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Tossing Out the Junk

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Over at the ID The Future podcast, Casey Luskin has been doing a series on “the top 10 problems with biological and chemical evolution.” Some of the problems he discusses will no doubt be of more interest to certain listeners than to others. However, the segment on junk DNA is particularly worth hearing (about 13 minutes).

For those who have been following the debate closely there may not be much new in the segment, but it provides a relatively up-to-date review of some of the recent research, with multiple citations that are useful when talking with a friend or colleague who may still be stuck in the naive and outdated idea that the genome is awash in junk.  Better yet, ask your friend if they have 15 minutes and an open mind, and then let them have a listen.

It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.  Even with the proliferation of functions for non-coding DNA, we still hear regular pronouncements from the purveyors of the materialist creation myth that “yes, there may be some function for non-coding DNA, but most of it is still junk.”

The whole idea of pervasive junk in our DNA is so naive and absurd as to boggle the mind.  Thankfully, the trajectory of the evidence is clearly trending toward a more rational and complete assessment of DNA.  Yes, hindsight is 20/20, and soon enough every biologist worth her salt will claim that she “always knew” that most DNA had function.  But let us not forget that there were a few lone voices, including prominent ID proponents, long arguing for pervasive function — in the face of ridicule and the stifling, science-limiting attitude of the Darwin establishment about their beloved icon of “junk” DNA.

Comments
Querius, you're making a potentially unjustified assumption in your last question. What makes you think that any knowledgeable biologists ever considered the mere existence of junk DNA to be evidence of evolution? As for your first three questions, Moran has already answered them in this article: http://sandwalk.blogspot.com/2013/10/non-darwinian-evolution-in-1969-case.htmlNullifidian
May 14, 2015
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wd400 and Larry Moran, Quiz - 12 points 1. Who popularized the term "junk DNA"? 2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA? 3. What was the proposed reason in the paper for so much junk? 4. Why was it considered strong evidence for evolution? -QQuerius
May 14, 2015
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Ever since it became apparent that the only causally adequate explanation for the contents of the protein coding regions of DNA memory was intelligent agency, it was entirely reasonable to expect that much of the rest of DNA memory would turn out to be functional. It always seemed to me to be reasonable to expect that some of the rest of it was currently unused but might have been left in a state that would reveal something about prior functionality that no longer exists, but would remain functional in the sense that it was available for use by new functionality. If that sounds like that is how a computer programmer would look at it, that is because it is, at least for this one. ;o) How do we, in understanding the rest of DNA memory, get to where we are in understanding the protein coding regions of DNA? As a computer programmer who has worked at the level of CPU machine instructions, having written applications in assembler language, and written applications to simulate the instruction set of a CPU for diagnostic purposes, let me explain from my perspective of the utilization of digital information, why understanding the rest of it will probably be much more difficult. There is a direct correspondence between the bit pattern of an executable instruction in memory and one of the machine instructions from the set of those of which the CPU is capable. Repeated observations of how the bit patterns read in from executable memory caused the CPU to respond as programs execute would soon reveal the complete instruction set of the CPU. Understanding the correspondence between the bit patterns in executable memory locations and the instruction set of the CPU is not the same as understanding that a given range of such memory locations comprise, say, a word processor. Understanding that correspondence would do nothing to help one understand that another range of memory addresses contained ASCII encoded characters, or a JPEG image, or some other kind binary data. My point is simply that what we understood first, unsurprisingly, was that which was most easily detected by observation. Where functionality is not revealed by a direct and observable correspondence between the contents of digital memory and some activity, such as the assembly of protein machines, does not mean that there is no functionality, but only that the functionality may be much more indirectly associated with the contents of digital memory.harry
May 14, 2015
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C-Value Paradox A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.
Let's not bother with empirical findings. And by all means, let's not use genome size as a marker of relatedness. Can't you just imagine what the tree of life would look like then? Yech!Mung
May 14, 2015
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Here is a video along the same line:
Biological Information - Not Junk After All 11-29-2014 by Paul Giem - video https://www.youtube.com/watch?v=xO-7kVBA_JM In the book "Biological Information: New Perspectives" the chapter entitled "Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information" discusses the various functions of DNA and finds that non-functional DNA is a small minority.
Here is the paper:
Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009
After ENCODE came out a guy named Dan Graur about had a cow. Here is an analysis of the Dan Graur incident:
Biological Information – (The Dan Graur incident) Criticizing ENCODE 12-13-2014 by Paul Giem – video https://www.youtube.com/watch?v=zhlFJO1WqVk
Basically, the Darwinian critics of the ENCODE study, which found widespread functionality for supposed 'junk' DNA, said that biochemical functionality does not really determine if a sequence is actually functional, only 'conservation of sequence' determines what is functional. With that self-serving definition for functionality, a self-serving definition in which common ancestry is presupposed in the definition of functionality, they arrived at 8.2% functionality:
DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm
So basically, only if Darwinian evolution is assumed as true from the outset will Darwinists be willing to accept that a given sequence of 'junk' DNA may be functional!,, That is called 'assuming your conclusion into your premise' and is absolutely a horrible way to practice science! Needless to say, science itself does not presuppose common ancestry in the answers for functionality that it gives us, and thus, as should be obvious, functionality does not follow the presupposed 'conserved' pattern as Darwinists imagined it would:
Protracted Unrest Between ENCODE Researchers and Junk-DNA Advocates Goes On - November 26, 2014 Excerpt: It's not exactly Fergusson, Mo., but the battle between ENCODE researchers and junk-DNA holdouts goes on.,,, ,,,"Evolutionary conservation of primary sequence is typically considered synonymous with conserved function, but this finding suggests that this concept should be reinterpreted, because insertions of retrotransposon elements in new genomic regions are not conserved between species." In short, the Mouse ENCODE group takes direct aim at the arguments of Dan Graur and the other junk-DNA faithful, who say that everything evolution did not conserve is junk.,,, ,,,much of what Darwinian evolutionists had dismissed as junk appears functional. Non-coding regions of the mouse genome are transcribed, and appear to function in previously unimagined ways, such as regulation of gene expression, chromosomal stability, and maintenance of species identity. Carninci offers further thoughts: ,,,"we should rethink the relationship between genomic function and evolutionary conservation. Regulatory regions and long non-coding RNAs (lncRNAs) are not subject to the evolutionary constraints of protein-coding genes, which may help to explain the sequence drifts reported in these papers. However, it is striking that transcription-factor networks are conserved despite low conservation of their binding positions in the genome." http://www.evolutionnews.org/2014/11/protracted_unre091501.html
bornagain77
May 14, 2015
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Dr. Sternberg was mentioned in Casey's talk. Here is a fairly recent talk that Dr. Sternberg gave on the human genome that overturns the Darwinian claim that most of the human genome must be junk:
Podcast: Richard Sternberg - PhD in evolutionary biology - " On Human Origins: Is Our Genome Full of Junk DNA? part 1 http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna/ Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 2 (Major Differences in higher level chromosome spatial organization) 5:30 minute mark quote: "Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species" http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/ Podcast: Richard Sternberg PhD - " On Human Origins: Is Our Genome Full of Junk DNA? Part 3 http://intelligentdesign.podomatic.com/entry/2014-11-17T14_14_33-08_00 Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 4 http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-4/ Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 5 (emphasis on ENCODE and the loss of the term 'gene' as a accurate description in biology and how that loss undermines the modern synthesis of neo-Darwinism) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/
bornagain77
May 14, 2015
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Five Things You Should Know if You Want to Participate in the Junk DNA Debate Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It MeansLarry Moran
May 14, 2015
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It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.
No knowledgeable scientist ever said that all noncoding DNA was junk or that it was uninteresting. Back in 1968 every knowledgeable scientist was familiar with functional noncoding DNA so they would have been laughed out of the room if they ever made such a silly statement. Back then, we knew about centromeres, origins of replication, regulatory regions, and various genes for functional RNAs. We have been patiently explaining this to ID folk for two decades. If they continue to repeat this untrue statement then they are either lying or incredibly stupid ... or possibly both.Larry Moran
May 14, 2015
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I think my comment is pretty clear: the thing you claimed to be true is not. People didn't say the only DNA worth looking at was protein coding. You make several more mistakes in your follow up comments, you should probably learn a little bit about junk DNA before you comment on it further.wd400
May 14, 2015
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Mung@1 gets dangerously close to undermining the post. Keep thinking, and you'll get yourself in trouble around here. Mapou@2: "Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1" .....nGFR1 is a protein, FYI.REC
May 14, 2015
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"It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins." Can we get a reference of a prominent scientist stating that the only DNA worth talking about codes for proteins? Your statement is laughable.REC
May 14, 2015
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Podcast: A Bonus 11th Problem - "The Top 10 Problems with Darwinian Evolution": - Casey Luskin In this segment, Casey discusses a bonus eleventh problem: that humans display many behavioral and cognitive ability that offer no apparent survival advantage. http://www.discovery.org/multimedia/audio/2015/05/the-top-10-problems-with-darwinian-evolution-a-bonus-11th-problem/bornagain77
May 14, 2015
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Here's a challenge @907: https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-564761 (see the post @908 in that same thread).Dionisio
May 14, 2015
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OT: Epigenetics on steroids
Seasonal immunity: Activity of thousands of genes differs from winter to summer - May 12, 2015 University of Cambridge Summary: Our immune systems vary with the seasons, according to a study that could help explain why certain conditions such as heart disease and rheumatoid arthritis are aggravated in winter while people tend to be healthier in the summer. The study shows that the activity of almost a quarter of our genes (5,136 out of 22,822 genes tested) differs according to the time of year, with some more active in winter and others more active in summer. This seasonality also affects our immune cells and the composition of our blood and adipose tissue (fat). http://www.sciencedaily.com/releases/2015/05/150512112356.htm
bornagain77
May 14, 2015
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It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.
It might be, if it were true. EA: Meaning what? Are you claiming that the fact that large swaths of DNA do not code for proteins has not been used by evolutionary proponents to bolster the claim that such DNA is "junk"? This has been an extremely common and pervasive tactic of Darwinist proponents for decades. Embarrassingly, some are still using this tactic today in the face of contrary evidence. And now that even many Darwinists are reluctantly admitting that "some" non-coding DNA might have function, whence the continuing and repeated claims that most DNA is still junk? Why on earth would any rational person make such a claim? It is a classic argument from ignorance: "We don't know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true." Evolution-of-the-gaps thinking.wd400
May 13, 2015
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Junk DNA is as anti-science as you can get. Intelligent design always results in a hierarchical organization: big parts are made of small parts. It follows that the design of the genome must be a hierarchy, i.e., a genetic tree. Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1.Mapou
May 13, 2015
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But surely there's no selective advantage to all that junk. Can't we prove that it's junk by showing that it's not under selection?Mung
May 13, 2015
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