Big textbook author on junk DNA

_{Denyse O'Leary

July 14, 2015

'Junk DNA', News}

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Ken Miller is a feted Catholic scientist, friend of Darwinism, and foe of design in nature: From his 1994 textbook:

Hundreds of pseudogenes have been discovered in the 1 or 2% of human DNA that has been explored to date, and more are added every month. In fact, the human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design.

If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection to innovate, to test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution’s great successes.

ENCODE 2015 offers a different picture, and of course, Darwin’s followers were quick to denounce it in consequence:

One memorably said, “If ENCODE is right, then Evolution is wrong.”

No one we know of paid the fellow to say that. We all thought it was just another example of Darwin’s followers ignoring facts.

Meanwhile, our friend thinks that Ken Miller might be forced to backtrack.

No. It’s not like that. Miller doesn’t have to stop asserting whatever he wants and has the social power for, and can maybe get a court to enforce.

That is because Darwinism’s truth is that our brains are shaped for fitness, not for truth, and truth is sometimes adaptive and sometimes not. Miller is free to assert whatever is adaptive at this time. And that, rammed down others’ throats, is the only truth that ever is or was or shall or could be. In case you wondered.

Nothing depends on evidence. Our brains are not shaped so as to understand evidence as such, apart from fitness.

See also: The Myth of Junk DNA

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Comments

wd400: or are you saying cells change their mind about expressing genes! Yes, you've got it! If you grant that cells can decide which genes to express and which genes to suppress, it is not that big a stretch to think that the decision might change. If you think such decision making requires a mind, ok.Mung_{July 17, 2015
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Why send a message if you have nothing to say and there is no one to receive it?
... or are you saying cells change their mind about expressing genes!wd400_{July 17, 2015
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wd400, anything that moves information from one place to another (which is essentially what RNA molecules do) is a messaging system. And if "cells make RNAs that they immediately destroy", so what? How does that change anything? I create and destroy messages all the time. It's called 'editing'.Mapou_{July 17, 2015
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It’s simple. We know that RNA molecules are essentially part of a messaging system. Why send a message if you have nothing to say and there is no one to receive it?
Very little molecular biology and quite a lot of assumption in this. There is no "message system" and it's just true that cells make RNAs that they immediately destroy. If that doesn't make sense under your "messaging system" concept then you may need to update your concept.wd400_{July 17, 2015
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Virgil, the definition of "aberrant RNA" is built into our DNA. That's how. And how did it get there? It was put there by RNA, obviously. Little did the aberrant RNA realize they were signing their own death warrant. Life is so cruel.Mung_{July 17, 2015
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WD:
How do you know this?
It's simple. We know that RNA molecules are essentially part of a messaging system. Why send a message if you have nothing to say and there is no one to receive it?Mapou_{July 17, 2015
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our cells have a whole system dedicated to cleaning up aberrant RNAs.
And evolutionism explains that how, exactly?Virgil Cain_{July 17, 2015
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wd400: our cells have a whole system dedicated to cleaning up aberrant RNAs. Thank God that system only evolved after the RNA world!Mung_{July 17, 2015
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Of course it is. Every RNA molecule is produced for a purpose, whether or not we know what that purpose is.
How do you know this?wd400_{July 17, 2015
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The mere existence of such RNAs is not evidence tha tmost of the genome is functions.
Of course it is. Every RNA molecule is produced for a purpose, whether or not we know what that purpose is. But we'll find out soon enough as genetic theory gets better and we begin to build better computer models. DNA was made for the age of computers. So give it up, man. You're a minority holdout, a renegade. The Darwinist world has already swallowed their pride on this one. They admitted that they were wrong. Only the bozos and true believers are still arguing over it.Mapou_{July 17, 2015
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“Getting made into RNA” is a non-random, non-junk process
Not really. If DNA is unpacked and there are transcription factors around you'll get RNA molecules produced. Hell, our cells have a whole system dedicated cleaning up aberrant RNAs. The mere existence of such RNAs is not evidence tha tmost of the genome is functions.wd400_{July 17, 2015
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wd400
ENCODE told us most DNA gets made into RNA sometimes
"Getting made into RNA" is a non-random, non-junk process. There are a number of functions beyond coding for proteins. "Only about 15 percent of the human genome consists of protein-coding genes, but in recent years scientists have found that a surprising amount of the junk, or intergenic DNA, does get copied into RNA — the molecule that carries DNA’s messages to the rest of the cell. Scientists have been trying to figure out just what this RNA might be doing, if anything. In 2008, MIT researchers led by Institute Professor Phillip Sharp discovered that much of this RNA is generated through a process called divergent expression, through which cells read their DNA in both directions moving away from a given starting point. " http://www.lncrnablog.com/reading-dna-backward-and-forward/#more-1222 "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue--specific transcription in human cells." -- John Mattick and Marcel Dinger, "The extent of functionality in the human genome," The HUGO Journal, 7:2 (2013). "Results from the ENCODE project show that most of these [non-coding] stretches of DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes." -- Ines Barroso, "Non-coding but functional," Nature, 489:54 (Sept. 6, 2012). ht- Casey Luskin's 4-part series on ENCODE "Nonetheless, the lncRNAs identified by Leung et al5 have provided the field with exciting new clues into Ang II actions in VSMC and move us closer to decoding the encrypted message within noncoding RNA." http://circres.ahajournals.org/content/113/3/240.fullSilver Asiatic_{July 17, 2015
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"Interpretation" has very little to do with it. The best evidence for junk (genetic load, variation on genome size, correlation of that and strength of selection, lack of conservation...) remain. ENCODE told us most DNA gets made into RNA sometimes, which doesn't change much.wd400_{July 16, 2015
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OK wnd, are you agreeing with Dr Miller? Encode has provided us with much more data than we had back when Dr Miller made his evolutionary interpretation. Given what Encode has found, are you going to stick with the idea that junk DNA leftover from past transitions is cluttering up the genome? Let's hear your interpretation!tjguy_{July 16, 2015
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Fortunately, we now have hard data to show he was wrong
We do? What evidence is that?wd400_{July 15, 2015
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If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection to innovate, to test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution’s great successes.
This is a perfectly good evolutionary interpretation of the data. It makes total sense from an evolutionary stand point or worldview. The creationist/ID interpretation of the same data would have been (and it was and still is) different. The data is the same, but the interpretation is different. The same data can easily be interpreted in different ways. The data is what we know. The interpretation is our human attempt to make sense of the data. The important thing is what paradigm/worldview we use to interpret the data. In this case Miller's evolutionary interpretation of the data Was wrong. His evolutionary paradigm let him down and misguided him. Fortunately, we now have hard data to show he was wrong, but what if we didn't? Most poeople would still probably think he was right. This is a great illustration of why simply being able to explain something thru the evolutionary paradigm does NOT make it true or trustworthy. Without the ability to test the explanation or hypothesis, no matter how slick and true it might sound, we still don't know if it is true. We need to remember this when it comes to other evolutionary/materialistic explanations that cannot be tested. An explanation does not truth make. This goes for ID and creationism as well. As has been mentioned before, this highlights one of the problems of doing historical science. In seeking to arrive at the truth, using the right paradigm is more important than the data and the interpretation.tjguy_{July 14, 2015
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Darwinists have finally admitted that they were wrong and have thrown in the towel in the junk DNA fight, as seen in this quote from a recent New Scientist article:
A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive “junk” is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, “It’s a jungle in there. It’s full of things doing stuff.” And that is one of the most apt genome metaphors I’ve ever read. Recent insights into what some of this “stuff” is reveal problems with another classic idea: that DNA is the master controller of the cell, with information flowing in one direction from it, via RNA, to proteins. Some of ENCODE’s mystery RNAs control gene activity, others make changes that the cell remembers and passes on when it divides, and which can even be passed down generations. The RNAs may be one way the environment alters the behaviour of genes without changing their DNA sequences, a phenomenon known as epigenetics. Source: DNA is life’s blueprint? No, there’s far more to it than that
Darwinists: 0 IDists: 1 Oh, the shame. Oh, the humanity.Mapou_{July 14, 2015
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Ken Miller is a Catholic scientist? No wonder the Pope and the Catholic Church are so clueless. Birds of a feather.Mapou_{July 14, 2015
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No junk? Not a problem: natural selection is so efficient that useless code is soon discarded. Theory confirmed! In fact I'd say it's brilliant, except that would imply intelligence when we know there is none. But the true brilliance is framing a theory in such a way that it can accommodate any possible finding of fact. Junk? Confirmed! No junk? Confirmed! Unfalsifiability is the mark of purest science, isn't it?leodp_{July 14, 2015
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Mung, The wiki article on orphans is very good. Whether they are evidence for or against ID depends on ones starting point, but IIRC either Wells or Nelson was using them as evidence against evolution 5-6 years ago.RodW_{July 14, 2015
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In fact, the human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA ... What is an "orphaned" gene and why are “orphaned” genes evidence against intelligent design?Mung_{July 14, 2015
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Why Are Biologists Lashing Out Against Empirically Verified Research Results? - Casey Luskin July 13, 2015 Excerpt: no publication shook this (ID vs Darwin) debate so much as a 2012 Nature paper that finally put junk DNA to rest--or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the "vast majority" of the human genome shows biochemical function: "These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions."3 Ewan Birney, ENCODE's lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, "it's likely that 80 percent will go to 100 percent."4 Another senior ENCODE researcher noted that "almost every nucleotide is associated with a function."5 A headline in Science declared, "ENCODE project writes eulogy for junk DNA."6,,, Evolutionists Strike Back Darwin defenders weren't going to take ENCODE's data sitting down.,,, How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm--and by personally attacking, (i.e. ad hominem), those who challenge their position.,,, ,,, For example, back in 1994, pro-ID scientist Forrest Mims submitted a letter to Science warning against assuming that "junk" DNA was "useless."7 Science wouldn't print the letter, but that same year, anti-ID biologist Kenneth Miller published an article in a different journal making the opposite conclusion, namely that "the human genome is littered with pseudogenes, gene fragments, 'orphaned' genes, 'junk' DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design."8 Contrast Miller's assertion with a conclusion of Discover Magazine 18 years later in light of ENCODE's 2012 breakthrough report: "The key point is: It's not 'junk.'"9 http://www.evolutionnews.org/2015/07/the_encode_embr097561.html part 2 http://www.salvomag.com/new/articles/salvo32/the-encode-embroilment-part-II.php part 3 http://www.salvomag.com/new/articles/salvo33/the-encode-embroilment-part-III.phpbornagain77_{July 14, 2015
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Perjury? Explain?News_{July 14, 2015
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Ken Miller should be charged for perjury in court.Andre_{July 14, 2015
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