Junk DNA label a mistake? Genome region linked to heart failure

_{Denyse O'Leary

April 25, 2014

Intelligent Design}

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We’ll let ScienceDaily tell it:

In the new study, the investigators found that unlike other RNA molecules, expression patterns of long noncoding RNAs could distinguish between two major types of heart failure and between failing hearts before and after they received LVAD support.

“We don’t know whether these changes in long noncoding RNAs are a cause or an effect of heart failure,” Nerbonne said. “But it seems likely they play some role in coordinating the regulation of multiple genes involved in heart function.”

Look, if Darwin’s people say it’s junk, it’s junk. Why you asking, anyway?

Comments

BA: Thank you, I'll be checking that out at lunch time.Barb_{April 29, 2014
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PS: Cretans are liars should not be confused with they lie with every statement. As the Kantian CI shows, no community like that can exist. Just, they are prone to fibbing. The lie every time is interesting but cannot be factual.kairosfocus_{April 29, 2014
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BA77: Muy interesante. KF PS: Where do you keep on finding these things? Maybe you should set up a news nuggets blog?kairosfocus_{April 29, 2014
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AVS: Perhaps -- apart from reflecting on what "paradigm shift" and "scientific revolution" as well as "inescapable limitations of inductive reasoning" imply about prevailing consensuses across time [whether or not dressed in a lab coat] -- you need to pause and actually ponder the implications of this, from Lewontin reviewing Sagan's last book in Jan 1997, in NYRB:
the problem is to get them [hoi polloi] to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations, and to accept a social and intellectual apparatus, Science, as the only begetter of truth [[--> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]. . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [[--> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[--> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [And, if you think this is quote mined or idiosyncratic, kindly read the fuller cite and notes then follow on down and notice esp. what the US NAS and NSTA say.]
There is such a thing as an evolutionary materialist reigning orthodoxy in origins science (one that is trying to entrench itself by redefining "science" and its methods conveniently but question-beggingly). Seminal ID thinker Philip Johnson's retort in November that year, was dead on target:
For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
With all due respect, maybe, just maybe . . . you need to open your mind a tad and do some rethinking from a fresh vantage point. KFkairosfocus_{April 29, 2014
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Barb and Joe, you guys may like this: A Mono-Theism Theorem: Gödelian Consistency in the Hierarchy of Inference - Winston Ewert and Robert J. Marks II - June 2014 Abstract: Logic is foundational in the assessment of philosophy and the validation of theology. In 1931 Kurt Gödel derailed Russell and Whitehead’s Principia Mathematica by showing logically that any set of consistent axioms will eventually yield unknowable propositions. Gödel did so by showing that, otherwise, the formal system would be inconsistent. Turing, in the first celebrated application of Gödelian ideas, demonstrated the impossibility of writing a computer program capable of examining another arbitrary program and announcing whether or not that program would halt or run forever. He did so by showing that the existence of a halting program can lead to self-refuting propositions. We propose that, through application of Gödelian reasoning, there can be, at most, one being in the universe omniscient over all other beings. This Supreme Being must by necessity exist or have existed outside of time and space. The conclusion results simply from the requirement of a logical consistency of one being having the ability to answer questions about another. The existence of any question that generates a selfrefuting response is assumed to invalidate the ability of a being to be all-knowing about the being who was the subject of the question. http://robertmarks.org/REPRINTS/2014_AMonoTheismTheorem.pdfbornagain77_{April 29, 2014
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AVS: "why does the vast majority of the scientific world have no problem with the theory of evolution?" Scientific truth is not determined by how many people believe it.Barb_{April 29, 2014
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AVS:
Tell me BA, why does the vast majority of the scientific world have no problem with the theory of evolution?
Why can't that alleged vast majority figure out how to model unguided evolution? Why can't that alleged vast majority figure out how to test the claims of unguided evolution? Why is AVS so ignorant of science?Joe_{April 29, 2014
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Actually I should amend my statement from "no amount of evidence can ever falsify Darwinism" to "no amount of evidence, that a typical Darwinists will ever accept, can ever falsify Darwinism" Because, as far as science itself is concerned, Darwinian evolution has been falsified both empirically by the finding of non-local quantum entanglement in DNA and proteins, and mathematically by numerous angles: Dembski, Sanford, Axe, Wistar, etc.. etc..bornagain77_{April 28, 2014
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Yes thank you BA. "evolution is not science because a bunch of creationists said so and here's some copy/paste BS about consciousness" Great comment. Tell me BA, why does the vast majority of the scientific world have no problem with the theory of evolution? Oh, that's right, it's all a giant conspiracy! Duh. What a joke. I've about had enough, it's just not funny anymore, it's quite sad actually. Toodaloo.AVS_{April 28, 2014
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AVS as to your claim:
"you guys don’t do science"
Actually, it might surprise you to know that Darwinian evolution is not even a proper science in the first place, but is more properly thought of a as a pseudo-science. The reason this is so is primarily because Darwinian evolution has no mathematical demarcation criteria so as to potentially falsify it.
“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003) Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013 Except page 9: (Gregory) Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.4/BIO-C.2013.4
In fact each piece of the framework which undergirds Darwinian evolution falls completely apart upon scrutiny:
Darwinian Evolution is a Pseudo-Science - Part II https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit
Darwinian evolution's 'scientific' attempt to explain 'Intelligence/Consciousness' provides even more insight into the absurdity that is Darwinian evolution and also provides a clear example of what demarcates ID from the pseudo-science of Darwinian evolution:
Mind and Cosmos - Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False - Thomas Nagel Excerpt: If materialism cannot accommodate consciousness and other mind-related aspects of reality, then we must abandon a purely materialist understanding of nature in general, extending to biology, evolutionary theory, and cosmology. Since minds are features of biological systems that have developed through evolution, the standard materialist version of evolutionary biology is fundamentally incomplete. And the cosmological history that led to the origin of life and the coming into existence of the conditions for evolution cannot be a merely materialist history. http://ukcatalogue.oup.com/product/9780199919758.do David Chalmers on Consciousness (the Hard Problem) - video http://www.youtube.com/watch?v=NK1Yo6VbRoo 'But the hard problem of consciousness is so hard that I can't even imagine what kind of empirical findings would satisfactorily solve it. In fact, I don't even know what kind of discovery would get us to first base, not to mention a home run.' David Barash - Materialist/Atheist Darwinian Psychologist "We have so much confidence in our materialist assumptions (which are assumptions, not facts) that something like free will is denied in principle. Maybe it doesn’t exist, but I don’t really know that. Either way, it doesn’t matter because if free will and consciousness are just an illusion, they are the most seamless illusions ever created. Film maker James Cameron wishes he had special effects that good." Matthew D. Lieberman - neuroscientist - materialist - UCLA professor
ID certainly does not suffer the embarrassment, as Darwinian evolution does, of having no mathematical demarcation criteria so as to separate it from pseudo-science:.
Evolutionary Informatics Lab – Main Publications http://evoinfo.org/publications/
Moreover, Intelligent Design can easily be falsified by empirical evidence, whereas, in my honest opinion, no amount of evidence can ever falsify Darwinism:
“Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.” - Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design – video http://www.youtube.com/watch?v=N8jXXJN4o_A
bornagain77_{April 28, 2014
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Ah yes, so doing something twice, isn't the same as repeating something? Are you going to redefine every word in the english language now? You don't have to tell me about the science lab. And no, it's not as simple as just computer time. The sequences eventually need to be sifted through for their relevance at a level that the computer simply cannot do. Just take a look at the number of author's in the paper, versus the number of authors on the first study. A lot more work had to go into the second study in the form of man-power, not computer power. If you IDists are so much better at science, then why don't we see your work popping up all over the place? Oh that's right, because you guys don't do science. =)AVS_{April 28, 2014
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AVS: Either way you slice it, they didn’t just “do the study twice” as you originally thought. Did I say that they had to "repeat" the study? No. Did I suggest that? No. I said that they had to do it "twice," meaning that if they had included lncRNA the first time around, even in mouse tissue, they would have found a connection and been that much ahead of the game. There are trade-offs in everything in life, even the science lab. But the entire point here is that the perceived view of lncRNA as "junk" meant that this is what would be left out due to constraints---you say because of all the data they would have had to sort through, but we're really talking about computer time, which is expensive, and is part of sequencing cost. Yes, there is a technical meaning to "unbiased," however, their "surprise" would not have been an IDist's "surprise." That's the carry-away message here.PaV_{April 28, 2014
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Either way you slice it, they didn't just "do the study twice" as you originally thought. They were two different studies, as I said. lnRNAs were not included in the scope of the first study simply because of the need to generate an analysis system for lnRNAs and because of the huge amount of data that would need to be analyzed. You are losing it over nothing. "If IDists had been doing the experiment..." Heh that's a good one.AVS_{April 28, 2014
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AVS: As I said, looking at lnRNAs simply did not fall within the scope of the first study. Yes, you said that. Why didn't they include them? That is, why didn't the lncRNAs fall within the scope of the first study. That's what is at issue here. We don't need you to pontificate. Explanations are preferred. They did not “do it twice” and you would realize this if you had any reading comprehension skills because you would have noticed that the two investigations were completely different studies. The first was done with mice, whereas the second was done with human heart tissue in normal and failing hearts. People who live in 'glass houses' shouldn't throw stones. Reading comprehension? Let's see: Here's AVS: " . . . the two investigations were completely different studies. And here is one of the authors of the study: "In fact, the field is evolving so rapidly that when we did a slightly earlier, similar investigation in mice . . . " Which of the two of us is correct here? Would you like to say? If you choose to continue to insist on the fact that they used mice the first time, and human heart tissue the second time, well . . . Aren't mice used as a proxy for humans in the lab? And isn't this usually because of ethical issues related to obtaining human tissue for experimentation? Well, if you read closely enough, you'll see that the human tissue became available to them the second time around, and so they used it. Otherwise we could presume that they would have used mouse tissue again. So, we're dealing with two differences between the earlier and later studies: the types of RNA they were searching out were different, and the type tissue being used was different. The tissue being used was different simply because it had become available the second time around. Did you read anywhere in the paper where they suggested that the lncRNAs had anything to do with using the "mouse tissue" the first time, and "human tissue" the second time? I didn't. Thus, the fundamental difference has to do with the RNA sequences that they searched for and included in their second study. And what was that RNA? Well, it was "junk RNA," lncRNA to be exact. And they found that the lncRNA allowed them to distinguish the cause of heart failure better than any of the other RNA sequences they searched for. And so why is it an "unbiased" approach? Because "junk DNA" was included. IOW, we don't care what kind of RNA transcript we're looking at this time around, we're going to look for them all. Bottom line, however you slice it, the "bias" was that of excluding so-called "junk DNA=lncRNA" the first time around because of the constraints imposed by sequencing costs. If IDists had been doing the experiment, the emphasis of what RNA to be looking for, or not looking for, would have been different; and, based on the results, we would have been ahead of the curve. And that's the whole point here. Now, run along.PaV_{April 28, 2014
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Again, Pav, another example of a fundamental misunderstanding from the UD crowd. As I said, looking at lnRNAs simply did not fall within the scope of the first study. They included it in the second study. They did not “do it twice” and you would realize this if you had any reading comprehension skills because you would have noticed that the two investigations were completely different studies. The first was done with mice, whereas the second was done with human heart tissue in normal and failing hearts. I have already talked about this in another comment. This is a perfect example of why this site is a joke. You guys have no idea what you are talking about. No need to reply, you’ve demonstrated your scientific illiteracy aplenty.AVS_{April 28, 2014
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AVS: Relax ladies. The phrase “unbiased approach” just means that the system they used did not favor analysis of any certain type of transcript, long/short, coding/noncoding, etc. They did many reads (deep sequencing) of the transcriptome to make sure they were not missing anything, hence “unbiased.” I don't think I thought anything other than what you've stated. However, it is very likely that they used the "unbiased" approach because the "biased" approach didn't give them the answers to their questions. This, then, simply serves to underline the fact that they didn't think---ahead of time---that long nc stretches of DNA could do very much, and they had to be disabused of the idea. It is standard evolutionary biology that says that "junk" is really "junk." [Although the whole time denying it] So, they ended up having to do it twice because they were "biased", in the sense that the left out the nc DNA, since, of course, what purpose would that serve!! No need to reply. You're steadfast in your views, and I in mine. Others can come to their own conclusions.PaV_{April 28, 2014
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jerry @ 41
Why people answer these comments is beyond me.
I agree. My stupid mistake. :(Dionisio_{April 27, 2014
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English seems impossibly flawless for a non-native speaker
I was recently in Botswana on a tour and the tour guide in our jeep was a native from Botswana. He said his first language was Setswana but everyone in Botswana speaks English. He was about 30 years old and his English was impeccable and he had all the idioms and colloquialisms down perfectly. His accent seemed like someone who was from the US. I assumed he went to school here for several years. But he said he had never been out of Africa, was born in Zimbabwe and had a degree from a university in Namibia. I do not know how well he wrote but if you met him here you would think he was a well educated American. Maybe it was watching a lot of movies and TV shows. That is where you will pick up the informal spoken language. No one speaks the formal language you learn in a language course. However, that is what one often uses when writing. Blogs are different though. Also some people are just gifted in language skills. I had a high school classmate who was average is a lot of ways but when tested in college found out he had extraordinary language skills. He then learned several languages and makes a good living that way negotiating business deals in foreign languages all of which he could speak fluently. (Arabic, Russian and German are some of them.)jerry_{April 27, 2014
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Can we ask the blog moderators to screen out anyone who drags down the discussions?
My son who is a web architect and developer said it would be easy to write a program that would eliminate the comments by a specific author if one wanted to. I could probably do it but it would take a couple weeks. Just run the thread through an app and put in the name of the author and presto all the comments from that author would be gone from your viewing. Of course the easy thing is never to answer a comment by this author that is not courteous or serious. Why people answer these comments is beyond me.jerry_{April 27, 2014
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Axel: Indeed, I had not understood well what you meant! :)gpuccio_{April 27, 2014
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Well, I seem to have displayed an extraordinary concordant world-blindness in my post, since neither Dionisio nor gpucci are writing in their native language in a foreign country! As regards the second paragraph, it must, indeed, be their use of prepositions and conjunctions that impresses us.Axel_{April 27, 2014
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I have an idea, how about make a thread for AVS to talk to himself? That way he can't complain about being censored or his posts being deleted, they are all just moved to a thread that we can all ignore and never look at because it has no meaningful content.sixthbook_{April 27, 2014
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Dionisio, your English seems impossibly flawless for a non-native speaker. Likewise GP. After living a few months abroad, it is said that people are wont to suffer from a degree of 'word-blindness' - a loss of fluency in their native tongue. It's always struck me as a little odd that academically-educated foreigners, while possessing an English vocabulary of more esoteric words, comparable to that in their own language, are - evidently with rare exceptions - fairly easily identifiable by their poorer fluency in their use of the smaller, Anglo-Saxon-type conjunctions, prepositions, and associated phrases. But vernacular speech is more idiosyncratic, isn't it? For Italian, multiply that by 10, a GP will vouch!Axel_{April 27, 2014
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Creationsgardener @ 35 I agree. Can we ask the blog moderators to screen out anyone who drags down the discussions? They opened OT threads, for OT comments. Good! (some unsolicited OT comments are probably mine). What about filtering out anyone who is disrespectful to most participants in the threads? I enjoy discussing with someone who has different opinions on subjects. That's actually interesting. But both sides must be willing to calmly listen to one another with respect. If I want to call someone ignorant, I don't have to look around, because I'm the one. Specially in this blog, where many participants display a visible willingness to share what they know in a nice friendly manner. Most of what you all write is above my pay grade. Not all the topics discussed in this blog are interesting to me, but some are very interesting. I've said before that I'm learning quite a bit from reading some OP and the follow-up comments. But greatly dislike the frequent distractions caused by annoying disrespectful comments that disrupt the discussions. Finally, let this be also a lesson to all, so we remember that it's important to be respectful to others. If anyone notice something disrespectful in my comments, please let me know about it, so I can correct it right away and apologize to you for my mistake. One of the several reasons I'm participating in this blog, is to learn how to write and express my thoughts to different people. I had never done it before. And English is not my first language. For years I worked as an intermediary tool, expressing someone else's ideas to computers, using programming languages. That's much easier than writing to thinking people like you all. So please, let me know if I write anything inappropriate. Thank you. Remember that God loves you. I know God loves me, and you all are much better persons than I am. :)Dionisio_{April 27, 2014
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AVS just drags down the comments every time he or she takes part. That you can argue with the extremely clear implications, even statements of this post shows you have no hope at seeing beyond your biases. You act like you are more intelligent than everyone but you actually look incredibly stupid and like a stubborn and misbehaving child. Please go away and work out your issues where you don't waste everyone's time.Creationsgardener_{April 27, 2014
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AVS in #11: "it’s not like they consciously chose to ignore lnRNAs," AVS in #19: "I never said it should be conscious,"gpuccio_{April 27, 2014
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I've tried to talk science with you. It ends with you claiming "I have this book that refutes you" and then leaving. Remember?AVS_{April 26, 2014
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AVS, do you want to talk science or trade insults? That's all I care to know. If you don't want to talk science let me know and I will ignore you. I have far better ways to spend my time.Mung_{April 26, 2014
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So it was you Mung? Well let me know when you're ready tell us all about how that book refutes what I had said. I've been doing both , feel free to add to any of the conversations. Or are you just making more empty threats and baseless claims? =)AVS_{April 26, 2014
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AVS:
Was it you Mung that tried to tell me you had a book about protocells that refuted what I was saying and then never provided said information? Refresh my memory.
I have numerous books that refute what you say, but much of what you say doesn't require resorting to any book. So let me refresh your memory. If you want to talk science, I stand ready, as do many others here at UD. If you want to trade insults, many others here at UD are probably just as willing. Do you want to talk science or trade insults?Mung_{April 26, 2014
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