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Origins of Genomic ‘Dark Matter’ Discoverd–Once Again, ID Predictions are Spot On

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This just in from Phys.Org.

Pugh added that he and Venters were stunned to find 160,000 of these “initiation machines,” because humans only have about 30,000 genes. “This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery.” . . .

The remaining 150,000 initiation machines—those Pugh and Venters did not find right at genes—remained somewhat mysterious.
These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists,” Pugh said. “In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins.” [Yeah, that’s right—you called it “junk DNA” and said it was proof contradicting design.] . . . . .

Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes. . . . . . .

These non-coding RNAs have been called the ‘dark matter’ of the genome because, just like the dark matter of the universe, they are massive in terms of coverage—making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there,” Pugh said. “Now at least we know that they are real, and not just ‘noise’ or ‘junk.’ Of course, the next step is to answer the question, ‘what, in fact, do they do?'”[Really?!! “Dark Matter?” You called it “junk-DNA”; it’s only now, now that you’ve been proven wrong on a grand scale that you’ve decided to call it “dark matter.”][P.S. This is what liberals do: when wrong, change the words; e.g., “global warming” = “climate change”, or, “pro-abortion” = “pro-choice”. You see, it all depends on what the meaning of “is” is.]

So, let’s see: 150,000 “initiation machines” (Wow, are there “machines” in the cell?) in the Non-Coding, and 10,000 in the coding portion. I wonder which is more important???? And what has ID been predicting since the late 1990’s? That the Non-Coding portion of the genome is where the bau-plan (blueprint, more or less) of the animal is to be found, and that proteins are but the building blocks (kind of forming the “parts list” of life’s manufacture); i.e., that ‘genes-coding’ portions of the genome are of less importance to life than the ‘non-coding’ portions. Here, it is 15:1 in favor of the Non-Coding—and in full agreement with ID predictions.

And, guess what, finally we get to put to rest the ‘junk-DNA’ argument. How do I know? Because it’s now called “dark matter.”

Comments
Phinehas:
In my view, a choice to have sex is a choice to be a legally responsible parent, caring for the life that may be a consequence.
Well said. I am all in favor of choice. But when you do choose, also choose to take responsibility for your choice. I am pro-choice and anti-abortion! Choose life.Mung
September 18, 2013
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Bruce David, "They regard you and those like you as religious fanatics bent on imposing your beliefs on the rest of humankind, no better than any other tyrant." Having seen the tone that this is in response to, I can sympathize with your tone here. However, those who are pro-life have very good reasons for viewing the Zygot and any transitional human developmental form thereafter as a person - an individual, a human being. The zygot of any other animal is distinct. You couldn't place a chimp zygot inside a human woman and have it come out as a human if such a procedure were even possible. So we know that it is uniquely human. Second, as far as being an individual - it has a DNA that is different than the mother's. That would seem to suggest that it is an individual other than the mother. Third, as far as being a person - our laws protect unborn babies who may be killed as the result of the murder of the mother. There's criminal prosecution for those who kill an unborn in that process, and it's considered murder. Clearly, our laws recognize the unborn as a person provided that the mother considers him/her as a person. We get a little schizophrenic when it comes to abortion though. Why do we have laws that protect the unborn as a person in one circumstance, but not another? I would say that in that regard, when our legal enlightenment improves, we will need to change the law. Which way will it go? If constitutional law prevails, it will go towards legislation protecting all human life inside and outside the womb. While predominantly "tyranical religious fanatics" are the ones pushing for such a law, it clearly does not require that sort of commitment. If you simply value the future of humanity, it requires such a commitment. How others view us should be inconsequential. We have a human duty to protect human life. That's the bottom line.CannuckianYankee
September 18, 2013
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I'm with Bruce David #6 #11 on this one.Box
September 18, 2013
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Ho-De-Ho. re. #14: Thank you. I think the attitude you bring to the conversation is right on.Bruce David
September 18, 2013
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I beg your pardon, the exchange I was referring to was between TSErik (not Erikson) and Elizabeth B Liddle. The thread was Debating Darwin and Design: Science or Creationism? (7) – Joshua Gidney’s Third Response And the posts were numbers 53, 65, 67. Hats off to both of you. Awfully sorry TSErik for my clanger. I almost made you sound like a mobile phone. My apologies.Ho-De-Ho
September 18, 2013
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Liz: I'm pretty sure Mung is aware of this. I certainly am keenly aware of it. I don't know what Mung believes, but this is why I personally focus on the responsibilities of parents as opposed to the right to life when it comes to the legal issue. In my view, a choice to have sex is a choice to be a legally responsible parent, caring for the life that may be a consequence. If one does not choose to have sex, then I would not personally hold them legally responsible as parents for any resulting life, though I believe there are still moral considerations beyond the legal ones.Phinehas
September 18, 2013
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Tally ho everyone. Just thought I'd say thank you for this marvelous post. What a find! And what sterling research, I mean to say, these fellows must have heads the size of dustbins to contain their evidently enormous brains. Golly. It does seem like one on the board for intelligent design predictions. Of course some may wag a finger and say "Poppycock! this is nothing more than a post hoc prediction." or words of similar impetus. However, I can vouch for that not being the case, from an incident that took place in a bookstore sequestered in the middle of England in the mid 90's. I had been thumbing through some science books which had images of the double helix printed in garish colours on their jackets, like only the 90's knew how. Positively lurid they were. Anyway, I was engaged with the passages about junk DNA which were in no way reticent in their claims. Evolution had hoarded a lot of garbage in the genome they said. Only a trifling amount was being used I was informed. At this point, I spied an acquaintance of mine whom I knew to be a devout sort of chap. Naturally I wanted to get his take on all this science. I'll never forget what the old beezer said to me after I had revealed my newly acquired knowledge. "Perhaps they are right and I am totally wrong" he said amiably "but do not stumble into the trap of thinking we have complete knowledge. If we were created then they will likely find a lot more function in the DNA." I remember thinking "Whatho, he has a point. We shall see." Lo and behold! 160,000 wossnames performing wonders in the junk heap. He was no scientist but his premises made a prediction which is being borne out. May I say that I think our friend Bruce David has a very good point which we all sides should heed. He puts it thus: "In a larger sense, your smug condescension toward those with whom you disagree serves only to solidify their opposition..." Could one put any more succinctly? I know I couldn't. Of course some may bristle at the term 'smug condescension' thinking that we are neither smug or condescending. The point of the matter - the crux if you will - is whether the person we are aiming our comments at feels that our tone is smug and condescending. If they do then our most powerful lines of reasoning (either for or against ID) on reaching our fellow debaters minds, find them boarded up for over-wintering. Take a lesson from the brave boys of the Great War. When they chose to make their point with mortars, nobody got anywhere. When they tentatively suggested a game of football since 'we all love a good kick-about', those two armies made more advances in 90 minutes than they did in the previous two years. We should take a leaf out of TSErikson's and Elizabeth Liddle's repartee on another thread and seek understand and accept the merits of the other persons position even if we cannot agree with the conclusion. Bridges do eventually get built this way. Let us be a sporting, not warring. Thank you for your observation Bruce David. I take your point.Ho-De-Ho
September 18, 2013
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Mung, you are aware, are you, that pregnancy can result from rape?Elizabeth B Liddle
September 18, 2013
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OT: I'm pro choice. No woman should be forced to have sex. If you don't want to get pregnant, choose not to have sex.Mung
September 18, 2013
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Axel,
Tell us why this is so, Bruce.
The fact that you have to be told speaks volumes. It means that you have no willingness to see the other's point of view, nor give them credit for being every bit as much sincere as you in their beliefs. The reason is that they simply do not agree that a zygote or an embryo is a person, and they see your attempt to limit the freedom of women to control the choices they make as an unconscionable assault on their freedom based on a religious conviction that they do not share. They see it as repugnant, repulsive, and morally contemptible. They regard you and those like you as religious fanatics bent on imposing your beliefs on the rest of humankind, no better than any other tyrant. Whether you agree or not is irrelevant. Until you are willing to exercise some compassion---in its meaning of being able to imagine yourself into another's experience---your moral indignation will only serve to harden the position of those whose minds you seek to change. vjtorley, re. #9:
The view that a “fertilized egg” is a person can be defended on purely secular grounds, without appealing to the notion of God or of a soul.
So? There are arguments which are compelling to anyone, and there are those which are compelling only to people who already accept the conclusion that the argument is trying to reach. The argument you so carefully provide in your link is of the latter variety. Here is my own reason for rejecting it (in a nutshell): to me a human being is a human body inhabited by a soul. Based on what I have read (primarily Journey of Souls and Destiny of Souls, both by Michael Newton) the soul does not join the developing fetus until there is a sufficiently developed brain for it to connect to. This happens some time during the third trimester. Since there is no soul joined to the body before that time, there is no person present, by definition.Bruce David
September 18, 2013
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I am also for freedom and very much pro-choice. Neither is contradicted by my belief that parents have a responsibility to love and protect their progeny both before and after birth.Phinehas
September 18, 2013
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Bruce David: The view that a "fertilized egg" is a person can be defended on purely secular grounds, without appealing to the notion of God or of a soul. See here.vjtorley
September 18, 2013
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'..and recognize that they are every bit as certain that they are right as you are, and to understand why this is so.' Tell us why this is so, Bruce. As for your secular 'fundie' tosh about freedom, well that takes some beating. Do you really think that freedom is an absolute? That the option of a mother to have her child killed, even when fully formed as a person, is freedom? You are a sick man, Brucie. Even some pro-abortion women don't view it as freedom, that there are any winners. They see it as a grim, painful choice they made. And for many, the pain never fully goes away. And there is an old Gospel axiom, which you will of course count as nonsense. It approximates to: 'If you are not for the good, you are for the bad, so that 'I am not pro-abortion' is lame, to put it mildly.' But then I'm an old 'fundie', aren't I! Just not a secular one. Any freedom worth a cracker involves a degree of personal responsibility.Axel
September 18, 2013
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This is just sheds more light on evolution. Science is self-correcting, you know.lifepsy
September 18, 2013
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PaV: As a liberal, I would like you to know that I am not pro-abortion. It is a matter of indifference to me whether a particular woman gets an abortion or not. What does matter a great deal to me is that she not be forced to carry a pregnancy to term if she does not wish to do so because some religious fundamentalists have made the quite arbitrary determination that in their opinion a fertilized egg is a person. I am for freedom, which makes me pro-choice. I am neither for nor against abortion. The fact that this distinction is apparently lost on you calls into question your intellectual capacity to make important distinctions at all. I would be more careful how you characterize people with whom you disagree if I were you. You can easily end up looking foolish. In a larger sense, your smug condescension toward those with whom you disagree serves only to solidify their opposition. Your judgment of people who firmly and sincerely believe that they are in the moral right only serves to make them angry and more entrenched. Do you want to be part of the problem or part of the solution? If you want to be part of the solution, the first thing you will have to do is stop demonizing your opposition and recognize that they are every bit as certain that they are right as you are, and to understand why this is so.Bruce David
September 18, 2013
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Well all bow down and worship chance and luck.... they sure made us wonderfully complicated.Andre
September 18, 2013
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Moose: This is from the abstract: Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcription factor IIB (TFIIB) and RNA polymerase (Pol) II. Using ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing), we identify approximately 160,000 transcription initiation complexes across the human K562 genome, and more in other cancer genomes.PaV
September 18, 2013
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Hilarious stuff, PaV! Literally LOveryL! Especially the last sentence. You couldn't make it up. But I know people who can...Axel
September 18, 2013
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I would really appreciate a definition for "initiation machine".Moose Dr
September 18, 2013
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Arthur Hunt might want to comment on this.PaV
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