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Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Genetics » Junk DNA has function

Junk DNA has function

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1 Junk DNA has function on Thu Jul 10, 2014 8:42 pm

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Junk DNA has function

http://reasonandscience.heavenforum.org/t1812-junk-dna-has-function

The argument of the new scientific development 
1. Ken Miller a Brown University biology professor and a staunch propagator of evolution theory said: “Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants of the past history...
2. "Chance experiments in gene duplication" means somebody, a person is experimenting. There is no experience of a non-person experimenting.
3. The new discoveries of science teach that the so-called pseudogenes are really functional[1], not to be considered any more as just “junk” or “fossil" DNA. Surely, many functional pseudogenes and novel regulatory mechanisms remain to be discovered and explored in diverse organisms. (RNA Biology 9:1, 27-32; January 2012; G 2012 Landes Bioscience) 
4. God is a must. His intelligence is seen in the mind-boggling complexities.
5. God exists.

NOTES:
1. Functional pseudogenes in mouse and humans:
a. 60% of the processed pseudogenes are conserved in both mammalian species. This suggests important biological functions.
b. "pseudogenes in mouse have been confirmed to produce stable transcripts”… many pseudogenes are known to be transcribed in humans.
c. Discovered functions for pseudogenes include:
i. They may function as "intracellular inhibitors in cell development" where pseudogenes can "suppress the translation of the functional counterparts."
ii. They may regulate gene expression through RNA interference (RNAi), where small interfering RNAs (siRNAs) can be generated by pseudogenes that play roles in RNAi pathways.
iii. They may produce transcripts which serve as "endogenous competitive RNAs to their cognate genes," also helping to regulate gene expression.
iv. They may yield transcripts which produce functional proteins. One example given is the nanog pseudogene which is known to yield proteins in cancer cell lines.


The evidence of intron’s fine tuning
1. ncRNAs carry out a function at the interface between DNA and specific chromatin modification marks, through stabilization of the association of PRC2 with chromatin. Intronic RNAs arise as candidates to carry out roles as ‘transcription factors’ that are responsible for fine-tuning mammalian transcriptional programs. (Intronic RNAs mediate EZH2 regulation of epigenetic targets)
2. Intronic sequences contain a number of ncRNAs (conservative estimates suggest that 65% of noncoding transcripts map to intergenic regions and 35% to intronic regions38), including many well-characterized regulatory small ncRNAs, such as snoRNAs, small nuclear RNAs (snRNAs), piRNAs or miRNAs39, 40, their expression being coordinated with the intronic context from which they originate. In addition, a recent study reports close to 80,000 and 40,000 long intronic expressed sequence tag (EST) contigs in human and mouse genomes, respectively41. They suggest that 80% of all spliced human protein-coding genes have transcriptionally active introns.
3. The more complexities and the more complex systems with their complex subsystems are discovered, the more the intelligent design by an intelligent designer is proved. That intelligent designer all men call God.
4. God exists.


The argument of the pseudogenes with function
1. Evolutionary biologists long regarded pseudogenes as nonfunctional junk. They thought these are a class of DNA elements that represents the remains of genes that lost their function due to mutations. Based on their characteristics biologists assumed that pseudogenes lack function solely. Experimentally, this theory was unverified for decades—until the recent advent of genomics. Discoveries by molecular biologists and geneticists have delivered a scientific upset: pseudogenes display function. Specifically, they play a role in regulating gene expression. 1
2. The researchers from Sweden have uncovered a second possible function for pseudogenes. They developed a new method of identifying and determining which genes are used to make proteins. Using their method, they discovered a number of previously unidentified genes in the human and mouse genomes. About 35 percent of the newly identified genes are pseudogenes that the cell’s machinery uses to produce proteins—a completely unexpected result. As one of the researchers noted, “Our study challenges the old theory that pseudogenes don’t code for proteins.”
3. The recognition that pseudogenes display a range of functions mitigates one of the most compelling arguments for common descent and instead of that reflects a common design. In other words, most –the one’s studied-, if not all, of the genome, including pseudogenes have purpose. Such a detailed and purposeful design provides another evidence for the designer all men call God.
4. God exists.

References:
1. Karolinska Institutet, “Protein Coding ‘Junk Genes’ May Be Linked to Cancer,” ScienceDaily, posted November 17, 2013, http:/www.sciencedaily.com/releases/2013/11/131117155500.htm.


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The standard scientific doctrine, only now being slowly and laboriously overturned – despite the resistance of the old guard – is that DNA wanders randomly to such an extent that the entire collection working faultlessly in every life form on Earth has arrived only by trial and error.  In reality there are DNA systems which have existed unchanged – to judge from the outer forms which they support and reproduce – for hundreds of millions of years, completly refuting the “random wandering gene” theory.

Natural selection itself has already been discredited as a shaping force, by the scientific establishment: studies of gene sweeps published in Scientific American (October 2010) show it has only acted in cases where an envrionmental pressure remained constant for tens of thousands of years, an exceptionally rare occurrence.  The massive store of apparently unused DNA components in every cell, which Richard Dawkins, incredibly, once dismissed as “99% junk”, now appears to hold multiple layers of subtle logic which are only beginning to be unravelled, with serious and long-lasting implications.



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

http://whoisyourcreator.com/topics/junk-dna-the-biggest-blunder-of-evolutionary-based-science/

Geneticists once believed that DNA sequences (genes) were the key to building and maintaining healthy cells. When all sorts of peripheral genetic elements 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. Come to find out, these regulatory elements are the key to cellular health and development, as well as the primary link to disease when not operating properly.

For over 50 years, evolutionary-based researchers have arrogantly denied the critical nature of “junk DNA,”which has been discoverely to consist of over 98.5% of DNA. The study of how these regulatory elements can change a gene’s function without altering its DNA sequence is called “Epigenetics”and it’s now the most funded area in genetic research:

“All the cells in the body have the same DNA sequence (genome), but it is how this DNA sequence is interpreted that results in the formation of different cell types. Epigenetic changes control how a DNA sequence is interpreted, specifically how different genes are switched on and off in different cell types, tissues and organs.” …
‘This suggests that DNA modifications are more dynamic than we previously thought.” 

Cambridge Unversity and Babraham Institute, “Cambridge technique to transform epigenetics,” April 20, 2012, Business Weekly.

http://www.businessweekly.co.uk/biomedtech-/13983-cambridge-technique-to-transform-epigenetics

“DNA is normally packed tightly into the nucleus of a cell and housed into chromosomes. Within chromosomes lie many chemical perturbations that modify how genes are expressed, without anything to do with the underlying DNA sequence, explained Aline Cerf, a postdoctoral associate who led the study. Studying these chemical modifications is a relatively new field called epigenetics.”
Cornell University, “Researchers suspend, image single DNA molecules,” October 31, 2011, Physorg.com.

http://phys.org/news/2011-10-image-dna-molecules.html
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 evolutionary-based science’s biggest blunders is still the most insidious
obstacle standing in the way of medical discovery and progress, 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 Genome’s ‘Dark 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

“Pseudogenes have long been labeled as ‘junk’ DNA, failed copies of genes that arise during the evolution
of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to
harbor the potential to regulate their protein-coding cousins.”
Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul
Francisco Carter, “Pseudogenes: Pseudo-functional or key regulators in health and disease?,” RNA, Vol.
17:792-798 (March 2011).
http://rnajournal.cshlp.org/content/early/2011/03/11/rna.2658311

“This new discovery challenges half a century of fundamental assumptions in biology…
Scientists have known about this redundancy for 50 years, but in recent years, as more and more genomes
from creatures as diverse as domestic dogs to wild rice have been decoded, scientists have come to
appreciate that not all redundant codons are equal.”
University of California, San Francisco, “Researchers discover new layer of genetic information that helps
determine how fast proteins are produced,” March 28, 2012, Physorg.com.
http://www.physorg.com/news/2012-03-layer-genetic.html

“The research published in Cell, online the 23rd of November, shows the mechanism is found in a DNA
sequence that was thought, incorrectly, to play no role. This long string has seven enhancers which, when
combined with one another, modulate the activity of the genes responsible for the formation of the fingers –
an important fundamental discovery for the field of genetics.”
Ecole Polytechnique Federale de Lausanne, “Finger (mal)formation reveals surprise function of desert DNA,”
November 23, 2011, Medicalxpress.com.
http://medicalxpress.com/news/2011-11-finger-malformation-reveals-function-dna.html

“Scientists at the Broad Institute of MIT and Harvard have discovered that a mysterious class of large RNAs
plays a central role in embryonic development, contrary to the dogma that proteins alone are the master
regulators of this process.”
MIT, “New roles emerge for non-coding RNAs in directing embryonic development,” August 28, 2011,
Physorg.com.
http://www.physorg.com/news/2011-08-roles-emerge-non-coding-rnas-embryonic.html

NOTE the comment at the end of article from Xianfa Xie, Center for Genomics and Systems
Biology, New York University:
“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 just a bunch of useless genetic
remnants that are left-over from evolutionary predecessors, many zealous evolutionists are still
preaching their nonsense:

“And I know scientific revolutions; scientific revolutions are friends of mine; and believe me, epigenetics is
no scientific revolution.”
Jerry Coyne, University of Chicago, “Is ‘epigenetics” a revolution in evolution?” August 21, 2011, The
Richard Dawkins Foundation.
“I now groan audibly when a journalist (usually from continental Europe where they spend too much time
learning philosophy rather than science) asks me the now inevitable ‘what about epigenetics?’ question. It is
a real disease among science journalists, this unseemly eagerness to find something that enables them to
say ‘Darwin was wrong’ (New Scientist under Roger Highfield is a lamentable example). I am heartily sick of
the ‘epigenetics’ bandwagon and almost look forward to the next one, whatever it turns out to be.”
Richard Dawkins, “Is ‘epigenetics’ a revolution in evolution?” August 21, 2011, The Richard Dawkins
Foundation.
This is a 2-for-1 link that reveals the ignorance of Professors Larry Moran and PZ Myers, who still teach
their nonsense to their students:
(NOTE: At least Larry Moran admits that some previously described “junk DNA” is actually usefull – See
#1,2,3)
http://sandwalk.blogspot.com/2011/12/jonathan-mclatchie-and-junk-dna.html

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”:

“Once considered unimportant ‘junk DNA,’ scientists have learned that non-coding RNA (ncRNA) — RNA
molecules that do not translate into proteins — play a crucial role in cellular function. Mutations in ncRNA are
associated with a number of conditions, such as cancer, autism, and Alzheimer’s disease.”
Tel Aviv Univerity, “’Junk DNA’ can sense viral infection,” April 24, 2012, Medicalxpress.com
http://medicalxpress.com/news/2012-04-junk-dna-viral-infection.html

“MicroRNAs are non-coding genes that often reside within ‘junk DNA’ and regulate the levels and functions
of multiple target proteins — responsible for controlling cellular processes in the brain …
James Uney, Professor of Molecular Neuroscience in the University’s School of Clinical Sciences, said: ‘These
findings are important as they show that very small changes in microRNA genes will have a dramatic effect
on brain function and may influence our memory function or likelihood of developing neurodegenerative
diseases. These findings also suggest that many more human mirror microRNAs will be found and that they
could ultimately be used as treatments for human neurodegenerative diseases such as dementia.’”
University of Bristol, “Doubling the information from the Double Helix,” April 27, 2012, Physorg.com.
http://phys.org/news/2012-04-helix.html

“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


http://creationwiki.org/Junk_DNA

What may currently fall under evolutionary presupposition of leftovers is rather, after the aforementioned history, merely the result of losing genetic expression. That is a view with which can be seen as entirely consistent with a creationism-based model.

http://www.sciencedaily.com/releases/2014/03/140331153641.htm

Recent research has identified non-coding DNA sequences that are found in nearly all plants and appear to have roles in basic processes such as tissue and organ development, response to hormones, and regulation of gene expression.



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2 Re: Junk DNA has function on Mon Oct 19, 2015 5:20 pm

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An article in the 7 September 2012 issue of Science was titled "ENCODE project writes eulogy for junk DNA". "This week, 30 research papers... sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose". "The ENCODE effort has revealed that a gene's regulation is far more complex than previously thought, being influenced by multiple stretches of regulatory DNA located both near and far from the gene itself and by strands of RNA not translated into proteins, so-called noncoding RNA."--

Pennisi, Elizabeth. 7 September 2012. Science, Vol. 337, pp. 1159-1161.

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3 Re: Junk DNA has function on Sat Nov 21, 2015 8:28 am

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Signature of the cell, page 320

Cell and genome biologists have also discovered that these supposedly “useless” nonprotein-coding regions of the genome: (1) regulate DNA replication,27 (2) regulate transcription,28 (3) mark sites for programmed rearrangements of genetic material,29 (4) influence the proper folding and maintenance of chromosomes,30 (5) control the interactions of chromosomes with the nuclear membrane (and matrix),31 (6) control RNA processing, editing, and splicing,32 (7) modulate translation,33 ( 8 ) regulate embryological development,34 (9) repair DNA,35 and (10) aid in immunodefense or fighting disease36 among other functions. In some cases, “junk” DNA has even been found to code functional genes.37 Overall, the nonprotein-coding regions of the genome function much like an operating system in a computer that can direct multiple operations simultaneously.38 Indeed, far from being “junk,” as materialistic theories of evolution assumed, the nonprotein-coding DNA directs the use of other information in the genome, just as an operating system directs the use of the information contained in various application programs stored in a computer. In any case, contrary to the often heard criticism that the theory makes no predictions, intelligent design not only makes a discriminating prediction about the nature of “junk DNA”; recent discoveries about nonprotein-coding DNA confirm the prediction that it makes.39

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Is there "junk" in our DNA as predicted by theory "evojunk"?




Figure 1. The junk DNA, one of the great "(un) forecasts" of evolution.
The biochemical evolution assumes that new information,  that one necessary for the construction of higher organisms arises when existing genes are "duplicated". Then these duplicated genes mutate, which transform the new "doubled genetics" into something useful and more sophisticated. This process - which turns two "cake recipes" in a "feastmeal" - would not have been, however, very efficient. This low efficiency would then left behind, fossilized in our genome, a enormity of gene enormity - such as "junk DNA". The process can be exemplified as follows: a gene that express "cake" on the life of the cake recipe is duplicated in "birds-flour" and sits there waiting for the change and the time to act on it. Suddenly, a mutation occurs and "cake-cake" becomes "bullet-cake" and then "bullet-lap" and finally "bullet-coconut" and there we have an increase in revenue, with now two genes that express "cake" and "coconut bullet". Understood?

In other words, the "junk" in our DNA, 97% of it would be the result of mutations that were neutral and therefore not eliminated by natural selection. Or also would be duplicated genes that did not develop as they should, and parked in things like "bullet-lap" or functional genes that have changed beyond due. As a result, then, this "dirty" evolutionary process "trash" of our evolutionary history was fossilized in our genetic code as "junk DNA," which would form today 97% of all our DNA. Molecular taxonomists then use the "evolving concept" of "junk DNA" as a molecular clock as a silent record of mutations that escaped the action of natural selection over millions of years. Then searching such "junk", taxonomists built "evolutionary trees" quite prepared for the different species.

Recently, however, the ENCODE project showed a story well, but quite different from that of "evolutionary junk". Evaluating the human genome, they found that 93% of the genome is actually transcribed. It was also discovered a complexity unrivaled in the transcription of the genome, with information scattered in different levels, blocks and DNA layers in an optimization strategy and diversification of information that defies human understanding. The information was not found in line but spread by DNA as a whole, there is a whole "metadata" logged in "junk DNA" which thus coordinates the entire a real ballet of multidimensional connections. With our approximately 25,000 genes produce so hundred thousands of proteins. The "exons" DNA discovered also are not specific to each gene, but are "floating modules" in a performance of unmatched genetic mastery. Both the "sense" tape as the tape "antisense "DNA are transcribed as everything is useful and versatile, and the efficiency is maximum. Worse, the code is read from left to right and also from right to left. Reading the DNA also starts at various points and so have reading strategies known as "genetic overlapping" and "alternative splicing". The DNA then acted a real "stunning paraphernalia" unprecedented engine optimization, compression, encryption and zipping of information that challenges the human mind, and probably goes beyond our current ability to decipher it.

No information engineer ever came close to drawing up - or even dared dream of such  encryption strategy and storage optimization and transmission of information as the DNA gene and its "junk". An analogy that might help you better understand the DNA is what compares with a poem. While reading this poem, you discover that reading it from back to front, another poem unfolds. Oh you also realize that by combining blocks of this poem, one finds other embedded poems there. Oh you read a sentence that DNA by analogy could be "ELI AMA LIA" but moves forward in a letter to read, and find other embedded phrase, as for example "LIA MAL". Move yet for the second letter, and find another phrase: "AMI ALI". Elsewhere in the poem, you find the "YELLOW" instruction and finds that built it, using spacers, words are stored "Love", "SEA", "AR" and "ELO" and the cell "know" how to recognize these nuances in the reading time because the spacers placed between the words of blocks. And even worse, with the discovery of "duons", it is clear that the phrases recorded there have double meaning, ie they can be read in "languages" different by the cell. For example, think of the word "TOMATO" which in English would read, "TO MATE" with another distinct meaning.

Remember that the mechanism offered by the (A) evolution to transform the "primordial germ" into the microbiologist of today is that of (B) gene duplication followed by random mutations in the new pair of genetic twins. This process, if true, would have created a lot of (C) garbage in our DNA. Ie: A = B + C Since 97% of our DNA is "junk", they say we have that C is a fact, then A and B are also facts. But the data show today "junk" is almost ZERO in our DNA. Ie C is false, and logic tells us then that A and B are also false! The junk DNA is gone, and with it apparently  the theory of evolution was gone as well, thrown in the trash by the "junk DNA". Oh you answer me then: What would then be able to create a DNA over 3 billion base pairs with perhaps almost 100% pure information? And an arbitrary information, zipped, encrypted, and "duonizada"? Chance or intelligent design?

A organized multi-layered nanomolecular information system  as DNA, causes also a huge logistical challenge for the cell. One is the use of DNA simultaneously for multiple functions. This "overlap" [overlap] with amazing features reveals a control system with resolutions involving multilayered organization, tangled in time and space. One of the biggest challenges of this intricate tangle and information system, which challenges the understanding of intelligent minds, arises when the cell divides. In the division at the same time and same place, the cell needs to maintain its metabolic functions governed by DNA, but also need to copy its DNA. That is, the cell copy a software while it is up and running. How can this cell learn "computer miracles", and do it from your most tender beginning because multiply is the paramount task of Life? Without this strategy, the cell would be unable to reproduce. But the cell does something that is still one "computer failure". To this day Bill Gates and his whole legion of "intelligent minds" Microsoft has not learned to do what the cell does from its 1.0 original version. "Close all their programs to upgrade Windows, "is it not so that Bill Gates recommends ? But how the cell avoids the 'deadly conflicts" between the copy machine, you need to unpack the strands of DNA through the process of reading, which needs information that is being copied? Involving three billion base pairs? And in a multidimensional information system all intricate and intertwined? In a huge software? The answer is these questions is shocking. The solution that the cell "forsaw" involves a strategy of extreme beauty and ingenuity. Replication (self-cloning) does not start at a specific point, but diversifies into thousands of different points along the DNA. But who or what controls then all this and decide at what point to start? And when you start? Little is known about this amazing process, but it turned out that the points used along the DNA are exactly in what areas, at the time, are not being used to manage cell metabolism. Not just have a broad knowledge of multidimensional control system time-space, but what is already known, added to the huge problem it solves, are a spectacle of a computer engineering high sophistication and unparalleled creativity. Note that the wrong way so than the evolution proposes, random mutations into an intricate multilayer and multifunctional system like this, zipped and encrypted, would be catastrophic and would destroy many functions at one time, making it impractical not only functioning as a copy DNA.

Referências e notas.

1. "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic- Epigenetic System," Richard Sternberg, Annals of the New York Academy of Sciences, 981, 154, 2002.

2. The Myth of Junk DNA, Jonathan Wells, Discovery Institute Press, 2011.

3. William A. Dembski, um dos teóricos da TDI, predisse a "funcionalidade" do DNA lixo quando afirmou: "Assim, do ponto de vista evolucionário, nós esperamos bastante DNA inútil. Se, por outro lado, os organismos foram intencionalmente planejados, nós esperamos que o DNA, o quanto possível, exiba função. O Design encoraja os cientistas a procurar por função enquanto que a evolução desencoraja isso." Science and Design, in First Things, Outubro de 1998. http://www.firstthings.com/article/1998/10/001-science-and-design

4. John S. Mattick, diretor do Institute for Biociência Molecular na Universidade de Queensland em Brisbane, Australia, disse que o DNA lixo pode ter sido "um dos maiores erros na história da biologia molecular." in Wayt T. Gibbs, "The Unseen Genome: Gems Among the Junk," Scientific American (Nov. 2003).

5. Richard Sternberg e o expoente geneticista James A. Shapiro concluíram que "um dia, nós pensaremos, do que costumava ser chamado de 'DNA lixo', como sendo um componente crítico "especialista" dos regimes de controles celulares." Richard v. Sternberg e James A. Shapiro, "How Repeated Retroelements format genome function," Cytogenetic and Genome Research, Vol. 110: 108--116 (2005). Esse dia parece já ter chegado com as descobertas do Projeto ENCODE. https://www.encodeproject.org/[/b]



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5 Re: Junk DNA has function on Sat Jul 02, 2016 2:19 pm

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  • Structural roles such as packaging chromosomes and preventing DNA "from unravelling and becoming damaged," acting as "anchor points when chromosomes are shared equally between different daughter cells and during cell division," and serving as "insulation regions, restricting gene expression to specific regions of chromosomes."

  • Regulating gene expression, as "Thousands and thousands of regions of junk DNA are suspected to regulate networks of gene expression."

  • Introns are extremely important:

  • The bits of gobbledygook between the parts of a gene that code for amino acids were originally considered to be nothing but nonsense or rubbish. They were referred to as junk or garbage DNA, and pretty much dismissed as irrelevant. ... But we now know that they can have a very big impact. (pp. 17-18)


  • Preventing mutations by separating out gene-coding DNA.

  • Controlling telomere length that can serve as a "molecular clock" that helps control aging.

  • Forming the loci for centromeres.

  • Activating X chromosomes in females.

  • Producing long non-coding RNAs which regulate Hox genes or regulating brain development, or serving as attachment points for histone-modifying enzymes helping to turn genes on and off.

  • Serving as promoters or enhancers for genes, or imprinting control elements for "the expression of the protein-coding genes."

  • Producing RNA which acts "as a kind of scaffold, directing the activity of proteins to particular regions of the genome."

  • Producing RNAs which can fold into three-dimensional shapes and perform functions inside cells, much like enzymes, changing the shapes of other molecules, or helping to build ribosomes. As she notes: "We've actually known about these peculiar RNA molecules for decades, making it yet more surprising that we have maintained such a protein-centric vision of our genomic landscape." (p. 146)

  • Serving as tRNA genes which produce tRNA molecules. These genes can also serve as insulators or spacers to stop transcription from spreading from gene to gene.

  • Development of the fingers and face; changing eye, skin, and hair color; affecting obesity.

  • Gene splicing and generating spliceosomes.

  • Producing small RNAs which also affect gene expression.


http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html

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