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> “Junk” DNA – The Biggest Blunder of Evolutionary-Based Science

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	“The commercial media is both ignorant of and blocks coverage of stories about non-centrality of the gene because its science advertising dollars come from the gene-centered Darwin industry. With declining ad revenue already widespread, and employee layoffs and contract buyouts in the editorial departments of news organizations like Newsweek, Time, the Washington Post as well as the New York Times – reporting on an evolution paradigm shift could mean the loss of even more advertising and/or yet another editor’s job. But neither will most science blogs report there’s a paradigm shift afoot because they share the same ideology as the corporate media. At the same time, the Darwin industry is also in bed with government, even as political leaders remain clueless about evolutionary biology. Thus, the public is unaware that its dollars are being squandered on funding of mediocre, middle-brow science or that its children are being intellectually starved as a result of outdated texts and unenlightened teachers.” —Suzan Mazur "Altenberg 16 An Exposé Of The Evolution Industry Will the Real Theory of Evolution Please Stand Up?" An E-Book in 6 Parts - Part 1 - Chapters 1, 2 & 3, 6 July 2008. http://www.scoop.co.nz/ stories/HL0807/S00053. htm#introduction

“Junk” DNA – The Biggest Blunder of Evolutionary-Based Science

Geneticists once believed that protein-coding genes were the key to building and maintaining healthy cells. When all sorts of other non-coding genetic sequences were discovered, evolutionary geneticists referred to them as “junk DNA” on the assumption that they were nothing but useless remnants left over from evolutionary predecessors.

For over 50 years now, evolutionary-based researchers have arrogantly denied the critical nature of these regulatory elements, but it is now known that “junk DNA” makes up approximately 98.5% of an organism's DNA. Regulatory elements control genes and they are the key to cell health and development and primary link to disease when not functioning properly. (The study of how “junk DNA” can change a gene's function without altering its DNA sequence is often referred to as 'epigenetics.')

Upon resigning as Director, Francis Collins regretfully stated that the National Human Genome Research Institute's gene-centered approach was misguided and had been “dismissive” of regulatory elements, i.e. “junk DNA”:

• “A slew of recent but unrelated studies of everything from human disease to the workings of yeast suggest that mysterious swaths of molecules - long dismissed as 'junk DNA' - may be more important to health and evolution than genes themselves …
  'It's a radical concept, one that a lot of scientists aren't very happy with,' said Francis S. Collins, director of the National Human Genome Research Institute. 'But the scientific community is going to have to rethink what genes are, what they do and don't do, and how the genome's functional elements have evolved.'”
  “DNA unraveled,” September 24, 2007, The Boston Globe.
  http://www.boston.com/news/globe/health_science/articles/2007/09/24/dna_unraveled/
  
• "Ah - so much of the genome - after all only about 1.5% of it is coding for protein. The rest of it is probably involved in this regulatory stuff, and for a long time were were a bit dismissive about that 98.5% of it and said that a lot of it was kind of a junk. I don't think people are using the word "Junk" any more when they are talking about the genome, because the more we study, the more functions we find in that "filler" - which is not a "filler" at all."
  2008, Francis Collins interview with Charlie Rose, begin at 10:35 for regulatory element discussion and quote.
  http://www.charlierose.com/view/interview/9193

In 1956, many scientists, including Nobel laureate Barbara McClintock, proposed that “junk DNA” was essential and functional genetic material. But, since that view didn’t fit with the presupposition of evolutionary philosophy, their proposals were dismissed and the next 50-60 years of research was primarily focused on pursuing the dogma that genes controlled everything:

• “Bejerano and his colleagues aren't the first to suggest that transposons play a role in regulating nearby genes. In fact, Nobel laureate Barbara McClintock, PhD, who first discovered transposons, proposed in 1956 that they could help determine the timing for when nearby genes turn on and off."
  Stanford University Medical Center, “'Junk' DNA Now Looks Like Powerful Regulator, Scientists Find,” April 24, 2007, ScienceDaily.
  http://www.sciencedaily.com/releases/2007/04/070423185538.htm

This ignorance has proven to be one of evolution’s biggest blunders and has been the most damaging obstacle in medical discovery and progress. What is more alarming is that there are many researchers who refuse to subscribe or are still ignorant of this paradigm shift, even though it “became apparent in 2001, when the human genome sequence was first published.”:

• “Gene regulation has turned out to be a surprisingly complex process governed by various types of regulatory DNA, which may lie deep in the wilderness of so-called junk DNA that lies between genes. Far from being humble messengers, RNAs of all shapes and sizes are actually powerful players in how genomes operate. Finally, there's been increasing recognition of the widespread role of chemical alterations called epigenetic factors that can influence the genome across generations without changing the DNA sequence itself. The scope of this 'dark genome' became apparent in 2001, when the human genome sequence was first published.”
  Elizabeth Pennisi, “Shining a Light on the Genomen's 'Dar Matter',” Science, Vol. 330 (6011):1614, December 17, 2010.
  http://www.sciencemag.org/content/330/6011/1614.short
  
• “For me, the most important outcome of the human genome project has been to expose the fallacy that most genetic information is expressed as proteins … In contrast to protein-coding genes, the extent of noncoding intronic and intergenic sequences increases markedly with complexity; only 1.5% of the human genome encodes proteins ...
  These observations suggest that we need to reassess the underlying genetic orthodoxy, which is deeply ingrained and has been given superficial reprieve by uncritically accepted assumptions about the nature and power of combinatorial control.”
  John Mattick, University of Queensland, “The genomic Foundation Is Shifting,” February 18, 2011, Science Magazine Vol. 331 no. 6019 p. 874.
  http://www.sciencemag.org/content/331/6019/874.1.full
  
• “Slowly the importance of the epigenome in cancer development is being appreciated. “Geneticists are hugely more aware of the importance of epigenetics in the development of cancer,” observes Baylin. When it comes to cancer prevention, the future could lie in arresting the reversible epigenetic changes before irreversible mutations take hold.”
  

NOTE the comment at the end of article from Xianfa Xi, Ph.D. Biological Scientists with a focus on evolutionary genetics, University of Notre Dame:
“I hope all cancer researchers will see this article. Last year at the 75th Anniversary Symposium on Quantitative Biology at Cold Spring Harbor, when I commented, after quite a few high-profile talks on genetic analysis of cancer, that the whole field of cancer genetics might have been on the wrong path by focusing on genetic mutations and epigenetics should instead be the way to go for cancer studies, the speakers and much of the audience seemed to be stunned. For many reasons, the simplistic view that everything in biology is determined by DNA sequence has dominated biology, medical research, and the study of evolution for over half an century. But this has inhibited the development of many innovative ideas in biology, prohibited a holistic and comprehensive view of life and the mechanism of evolution, and delayed medical research on cancer and many other diseases for a few decades.”
“Epigenetics: Unravelling the cancer code,” March 23, 2010, Nature.
http://www.nature.com/nature/journal/v471/n7339_supp/full/471S12a.html

Unwilling to deny the ridiculous assumption that “junk DNA” is proof for evolution, many zealous evolutionists have yet to throw in the towel:

The most famous evolutionist promoting the myth of “junk DNA” is Richard Dawkins, who coined the term ‘parasitical’ when referring to ‘repetitive DNA’ in his 1976 book called “The Selfish Gene.” As far as we know, Dawkins is still beating the drum and hasn't recanted:

• “For the genome is littered with dead genes. Huge wastes of DNA territory comprise a graveyard of discarded, superseded old genes (plus meaningless sequences of nonsense DNA that never functioned) with occasional islands of current, extant genes that are actually read by the translating machinery and turned into action. Dead, untranslated genes are called pseudogenes.”
  Richard Dawkins, “Dawkins on Darwin,” published in The Times UK, February 11, 2009. http://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article5707143.ece

As of May 2010, political and zealous anti-God host of Pharyngula blog PZ Myers was continuing to promote the “junk DNA” myth to his followers:

• “There clearly are still mysteries in there – they do identify a few novel transcripts that come up out of the intergenic regions – but they are small and rare, and the fact of their existence does not imply a functional role, since they could simply be byproducts of other processes. The only way to demonstrate that they actually do something will require experiments in genetic perturbation.
  The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.”
  PZ Myers, biologist and associate professor, “Junk DNA is still Junk”, May 19, 2010, Pharyngula blog.
  http://scienceblogs.com/pharyngula/2010/05/junk_dna_is_still_junk.php
  

In the following quote, note that the researchers acknowledge that non-protein coding genes play “critical roles in both health and disease,” but then they later regress back to believing that most might be just “’genomic noise’ without any biological function.”:

• “A research team at the Broad Institute of Harvard and MIT and Beth Israel Deaconess Medical Center has uncovered a vast new class of previously unrecognized mammalian genes that do not encode proteins, but instead function as long RNA molecules.
  Their findings, published in the February 1st advance online issue of the journal Nature, demonstrate that this novel class of 'large intervening non-coding RNAs' or 'lincRNAs' plays critical roles in both health and disease, including cancer, immune signaling and stem cell biology …
  'The challenge in finding these lincRNAs is that they have been hiding in plain sight,' said John Rinn, a Harvard Medical School assistant professor at Beth Israel Deaconess Medical Center and an associate member of the Broad Institute of Harvard and MIT. 'The human and mouse genomes are already known to produce many large RNA molecules, but the vast majority show no evolutionary conservation across species, suggesting that they may simply be 'genomic noise' without any biological function.'”
  Broad Institute of MIT and Harvard, “New Class Of Non-Protein Coding Genes In Mammals With Key Functions Uncovered,” February 9, 2009, ScienceDaily.
  http://www.sciencedaily.com/releases/2009/02/090201141601.htm

Why do so many evolutionists resist the truth? Because many of them can’t think past their evolutionary-based presupposition that evolution is true so genetic material MUST correlate with common descent and what they've been told … regardless of the evidence!

Because evolutionary-based presuppositions are the foundation of almost ALL research dollars, we are now paying for this horrific blunder. Since it has been discovered that most diseases, especially cancer, are caused by alterations with “junk DNA” instead of the protein-coding genes themselves, imagine the medical treatment and cures we could be experiencing today if evolutionists would only have kept an open mind. Slow to come around, there is hope and some evolutionary-based geneticists are finally changing their minds about “junk DNA”:

• “In fact, it looks so useless that, until recently, many scientists considered it to be just a leftover artifact of eons of evolution.Recently, however, research has shown that defects in the development or function of primary cilia are associated with many human disorders, including polycystic kidney disease, skeletal malformations, neural tube defects, as well as obesity. Clearly there's more here than meets the eye. Scientists have since decided that the primary cilium works as a kind of antenna to help the cell respond to outside chemical signals and mechanical forces.”
  Stanford University Medical Center, “Mysterious cilium functions as cellular communication hub, study shows”, June 24, 2010, Physorg.
  http://www.physorg.com/news196605108.html
  
• “Gerstein and postdoctoral associate Nitin Bhardwaj analyzed regulatory networks of five diverse species, from E. coli to human, and rearranged those systems into hierarchies with a number of broad levels, including 'master regulators,' 'middle managers' and 'workhorses.' In most organisms, master regulators control the activity of middle managers, which in turn govern suites of workhorse genes that carry out instructions for making proteins.”
  Yale University, “Molecular Middle Managers Make More Decisions Than Bosses”, March 29, 2010, Physorg.
  http://www.physorg.com/news189083953.html
  
• “When the human genome was fully sequenced in 2004, approximately 20,000 genes were found. However, it was discovered that living cells use those genes to generate a much richer and more dynamic source of instructions, consisting of hundreds of thousands of genetic messages that direct most cellular activities. Frey, who has appointments in Engineering and Medicine, likens this discovery to 'hearing a full orchestra playing behind a locked door, and then when you pry the door open, you discover only three or four musicians generating all that music.'
  To figure out how living cells generate vast diversity in their genetic information, Frey and postdoctoral fellow Yoseph Barash developed a new computer-assisted biological analysis method that finds 'codewords' hidden within the genome that constitute what is referred to as a 'splicing code'. This code contains the biological rules that are used to govern how separate parts of a genetic message copied from a gene can be spliced together in different ways to produce different genetic messages (messenger RNAs). 'For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,' says Frey.”
  University of Toronto, “Researchers crack 'splicing code,' solve a mystery underlying biological complexity”, May 5, 2010, Physorg.
  http://www.physorg.com/news192282850.html
• “Pseudogenes are relics of former genes that no longer possess biological functions. They are abundant in the genomes of complex organisms such as vertebrates and flowering plants and provide a useful resource for studying mutation rates and neutral evolutionary patterns. Processed pseudogenes can be regarded as fossilised footprints of past gene expression, permitting a peek into ancient transcriptomes … Recent studies found some pseudogenes to possess apparent functions in gene regulation, creating a difficulty in defining pseudogenes.”
  Encyclopedia of Life Sciences, “Pseudogenes and Their Evolution,” November 15, 2010, Wiley Online Library.
  http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0005118.pub2/abstract
  
• “An entire class of seemingly useless genetic components may actually regulate gene activity, suggests a study that — though preliminary — has potentially transformative implications for biology.
  The findings involve apparently redundant copies of genes, called 'pseudogenes,' and RNA molecules that would normally carry out genetic instructions, but appear to be disabled.
  'This is a completely new way by which genes can be regulated. It’s something that up to this point has been undiscovered,' said Leonardo Salmena, a Harvard Medical School geneticist and co-author of the study, published June 23 in Nature.'”
  Wired Science, “New Form of Gene Regulation Hints at Hidden Dimension of DNA”, June 24, 2010, Wired.
  http://www.wired.com/wiredscience/2010/06/expanding-genome/#ixzz0rruDbndo
  
• “We also demonstrate that the transcripts of protein-coding genes such as PTEN are biologically active. These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs. “
  Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, “A coding-independent function of gene and pseudogene mRNAs regulates tumour biology,” April 26, 2010, Nature.
  http://www.nature.com/nature/journal/v465/n7301/pdf/nature09144.pdf
  
• “By blocking the function of a type of genetic material called microRNA, researchers have dramatically decreased the size of a cancerous tumour in a mouse model.
  'MicroRNAs originate from part of our DNA that has long been thought of as junk DNA. Much is still unknown but we know they can interfere with the functioning of genes and can control the production of proteins in the body,' said QIMR researcher Dr Susan Woods.”
  Queensland Institute of Medical Research, “MicroRNA to cambat cancer,” September 28, 2010, Physorg.
  http://www.physorg.com/news204867760.html
  
• “The research results, published in the July 22 issue of the journal Nature, add to the growing body of evidence that so-called 'junk DNA' is anything but rubbish. The term 'junk DNA' is commonly used to describe the portion of the genome that doesn't contain genes, which are pieces of DNA that code for the production of proteins and other molecules that have specific functions. The noncoding region is often surprisingly large; in humans, some 98 percent of the genome merits 'junk' status. But according to David Ste' is crucial for turning the information encoded in genes into useful products.”
  Princeton University, “Redundant genetic instructions in 'junk DNA' support healthy development,” July 16, 2010, Physorg.
  http://www.physorg.com/news198500666.html
  
• “While miRNAs were first discovered in 1993, scientists did not link them to gene regulation until nearly ten years later. Now, scientists are working to understand how miRNA expression is controlled, what genes miRNAs target, and how varying levels of miRNAs are related to human disease, particularly heart disease and cancer.”
  Tufts University School of Medicine and Tufts Medical Center, “Newly Identified RNA Sequence Is Key in microRNA Processing,” August 21, 2010, ScienceDaily.
  http://www.sciencedaily.com/releases/2010/08/100816110413.htm

	“IT WILL TAKE YEARS, perhaps decades, to construct a detailed theory that explains how DNA, RNA and the epigenetic machinery all fit into an interlocking, self-regulating system. But there is no longer any doubt that a new theory is needed to replace the central dogma that has been the foundation of molecular genetics and biotechnology since the 1950s.” —W. Wayt Gibbs Senior writer at Scientific American, “The Gems of "Junk" DNA,” Scientific American, November, 2003. (Gibbs was one of two recipients of the first annual Winstar Institute Science Journalism Award for his coverage of epigenetics.) http://www.mindfully.org/GE/2003/Junk-GenomeNov03.htm