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, 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.
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.
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.
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
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.
“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.
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.
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.
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
“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.
“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).
“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.
“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.
“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,
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.
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
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
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
“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.
“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.
“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.
“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.
“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.
“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.
“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.
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.
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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