolutionary biologists for whatever reason. If that's true why publish findings which, according to the conspiracy theorists, could undermine confidence in the whole enterprise? In fact, why bother to do the research at all?

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    1. worldwide conspiracy of evolutionary biologists

      AKA a church. ahahaha...

      Delete
    2. "As for it being a surprise, since nobody knew they were there in such numbers before, that's as true for EID/creationists as it is for evolutionists."

      Utterly and obviously false. ID expects and predicts a much higher level of complexity than Darwin ever did

      Delete
    3. A new discovery does not necessarily mean a surprising discovery, at least to anything like the extent that Evolutionists express it so regularly, in relation to some finding, when some new feature of the natural world falsifies one their tenets.

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  7. CH: As one evolutionist admitted, “You just wonder when these surprises are going to stop.”

    J: They're not just surprises in the simple sense. They're surprises in the sense that they render guesses about fixed-mutation rates utterly speculative. And that, in turn, renders any inferences based on those rates ad-hoc themselves. There's nothing predictable in the theory that gets us beyond AIG style SA. And that's why the UCA'ists theological arguments seem so necessary to their claims about "overwhelming evidence."

    But of course, even that move is of no avail. For once even the mind isn't intelligently designed to infer in a truth-approximating way, inference itself is not knowably distinguishable from pure speculation. It's just a different mode of speculation. There is nothing entailed in the UCA'ists' presumed pre-consciousness conditions of the universe that implies consciousness would arise, much less with a truth-approximating inferential capacity.

    This is why Theobald is right--the UCA'ist can't, with the consensus view, non-arbitrarily rule out solipsism, epiphenominalism, LastThursdayISM, and the rest of the infinite views he/she rejects. This why they have no problem making their arbitrary claims about the existence of "over-whelming" evidence. They literally live in an arbitrary epistemology.

    So, I and TWT, CH is not arguing against the possibility of UCA. He's arguing against the claim that there is "overwhelming evidence" for it. There is no such thing.

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  8. When surprises stop, a science dies.

    Think of a science that no longer has any surprises. Classical mechanics comes to mind. Or geometrical optics. Both are valid scientific theories, but they stopped developing a long time ago. Any science that is in active development brings up surprises, almost by definition.

    So the answer to that question is not any time soon. That's true of evolutionary biology, cosmology, and condensed matter physics.

    In contrast, no surprises are expected in the field of scientific creationism. Amirite?

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  9. O, you're right that science is tentative and, therefore, can't rule out surprises. But what has happened is that the word "evidence" has assumed a relatively new meaning that is not being clarified to the unsuspecting public. By the old inductive definition of evidence, there is NO evidence of naturalistic UCA. But by the NEW definition of evidence, there is some evidence for it, though not a great deal.

    The problem is that the new meaning of evidence is derived by arbitrarily ruling out the finality of explanation entailed in a teleological epistemology. This, in turn, means all explanations involve, ultimately, an infinite set of ad-hoc hypotheses. This, in turn, makes relative plausibility calculations impossible, for all practical purposes.

    In short, the new meaning of "evidence" only works deceptively at the micro-level. Viewed holistically, at a more macro level, it is obviously illusory. The unsuspecting public doesn't realize these "games" are being played with what was once truly conventional language.

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  10. Jeff,

    No modern* scientific theory incudes teleological explanations. Evolutionary biology is not exceptional in that regard.

    *That includes Newtonian mechanics.

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    1. There isn't any "theory" of evolution, oleg. If you think there is then please provide a link to it.

      And Newton did include teleology.

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    2. Chubby Joke G

      There isn't any "theory" of evolution, oleg. If you think there is then please provide a link to it.


      Hey Chubs, that was a great meltdown you had Friday at ATBC! All that screaming and cursing by you - most entertaining one in years!

      I see you're still so ronery at your shithole blog you have to come back trolling over here. Oh well, it was peaceful while it lasted.

      Delete
    3. I see that you still have nothing to offer but false accusations and momma's boy BS

      Delete
  11. O: No modern* scientific theory incudes teleological explanations. Evolutionary biology is not exceptional in that regard.

    J: To the extent that it predicts, you're right. But that extent is so trivial that it's consistent with Ken Ham's view of natural variation.

    O: *That includes Newtonian mechanics.

    J: His mechanics were natural. But his epistemology, per se, was teleological and, therefore, entailed a finite finality to explanation.

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    1. Jeff, Newtonian mechanics is not synonymous with Newton's original thinking. Some of his ideas involved divine intervention—specifically his thoughts on the formation of the solar system. These ideas did not survive to this day. We have a modern theory of star formation that requires no divine intervention. Newton's theory of gravity and his laws of mechanical motion do not rely on teleology, and those are the theories that remain with us.

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    2. Your modern theory of star formation needs quite a few untestable assumptions and yes all of what Newton wrote was about design and a designer.

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  12. O: Newton's theory of gravity and his laws of mechanical motion do not rely on teleology, and those are the theories that remain with us.

    J: Explanation, to be valid in any normative sense, requires a teleological epistemology. I can conceive of multiple explanations for event sequences. But how do I know one is better in any conceivable sense than the other apart from teleology? How do I know the events occurred as per my apparent memories (i.e., how do I know apparent memories are actual memories?).

    Once you posit that you have not always existed, you have posited that your conscious experience also began. Now, explain that event naturalistically. If you can't, you can't explain anything more specific about that consciousness. And therefore, you can't explain the "validity" of inference, etc so as to distinguish it from speculation.

    You have no epistemology, as a naturalist that posits a FIRST historical conscious experience, that can account for NORMATIVE thought. Thus, nothing you believe is demonstrably better than what anyone else believes IF you're right about naturalism. That's why science is not demarcatable from non-science per naturalism.

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  13. Jeff: "Explanation, to be valid in any normative sense, requires a teleological epistemology."

    I suppose it depends on what you mean by an "explanation." A scientific theory, at any rate, requires experimental verification, not teleology. Newton's theory of gravity has been validated by experimental confirmations. Evolutionary theory is no different in this regard.

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    1. What evolutionary theory, oleg? Can you post a link to it so we can read it?

      Delete
  14. This comment has been removed by a blog administrator.

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  15. Jeff,

    Last Thursdayism is irrefutable. That does not make it an interesting hypothesis.

    Science uses a lower standard of proof than formal logic. That does not reduce its usefulness. Take it or leave it.

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  16. O: Newton's theory of gravity has been validated by experimental confirmations. Evolutionary theory is no different in this regard.

    J: But once you flesh out what "validated" means, you'll see that all we're ever meaning by that is that such explanations SATISFY in some specific way/sense. But how, on naturalism, is my satisfaction knowably correlated to truth or plausibility? That's what only teleology can explain, true or not.

    There's an infinite set of logical possibilities that are UNsatisfying and, therefore, rejected. But how is hypothesis rejecting based on the criteria of my satisfaction inconsistent with radical non-regularity of events, solipsism, epiphenominalism, a 100-yr old universe, etc on the assumption of naturalism? We need to explain a correlation of satisfaction TO plausibility/truth.

    But I can conceive of a teleological explanation that correlates real plausibility to my satisfaction in the ultimate sense. But that involves conceiving of the designer as sympathetic and therefore deriving the greatest long-term satisfaction from the greatest long-term satisfaction of designed, sentient beings.

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  17. J1: But how is hypothesis rejecting based on the criteria of my satisfaction inconsistent with radical non-regularity of events, solipsism, epiphenominalism, a 100-yr old universe, etc on the assumption of naturalism?

    J2: I should have said, "on the assumption of an a-teleological explanation of conscious experience," if naturalism is taken to mean determinism. But even determinism is consistent with solipsism and epiphenominalism.

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  18. Jeff: "But once you flesh out what "validated" means, you'll see that all we're ever meaning by that is that such explanations SATISFY in some specific way/sense. But how, on naturalism, is my satisfaction knowably correlated to truth or plausibility? That's what only teleology can explain, true or not. "

    I have adressed most of it in my reply to your deleted comment.

    To add to that, teleology may or may not be right. You could formulate a teleological theory with logical precision. Unfortunately, there is no way to test that. You can have a hypothesis that is perfectly sound on the logical level, but it is untestable. So in this case it's the word of one philosopher against the word of another.

    With science, it's different. Unlike philosophers, scientists don't duke it out among themselves. They do it to some extent, but scientific disputes aren't the ultimate judgment on scientific theories. Eventually any scientific theory is up against a more formidable judge: Nature. A scientific theory either advances our understanding of Nature or it doesn't. To do so, a theory must make specific predictions and these predictions be tested experimentally. Successful theories remain with us. That's how science works, for better of for worse. Demanding that science follow the rules of philosophy is silly and misguided.

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  19. O: To do so, a theory must make specific predictions and these predictions be tested experimentally.

    J: Right, and current NATURALISTIC evolutionary theory doesn't predict anything beyond Ken Ham separate ancestry. So why would I care that there's lots of scientists who, nevertheless, believe in UCA?

    O: Successful theories remain with us. That's how science works, for better of for worse.

    J: And everyone agrees with that except Eastern anti-realists, etc.

    O: Demanding that science follow the rules of philosophy is silly and misguided.

    J: And what rules would those be? I'm not aware of a philosophical consensus in opposition to what you and I are agreeing to. What CH and I are in agreement with is that the naturalistic portion of the ToE predicts precious little, none of which has any relevance to the relative plausibility of UCA and SA.

    If all you're saying is that science should continue to push at the boundaries of what is currently known about the kinds and degrees of naturally caused biological variation, then you have no disagreement from CH or me--or any other ID'ist that I'm aware of. We ask that the false claims about evidence be stopped so academic freedom, etc can flourish.

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  20. Jeff: "Right, and current NATURALISTIC evolutionary theory doesn't predict anything beyond Ken Ham separate ancestry."

    That's clearly false. Theory of evolution posits universal common ancestry, among other things. This hypothesis can, and has been, tested by building a tree of phylogenetic relations between extant species and checking the relations inferred through, say, morphological analysis against genetic information.

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    1. O: That's clearly false. Theory of evolution posits universal common ancestry, among other things. This hypothesis can, and has been, tested by building a tree of phylogenetic relations between extant species and checking the relations inferred through, say, morphological analysis against genetic information.

      J: It's your claim that is clearly false. Tree-generation rules have no known correspondence to the phenotypic/morphological/extinction effects of temporally-sequenced mutations. Heck, we're not done even learning WHAT DNA sequences CAUSE. Phenotypes are not predictable to any relevant degree, much less to the level of UCA-style trajectories.

      Explanation is deductive. No one has come close to showing that what is known about variation can IMPLY, per some posited environmental succession, that viable transitions would bridge the morphological gaps, much less in the posited time-frame.

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    2. Jeff, it's really simple. We can generate phylogenetic tree on two independent bases: (1) morphological characteristics, (2) genetic distance. We can check whether the trees generated in these independent ways agree, as evolutionary theory predicts. This is how scientific theories are tested.

      Let me give you a similar example from physics. In the 18th century Fresnel proposed a first wave theory of light. It was not a complete theory. It did not explain everything in optics (e.g., it lacked an explanation for polarization of light). But it did make a nontrivial prediction that light would go around an obstacle. An experiment to confirm that was conducted by Arago (see Arago spot). That was enough to establish Fresnel's wave theory of light as a favorite over Newton's corpuscular theory.

      Scientific theories never provide a final explanation that you require. They represent piecemeal knowledge. But that knowledge is much more solid than philosophical theories.

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    3. oleg:

      Theory of evolution posits universal common ancestry, among other things.

      As it turns out, it's not so universal. The exceptions are many and glaring. Big ID, by contrast, predicts a non-nested tree of life. In other words, an organism can inherit genetic material that come from distant branches of the tree. Why? Because that's what intelligent designers do. I call it design reuse via lateral inheritance. In other words, most branches are strictly nested but some are not. This is what we can expect from intelligent design over time. We know this is true from observing human designers.

      By the way, I use the term 'Big ID' to refer to an extension of the ID hypothesis that goes beyond strict design detection.

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    4. O: Jeff, it's really simple. We can generate phylogenetic tree on two independent bases: (1) morphological characteristics, (2) genetic distance. We can check whether the trees generated in these independent ways agree, as evolutionary theory predicts. This is how scientific theories are tested.

      J: First of all, the tree generation rules are modified all the time to accomodate newly-found anomalies. Second, those rules have NO known correspondence to mutational effects. Thus, they have nothing to do with a naturalistic causal theory. Similarity, per se, is not a cause, O. Temporal relationality, per se, is not a causal relation. You need a CAUSAL theory that IMPLIES that simlarities and temporal relations relate CAUSALLY in the way you posit.

      Just showing that such relationships can be used to generate trees was known by people who never inferred UCA at all. Because they're not necessarily related at all, much less causally, much less deterministically.

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    5. Jeff: "Temporal relationality, per se, is not a causal relation. You need a CAUSAL theory that IMPLIES that simlarities and temporal relations relate CAUSALLY in the way you posit. "

      Jeff, this is some philosophical gibberish that I don't care much for. Science is different from philosophy. If you wish to apply the same rules then you don't understand science and we won't make much progress understanding each other.

      Best,

      Oleg

      Delete
    6. Actually, O, it's modern physicists that posit causeless events and other counter-intuitive notions. I don't. E.g., there are some who posit that radioactive decay might be uncaused. So you are just dead wrong to claim that science doesn't distinguish between temporal and causal relationality. That's why the whole philosophy vs. science deal is just bogus.

      There are logical possibilities and plausibility criteria. There's nothing more to it than that. Scientists and philosophers may disagree on what logical possibilities are relevant to the particular methodological plausibility criteria they use, but that doesn't change the fact that induction only works with the assumption that events ARE caused and that explanation has finality and finitude to it. Such finality and finitude is only possible per a teleological approach.

      Subtract either of those axioms, and inductive plausibility criteria is out the window. At that point, I have no idea what you mean by evidence until you define it. So far, no one has.

      Not one future event is implied by the fact that critters are classifiable in terms of relationships that are graphically depicted by trees. It has nothing to do with specific causal theories. This should be obvious since that fact is articulable in ONE proposition. Nothing follows (i.e., is implied by) the truth of one proposition other than the falsity of its negation. Thus nothing is predicted by it. A prediction IS, by definition, an implication of a hypothesis that is articulable in 2 or MORE propositions.

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    7. Jeff: "Actually, O, it's modern physicists that posit causeless events and other counter-intuitive notions."

      Counter-intuitive does not mean wrong. Out intuition has developed in the context of macroscopically large objects. There is no reason why microscopic world should obey the same rules. So sometimes our intuition can be an impediment.

      That turned out to be the case with quantum mechanics. Our classical intuition told us that we can know both the coordinate and velocity of a particle with arbitrary precision (as long as we have precise measuring tools). That turned out to be not true at the microscopic scale: there is an inherent uncertainty in a simultaneous measurement of these quantities. It is simply impossible to know both the coordinate and velocity of a particle. No one, God included, can do that.

      There are even stranger things than that. If you prepare an electron in a state with its magnetic moment pointing up the vertical axis and then measure its component along a horizontal axis, you will always get values +1/2 and –1/2 (in certain units) with equal probabilities. So far as we know, the outcome is genuinely random: the value of the horizontal projection is undetermined prior to the measurement. No one, including God, knows what it was initially. (It is, in a very real sense, both +1/2 and –1/2.) We have good reason to say that there is no cause that determines the outcome of that measurement. Strange? Yes. Counter-intuitive? You bet. Wrong? Likely not.

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    8. I never had an intuition that we could "measure" absolutely every quantifiable property. If events are caused, to measure is to affect. But to affect is to modify properties. Thus, it seems to me that there is a limit as to what humans can measure with absolute accuracy.

      The point is, there is no philosophy vs. science dichotomy once you posit uncaused events. That IS a philosophical stance. It is neither intuitive (for the reason I gave above) nor proveable.

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    9. Moreover, though logic texts are typically taught by those that have philosophy degrees, it doesn't follow that they're arguing for world-views in those classes. They are teaching the most universally used rules of logic.

      Indeed, when you say of uncaused events, "There is no reason why microscopic world should obey the same rules," you are misusing the word "rule." There are NO rules for uncaused events, by definition. They're totally unpredictable, by definition.

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    10. oleg:

      Maybe "counter-intuitive" is wrong!

      Looka here:

      http://phys.org/news/2013-03-uncertainty-principle-physicists-polarization-states.html

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    11. Are you sure, Lino, that their results are in contradiction with standard quantum mechanics?

      Delete
    12. oleg:

      The answer to your question is both 'yes' and 'no.' And that's because they get 'around' the uncertainty principle by using a series of 'weak' tests. So, for direct measurement, the limitation still applies; but it can be gotten around.

      One of the implications of the uncertainty principle is that the world becomes immeasurable, with the implication that there is nothing underneath that can be gotten at. That's, more or less, the Copenhagen view. This experiment gets around the limits QM gives and finds actual, measurable phenomena. Maybe this doesn't render the uncertainty principle false, but it certainly questions the Copenhagen view of things---which is, of course, "counter-intuitive."

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  21. Liar for Jesus Jeff

    We ask that the false claims about evidence be stopped


    If you know of any false claims about evidence, write up a report and contact the peer-reviewed journal where the claims were published. Don't forget to include your conclusive evidence the claims are false. Merely claiming they are false based on your ignorance and personal incredulity won't cut it.

    so academic freedom, etc can flourish.

    Academic freedom doesn't mean any fantasy you can dream up automatically gets taught in schools. It means you have freedom to present your ideas to the scientific community for critical review, which you clowns have had all along. As always you IDiots demand inclusion without doing any of the work and without providing any positive evidence.

    You'll be happy to know that three of these bogus 'academic freedom' bills died in committee last week. People in Oklahoma, Arizona, and Indiana aren't as stupid as you IDiots think.

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    1. Moronton, you assume ID'ists want to teach ID in exclusion to consensus views. That's not the case. But I realize you need to lie over and over to cover for you absolute inability to just articulate an argument for your view.

      What ID'ists want is to be able to state, without professional repercussions, the same KNOWN problems (problems per induction, i.e.) that at least some UCA'ists acknowledge while publicly avowing their own inference to libertarian causality if asked. Only narcissists have a problem with that.

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    2. LOL! Poor Liar for Jesus Jeff. Four months in and he's still blithering about how he used his worthless philosophy training to disprove 150+ years of positive scientific evidence.

      Let me know when you write up that monumental disproof and submit it to any professional science journals, OK LFJJ?

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    3. Liar thorton- there isn't any positive evidence for evolutionism.

      Heck there still isn't a testable hypothesis.

      You lose, again, as usual

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    4. So, we're supposed to take Thornton seriously with all those personal attacks, prejudicial conjectures, unargued philosophical biases, arbitrary assertions, cherry-picked "facts", poisoning the well, appeal to motive, ridicule and more? Not bloody likely.

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  22. Here's what you need to do, Moronton, to show you have any grasp of logic. Tell all the theistic evolutionists that they are being inductively arbitrary in positing a designer for any feature of the universe since, per induction, you shouldn't posit that which is unnecessary to explain. After all, positing an infinite set of ad-hoc hypotheses to get around teleological finality is utterly inductive, right?

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  23. This is from the Nature article, and contains important information:

    Instead, the predominance of linear RNAs may have been the artefact. Typical RNA-sequencing methods isolate only those mol­ecules with characteristic molecular ‘tails’. With their ends joined together, round RNAs lack those tails, so have generally been overlooked.

    But advances in sequencing have allowed biologists to accumulate large data sets of RNA sequences, including some from RNA without tails. Last year, Julia Salzman, a molecular biologist at Stanford University School of Medicine in California, and her colleagues sent the first missive from the circular universe. They reported finding a plethora of circular human RNAs while searching for RNA molecules that conventional methods might have missed3. And when Rajewsky and his colleagues mined databases for circular RNA molecules, they found thousands in nematode worms, mice and humans.

    “It’s yet another terrific example of an important RNA that has flown under the radar,” says Sontheimer. “You just wonder when these surprises are going to stop.”

    [Rajewski]: “They are so abundant, there are probably a multitude of functional roles,” she says.


    The more we learn, the more Darwinism becomes inadmissible as a viable theory.

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    1. Lino,

      I have responded to your query at The Skeptical Zone.

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  24. I am one of the scientists working on circular RNAs (See Jeck et. al. 2012 in RNA), and probably ought to know better than to respond here, but the willful ignorance is just baffling. In fact my article points to a possible mechanism of circular RNA formation and evolution (through transposable elements, in particular the ALU repeat element). Science is complicated, and before you say that something CANNOT be explained, perhaps you should read up about it to see if, in fact, it already has been.

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    1. William:

      I am one of the scientists working on circular RNAs (See Jeck et. al. 2012 in RNA), and probably ought to know better than to respond here, but the willful ignorance is just baffling. In fact my article points to a possible mechanism of circular RNA formation and evolution (through transposable elements, in particular the ALU repeat element). Science is complicated, and before you say that something CANNOT be explained, perhaps you should read up about it to see if, in fact, it already has been.

      Thank you for pointing us to your 2012 paper on circular RNA that explains how it evolved:

      http://www.ncbi.nlm.nih.gov/pubmed/23249747

      Just to be clear, we did not say that the evolution of circular RNAs “CANNOT be explained.” We did point out that (i) the fact that exons code for circular RNAs constitutes yet another genetic information layer, making protein evolution even more challenging, and that (ii) evolutionists have no scientific explanation for how circular RNAs could have evolved.

      Now that you have pointed us to your paper we can retract that latter statement. One question for you though: Why do you think your 2012 paper provides such a scientific explanation of circular RNA evolution?

      Your paper said nothing about how exons could have evolved to include the circular RNA information layer. That would be on top of all the other information exons code for, such as for the protein and its multiple functions, instructions for transport and other interactions, for mRNA stability, mRNA editing, DNA copy error correction, the speed of translation, avoiding an amyloid state, for any other genes that overlap with the gene, and for controlling tRNA selection which can help to respond to different environmental conditions.

      You did cite another study that found circular RNA in Archaea so you concluded that “the production of RNA circles is evolutionarily ancient.” But that just aggravates the problem, since that means that the circular RNA signals must have evolved early, long before there were multicellular organisms, for instance.

      You also found circular RNA similarities between humans and mice, including the ALUs in the flanking introns. But aside from stating that these similarities reveal an evolutionary relationship, you again said nothing about *how* the circular RNA could have evolved. You seem to be saying that the observation of similarity implicitly constitutes a scientific explanation for *how* circular RNAs evolved.

      In fact you mention evolution only four times, and in each instance you simply are making the assumption that circular RNA similarities reveals an evolutionary relationship.

      So we’re happy to retract our statement, but need a little guidance first. Thanks again.

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    2. I replied to the relevant post, I hope we can continue a productive discussion. I'm very impressed and thankful that you read my paper, it is the result of years of work as a graduate student. I hope the tone of my reply to the other article is more useful than this one.

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    3. For some reason my reply is not showing there. Anyway, I'll put the briefest of summaries here:

      ALU elements are a self replicating genomic element. This means that they frequently insert themselves randomly through the genome. This random insertion may cause the formation of circular RNAs. If the formation of certain circular RNAs increases fitness, then those individuals will flourish in the population.

      You are right that it is a hypothesis, not a proof, but proof with a mathematical level of rigor is almost never possible in science. I think the nice thing about the hypothesis is that it makes useful predictions that we can then test as we examine circular RNAs in other species, and in experimental systems.

      Anyway, I appreciate your attention to detail in this, and would be happy to continue the dialogue.

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    4. William:

      Thank you for the thoughtful comments. I think your hypothetical explanation for the evolution of circular RNA is fine, insofar as it goes. But it raises several issues.

      1. Your explanation entails the pre existence of genes that are alternatively spliced. You say there are explanations for the evolution of alternative splicing, but those explanations are speculative with details missing. The splicing machinery itself is a huge problem, calling for the evolution of many proteins which must work together. Yet evolution cannot explain, beyond speculation, how even a single protein could evolve. Likewise your explanation for the origin of circular RNAs is speculative. And none of this is unusual. Evolutionary theory entails a large number of such speculative explanations. How then can we say that evolution is a scientific fact if it relies on so much speculation?

      2. You say that your explanation for the origin of circular RNAs is a hypothesis, not a proof, but proof with a mathematical level of rigor is almost never possible in science. Well apparently it is possible, or at least something close to that level of rigor, with the theory of evolution itself. How is it that such a heroic theory (i.e., the species arose by themselves, which is to say spontaneously) could be known to be a fact, when its myriad explanations and sub hypotheses are so full of speculation and often turn out to be unlikely or false?

      3. Your explanation entails the pre existence of genes that are alternatively spliced. That means that evolution must have created the various splicing signals and splicing machinery. That in itself is a huge problem as mentioned above in #1, but leaving that aside for a moment, this means that your explanation calls for a high level of serendipity. Remember evolution has no foresight. So in the evolution of the splicing machinery, there must be no knowledge or selection for the future role as creator of circular RNA. So evolution must have evolved the splicing machinery which, as luck would have it, turned out also to construct the crucial circular RNAs.

      4. The serendipity problem described above in #3 also applies to the Alu’s. These junky DNA elements, as luck would have it, just happen to cause RNA to go circular.

      5. Of course there is the whole problem of coding for the circular RNA. We don’t know exactly how flexible the sequence can be and still get the job done, but even minor levels of required coding cause problems. You not only need the Alu’s just happening to insert on the exon’s flanks, but you need the exon to have the right coding so that its transcript can double as a circular RNA and do that job it does. Your likelihood of getting the right mutations (Alu insertions and DNA coding) is low and the number of evolutionary attempts required is large. Meanwhile a crucial function is not being performed. Or perhaps the function is not crucial, but only becomes crucial later in evolutionary history after the circular RNA is selected. But now you have even more serendipity.

      6. The problem of coding for the circular RNA also applies to the gene more generally. As I mentioned in the OP, there are several “layers” of information in a typical protein-coding gene. Evolution fails to explain, beyond speculation, how even a single protein could evolve that merely folds and performs a single function, let alone evolve all the additional layers of information. Well with the circular RNA you’ve just added yet another layer of information.

      Evolutionists claim evolution to be a fact. But there are all kinds of serious problems with the theory.

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    5. I think you've succeeded, in your arguments, of pushing back the question of "How" back another level. I take it that you are conceding that circular RNAs could have evolved from those states (splicing + ALU elements), given their existence?

      The only point that seems to address the mechanism I proposed is #5. To answer this I'd only ask that you look into ALU elements further, and transposable elements in general. These elements are extremely abundant in the genome, and the serendipity of their occasionally landing in a useful place and being selected for is not a far stretch of the imagination.

      I have, I think, explained sufficiently how circular RNAs might have evolved from the preexisting states. I will not try to take on the question of how every preexisting state evolved. This isn't what the post was about, and it's not what my response to your post was intended to take issue with.

      Frankly the reason I was so surprised to find your post is that, of all the difficult to explain things in biology (the existence of splicing itself actually being a formidable example) you chose to take issue with circular RNA! Circular RNAs, to me, may be one of the most easily explained biological elements. In fact, I frequently am made to argue with people circular RNAs have any function at all, since to many biologists their 'accidental' formation seems so obviously simple, and evidence for selection is not as strong (yet).

      As an aside, honestly I think I have much less of a problem with anti-evolutionists than other scientists, since asking questions and taking us to task can only help the process of scientific inquiry as a whole. There are many mysteries in this world, and I hope that we are both doing our best, honest attempt to understand them. As for the issue of "evolution as fact", I think we all do well to approach discourse with humility and respect for the power of human reason, but also respect for its failures. We can all learn from each other.

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    6. William:

      I think you've succeeded, in your arguments, of pushing back the question of "How" back another level. I take it that you are conceding that circular RNAs could have evolved from those states (splicing + ALU elements), given their existence?

      The only point that seems to address the mechanism I proposed is #5. To answer this I'd only ask that you look into ALU elements further, and transposable elements in general. These elements are extremely abundant in the genome, and the serendipity of their occasionally landing in a useful place and being selected for is not a far stretch of the imagination.


      No, even given the existence of all these things, the origin of circular RNA via your hypothesis is not obviously feasible. #5 presents the problem, as you note, but your response is simply about Alu's the TE's. You disregarded the sequence requirements. Is an existing gene likely to code for a functional circular RNA? If not how many mutations are likely to be needed? Is there a gradual pathway where one mutation can be added at at time?

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    7. Let's look at the numbers:

      That transposable elements exist is certainly not in dispute, since there are many that remain active in many plant genomes and there are some active ones in animals as well. Roughly (ballpark) 1% of the human genome is composed of transposable elements. By their very nature, these elements resemble one another, since they represent duplications of identical sequence throughout the genome. This self-resemblance appears to be the feature that promotes circular RNA, since this means that the elements can pair in the pre-mRNA.

      There are approximately 30,000 genes. Of these, each contains dozens (if not hundreds) of exons, but let's ignore that and say that each gene is just 1 exon (this will actually give us an underestimate of the likelihood of generating circular RNA).

      This makes for 30,000 potential "targets" for ALU or other transposable element insertion. Now let's think about the size of each of these targets. Our results (using biochemical methods, no evolution required here, just everyday science) suggest that about 200-1000bp worth of sequence flanking an exon are relevant to ALU element formation. This means that the chance of an exon flank, generally, of having an ALU element in it (I am ignoring all other transposable elements) turns out to be about 1/50 (the flank region can contain multiple ALUs, which is why this is > 1%)

      Since we need an ALU element on either side, that makes the chance of an ALU element on both sides of an exon 1/2500. We must half this number because only 1/2 of the time will these ALUs be in an inverted orientation. This means that ALU elements alone, in the absence of any selection whatsoever, and assuming only single exon genes (a ridiculous assumption!) should promote the formation of at least 6 circular RNAs. I am aware that the math is not water-tight here, but let's treat it as a rough estimate.

      If we add heterogeneity in the insertion locations of ALUs between individuals, the existence of other repetitive elements, and the fact that there are MANY more than 1 exon per gene, it becomes likely that a large number of circular elements should be generated. As the Nature papers suggested, these circular RNAs appear to act as miRNA sponges. miRNA binding sequences are very small, degenerate, and common in the genome. Among these thousands of circular RNAs, miRNA binding sites are expected to be quite common. If this represents a useful functional addition to the organism, one can imagine that the sequences nearby could evolve to contain many additional binding sites for the relevant miRNA, as it appears is the case in CDR1as and SRY.

      This further ignores additional facts about circular RNAs. What if, instead, the operate simply to modulate the expression of their source linar transcript (this has been called the 'mRNA trap hypothesis'). In this case, all the circular RNA has to do is lower the expression of a gene in a way that's advantageous. Depending on how optimized you believe expression levels to be at the basal level, this may actually be incredibly likely to be advantageous, at least occasionally. In fact, this is one function we proposed for circular RNAs in the HIPK3 gene, though additional evidence is needed.

      That narrative is the best I can offer given the facts at hand, in these early days of research into circular RNA. It is, I think, a less bold claim to say that these transcripts might be explained by evolutionary processes than to assert positively that they cannot be. I would not take issue if you concluded that they were "difficult to explain" or perhaps "not yet explained". That statement at least makes it clear that you are open to discussion.

      I mean all this respectfully, and enjoy this discussion.

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    8. William:

      Thank you for that comment and if, as you suggest, the sequence requirements for functional circular RNA, beyond what is already present in the DNA, is minimal, then I agree that that concern is greatly lessened. From what I understand the sequence requirements are not this easy for at least some circular RNAs, so I suspect your scenario is optimistic in that sense. But if you are correct, then yes, that concern is lessened, no doubt.

      But note that this aggravates even more so the other concerns. That is, we're pushing a lot of problems upstream by saying evolution had, serendipitously, preconstructed most all of the needed elements (DNA sequences, splicing machinery, Alu's, etc) and so functional and crucial circular RNAs just happened to arise with no problem. Another "as luck would have it..." scenario.

      It is, I think, a less bold claim to say that these transcripts might be explained by evolutionary processes than to assert positively that they cannot be. I would not take issue if you concluded that they were "difficult to explain" or perhaps "not yet explained". That statement at least makes it clear that you are open to discussion.

      But that is precisely what I did say. I did not "assert positively" that circular RNAs cannot be explained according to evolution. I said they haven't been explained and that there are significant difficulties.

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    9. You're right, your statement, simply, was this:

      "Not surprisingly, beyond “oh, evolution did that,” evolutionists have no scientific explanation for how circular RNAs could have evolved."

      Still, I think that we have much more than "oh, evolution did that".

      I will concede that our explanation is imperfect (of course it is, we only have so much ability to prove *any* historical theory), and I have not laid out an explanation starting with the first protocell, all the way through mammalian splicing, and up through circular RNA. However I have described how an early mammalian genome might have begun to acquire circular RNA by the action of transposable elements. This makes mathematical sense, given the abundance of exons, ALU elements, and the degeneracy of miRNA binding sites.

      I am glad that I have lessened your concern in this area. I think all theories as vast as evolution need their detractors as well as their advocates, and you do a service to the discipline to keep us honest. I especially appreciate that you so closely read our paper. I would ask, humbly, that you edit the post about "A Marshall McLuhan Moment" to note that I have responded.

      I look forward to future discussions.

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    10. William:

      Change made. Thanks so much for the discussion!

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  25. My post, above, was intended as sarcasm, Cornelius.

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    1. Paul, which post specifically are you referring to?

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