I would say, in terms of junk DNA, we don’t use that term any more ’cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn’t functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu’s, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that’s where the epigenome gets involved, and is teaching us a lot.

http://www.uncommondescent.com/intelligent-design/francis-collins-admits-his-own-prediction-about-junk-dna-was-false/

Here’s what Collins said in 2006 .....

Darwin’s theory predicts that mutations that do not affect function (namely, those located in “junk DNA”) will accumulate steadily over time. Mutations in the coding regions of genes, however, are expected to be observed less frequently, since most of these will be deleterious, and only a rare such event will provide a selective advantage and be retained during the evolutionary process. That is exactly what is observed.

......

bornagain November 11, 2015 at 6:56 pm

The genome, contrary to what Darwinists desperately want to believe in their ‘God would not have done it that way’, theology

“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. . . . 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.”
– Ken Miller

“Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution … we expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed … the evolutionary prediction that we’ll find pseudogenes has been fulfilled—amply … our genome—and that of other species—are truly well populated graveyards of dead genes”
– Jerry Coyne

“We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo¬genes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production. Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.”
– Michael Shermer

Contrary to that Darwinian ‘God would not have done it that way’ theology, the genome is fantastically complex and gives all the hallmarks of having been designed by an Intelligence far greater than man’s intelligence.

First off, the information storage capacity of DNA vastly exceeds the best efforts of man to store information in his computers. In fact, 1 gram of DNA can store the total world information content

Information Storage in DNA by Wyss Institute – video
https://vimeo.com/47615970
Quote from preceding video:
“The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
Sriram Kosuri PhD. – Wyss Institute

Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA – January 29, 2013
Excerpt: researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they’ve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,,
http://www.evolutionnews.org/2.....68641.html

DNA: The Ultimate Hard Drive – Science Magazine, August-16-2012
Excerpt: “When it comes to storing information, hard drives don’t hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare.”
http://news.sciencemag.org/sci.....-code.html

Secondly, the complexity of the programming language encoded in the genome far exceeds man’s achievements at encoding. For instance, there is overlapping coding, i.e. one code written on top of another code, written on top of another code, written on etc..:

Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
https://www.youtube.com/watch?v=fDB3fMCfk0E

In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.
Concluding powerpoint of the lecture (at the 1 hour mark):

“Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
Edward N. Trifonov – 2010

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
Excerpt: In the last decade, we have discovered still another aspect of the multi-dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
http://www.worldscientific.com.....08728_0006

Along the same line, this following recent paper that came out the other day found that the ‘grammar’ of the human genetic code is far more complex than even the most intricately constructed spoken language

Complex grammar of the genomic language – November 9, 2015
Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,,
,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.
Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.
http://www.sciencedaily.com/re.....140252.htm

Moreover, as if that was not more than enough to falsify the notion that unguided material processes could have possibly produced the information in the genome, it is now found that the genome is also performing quantum computation on a scale that puts man’s best efforts at quantum computation thus far to shame.
First off,

Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
http://www.sciencedaily.com/re.....123522.htm

Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.

NP-hard problem – Examples
Excerpt: Another example of an NP-hard problem is the optimization problem of finding the least-cost cyclic route through all nodes of a weighted graph. This is commonly known as the traveling salesman problem.
http://en.wikipedia.org/wiki/NP-hard#Examples

Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:

Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013
Excerpt: quantum computing is, “in some cases, really, really fast.”
McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,,
“This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.”
http://www.sciencedaily.com/re.....122828.htm

bornagain November 11, 2015 at 6:56 pm

Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA.
And DNA just so happens to have quantum entanglement/information embedded along its entire length so as to enable it to be able to perform quantum computation on such a massive scale

Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
https://youtu.be/2nqHOnVTxJE?t=1176

Of related note:

Scientists achieve critical steps to building first practical quantum computer – April 30, 2015
Excerpt: If a quantum computer could be built with just 50 quantum bits (qubits), no combination of today’s TOP500 supercomputers could successfully outperform it (for certain tasks).
http://phys.org/news/2015-04-s.....antum.html

Quantum Entanglement and Information
Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
http://plato.stanford.edu/entries/qt-entangle/

There is much more that could be pointed out about the genome that completely refutes the Darwinian notion that our genome is mostly junk, but hopefully the small glimpse provided above will give someone an indication just how far off base some of those Darwinists, like Moran and his atheistic cheerleaders, are in their ‘theological’ insistence that the DNA is not what we would expect if God designed it.

Contrary to their theological argument of “God would not have done it that way”, I hold that “God most certainly would have done it that way!”