How Junk DNA confirms intelligent design predictions

How Junk DNA confirms intelligent design predictions

https://reasonandscience.catsboard.com/t2359-how-junk-dna-confirms-intelligent-design-predictions

As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that 'junk' DNA was 'useless.'" Science wouldn't print Mims' letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things:
[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it. 15

The more scientific knowledge advances and unravels, important biochemical functions of junk dna are discovered, which doesn't favour the views of proponents of naturalism.  Complex instructional information is used on various levels, not only in the genome, but also in the epigenome, and a big responsability goes to the noncoding DNA regions, and what was supposed to be Junk DNA, HAS been uncovered to have several essential functions to form complex organisms. 

 Dr. Mae-Wan Ho mentions " a vast RNA underworld where RNA agents not only decide which bits of text to copy, which copies get destroyed, which bits to delete and splice together, which copies to be transformed into a totally different message and finally, which resulting message - that may bear little resemblance to the original text - gets translated into protein. RNAs even get to decide which parts of the sacred text to rewrite or corrupt. The whole RNA underworld also resembles an enormous espionage network in which genetic information is stolen, or gets re-routed as it is transmitted, or transformed, corrupted, destroyed, and in some cases, returned to the source file in a totally different form. 

RNA's of course do not decide anything ( thats one of the often used anthropomorphised language that should be tabu in evolutionary writings ) . RNA's, transcribed from " junk dna" are PROGRAMMED, or INSTRUCTED to exercise many tasks in the organism. These instructions can only be the result of preloading by intelligence, since a stepwise evolutionary manner is not possible. Jerry Coynes assertion that natural selection is capable of the task is unsupported pseudoscientific nonsense. 

An interesting paper reports that eukaryotic cells use a variety of strategies to control their transcriptional output that employ a large number of regulatory factors that, in turn, must be tightly regulated. Introns, as genetic entities or RNA segments ( previously held as junk ), facilitate or participate in this amazing regulation feat by sheltering information for small regulatory RNAs allowing for concerted expression of multiple molecules in a given context, influencing where and when a messenger RNA is spliced and translated, preventing or attenuating translation off context or, on the contrary, diversifying the type and function of the molecules produced depending on the internal and external environment.

Observe the nomenclature, which goes like a redline through many scientific biology papers: strategies, control, regulatory, tightly regulated, amazing regulation feat, concerted expression, preventing or attenuating translation. All this is far from useless , random , genetic junk and waste, but is essential  coded, instructional complex genetic information. A stepwise arise  is not possible; either the process is fully regulated and setup right from the beginning, or nothing goes. 

There  remains a portion which is non-functional, as for example:

http://www.sciencedirect.com/science/article/pii/S0960982212011542

Transposable elements in humans, called Alu, occur in about a million copies and accounts for about 10% of our genome. Almost all copies of transposons in genomes are partial or defective elements that were inserted in the evolutionary past and are now decaying away, largely by neutral mutational drift.

A good part of Junk DNA is junk through endogenization of viral DNA and pseudogenization , unconstrained evolving introns, pseudo genes through gene duplications etc.  This does not falsify IDs predictions however. It means that a part of this part of the genome is indeed the result of evolutionary remainings. 




Blue: titles
Bolt: important
Red: very important
Green: my remarks
Blue: deseases

MicroRNAs are predicted to control the translational activity of approximately 30% of all protein-coding genes in mammals  12

Biogenesis of Mammalian MicroRNAs: A Global View 13
MicroRNAs (miRNAs) are approximately 22-nucleotide-long non-coding RNAs that are important regulators of gene expression in eukaryotes. miRNAs are first transcribed as long primary transcripts, which then undergo a series of processing steps to produce the single-stranded mature miRNAs. 

There would be no use for miRNA's, unless regulation of gene expression is required. 

Mammalian Introns: When the Junk Generates Molecular Diversity 6  
Splicing of introns has been directly implicated in the production of small regulatory RNAs. Hence, splicing of introns also appears to provide plasticity to the type of RNA produced from a genetic locus (coding, non-coding, short or long). Introns have been regarded for a long time as “junk DNA” and remnants of archaic ancestral genomes. Accumulating evidence lent support to their fundamental importance in the regulation of mammalian gene expression programs, from transcriptional initiation, termination and stability, through recruitment of the exon-junction complex to recruitment of chromatin remodelers through the spliceosome.
Eukaryotic cells use a variety of strategies to control their transcriptional output that employ a large number of regulatory factors that, in turn, must be tightly regulated. Introns, as genetic entities or RNA segments, facilitate or participate in this amazing regulation feat by sheltering information for small regulatory RNAs allowing for concerted expression of multiple molecules in a given context, influencing where and when a messenger RNA is spliced and translated, preventing or attenuating translation off context or, on the contrary, diversifying the type and function of the molecules produced depending on the internal and external environment.

Observe the nomenclature, which goes like a redline through many scientific biology papers: strategies, control, regulatory, tightly regulated, amazing regulation feat, concerted expression, preventing or attenuating translation. All this is far from useless , random , genetic junk and waste, but is essential  coded, instructional complex genetic information.  Only intelligent minds are capable of producing this,  and requires the intervention of intelligence, and forplanning and organisation. A stepwise arise  is not possible; either the process is fully regulated and setup, or nothing goes. 

Natural antisense transcripts 4
Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be ‘junk DNA’.

How could that regulation have been achieved ? trial and error ? 

MicroRNAs--"Once Dismissed as Junk"--Confirmed To Have Important Gene Regulatory Function 2
In 2008 Scientific American noted that microRNAs were "once dismissed as junk" and said the following:
Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called "junk DNA," sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.

ENCODE showed that there are millions of regulatory particles, at least 18,000 small and large RNA particles. These newly discovered microRNA added to the enhancers and repressors of old.

This shows there is a essential function for microRNA's, and they need coded information to exercise their function. 

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription 14
Several regions of the human genome that are believed to be enhancers, are transcribed into short enhancer RNAs (eRNAs). These are thought to act as scaffolds that regulate the 3D architecture of chromosomes in the vicinity of their transcription site 

Junk DNA: Is Preventing Breast Cancer a Function? 5

Each time a function is found for a piece of non-coding DNA, the "junk DNA" myth gets more mythological. Here's a function that has been revealed for a certain long, non-coding transcript of DNA into RNA (lncRNA). It helps prevent breast cancer and ovarian cancer.

Junk DNA' made visible before the final cut 7
Snippets of information contained in dark matter ( junk DNA )  can alter the way a gene is assembled. "These small sequences of genetic information tell the gene how to splice, either by enhancing the splicing process or inhibiting it. The research opens the door for studying the dark matter of genes.

RNA-mediated epigenetic regulation of gene expression 10
Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds and then mediating the recruitment of histone and DNA methyltransferases. In addition, recent advances suggest that chromatin-associated long non-coding RNA scaffolds also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.

Chromatin Regulation by Long Non-coding RNAs 11
A class of noncoding RNAs referred to as long noncoding RNAs or lncRNAs have proven to be of particular interest. These transcripts are distinguished from other classes by
their length and inability to produce protein. Similar to mRNAs, they are transcribed by RNA polymerase II, capped, spliced, and polyadenylated. Given the diversity and quantity of lncRNAs, it seems likely that their functions are as numerous as those of proteins Biologically, lncRNAs function in a wide variety of processes, including X-chromosome inactivation (XCI), genomic imprinting, development, and metastasis
Chromatin Modifications Play Key Roles in Development and Cell Identity
.Interactions between the nucleosomes, the underlying DNA, and a variety of other components are altered by targeted physical disruption or enzymatic modifications, which results in changes in the accessibility of the DNA sequence. Consequently, these changes in chromatin structure have dramatic effects on gene expression patterns and are vital in establishing cell identity. lncRNAs are not passive or transient components of chromatin, in fact they play a key role in one of the most dramatic chromatin compactions in development. 

Regulation of Eukaryotic Cell Differentiation by Long Non-coding RNAs
Individual examples of lncRNAs that modulate developmental processes have been studied in detail over the past two decades. For instance, Xist plays a well-characterized essential role in X-chromosome inactivation in female mammals via epigenetic silencing , and H19 regulates growth during embryogenesis via imprinting of the maternal Igf2 allele. 

Dr. Mae-Wan Ho writes : 8 
RNA agents not only decide which bits of text to copy, which copies get destroyed, which bits to delete and splice together, which copies to be transformed into a totally different message and finally, which resulting message - that may bear little resemblance to the original text - gets translated into protein. RNAs even get to decide which parts of the sacred text to rewrite or corrupt. The whole RNA underworld also resembles an enormous espionage network in which genetic information is stolen, or gets re-routed as it is transmitted, or transformed, corrupted, destroyed, and in some cases, returned to the source file in a totally different form.

RNA's do not decide anything ( thats one of the often used anthropomorphized language that should be tabu in evolutionary writings ) . RNA's are PROGRAMMED to exercise their precise job in the organism. These instructions must be preloaded and programmed by intelligence, since a stepwise evolutionary manner is not possible.

Jerry Coyne responded : 

epigenetics is not something that radically revises our view of genetics and evolution, for it’s something that some parts of DNA do to other parts of DNA, and those instructions have evolved by natural selection.



How does Coyne know that natural selection has that hability ? Seems to me a just so assertion without any evidence to back up the claim. 

1  http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution
2. http://www.scientificamerican.com/article/hidden-treasures-in-junk-dna/
3. http://www.evolutionnews.org/2016/02/junk_dna_is_pre102591.html
4. https://hmg.oxfordjournals.org/content/early/2014/05/28/hmg.ddu207.full.pdf
5. http://www.evolutionnews.org/2016/02/junk_dna_is_pre102591.html
6. file:///D:/Downloads/ijms-16-04429.pdf
7. https://www.sciencedaily.com/releases/2013/01/130107100057.htm
8. Subverting the Genetic Text
9. Mae-Wan Ho and Suzan Mazur: the blind leading the blind about evolution
10. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376354/
11. Molecular Biology of Long Non-coding RNAs page 1
12. https://en.wikipedia.org/wiki/Noncoding_DNA
13. http://www.sciencedirect.com/science/article/pii/S1672022912000563
14. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109059/
15. http://www.ideacenter.org/contentmgr/showdetails.php/id/1437

«Another complication is that many of the long non-coding RNAs are found in the same region as classical protein-coding genes. Sometimes they may be in exactly the same position, but encoded on the opposite strand, just as we saw for Xist and Tsix in Chapter 7. Others may be found «within the stretches of junk that lie between two amino acid-coding regions in a single gene, which we first encountered in Friedreich’s ataxia in Chapter 2 (see page 18). There are lots of ways in which the long non-coding RNAs may be co-located in the same region as protein-coding genes and this creates substantial experimental difficulties if trying to investigate function.
Usually the functions of genes are tested by mutating them. There are all sorts of mutations that can be introduced but the most commonly used will either switch the gene off or will lead to it being expressed at a higher level than normal. But because so many of the long non-coding RNAs overlap with protein-coding genes, it’s hard to mutate one without mutating the other at the same time. We then face the problem of knowing whether the effects we see are due to the change in the long non-coding RNA or in the protein-coding gene.»

Carey, Nessa. «Junk DNA: A Journey Through the Dark Matter of the Genome.»



Messenger RNA from one direction in the genome may code for a protein, but the same region copied backwards simply codes for a non-coding RNA that cannot be translated into a protein. Sometimes this creates auto-regulatory loops in our cells, limiting expression of certain genes.

Researchers have reported that about a third of protein-coding genes also produce non-coding RNA from the antisense strand. However, the antisense is usually produced at lower levels, often no more than 10 per cent.

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 2010 Dec 10;143(6):1018–29
http://www.cell.com/cell/pdf/S0092-8674(10)01300-0.pdf

https://www.apologeticscentral.co.za/articles/ERV.html?fbclid=IwAR2bbreABxpdyK823BTaYt4hevRBb7baKdS2oYL_V590q8mlRwrmwtWTRrQ

Non-Coding DNA “Extremely” Conserved, Essential for Regulation   11/26/2004


https://web.archive.org/web/20121130144326/http://creationsafaris.com/crev200411.htm


A paper in PLOS Biology¹ compared non-coding DNA from widely-separated vertebrates and found them not only “extremely conserved” in many cases, but essential for regulating the gene-coding regions.

Understanding the intricate and finely tuned process of gene regulation in vertebrate development remains a major challenge facing post-genomic research.  In order to begin to understand how genomic information can coordinate regulatory processes, we have adopted an approach integrating comparative genomics and a medium-throughput functional assay. Nearly 1,400 non-coding DNA sequence elements were identified that exhibit extreme conservation throughout the vertebrate lineage.... Most, if not all, of the CNE [conserved noncoding element] sequences appear to be associated with genes involved in the control of development, many of them transcription factors.  A significant proportion of genes identified in this study are homologous to those identified in the sea urchin and other invertebrates as master regulators of early development, leading us to believe that they interact in GRNs [gene regulatory networks].  Consequently, it is extremely likely that the CNEs identified compose at least part of the genomic component of GRNs in vertebrates, acting as critical regions of regulatory control for their associated genes.  Such regions would mediate up- or down-regulation of expression, effecting a cascade of downstream events.

They speculate that these sequences are not mere binding sites, because that would not explain the high degree of sequence conservation.  “Consequently,” they say, “we have not ruled out the possibility that the CNEs may have a completely different mode of action or act in numerous different ways.”  The team of 16 scientists from the UK were struck with the similarity of these noncoding sequences between human, rat, mouse and pufferfish.  They performed some limited functional analysis on the sequences and found that some affect genes that are physically distant, often megabases away.  Though apparently essential, “They are amongst the most highly conserved of all sequences in vertebrate genomes yet they are completely unrecognisable in invertebrates.”  It seems, however, that invertebrates have analogous sequences for gene regulation, as stated in their introduction:

Identification and characterisation of cis-regulatory regions [i.e., on the same strand of DNA] within the non-coding DNA of vertebrate genomes remain a challenge for the post-genomic era.  The idea that animal development is controlled by cis-regulatory DNA elements (such as enhancers and silencers) is well established and has been elegantly described in invertebrates such as Drosophila and the sea urchin.  These elements are thought to comprise clustered target sites for large numbers of transcription factors and collectively form the genomic instructions for developmental gene regulatory networks (GRNs).  However, relatively little is known about GRNs in vertebrates.

More work will need to be done to find out if this is true for vertebrates, as it appears from this study, and if so, how these vertebrate CNEs work.  Some could prevent gene expression, for example, as well as enhance it.  “Whatever their mode of action, the striking degree of conservation displayed by this set of CNEs suggests they play critically important functional roles,” they deduce.  In conclusion, they state, “Given their strong association with genes involved in developmental regulation, they are most likely to contain the essential heritable information for the coordination of vertebrate development.”

---

¹Woolfe et al., “Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development,” PLOS Biology, Vol 3 Issue 1 (Jan 2005), published online 11/15/2004: DOI: 10.1371/journal.pbio.0030007.

The authors make only the meagerest references to evolution, none of it helpful to the Darwin Party.  They merely state as matters of belief the “evolutionary divergence” between humans and mice, and make other similar assumptions that said divergent animals evolved from a common ancestor.  They merely assume some genes evolve quickly and others slowly.  But when it comes to explaining how such extremely conserved sequences could survive the inexorable pressure of natural selection for oodles of aeons, they admit there is nothing but guesswork:

A number of other ideas on the evolutionary mechanisms responsible for “ultra-conservation” have been suggested, involving decreased mutation rate, increased DNA repair, and multiply-overlapping transcription factor binding sites, but without more functional studies such hypotheses remain speculative.

Elsewhere, they remark with astonishment about specific examples of CNEs in all four species (human, rat, mouse, pufferfish) that show 100% identity, “demonstrating an extraordinary level of conservation for genomes separated by 900 million years of divergent evolution.”  Maybe no divergent evolution.  Maybe no 900 million years.
    So, any biologists around still wanting to assume this non-coding material is “junk DNA”?  Stop wasting your life work, your lab equipment, and your grant money.  Get with the program – the ID program.  Get out there and find out what it was made for.
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