Home » Intelligent Design » The Rest of the Science Community Starting to Catch Up With ID on “Junk” DNA (It Ain’t)

The Rest of the Science Community Starting to Catch Up With ID on “Junk” DNA (It Ain’t)

The ID community, including many writers here at UD, has been predicting for years that so-called junk DNA would be  found to be functional.  The Darwinists have scoffed.  Now ID proponents are being vindicated.  My prediction:  The Darwinists will change their story to “we’ve been saying this all along.”

The Washington Post reports on the breakthrough research published in Nature.

Most of a person’s genetic risk for common diseases such as diabetes, asthma and hardening of the arteries appears to lie in the shadowy part of the human genome once disparaged as “junk DNA.”

Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades.

Those are among the key insights of a nine-year project to study the 97 percent of the human genome that’s not, strictly speaking, made up of genes.

The Encyclopedia of DNA Elements Project, nicknamed Encode, is the most comprehensive effort to make sense of the totality of the 3 billion nucleotides that are packed into our cells.

The project’s chief discovery is the identification of about 4 million sites involved in regulating gene activity. Previously, only a few thousand such sites were known. In all, at least 80 percent of the genome appears to be active at least sometime in our lives. Further research may reveal that virtually all of the DNA passed down from generation to generation has been kept for a reason.

This concept of ‘junk DNA’ is really not accurate. It is an outdated metaphor,” said Richard Myers of the HudsonAlpha Institute for Biotechnology in Alabama.

Myers is one of the leaders of the project, involving more than 400 scientists at 32 institutions.

Another Encode leader, Ewan Birney of the European Bioinformatics Institute in Britain, said: “The genome is just alive with stuff. We just really didn’t realize that beforehand.”

“What I am sure of is that this is the science for this century,” he said. “In this century, we will be working out how humans are made from this instruction manual.”

The new insights are contained in six papers published Wednesday in the journal Nature. More than 20 related papers are appearing elsewhere. . .

The new research helps explain how so few genes can create an organism as complex as a human being. The answer is that regulation — turning genes on and off at different times in different types of cells, adjusting a gene’s output and coordinating its activities with other genes — is where most of the action is. . . .

In one paper, a team led by Thomas R. Gingeras of Cold Spring Harbor Laboratory in New York reported that three-quarters of the genome’s DNA is “transcribed” into a related molecule, RNA, at some point in life. A small amount of that RNA is then “translated” into protein. Much of the rest appears to have gene-regulating activities that remain to be discovered.

In a telephone conference call with reporters, several of the researchers likened the 4 million regulatory sites to electrical switches in a hugely complex wiring diagram.

By turning switches on and off, and varying the duration of their activity, a nearly infinite number of circuits can be formed. Similarly, by activating and modulating gene function, immensely complicated events such as the development of a brain cell or a liver cell from the same starting materials is possible.

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119 Responses to The Rest of the Science Community Starting to Catch Up With ID on “Junk” DNA (It Ain’t)

  1. This paper is a bombshell. I like this quote from the following video:

    Scientists go deeper into DNA (Video report) (Junk No More) – Sept. 2012
    http://bcove.me/26vjjl5a

    Quote from preceding video:
    “It’s just been an incredible surprise for me. You say, I bet it’s going to be complicated’, and then you are faced with it and you are like ‘My God, that is mind blowing.’”
    Ewan Birney – senior scientist – ENCODE

    The denial of this overwhelming evidence against Junk DNA, that I’ve seen thus far from Darwinists, really is illuminating as to revealing the dogmatic philosophical bias that Darwinists have as to ever evaluating the evidence fairly.

  2. Around 9:30 minute mark of the following podcast, Casey Luskin speaks on this dogmatic ‘no concession’ policy of neo-Darwinists as to ever admitting they were wrong:

    “ENCODE Project Finds Mass Functionality for “Junk” DNA” – podcast
    http://intelligentdesign.podom.....0_13-07_00

  3. Very interesting quote:

    “In a telephone conference call with reporters, several of the researchers likened the 4 million regulatory sites to electrical switches in a hugely complex wiring diagram.

    By turning switches on and off, and varying the duration of their activity, a nearly infinite number of circuits can be formed. Similarly, by activating and modulating gene function, immensely complicated events such as the development of a brain cell or a liver cell from the same starting materials is possible.”

    Emphasis mine. Does the phrase “immensely complicated events” ring a bell for us in ID? I bit ot does :)

    Now our “friends” (the darwinists), in the spare time left by their unsuccessful attempts at explaining how the basic protein domains came into being, must also explain how the right circuits were generated among the search space of a “nearly infinite number of circuits”. I am not surprised that they are a little bit displeased…

  4. I don’t believe I’ve ever seen a larger, more collective backtracking than I have when reading Darwinists’ reactions to the ENCODE Project’s discovery. This is unintentional comedy at it’s finest.

  5. Backtracking? Pretty much everyone is saying the “80% functional” number is wrong. Even the project leader, Ewan Birney, more or less admitted it’s not credible for standard definitions of “functional”.

    So it’s the ENCODE leaders that are backtracking, not the scientific community.

  6. And, onion test. Answer it or you don’t have an argument.

    http://www.genomicron.evolverz.....nion-test/

  7. I like this article:

    A lesson from ENCODE about the limits on Human Reason – David Ropeik
    Excerpt: In what should be another blow to the hubris of human intellect, we have a new entry in the long and ever growing list of “Really Big Things Scientists Believed” that turned out be wrong.,,,

    Well, there’s going to be a lot of editing on Wikipedia in the days and weeks to come, and it’s time to reprint the basic biology textbooks, because extensive research into the mystery of what most of DNA is doing there has discovered that the ‘junk’ isn’t junk at all. Most of it has all sorts of jobs. Science Journalist Ed Yong has written a wonderful summary of this work here. The nut of it is:

    “A massive international project called ENCODE – the Encyclopedia Of DNA Elements – has moved us from “Here’s the genome” towards “Here’s what the genome does”. Over the last 10 years, an international team of 442 scientists have assailed 147 different types of cells with 24 types of experiments. Their goal: catalogue every letter (nucleotide) within the genome that does something.

    “For years, we’ve known that only 1.5 percent of the genome actually contains instructions for making proteins, the molecular workhorses of our cells. But ENCODE has shown that the rest of the genome – the non-coding majority – is still rife with “functional elements”. That is, it’s doing something.”

    In many ways, this puts us back to the ABCs of DNA. So toss out a lot of what you know. Only, that won’t be easy. Given the nature of human cognition, it is innately difficult to let go of what you ‘know’ and keep a truly open mind. Just look at history. Big ideas, once set into place and ascribed to by the ‘experts’ in a given field, are hard to get people to think about in new ways. This intellectual inertia can do great harm.
    http://blogs.nature.com/soapbo.....an-reason/

  8. Nick as to the onion test, let’s see if you can detach your ‘intellectual inertia’ for a moment:

    Nick, as with you philosophically (and dogmatically) driven belief in Junk DNA, human ignorance for why the genomes are the varying sizes they are is not a actual argument for the Darwinian origin of those varying sizes! In fact some very credible reasons have been put forth for why it would make ‘engineering sense’ to vary genome sizes as such:

    i.e. There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;
    http://en.wikipedia.org/wiki/C-value_enigma

    And yet, even though this C-value enigma is somewhat (very?) paradoxical to the materialistic, neo-Darwinian, point of view, since information is presupposed to simply ‘emerge’ from a material basis and there clearly is no linear correlation to amount of material present and amount of information expressed, from a design point of view we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ for any particular life-form that was designed; For examples of such constraints,,:

    “There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus – which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.”
    Jonathan Wells – The Myth Of Junk DNA – page 85

    Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place – July 2011
    Excerpt: “Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known,” Yu said. “Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome.”
    http://pos-darwinista.blogspot.....evela.html

    THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS
    Excerpt: this show(s) that,,, the higher total life energy per unit body mass leads to smaller C-value.
    http://www.sustz.com/Proceedin.....ANASOV.pdf

    As well, at the 7:00 minute mark of this following video, we find that ‘genome length vs. mass’ gives a enigmatic 1/4 power scaling on the plotted graph for a wide range of different creatures. Thus, once again, giving strong indication of a design constraint that was/is imposed, top down, on genome length, and which is inexplicable from the neo-Darwinian framework:

    4-Dimensional Quarter Power Scaling In Biology – video
    http://www.metacafe.com/watch/5964041/

    Chargaff’s “Grammar of Biology”: New Fractal-like Rules – 2011
    Excerpt from Conclusion: It was shown that these rules are valid for a large set of organisms: bacteria, plants, insects, fish and mammals. It is noteworthy that no matter the word length the same pattern is observed (self-similarity). To the best of our knowledge, this is the first invariant genomic properties publish(ed) so far, and in Science invariant properties are invaluable ones and usually they have practical implications.
    http://arxiv.org/ftp/arxiv/pap.....2.1528.pdf

    Why the “Onion Test” Fails as an Argument for “Junk DNA” – Jonathan M. – November 2, 2011
    Excerpt: The so-called onion test, or indeed the “C-value enigma,” is predicated on unsupportable assumptions about the physiological effects of — and/or requirements for — larger genomes, many of which are contradicted by the scientific evidence.
    http://www.evolutionnews.org/2.....52321.html

  9. So aside from this being yet another failed Darwinian prediction, what’s the big deal? Can someone please explain what’s going on in simple terms?

    Thanks.

  10. The rate-independent symbol structures make life and evolution possible. Deal with it, or you don’t have an argument.

  11. 11

    Nick is in full spin mode. Here is my prediction. Nick and his buddies will say ENCODE isn’t really saying what you think they are saying until that becomes totally unsupportable. Then they will start saying that they never really believed most of the DNA was junk. In fact, Darwinian theory predicts exactly what ENCODE has found.

    The whole thing is like the husband who was caught by his wife in flagrante delicto carrying on with another woman. The man tries to brass it out and denies the affair. The wife says “but I caught you in the very act,” to which the man replies “who are you going to believe, me or your own eyes?” Nick asks us to believe him and not our own eyes.

    Nick, no amount of spin on your part is going to make this anything other than a devastating loss of the “junk DNA” crowd. Why don’t you show a little class and fess up that you and your buddies have been wrong all along when you claimed the vast majority of human DNA is junk.

  12. Here ya go Nick.

    just say it wasn’t you

  13. Hey Barry. Answer me this:

    1. What definition of “function” did ENCODE use?

    2. Is that a good definition, in accord with standard English usage?

    3. Why isn’t it valid to point out that even the project leader, Ewan Birney, expressed qualms about the 80% number and chose it mostly to get attention?

    4. If most of our DNA is functional, why do some other vertebrates (and plants) make a vertebrate with 10 times less DNA, and other vertebrates use 10 times more? We all have about the same number of genes, the differences are due mostly to repetitive elements. Why isn’t it reasonable to think that the minimal genomes contain what is actually needed, and the critters with 10 times bigger genomes (us) and 100 times bigger genomes (e.g. salamanders) have a lot of DNA that it pretty much dispensable, i.e., junk?

  14. 14

    Nick,

    I will not rise to your bait. Your attempt to deflect from the fundamental findings at ENCODE are sad.

    Tell you what. I will answer your questions just as soon as you admit that everyone who said the vast majority of human DNA is “junk” was wrong. Again, I won’t be holding my breath.

  15. Nick Matzke:

    4. If most of our DNA is functional, why do some other vertebrates (and plants) make a vertebrate with 10 times less DNA, and other vertebrates use 10 times more?

    LoL! the first part “If most of our DNA is functional…” has nothing to do with the second. Desperation is not a good position to argue from, Nick.

    But anyway- Why do old computers contain many more discrete components than their modern counterparts? Why are old computer languages more cumbersome and contain more coding lines than their modern counterparts?

    BTW Nick, how many different proteins do we have compared with the number of genes?

    I used to work for a computer/ technology company that used redundancy- every board was backed up by another- if the main board failed it automatically switched to the other. AND each board was also redundant- each side a mirror image of the other, both running and checking each other to make sure they had the same 1s and 0s. We could have removed 75% of the system and it still would have functioned, ie 75% was dispensable junk by Nick’s “logic”.

    However far from being dispensable junk redundancy is a design feature with those systems.

    Also there is another feature of genomes that Nick’s position doesn’t even consider-> that it also serves as a data storage device just as hard drives, flash drives, PROMS, etc do. Meaning there is actual software directing gene expression & alternative gene splicing and determining final form. The DNA just helps in carrying out the instructions it contains.

    See also the onion test answered

  16. Applying Nick’s “logic” to soda- Coke cannot taste good because Moxie tastes like crap.

  17. Here are a few points for you to chew on Nick as you defiantly cling to your colossal error of junk DNA:

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin September 5, 2012
    Excerpt: “And what’s in the remaining 20 percent?,,, ENCODE only(!) looked at 147 types of cells, and the human body has a few thousand.,, If every cell is included,,, “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”"
    http://www.evolutionnews.org/2.....64001.html

    ENCODE: The Encyclopedia of DNA Elements (Interviews with members of the ENCODE Project) – video
    http://www.youtube.com/watch?v=PsV_sEDSE2o
    Quotes from preceding video:
    “This metaphor about Junk DNA has become very entrenched. It has been entrenched publicly and entrenched scientifically. And ENCODE totally challenges that. We just don’t have big, blank, boring, bits of the genome. All the genome is alive at some level.”
    “There are about 2000 DNA binding proteins in the genome. We looked at about 100 of those, 115 of those, so there is a long way to go yet, there is a lot more to study.”

    “Junk DNA” is found to have 100% purpose in an astonishing way in this following paper:

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2......html#more

    virtual 100% functionality for DNA was established by another method here:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Moreover this study suggests that the simplistic definition of a gene is gone bye-bye:

    ENCODE project: In massive genome analysis new data suggests ‘gene’ redefinition – September 5, 2012
    Excerpt: The vast amount of data generated with advanced technologies by Gingeras’ group and others in the ENCODE project is likely to radically change the prevailing understanding of what defines a gene, the unit we routinely use, for instance, to speak of inheritable traits like eye color or to explain the causes of and susceptibility to most diseases, running the gamut from cancer to schizophrenia to heart disease.
    http://medicalxpress.com/news/.....-gene.html

    This following video is a bit more clear as to exactly why the term ‘gene’ is far too simplistic

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    As well this study found that the 3-Dimensional structure of the genome is found to play a important role:

    Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role – September 2012
    Excerpt: There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.
    http://www.nytimes.com/2012/09.....wanted=all

    Related ’3-Dimensional’ notes

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

  18. Moreover, very unexpectedly from the atheistic Darwinian mindset, the 3-D arrangement of DNA is found to determine ‘the form of the endogenous electric field’

    Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
    Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.

    Here is a ‘jaw dropping’ video of a 3 dimensional ‘electric field’ in action:

    The (Electric) Face of a Frog – video
    http://www.youtube.com/watch?v=ndFe5CaDTlI

    Moreover, as if the preceding was not bad enough for dogmatic neo-Darwinists like Matzke and Moran who refuse to admit they are wrong on Junk DNA, body plans are not even encoded solely by the DNA code in the first place (as is required in the genetic reductionism model of neo-Darwinism). This inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance and ‘epigenetic’ studies.

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/4187488

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    The Mysterious Epigenome. What lies beyond DNA? – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    Besides this mysterious epigenetic information, there is also now found to be ‘non-local quantum information’ along the entirety of the DNA molecule which we really have no clue as to what it is doing:

    Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
    http://www.metacafe.com/watch/5936605/

    As well, besides the quantum information/entanglement in DNA that no one really has a firm clue as to exactly what it is doing, there are hints of another whole level of information hidden within the genome that, as well, no one has a clue what it is doing:

    DNA Caught Rock ‘N Rollin’: On Rare Occasions DNA Dances Itself Into a Different Shape – January 2011
    Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
    http://www.sciencedaily.com/re.....104244.htm

    Of related interest is this very recent breakthrough which stored 700 terrabytes of functional information on just one gram of DNA!

    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

    Notes of interest:

    What Is The Genome? It’s Certainly Is Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    DNA – Replication, Wrapping & Mitosis – video
    https://vimeo.com/33882804

  19. Barry @14, you are being disingenuous in your response to Nick. The definition of function used by ENCODE is paramount to the discussion.

  20. paulmc- so is the definition of dispensable junk.

  21. Here is a particularly good read from Sean Eddy on ENCODE’s findings. You’ll see that junk DNA is functional because of ENCODE’s definition.

  22. paulmc accuses Mr Arrington of being disingenuous:

    Barry @14, you are being disingenuous in your response to Nick. The definition of function used by ENCODE is paramount to the discussion.

    Really paulmc??? Disingenuous paulmc??? that’s funny because the reality of the situation is that it is neo-Darwinists who are the ones who have been completely disingenuous towards the evidence for functionality in DNA. This ‘disingenuousness’ is especially surprising since the initial 2007 ENCODE findings came out urging a more ‘neutral’ view of non-coding regions. If science were to have operated as it should, this warning should have put severe dampers on Darwinian claims. But it did not, which goes to show, once again, that it is not about the science with Darwinists!!!:

    i.e.

    Concluding statement of the ENCODE study:
    “we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome.”
    http://www.genome.gov/Pages/Re.....e05874.pdf

    Did neo-Darwinists listen to these words of caution paulmc? No of course not! Despite the fact that researchers are dealing with complexity that is orders of magnitude greater than anything ever built by man in computer programs,,,

    Human Genome “Infinitely More Complex” Than Expected – April 2010
    Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.”
    http://www.creationsafaris.com.....#20100405a

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    ,,,the Darwinists are, for purely philosophical/religious reasons as far as I can tell, dead set against ever admitting to any hints of Design in life whatsoever. In fact, it is held in some quarters that this irrational stance (indeed unscientific stance) by Darwinists has severely hindered scientific progress:

    Matheson’s Intron Fairy Tale – Richard Sternberg – June 2010
    Excerpt: The failure to recognize the importance of introns “may well go down as one of the biggest mistakes in the history of molecular biology.” –John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American,,,
    http://www.evolutionnews.org/2.....35301.html

    On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. – Richard Sternberg
    Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    and this irrational stance of Darwinists can even be argued to have hindered medical progress:

    International HoloGenomics Society – “Junk DNA Diseases”
    Excerpt: uncounted millions of people died miserable deaths while scientists were looking for the “gene” causing their illnesses – and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes).”
    http://www.uncommondescent.com.....ent-357177

    No paulmc, IDists may not be perfect, no human is for that matter, but neo-Darwinists take the cake on being disingenuous towards the evidence for finding functionality in DNA!

    further note:

    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

  23. Perhaps you should have read the link in @21 before posting? “Functional” is defined so broadly that junk is subsumed within it.

  24. paulmc, actually Darwinists have junk defined so broadly that functionality is subsumed within it.

  25. About the C-Value paradox

    I remember reading a paper from Lynch that 1-50bp deletions in humans were 3 times as likely as insertions. Could lungfish, salamanders, and onions have some process in the replication that has gone wrong, causing them to accumulate extra nucleotides over time? (and therefore it would be junk).

    I suppose this is the same as the Darwinian explanation, and also perfectly compatible with ID, esp. given degeneration?

  26. Junk DNA has no bearing on phenotype. Functional DNA for most people would be everything else, rather than just everything that has a degree of biological activity. As Eddy points out – and others have too – you would expect random generated sequences inserted into a genome to qualify as functional under ENCODE.

    Therefore it is the definition of function and not of junk that is too broad here.

  27. paulmc:

    Junk DNA has no bearing on phenotype.

    True, but that does NOT mean that all the DNA that has no bearing on phenotype is junk.

  28. paulmc:

    Junk DNA has no bearing on phenotype.

    Hang on. Just want to make sure I caught this. Are you saying that some 90% of our DNA (the “junk” figure, plus or minus a couple of percentage points) has no bearing on phenotype?

  29. Eric,
    no, not quite – I’d say that 90% of the genome shows no evidence of conservation, and while much of it is likely to be junk, it is not possible to firmly conclude it is *all* junk without a stronger basis. With that said, there is also much that we do know, which allows us to put upper and lower limits on junk.

    Firstly, the ENCODE extrapolation suggests a final figure might be 20% functional (by traditional definitions) and 80% junk. Secondly, in the past I have referred repeatedly to Larry Moran’s quantitative account of genome composition as being a good guide – the junk component there being estimated as between 65% to 90%.

    The majority of the human genome is junk by any of these definitions.

  30. Junk DNA has no bearing on phenotype.

    Really??? That’s a pretty radical claim paulmc! Indeed:

    A phenotype (from Greek phainein, ‘to show’ + typos, ‘type’) is the composite of an organism’s observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird’s nest). Phenotypes result from the expression of an organism’s genes as well as the influence of environmental factors and the interactions between the two.
    http://en.wikipedia.org/wiki/Phenotype

    Definition of PHYSIOLOGICAL
    1 of or relating to physiology
    2 characteristic of or appropriate to an organism’s healthy or normal functioning
    3 differing in, involving, or affecting physiological factors

    Thus if:

    Junk DNA has no bearing on phenotype.

    As paulmc claims then Junk DNA would have to be perfectly neutral biochemically and place no unnecessary energetic burden on the cell affecting its normal, healthy, functioning. But that belief in perfect biochemical neutrality is preposterous!

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    For the cell would have to expend energy replicating totally useless DNA and, according to this new research by ENCODE, transcribing it into massive amounts of RNA, where, according to Darwinists, it does absolutely nothing useful, but is just a unnecessary energetic burden on the cell???,,,

    …And so goes the completely insane swamp land of evolutionary apologetics.

    notes:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.

    High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley)
    “In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load…the presence of a large class of mildly deleterious mutations can never be ruled out.”
    http://www.sciencemag.org/cgi/...../5434/1748

    Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally – September 2010
    Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).
    http://www.uncommondescent.com.....literally/

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video (Notes in description)
    http://vimeo.com/35088933

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE

    Human evolution or extinction – discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) – video
    http://www.youtube.com/watch?v=aC_NyFZG7pM

  31. I wonder if ENCODE did a graph comparing the Transcription Regulation in humans to a Call Graph of a computer operating system as the following video does for e-coli:

    What Is The Genome? It’s Certainly Not Junk! – Dr. Robert Carter – video
    http://www.metacafe.com/watch/8905583/

    It would certainly be very interesting to see the comparative differences between the e-coli and Human Transcription Regulation networks since humans have a vastly more expansive regulatory network than e-coli does

    Related notes:

    Global project reveals just how active our ‘junk’ DNA is – Sept. 2012
    Excerpt: They found that, across the genome, about 19 per cent of our DNA may code for RNA switches that turn genes on or off. “We see way more switches than we were expecting, and nearly every part of the genome is close to a switch,” project coordinator Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, told New Scientist.
    The switches also appear to be spread out over the genome, with some being located at a distance from the gene they are controlling. Around 95 per cent of the genome appears to be very close to a switch, suggesting that almost all of our DNA may be doing something important.
    http://www.newscientist.com/bl.....at-ou.html

    “Millions of DNA Switches That Power Human Genome’s Operating System Are Discovered.” (http://www.sciencedaily.com/re.....135326.htm

    An expansive human regulatory lexicon encoded in transcription factor footprints
    http://www.nature.com/nature/j.....11212.html

    The accessible chromatin landscape of the human genome
    http://www.nature.com/nature/j.....11232.html

  32. per crev.info

    ENCODE Study Forces Evolutionists to Retract “Junk DNA” Myth
    http://crev.info/2012/09/encode-study-junk-dna/

  33. Can someone explain to me why scientists use the words functional and junk interchangeably…An answer from you Paul would be nice.

    Also, Maybe it’s time for a redefining of terms in the case of the word “Functional” in evolutionary science. Scientists, I feel, want to use the “junk DNA” words because they think it hurts the idea of an IDer. I agree, it does, but if there was never any real USELESS junk in the genome, and scientists have know that for a while, than I accuse scientists of a half-truth, if not lying for years!

    Functional, nonfunctional, junk…it’s all conflated now, especially if you are right Paulmc. The question I would like answered is…do these non-coding sequences have(serve) a purpose in our genome? (the importance of its usage is besides the point)…if yes than ID would predict that…if no than it hurts ID. I don’t claim to know the answer just yet.

  34. paulmc:

    . . . I’d say that 90% of the genome shows no evidence of conservation . . .

    Hang on. Weren’t we being told that we share 95%, 98&, 99% (pick the favorite number) of our DNA with chimps? Now you’re suggesting that there is no evidence of conservation of 90% of our DNA. So either our DNA has conserved the vast majority (and thus remains very similar to our common chimp ancestor), or there isn’t any conservation (and thus the idea of DNA similar to the common chimp ancestor has to be questioned).

  35. Perhaps you should have read the link in @21 before posting? “Functional” is defined so broadly that non-functional is subsumed within it.

    So you’re accusing these scientists of being illogical?

  36. Eric, conservation = purifying selection.

  37. Mung, I’m sure their logic is just fine. Their definitions not so much.

    As I explained in the first ENCODE thread here, and others have explained all over the internet (including Ewan Birney, ENCODE coordinator) – ‘functional’ under ENCODE means something very broad. The definition subsumes what most of us would call junk. They effectively redefine ‘functional’ as ‘biologically active’. In Birney’s words:

    Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.

    So, for a start, functional is defined to automatically include every intronic base in the genome (60% of the genome already) on account of those bases being transcribed. ENCODE effectively redefine junk as anything that doesn’t meet the criteria Birney describes above(i.e. very little).

    They argue the purpose of this is to give a precise definition of functional, yet other definitions are possible. The other definitions wouldn’t have made such punchy headlines.

  38. 38
    critical rationalist

    BA: The ID community, including many writers here at UD, has been predicting for years that so-called junk DNA would be found to be functional. The Darwinists have scoffed. Now ID proponents are being vindicated. My prediction: The Darwinists will change their story to “we’ve been saying this all along.”

    The assumption that Darwinists will change their story suggests finding errors in a theory is somehow a bad thing. This is illogical, as it conflicts with our current, best explanation for the growth of knowledge. Namely, all theories contain errors of varying degree and that finding them is how knowledge grows. It also assumes some ultimate explanation can be found.

    For example, even when found to be in error as a whole, as it was in this case, a theory that only roughly 2% of the genome has a specific purpose is better than the vague claim that 100% of the genome “should be functional”. This is because it encompasses the theory that roughly 2% of the genome a specific function, rather than some other specific function, which can be found in error.

    Merely assuming the entire genome “should be functional” does not stick its neck out in a way that allows itself to be criticized. Furthermore, if we do not conjecture a specific theory of what specific function they do perform, then we do not know what tests to run. And without tests, we do not know what observations to make. So, merely saying “all genes should be functional” doesn’t tell us where we should look or what we should look for.

    In addition, a replicators, we know that genes to serve a purpose. They play a casual role in getting copied. So, of course, they “do something”. The question is, what hard to vary role do they play in adaptations of biological organisms.

    IOW, proposing the remaining 98% of the genome did not play a role in building biological adaptations means that the 2% should play the entire role. That’s a testable prediction that can be criticized.

    Surviving criticism and *not* surviving criticized is a win win situation, which doesn’t represent a blow to human intellect. In fact, it’s just the opposite. Our ability to devise specific tests that would falsify one theory, but not the other, is an example of human intellect. This is what allows us to make progress.

    Furthermore human designers regularly make things that are merely cosmetic or inadvertently end up creating things that serve no purpose. In addition, a designer could make genes non functional in an attempt to obscure its role in the process. IOW, it’s not clear why you would expect an abstract designer with no defined limitations to make all genes functional.

  39. paulmc,

    ‘functional’ under ENCODE means something very broad.

    But no so broad as to include all DNA.

    IOW, even under ENCODE there is still room for “non-functional” DNA, aka “junk”. True?

    The definition subsumes what most of us would call junk.

    But not all of what most of you would consider junk. And that, sir, is the point, isn’t it?

    The definition subsumes some of what most of you would call junk, and perhaps even most of what most of you would call junk.

    So let’s not pretend like ENCODE has done away with “junk DNA.” There’s still some hope for most of you.

    They effectively redefine ‘functional’ as ‘biologically active’.

    ok. But I think the real issue is purpose. Does it serve any purpose? Is that still an open question in your mind? Or are you still convinced that it serves no purpose?

    I have to wonder why they would call it functional if it serves no purpose. Why not just call it biologically active?

    As far as I am concerned, “junk DNA” didn’t mean “biological inert DNA,” but rather “purposeless DNA.”

    Am I wrong?

  40. Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades.

    here

    Just bad science reporting?

  41. paulmc you state:

    I’m sure their logic is just fine.,,

    Unfortunately for you, the neo-Darwinian, atheistic/materialistic, foundation for logic is far from fine on this particular matter, or for any other subject in science for that matter, since atheistic materialism winds up in abject epistemological failure (A.Plantinga, Boltzmann’s Brain).

    Indeed, Modern Science was born in the matrix of Christian Theism by presupposing the world was intelligible to the human mind because we are made in the image of the Creator Who made the universe and all life in it. Indeed science was born by presupposing that ‘functionality’ would be discovered in the universe and in life before any functionality was even known to exist in the world or in life. Atheistic materialism, which undergirds neo-Darwinian thought, with its demand for unguided randomness at its foundational base, is simply completely at odds with that very fruitful heuristic that was born out of Judeo-Christian presuppositions. Indeed Neo-Darwinian evolution with its demand for ‘non-functionality’, i.e. for junk, vestigial, etc.., is simply a complete hindrance to science properly done! This undo hindrance that atheistic materialism places on science is already self evident in this new area of investigation of ‘Junk DNA:

    “The failure to recognize the importance of introns “may well go down as one of the biggest mistakes in the history of molecular biology.”” –John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American,,,

    On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. – Richard Sternberg
    Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    I could list many more areas where atheistic materialism has hindered science in such a way. Thus paulmc however reasonable you may think your arguments to be for presupposing ‘non-functionality (I personally find your arguments baseless), the fact is that you are in fact very unreasonable in trying to advance your position!

  42. The project’s chief discovery is the identification of about 4 million sites involved in regulating gene activity.

    Non-functional but biologically active sites involved in regulating gene activity? Still “junk”?

  43. Indeed, Modern Science was born in the matrix of Christian Theism by presupposing the world was intelligible to the human mind because we are made in the image of the Creator Who made the universe and all life in it.

    http://www.amazon.com/dp/0199550018

    http://www.amazon.com/dp/0199594937

  44. NickMatzke_UD:

    And, onion test. Answer it or you don’t have an argument.

    Really? That’s the best you can do? What does the “onion test” have to do with the human genome, which is, after all, the subject of the OP?

    ok, Nick.

    Why is there something, rather than nothing?

    Answer it or you don’t have an argument.

  45. Off Topic

    Here is a free course on wishfulthinking genetics and evolution
    https://www.coursera.org/course/geneticsevolution

  46. Mung — I’ll run a couple of your posts together and respond to the lot. Firstly:

    But no so broad as to include all DNA.

    Actually, Birney suspects that by the end of ENCODE (another 5 years) the figure will be 100% under their definition.

    The definition subsumes some of what most of you would call junk, and perhaps even most of what most of you would call junk.

    So let’s not pretend like ENCODE has done away with “junk DNA.” There’s still some hope for most of you.

    That’s exactly what they have done. ENCODE has effectively defined away junk DNA, as I have explicitly outlined. Again, the expected figure of functional DNA in the human genome by the end of ENCODE is 100%, once the project is complete. This is not because it’s all contributing to phenotypes, but because it has binding sites or gets transcribed, etc.

    Again, consider what happens when there is a random insertion into the genome – say 30 random bp inserted in the middle of an intron. The intron is still removed in the production of the mature mRNA molecule, and there is no appreciable effect on the organism. I would say that there has been an increase in the junk content of the genome, ENCODE would literally claim that there has been a functional expansion of the genome.

    But I think the real issue is purpose. Does it serve any purpose? Is that still an open question in your mind? Or are you still convinced that it serves no purpose?

    To be clear — if you randomly generate a sequence and insert in the genome it would be “functional” under the definition used by ENCODE. Surely, this is not a standard that an ID advocate would accept as functional.

    As far as I am concerned, “junk DNA” didn’t mean “biological inert DNA,” but rather “purposeless DNA.”

    Am I wrong?

    Nope, you’re not wrong. I wouldn’t use the word purpose, but I know what you mean and you are right as far as I am concerned. This is the heart of the matter and why so many scientists are unhappy with ENCODE’s characterisation.

    Non-functional but biologically active sites involved in regulating gene activity? Still “junk”?

    No, I wouldn’t say so. Sites involved in gene regulation are not junk, even though many of the interactions might be of little significance (as we expect many interactions to arise by chance). Michael Eisen has an excellent discussion of this from his own work. The point is not that the human genome is complex — of course, it is — the point is that beyond the four million switches are large swathes of DNA that have arisen by retrotransposon duplication and mutated to non-function, by traditional definitions. ENCODE still considers them functional by definition.

  47. as to:

    the point is that beyond the four million switches are large swathes of DNA that have arisen by retrotransposon duplication and mutated to non-function,

    nothing like presupposing your conclusion for non-functionality into the very question being asked for functionality is there paulmc??? Like I said before atheistic materialism is a hindrance to science and certainly does not provide a fruitful heuristic for discovery!

  48. Mung:

    What does the “onion test” have to do with the human genome, which is, after all, the subject of the OP?

    It has a lot to do with it. If we want to make the positive case that the majority of non-coding DNA in humans is functional in the traditional sense — i.e., it is necessary to regulate the genome — then we need to have a functional explanation of genome size that can explain a few things:

    1) What is so complex about an onion, compared to a human, that it needs substantially more non-coding DNA than we do?

    Now, it is possible that we simply don’t understand the complexity of the onion, and perhaps it really is much more complex than we are. There is no evidence for this, but even if we accept this:

    2) Why does one species of onion need 4x as much non-coding DNA as another biologically and ecologically similar species of onion (both in the genus Allium)?

    This is not to say that there is no possible explanation for the differences in these two onion species. However, there is no clear functional explanation, yet we need one before we would conclude that the enormous variation in genome size is actually necessary DNA. Lacking such an explanation, we fall back to the far simpler explanation — that much of the excess non-coding DNA is not biologically necessary. This is our null position, because we understand the processes that cause the accumulation of DNA well and can see these processes operate.

    However, if we accept that this is possible for onions, we should also be open to the possibility that not all of the non-coding DNA in humans is necessary either. For example, within the vertebrates there is much genome size variation. Why is the fugu genome only 400Mb when ours is about 9x larger? Is it because we need that much additional regulation? Or, like the onions, is this more likely to represent an excess of non-coding DNA?

  49. paulmc:

    Perhaps I’m misunderstanding your terminology. I understand purifying selection to refer to natural selection acting to eliminate deleterious characteristics. (We could quibble a long time about the whole concept of ‘selection,’ let’s set that aside for now.)

    So if I’m understanding your reference to genome “conservation,” what you’re suggesting is that all the junk DNA (65%, 80%, 90%, whatever% of DNA) shows no evidence of elimination of deleterious characteristics?

    I just want to make sure I’m understanding your point.

  50. paulmc:

    That’s exactly what they have done. ENCODE has effectively defined away junk DNA, as I have explicitly outlined.

    No, they haven’t. As I have explicitly outlined, lol.

    Again, consider what happens when there is a random insertion into the genome – say 30 random bp inserted in the middle of an intron. The intron is still removed in the production of the mature mRNA molecule, and there is no appreciable effect on the organism. I would say that there has been an increase in the junk content of the genome, ENCODE would literally claim that there has been a functional expansion of the genome.

    Now you’re just making things up.

    WHY would Encode claim there has been a “functional expansion” of the genome?

    According to your own admission the insertion would not change anything. It would still be removed. So Encode would discern no difference at all.

    To be clear — if you randomly generate a sequence and insert in the genome it would be “functional” under the definition used by ENCODE.

    Why?

    If you randomly generate a sequence and insert it into the genome, what are the possible scenarios?

    Surely one of the possible scenarios includes changing a formerly “functional” sequence into a “non-functional” sequence.

    If not, why not?

    Nope, you’re not wrong. I wouldn’t use the word purpose, but I know what you mean and you are right as far as I am concerned. This is the heart of the matter and why so many scientists are unhappy with ENCODE’s characterisation.

    :)

    I am not sure why any scientist would object. It’s there for a reason has to trump it’s there for no reason at all.

    But for me, the jury is still out. The issue is not “functional” DNA but rather “purposeful” DNA.

  51. paulmc,

    Get back to me when you have a species of human that “needs” 4x as much non-coding DNA as another biologically and ecologically similar species of human.

  52. Eric – yes, that’s right. In fact, it is not possible for the majority of the bases in our genome to be subject to purifying selection at the current mutation rate.

  53. Mung:

    Now you’re just making things up.

    WHY would Encode claim there has been a “functional expansion” of the genome?

    According to your own admission the insertion would not change anything. It would still be removed. So Encode would discern no difference at all.

    But this is their definition Mung – and is the main point! A stretch of DNA is called ‘functional’ in ENCODE simply if is transcribed. Because introns are transcribed — even though they are removed in the production of the mature mRNA from which a protein is translated — they are considered functional, even if they are entirely biologically inert in every other sense.

    ENCODE does discern a difference here because it is annotating this section of the genome as being intronic. Therefore an expansion in this region contributes to the functional component of the genome under ENCODE.

    If you randomly generate a sequence and insert it into the genome, what are the possible scenarios?

    Surely one of the possible scenarios includes changing a formerly “functional” sequence into a “non-functional” sequence.

    If not, why not?

    Absolutely, one of the possibilities is mutating something functional. If a chunk of random sequence falls in an exon, for example, it is almost certainly going to be deleterious. These mutations are removed quickly by purifying selection – often they won’t produce a viable organism. Many, many other insertions do not have this effect because they occur in areas of the genome that are not subject to purifying selection – e.g. in the middle of a typical intron.

  54. Mung:

    Get back to me when you have a species of human that “needs” 4x as much non-coding DNA as another biologically and ecologically similar species of human.

    The point stands that if we can observe such enormous variations in genome sizes, they warrant explanation. The variation suggests the tendency towards accumulating non-coding DNA that lacks any evidence of function, and there is no biological sense in treating humans separately here. This is a phenomenon that occurs across the eukaryotes.

  55. Paulmc…what does it mean for the genome to have non-functional DNA? Or useless DNA? What is it?

  56. paulmc:

    The point stands that if we can observe such enormous variations in genome sizes, they warrant explanation.

    Absolutely. We agree. But the fact that we do not yet have an explanation for x (the genome size of various species of onion) does not mitigate against the facts that we do have at hand concerning the human genome.

    Please explain how onion genomes affect the human genome.

    What was the most recent common ancestor?

  57. paulmc:

    A stretch of DNA is called ‘functional’ in ENCODE simply if is transcribed.

    So what?

    The darwinian view is that transcription of ‘functionless’ DNA is a waste of energy and therefore should be selected against.

  58. Mung:

    Please explain how onion genomes affect the human genome.

    It should be fairly clear that it is not a case of the onion genome “affecting” the human genome. The challenge is to explain genomic variation broadly. You haven’t offered any reason to doubt that the variation in genome sizes between different onion species is due to anything other than junk.

    The point we learn from onions is that non-coding DNA cannot be assumed to be functional (in the traditional sense). We know that half of any typical mammalian genome comprises old, degenerate retrotransposons – sequences that accumulate by their mutational pressure. Such a volume of non-coding DNA is lacking in some other vertebrates like fugu as I mentioned before – this is the multicellular end of the c-value enigma: there are no patterns of differences in complexity between these organisms, only massive variation in their non-coding, nuclear DNA.

    However, variation in genome size broadly correlates to population size, as laid out finely in the Lynch et al. review paper I linked to above. And this ties closely into your next point:

    So what?

    The darwinian view is that transcription of ‘functionless’ DNA is a waste of energy and therefore should be selected against.

    The accumulations of non-coding DNA occurs incrementally. Each addition does not waste much energy, and in small populations, selection is too weak to remove such variation.

    While it is true that the ultradarwinist view would not allow to such accumulation, this view doesn’t represent mainstream evolutionary biology, and hasn’t for decades. A more pluralistic approach will accept that the well-established limits of selection in small populations, and the population-genomic consequences. Lynch lays all of this out in a quantitative framework, with thresholds for junk accumulation.

  59. paulmc:

    In fact, it is not possible for the majority of the bases in our genome to be subject to purifying selection at the current mutation rate.

    OK, just to make sure I understand what you are saying.

    1. Are you saying that because the mutation rate is too high (compared with our reproductive cycle), most of the mutations cannot be eliminated through purifying selection?

    2. If so, are you then further saying that because those mutations haven’t caused any identifiable problems then we can infer that those sequences were/are non-functional?

  60. paulmc:

    The accumulations of non-coding DNA occurs incrementally. Each addition does not waste much energy, and in small populations, selection is too weak to remove such variation.

    Sorry to butt in, but that sentence jumped out at me. So what we’re being told to believe is the following:

    1. In small populations with long lifecycles (like humans) selection is so strong and so effective that it was able to fix in the population numerous miniscule changes over a relatively short time period of a few million years that add up to huge differences between us and chimp ancestors.

    2. In small populations with long lifecycles (like humans) selection is so weak and so ineffective that it is unable to purge a massive quantity of junk that, even under the highly questionable assumption that such junk would not cause problems for cellular function, the junk at the very least: (i) utilizes the majority of the copying resources every cell division, (ii) utilizes a meaningful portion of the transcription resources on an ongoing basis, and (iii) produces nonsense RNA strands that have to be located, recognized and broken down, over and over, minute by minute, day after day, for generations.

    Sounds more like a convenient story than a coherent story.

  61. Why are none of my questions being answered!?!? I want to know what non-function DNA is! I also want to know why any scientist would label DNA as junk if it has a purpose. Can we get an illustration here also preferably applying this same kind of idea to vestigial organs?

  62. In software engineering, the concept of “coupling” is used to describe the the way that software modules interact with each other in accomplishing the overall function of a computer system. This concept was pioneered by Larry Constantine and Ed Yourdon in developing the Structured Design approach (Structured Design: Fundamentals of a Discipline of Computer Program and System Design, Prentice-Hall, 1979).

    They describe the differences between “loosely coupled” and “tightly coupled” systems (Wikipedia provides a good summary of the ideas involved).

    A tightly coupled module is difficult to modify or swap out for a superior alternative without a detailed knowledge of the way that related modules do their job. Tightly coupled systems have greater interdependency between their parts, require more coordination between parts, and require greater information flow to maintain function. Tightly coupled modules may even rely on modifying the functions of related modules. Loosely coupled systems have the opposite characteristics.

    In systems design, “loose coupling” is to be preferred to “tight coupling”.

    Loosely coupled systems evince good design (clear forethought about module functions, inter-module communications and the likely need to modify or enhance functionality in the future – all good teleological attributes.

    Tightly coupled systems, on the other hand, evince a lack of forethought, an ad-hoc approach to making things work, and a tendency to develop spaghetti code. In other words, tightly coupled systems tend to develop “organically” (designers and programmers modify the current structure in small ways to overcome the next immediate difficulty), rather than reflecting a long-term view of the function, development and maintainability of the overall system.

    The genetic control systems of cellular function are clearly “tightly coupled” in the sense used by Constantine and Yourdon. The expression of a protein from a gene template is mediated by a complex parallel set of genetically encoded transcription and timing controls, each of which is specific to the particular expression pathway, and has the ad-hoc characteristic of tight coupling.

    Hence, if design in natural biology is to be inferred by analogy to human-designed templates (we recognise design in non-human nature because it is analogous to examples of human design), then we are forced to the inference that biological systems are poorly designed. And worse yet – the more complex the cellular functions happen to be, the worse the design.

    Or to put it differently, if the complexity of cellular control systems demands that deliberate design is a superior explanation for their origin (compared to mutation plus natural selection, or neutral drift following by functional co-option), then we are also paradoxically forced to the conclusion that the actual deliberate design is inadequate to the long-term survival of the system.

    [In the interests of full disclosure, I should say that I have shamelessly plagiarised this idea from a more loosely coupled organism than I am.]

  63. It is so interesting watching Darwinists make ad hoc and ex post facto pronouncements.

    When pseudogenes are found to have function, thus undercutting their “junk DNA” argument, they say: “Oh, what’s the big deal. No one ever said that there was ‘junk-DNA’.”

    Then you have this study that shows that 80% of the genome is transcribed, and has some, minimal, “chemical” function, and they say: “See, under this definition, anything can be termed ‘functional.’ We all know that there’s all this ‘junk’ in the genome. Just look at the onion.”

    So, which way is it, boys? Have you never said there was junk, or are you saying there’s all kinds of junk?

    As usual, your answer will be whatever you perceive is needed to prop up a failed theory. Let’s hear it for Ptolemy.

    In the meantime, thanks for the entertainment.

  64. You know what I’d like to see?

    I’d like to see these guys who claim there is so much junk in the genome to “practice what they preach”!

    Wouldn’t it be nice if there was a way for them to delete whatever part of the genome they think is junk in the cells of their own children?

    Not that I would wish that on their kids, but I’d love for there to be a way for them to put their faith into practice and then we would be able to see what they really believe.

    How many of these guys would have been willing to delete 98% of the genome they claimed was junk in their own cells or in their kid’s cells? None, I’m sure, and that makes me question whether or not they really believe that.

    It’s like the tightrope walker asking people if they think he could take a guy piggy back across the falls. They all say yes and then he said “Who will volunteer?”

    Needless to say, there were no volunteers. It’s easy to claim you believe something – but when the rubber meets the road, the truth comes out.

  65. timothya @62, that is one of the most absurd things I have read in a long time. Neither you nor anyone else has the slightest clue about how biological systems could be better designed. Your failed analogy (setting aside for the moment your very questionable interpretation of tightly/loosely coupled module design) is just another in the long history of pathetic attempts to say “no designer worth his salt would have done it this way.” Never is a detailed analysis done; never is a better method put forward with enough detail to ever determine whether the vague assertions about ‘it could have been better’ are true. And lastly, as I think you mention, even if it is poorly designed, it doesn’t mean it wasn’t designed.

  66. PaV, I think you make an astute observation. There appear to be two trends in evolutionary thought right now in regards to junk DNA. The first, which we are starting to hear occasionally, is “What junk? We never really meant it was junk.” The second, championed by wd400 and paulmc here, is to dig in the heels and battle tooth and nail against every additional finding that suggests there might be more function than previously thought. The former approach will eventually become more common as more and more function (the only possible way the evidence can trend) is discovered. But it will be painful for the latter group, and I suspect we’ll see plenty more defintional/rhetorical battles waged by them in the next few years before they finally throw in the towel.

  67. paulmc:

    The challenge is to explain genomic variation broadly.

    Then why are you so narrowly focused on one species of onion?

    :)

  68. timothya @62, you have a lot of assumptions built into that argument that may or may not hold even for software systems, much less for an attempt to apply principles of software design to biological organisms.

    One could just as easily argue that what you have described are not separate modules that “ought” to be loosely coupled, but rather a single module that “ought” to be tightly coupled according to the software principle of encapsulation.

    Nice try though. Perhaps if you developed the argument further.

    I’m interested in the extent to which software design principles are present in biological systems. Biological Design Patterns anyone?

  69. Nah Eric, it’s like this.

    No one ever said every non-coding sequence was junk. Ohno, in the first papers about the idea was quite explicit about this. So finding this or that pseudo-gene now drives expression of some thing or other doesn’t disprove junk DNA.

    On the other hand, the ENCODE result includes every nucleotide of every intron in its definition of “function”. I don’t think any sane person could think every nucleotide of every intron was actually require for proper functioning of the cell (and to believe that, and that Fugu can get by fine with many times smaller introns in a real stretch), so clearly the ENCODE total is too high.

    (BTW, this is one of those topics that exposes how the verbal tic of calling evolutionary biologists “Darwinists” is really misleading – only ultra-Darwinian biologists would think the genome was full of functions. So, the people arguing for junky genomes are actually talking about non-Darwinian theories of genome evolution)

  70. wd400:

    On the other hand, the ENCODE result includes every nucleotide of every intron in its definition of “function”. I don’t think any sane person could think every nucleotide of every intron was actually require for proper functioning of the cell…

    That’s one way to set up a straw-man.

    But has the question “why introns” even been answered yet?

    To what extent are introns found in non-Eukaryotes?

    The biological origins of introns are obscure. After the initial discovery of introns in protein-coding genes of the eukaryotic nucleus, there was significant debate as to whether introns in modern-day organisms were inherited from a common ancient ancestor (termed the introns-early hypothesis), or whether they appeared in genes rather recently in the evolutionary process (termed the introns-late hypothesis).

    http://en.wikipedia.org/wiki/Intron

  71. Mung: I was not proposing human software design as template for understanding the structure and functioning of biological systems. In fact, I think digital computing is a particularly poor analogy of how biological systems work. I need to say this upfront, just so Eric doesn’t bark himself into a lather up the wrong tree again.

    I will include one partial response to Eric’s comment that:

    Neither you nor anyone else has the slightest clue about how biological systems could be better designed.

    This would be news to generations of plant and animal breeders, developers of genetically modified organisms, developers of gene therapy solutions, stem cell researchers etc etc, all of whom by different pathways are “investigating how biological systems could be better designed” (that is, better fit to human health and requirements). I used to do it for a living, so actually I do have a clue. Enough said.

    My point (and probably not a particularly important one) is this. Simply asserting designedness in non-human systems on the basis of prior knowledge about how humans design things is insufficient. If, in fact, undesigned, natural processes can create complexity, then you have simply fallen prey to an illusion.

    We need to look at how the complexity of human designs is materialised, and pay particular attention to how human designers typically achieve desirable features – functional fitness, sustainability, upgradability, adaptability. Software design is a reasonable example of how human designers go about achieving these attributes.

    Any computer program (that “works”) will be at least as complex as is required to deal with the processing problem at hand. The designer essentially has two canonical approaches to creating the necessary complexity.

    Either follow the structured design approach, in which individual functional modules are robustly designed to perform a “class” of function, and the overall program control module contains all of the complexity required to deal with the full range of potential processing inputs – deciding which functional module to call on the basis of the input case, assembling its input data, handling its output etc etc.

    Alternatively, the designer can embed all of the control switching capabilities into each functional module (or, as you point out, dump all control and processing functionality into one bag of code), so it can autonomously handle all possible input combinations.

    We would expect to see very different abstract structural characteristics of two programs written to solve a problem using the two approaches. The first would have a single, complex control structure with a minimal set of “functional” modules. The second would either have as many functional modules as there are input possibilities, or one undifferentiated processing structure with processing code, control code and variable definitions studded throughout like plums in a pudding.

    Now. When faced with a new input case, the designer of the first type will typically add a switch to the control module. The designer of the second type will typically modify an existing functional module to handle the new case, or even create a new module to deal with the new eventuality.

    Both approaches can, in principle, deliver the functional fitness attribute, but the structured design approach requires significantly less effort to deliver sustainability, upgradability and adaptability.

    The structure of cellular control in biological systems appears to be one of ad-hoc modification of existing processes to meet new input cases (of dazzling intricateness). It clearly exhibits the “one control system per function” model. This, in itself, is counter-evidence to the argument that there is a long-run intention for sustainability and adaptiveness behind the processes of biological systems, irrespective of whether they were designed in the first place.

    I happen to believe that the ad-hoc model of modifying existing systems is precisely what one would expect if the functional changes arise from random mutations in the genetic code, followed by selection under environmental pressure on the resulting phenotype. I would not expect to see a consolidated unitary control system. And it appears that reality confirms this prediction.

  72. Mung, it’s not a strawman, it’s ENCODE’s definition!

    And no, it’s not clear why intron’s exist, but it’s worth repeating evolutionary biology doesn’t require something to have a purpose in order to exist. Michael Lynch and his crew might well argue introns are non-adaptively complex

  73. wd400,

    Introns exist to make alternative gene splicing possible. And your position cannot explain alternative gene splicing.

    And we await your experiments in which you remove all introns and get a viable organism.

  74. Loljoe, even if that is true, most genes don’t make alternative products. so, why so many introns? And why so big?

  75. Joe. I didn’t say all introns are junk, Just that encode calling every nucleotide of every one if them functional is a bit of a joke.

  76. wd400-

    Your entire position is a joke because you cannot explain functional DNA and you cannot explain alternative gene splicing.

    And again FUTURE FUNCTIONS- ie theb reason not all genes make alternative products- why so big (introns)? Because they also house software.

    As I said eliminate them and see what you get.

  77. wd400:

    Nah Eric, it’s like this.

    No one ever said every non-coding sequence was junk. Ohno, in the first papers about the idea was quite explicit about this. So finding this or that pseudo-gene now drives expression of some thing or other doesn’t disprove junk DNA.

    No-one ever said anyone said that every non-coding sequence was junk. We’re talking about a broader concept here. paulmc and I are discussing selection and what evidence may or may not exist about selection’s action in the genome.

    On the other hand, the ENCODE result includes every nucleotide of every intron in its definition of “function”. I don’t think any sane person could think every nucleotide of every intron was actually require for proper functioning of the cell (and to believe that, and that Fugu can get by fine with many times smaller introns in a real stretch), so clearly the ENCODE total is too high.

    I’m not so interested in the ENCODE definition in what I am discussing, other than the fact of pervasive transcription and the implications of that. I realize you and others on the thread are focusing on the ENCODE definition. paulmc and I are talking about other aspects. However, in response to your comment I would note that you cannot assume that the ENCODE total is too high. You may end up being right that the definition is too broad and that some portions of some introns are not necessary for funcion. However, we will find more functions in the future, and we also know that some portions of DNA are important due to their placement, transcription timing ‘pause’ elements, and there is even multi-layered information in some elements. So it is not at all clear that 80% will be too high at the end of the day.

    (BTW, this is one of those topics that exposes how the verbal tic of calling evolutionary biologists “Darwinists” is really misleading – only ultra-Darwinian biologists would think the genome was full of functions. So, the people arguing for junky genomes are actually talking about non-Darwinian theories of genome evolution)

    Well, there may be better terms. Your classic ultra-Darwinist Dawkins, however, loves to proclaim how much junk DNA there is, so I’m not sure you’ve got your categories quite right either. :) And Darwinian evolution includes two general principles: variation plus selection. It seems the first aspect is pretty broad and picks up just about everything. Whether selection is acting or hasn’t acted yet, or is only slowly acting, is of course an open question. I understand your point, however, that there may be other specific stories about how certain features came about that one could view as less Darwinian. Most of which are just variations on the overall evolutionary ‘explanation’ that “stuff happens.”

  78. timothya,

    The structured approach has been replaced by the object-oriented approach. And before the structured approach there was some other “best” way to develop software.

    It’s probably not a good idea to just take one of them when seeking to find comparisons in biology. And as you can see, human understanding changes.

  79. wd400:

    And no, it’s not clear why intron’s exist, but it’s worth repeating evolutionary biology doesn’t require something to have a purpose in order to exist.

    Introns do not exist in all organisms. (I’m not trying to imply that you don’t know that, I’m sure you do.)

    So did they just magically appear in numerous lineages independently?

    Or have they been inherited from a common ancestor?

    When the first intron appeared, how did it spread throughout the population? Drift?

    I would think that one would assume that there was some initial selective advantage.

    So I don’t think it’s at all unreasonable to think that they had some purpose, at least in the beginning.

    Something new appears on the scene that gives the carrier and it’s descendants a reproductive advantage, by which means it is then spread through the population. Wash Rinse Repeat. Much less likely to happen if if serves no purpose.

  80. Mung,

    Introns evolved once, there used to be a debate about whether they were excised by prokaryotes or invented by eukaryotes, don’t know where we stand on that one today. Even if they are a eukaryote invention, it’s worth remembering that there are models of non-adaptive complexity (read the link in my earlier comment).

    Eric.

    OK, only about 10% of the genome is subject to purifying selection. Done?

  81. wd400:

    Introns evolved once…

    1. What is the evidence that introns evolved?

    2. Why did introns evolve at all?

    3. Why did introns evolve only once?

    …here are models of non-adaptive complexity (read the link in my earlier comment).

    Your link doesn’t work.

    But what I’m looking for are the models of non-adaptive junk, not models of non-adaptive complexity.

  82. I don’t really know why this is relevant, but the evidence for a single origin of introns is that fact they are limited to a single calde – Eukaryotes.

    Their orign is unclear – perhaps they started out as selfish elements, perhaps the splicisome etc is a relic from and RNA world that prokaryotes, with their much more efficient genomes, could remove. I’m not sure why it matters? I still think you’d have to be mad to think every nucleotide of every intron was functional.

    The non-adaptive origin of complexity paper is this one:
    http://www.ncbi.nlm.nih.gov/pm.....MC3121905/

    and all models of junk DNA are non-adaptive, that’s sort of the point.

  83. Well, I just think introns are very interesting and remain an unsolved puzzle for biology. I just have to decide I guess how much they can be explored in a blog.

    Perhaps one of the first things to reflect on is the fact that introns don’t exist in isolation. Would we even recognize an intron as an intron if there were not some biochemical process that excised them? But why would such a system as that arise, absent any introns in the first place? Yet another classic beef and egg problem?

    http://en.wikipedia.org/wiki/Intron

    http://en.wikipedia.org/wiki/RNA_splicing

  84. The existence of introns is certainly interesting, and a challenge to the panglossian view of the genome that some engineering-types have. But no matter the origin of introns, do really think every single nucleotide of every single intron is “functional” is a bit strange, which is one reason to discount ENCODE’s 80% number.

  85. wd400:

    But no matter the origin of introns, do really think every single nucleotide of every single intron is “functional” is a bit strange…

    Straw-Man

    Take Threonine for example:

    Threonine … Its codons are ACU, ACA, ACC, and ACG.

    As that final nucleotide in the codon “junk” because it can be any of the four and still result in the production of threonine? What ‘function’ does it have?

  86. It can’t be a strawman, because it is ENCODE’s definition!

    And no, the degenerate nature of the genetic code is not “junk” anymore than the fact you could change most residues in a protein and not alter the functions make most positions in proteins “junk”.

  87. wd400:

    The problem is not that “every single nucleotide… is “functional” “. The problem is if introns and other non coding sites are globally functional, and what functions they do have.

    As Mung has very correctly mentioned, not even in protein coding genes “every single nucleotide is “functional” “. That’s why we have a lot of neutral mutations. Even deletions of aminoacids can in some cases be irrelevant to the function of a protein.

    So, the function issue has to be judged on proper terms, and not at the single nucleotide level.

  88. Chop out a nucleotide in a protein coding gene and see how it works. Do the same to an intron…

  89. There was a discussion above about purifying selection (selection against deleterious mutations). One result from population genetics is that purifying selection isn’t very effective in small populations, so mildly deleterious mutations can be fixed in the population. (Humans have a small effective population size, historically, so this applies to us to some degree. It’s probably why transoposon insertions, which are probably only mildly deleterious, can be fixed in mammals) The result is that in very small isolated populations, deleterious alleles can build up quickly, increasing the mutation load severely. As it happens there is a paper in this week’s PNAS on such a case. ttp://www.pnas.org/content/109/37/E2496.abstract

  90. @NickMatzke_UD #6
    Hi Nick. About the onion test. It reads:

    Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

    I suppose one hypothesis, within an ID worldview, would be that there could be some nutritional value in the onion for other species. Pumping up the DNA size might simply pump up the nutrional content or variety of benefits.

    Example:DNA is Not Destiny article from Discover magazine (excerpt):

    Remarkably, the researchers effected this transformation without altering a single letter of the mouse’s DNA. Their approach instead was radically straightforward—they changed the moms’ diet. Starting just before conception, Jirtle and Waterland fed a test group of mother mice a diet rich in methyl donors, small chemical clusters that can attach to a gene and turn it off. These molecules are common in the environment and are found in many foods, including onions, garlic, beets, and in the food supplements often given to pregnant women. After being consumed by the mothers, the methyl donors worked their way into the developing embryos’ chromosomes and onto the critical agouti gene.

    (bold emphasis mine)

    So, an ID-ist might persue the discovery of overlapping genetic benefits between speices (e.g. humans and onions). This is a possible prediction that could not be made faithfully within the Darwinist view because it would apparently presume a feature of an organism (the onion) the exclusively serves the good of another organism(humans or other onion eaters).

    JGuy

  91. I think I used a bad example (methyl donors), but the hypothetical premise seems to hold potetial.

  92. The remarkable story of eukaryotic introns

    The “genes in pieces” (exon-intron) architecture of the protein coding (and some RNA-coding) genes in eukaryotes is a truly astonishing feature… Why would genes be interrupted by multiple non-coding sequences, most of which have no demonstrable function and are excised from the transcript by an elaborate molecular machine (evolved solely for this purpose) only to be destroyed? This almost defies imagination.

    …introns seem to have played a key role from the start of the evolution of eukaryotes…

    Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution

  93. Mung-

    If it defies imagination then they will either not want to discuss it, take LSD to help their imagination, or give the rest of us LSD to help ours.

  94. It may seem that the ID community celebrated too early on this. According to Jay Wile’s blog, a vast majority of pseudogenes are non-functional. And yes, I did leave a nasty note on there.

    http://blog.drwile.com/?p=8766

    Larry Moran’s blog says that the PR people screwed up the story and that Junk DNA is still alive.

  95. But are the pseudogenes really completely non-functional or are they a design feature that provides redundancy if a primary pathway is broken???

    The regulatory utilization of genetic redundancy through responsive backup circuits – 2006
    Excerpt: many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. … We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation.
    http://www.pnas.org/content/103/31/11653.full

    Either way Darwinism loses, i.e. if pseudogenes are a design feature of some type, such as providing redundancy, or some other design feature that hasn’t been looked for yet (given the extreme overlapping complexity of the coding in DNA), then the purported pseudogenes overtly support ID, and if the vast majority of pseudogenes really are broken genes, as Darwinists prematurely presuppose (think vestigial organ arguments that have now been overturned), then they provide further proof that Darwinian processes are excellent at breaking things but are powerless to create things!

    Of related interest form ENCODE, and shattering to the foundational Darwinian precept of the “Central Dogma’ i.e. DNA makes RNA makes Proteins, is the fact that ENCODE found that a ‘gene’ is not a gene anymore:

    …three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

    This supports and is consistent with earlier observations of a highly interleaved transcribed genome, but more importantly, prompts the reconsideration of the definition of a gene. As this is a consistent characteristic of annotated genomes, we would propose that the TRANSCRIPT be considered as THE BASIC ATOMIC UNIT OF INHERITANCE. Concomitantly, the term gene would then denote a higher-order concept intended to capture all those transcripts (eventually divorced from their genomic locations) that contribute to a given phenotypic trait. (Landscape of transcription in human cells. Sarah Djebali et al. Nature 2012 489: 101-108.)

    And:

    Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order framework around which individual transcripts coalesce, creating a poly-functional entity that assumes different forms under different cellular states, guided by differential utilization of regulatory DNA. (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.)
    http://www.evolutionnews.org/2.....64371.html

  96. BA77

    So if there are pseudogenes then ID is correct. If there are no pseudogenes then ID is correct. Isn’t this the type of reasoning Darwinists use? This sounds like a just-so story that they are always being blamed for. According to Jay’s blog, ID and creationism predicted the presence of pseudogenes but we all know that’s not right. Junk DNA is not a myth as previously thought and it kills one of ID’s best arguments. It might be time to go where the evidence leads…Darwin was right.

  97. But darwinism cannot explain the existence of genes…

  98. JLAfan2001, you are missing the entire point of experimental (empirical) science. Even Einstein’s theories (special and general relativity) were considered nothing more than conjecture until experimental proof was brought forth confirming time dilation for special relativity (now confirmed by multiple lines of experiment) and the experimental proof of the warping of 4-D space-time (i.e. bending of starlight during a eclipse) confirmed general relativity. In other words, why should Darwinism even be given the time of day, a free pass as far as Darwinists are concerned, as to explaining how genes arose when Darwinism has NEVER EVER been observed to create even a single functional gene and/or a functional protein in the first place??? whereas intelligence has been observed to create as such???

    Computer-designed proteins programmed to disarm variety of flu viruses – June 1, 2012
    Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, “to leapfrog over bottlenecks” to improve the activity of the binder.
    http://phys.org/news/2012-06-c.....ruses.html

    Stephen Meyer – The Scientific Basis Of Intelligent Design – video
    https://vimeo.com/32148403

    JLAfan2001 it is simply beyond ludicrous, indeed insane, for you to presuppose Darwinism as true for all of biology with no empirical basis to support your position that Darwinism can create functional complexity. Moreover for you to point to broken (vestigial) genes, which I grant Darwinism processes would be more than excellent at achieving, as proof that Darwinism is true simply because you can’t envision a Designer (God) allowing such genetic entropy to occur after He has implemented top-down design, is simply not even in the field of empirical science, and, in reality (not Darwinian fantasy land), such argumentation clearly is theological argumentation that you, and other Darwinists, have been using solely to try to support your empirically bankrupt, and philosophically motivated, theory!

    Notes:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    Where’s the substantiating evidence for neo-Darwinism?
    https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter – July 2012
    Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time.
    http://darwins-god.blogspot.co.....badly.html

    There is no evidence of Darwinian processes ever creating novel genes or proteins in humans whereas the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”

    I went to the mutation database website cited by John Avise and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.hgmd.org/

    I really question their use of the word ‘celebrating’. (Of note, apparently someone with a sense of decency has now removed the word ‘celebrating’). Such a high rate of detrimental mutations is further elaborated here by Dr. John Sanford:

    John Sanford on (Genetic Entropy) – Down, Not Up – 2-4-2012 (at Loma Linda University) – video
    http://www.youtube.com/watch?v=PHsu94HQrL0

    Notes from John Sanford’s preceding video:

    *3 new mutations every time a cell divides in your body
    * Average cell of 15 year old has up to 6000 mutations
    *Average cell of 60 year old has 40,000 mutations
    Reproductive cells are ‘designed’ so that, early on in development, they are ‘set aside’ and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,,
    *60-175 mutations are passed on to each new generation.

  99. This detrimental mutation rate is far higher than what even leading population geneticists agree is acceptable:

    Human evolution or extinction – discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) – video
    http://www.youtube.com/watch?v=aC_NyFZG7pM

    A graph featuring ‘Kimura’s Distribution’ for mutations, and how it completely falsifies evolution, is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    Further reflection on the implications of genetic entropy are discussed here:

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video (Notes in description)
    http://vimeo.com/35088933

    JLAfan2001, you mentioned following the evidence where it leads, those are wise words indeed. Why don’t you please follow your own advise??

  100. Just up at ENV:

    ENCODE Results Separate Science Advocates from Propagandists
    David Klinghoffer September 20, 2012
    http://www.evolutionnews.org/2.....64491.html

  101. Further Thoughts on the ENCODE/Junk DNA Debates – Jame Shapiro – Sept. 18, 2012
    Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of “DNA Elements” rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries.
    Diogenes and like-minded people argue that we knew enough in the 1970s to understand the basic principles of genome organization. They do not accept that the flood of new information from genome sequencing and the kind of methodologies exemplified by the ENCODE project will fundamentally alter our genetic concepts. While they are certainly entitled to these opinions, I think we have to recognize that they are nothing more than that — simply opinions that fly in the face of scientific history.
    http://www.huffingtonpost.com/.....93984.html

  102. BA77 and Joe

    My comment was not asking where genes come from or how Darwinism can’t explain the lack of functional genes. I will phrase it in some questions.

    Did ID predict that junk DNA would be a myth?
    Did ENCODE find junk DNA or non-functioning pseudogenes?
    If so, does this undermine the ID argument?

    All I want to know is are there or are there not any junk DNA in the genome?

  103. My comment was not asking where genes come from or how Darwinism can’t explain the lack of functional genes.,,,

    And you are ignoring this glaring, and profound, deficiency of evidence because why exactly????

    i.e. Why should I care one iota what you think about the evidence when you are basically reading tea leaves and calling it science whilst you are completely ignoring the elephant standing on your chest in the middle of your living room!?!

  104. Over at ENV:

    “The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.”

    It seems that even IDists are starting to reel in the reigns on their celebration of no junk DNA. If Jonathan M. is becoming cautious about 80%, why shouldn’t everyone else. Anything more to add, BA77? Keep in mind that this thread is about the issue of junk DNA not origins of life or CSI.

    I think the 80% will lower quite a bit in the future becoming a hard blow to ID.

  105. “I think the 80% will lower quite a bit in the future becoming a hard blow to ID.”

    Nothing prejudiced there! i.e. Why should I care one iota what you think about the evidence when you are basically reading tea leaves and calling it science whilst you are completely ignoring the elephant standing on your chest in the middle of your living room!?!

  106. as to which way the functionality percentage will go, well I’ll let the evidence speak for itself:

    Why All the Fuss Over Some Junk? – Jonathan Wells – September 25, 2012
    Excerpt: the four bloggers listed above are doing everything they can to discredit the ENCODE project’s estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is “pervasively transcribed,” suggesting functionality. The 2012 results, based on 1,640 datasets, documented that “the vast majority (80.4%) of the human genome” is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body.
    Clearly, we have a lot more to learn about our genome — but not if we start by assuming that most of it is junk.

    http://www.evolutionnews.org/2.....64721.html

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”"
    http://www.evolutionnews.org/2.....64001.html

  107. Why can’t you just admit ID and Jonathan Wells were wrong on this? It also seems there is bias on the other side because it very well could be junk which I suspect will be.

  108. “Why can’t you just admit ID and Jonathan Wells were wrong on this?”

    They weren’t! On the other hand Why can’t you admit to the overwhelmingly obvious fact that DNA, and the coding in DNA, is unfathomably complex, being several orders of magnitude more complex than anything our best computer engineers or computer programmers have ever built or programmed??? Or is going through life with you head stuck in the sand how you prefer to do science?

  109. notes only 4 grams of DNA can store the entire information content of the entire world:

    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

    Harvard cracks DNA storage, crams 700 terabytes of data into a single gram – Sebastian Anthony – August 17, 2012
    Excerpt: A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.,,, Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored.
    http://www.extremetech.com/ext.....ingle-gram

    DNA Stores Data More Efficiently than Anything We’ve Created – Casey Luskin – August 29, 2012
    Excerpt: Nothing made by humans can approach these kind of specs. Who would have thought that DNA can store data more efficiently than anything we’ve created. But DNA wasn’t designed — right?
    http://www.evolutionnews.org/2.....63701.html

    Harvard Scientists Write the Book on Intelligent Design—in DNA – Dr. Fazale Rana – September 10, 2012
    Excerpt: One gram of DNA can hold up to 455 exabytes (one exabyte equals 10^18 bytes). In comparison, a CD-ROM holds about 700 million (7 x 10^8) bytes of data. (One gram of DNA holds the equivalent amount of data as 600 billion CD-ROMs. Assuming a typical book requires 1 megabyte of data-storage capacity, then one gram of DNA could harbor 455 trillion books.)
    http://www.reasons.org/article.....ign-in-dna

    Biochemical Turing Machines “Reboot” the Watchmaker Argument – Fazale Rana – July 2012
    Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.
    http://stevebrownetc.com/2012/.....-argument/

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    DNA – Replication, Wrapping & Mitosis – video
    http://vimeo.com/33882804

    Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area:

    Welcome to CoSBi – (Computational and Systems Biology)
    Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. (of note: the preceding header, which was originally on the main page of the website ,is now missing)

    etc.. etc.. etc..

  110. I never said that I didn’t agree with any of things you mentioned. In fact, I do agree with it very much. I think any biologist out there would too. What I’m trying to find out is if all that complexity came to be after years of trial and error. Perhaps the junk DNA is proof of that.

  111. ‘What I’m trying to find out is if all that complexity came to be after years of trial and error.’

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2.....20071.html

    Where’s the substantiating evidence for neo-Darwinism?
    https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

  112. This raises an interesting question that even Behe brought up. Why would the Intelligent Designer (and we all know who that is even if ID wants to pretend they don’t) design malaria, HIV and E.coli? That would imply that the Intelligent GoDesinger was not all good.

  113. So do you want to argue theology or do you want to focus on the fact that you are empirically bankrupt for your preferred answer of Darwinism? Either way you lose!

    i.e. the argument from evil presupposes the existence of a absolute standard of good of the way things ought to be but are not. Exactly where do you derive this standard of good from to enable you to judge by if it did not in fact exist in reality?

    Stephen Meyer – Morality Presupposes Theism (1 of 4) – video
    http://www.youtube.com/watch?v=uSpdh1b0X_M

    Cruel Logic – video
    Description; A brilliant serial killer videotapes his debates with college faculty victims. The topic of his debate with his victim: His moral right to kill them.
    http://www.youtube.com/watch?v=4qd1LPRJLnI

    Albert Einstein and his answer to his Professor ! – video
    http://www.youtube.com/watch?v=fLOZDpE1rkA

  114. I admit that I went off in a different direction but it wasn’t because of proof or lack of it. I just thought that would be an interesting question to pose. All the videos that you posted were about moral evil. I was referring to natural evil. Malaria, HIV and E.coli don’t have moral codes but kill humanity because they were seemingly designed to. Why? Why does the design of nature require so much death and survival? This seems to be poor design right from the get go but in falls in line with the idea of natural selection.

  115. First you apologize for making a theological argument and state “it wasn’t because of proof or lack of it”, then instead of presenting any proof that Darwinian processes can produce functional information you go ahead and dig a deeper theological hole by bringing ‘natural’ evil into it, i.e. death. So I ask you again to you “do you want to argue theology or do you want to focus on the fact that you are empirically bankrupt for your preferred answer of Darwinism? Either way you lose!”

    The following book has a brief Biblical exegesis the fall of man affecting all of creation even to the point of death preceding the fall:

    The End Of Christianity – Finding a Good God in an Evil World -
    William Dembski PhD. Theology and Mathematics
    http://www.designinference.com.....of_xty.pdf

    i.e. God’s view of time is simply not linear, sequential, temporal, as we view time, but is eternal, timeless, knowing the beginning from the end,, thus explaining why when we sinned against almighty God it affected all of creation even in a future effecting the past manner. If you hold that such is not possible, well advances in quantum mechanics begs to differ with what you would prefer to believe

    Notes:

    Quantum physics mimics spooky action into the past – April 23, 2012
    Excerpt: The authors experimentally realized a “Gedankenexperiment” called “delayed-choice entanglement swapping”, formulated by Asher Peres in the year 2000. Two pairs of entangled photons are produced, and one photon from each pair is sent to a party called Victor. Of the two remaining photons, one photon is sent to the party Alice and one is sent to the party Bob. Victor can now choose between two kinds of measurements. If he decides to measure his two photons in a way such that they are forced to be in an entangled state, then also Alice’s and Bob’s photon pair becomes entangled. If Victor chooses to measure his particles individually, Alice’s and Bob’s photon pair ends up in a separable state. Modern quantum optics technology allowed the team to delay Victor’s choice and measurement with respect to the measurements which Alice and Bob perform on their photons. “We found that whether Alice’s and Bob’s photons are entangled and show quantum correlations or are separable and show classical correlations can be decided after they have been measured”, explains Xiao-song Ma, lead author of the study.
    According to the famous words of Albert Einstein, the effects of quantum entanglement appear as “spooky action at a distance”. The recent experiment has gone one remarkable step further. “Within a naïve classical world view, quantum mechanics can even mimic an influence of future actions on past events”, says Anton Zeilinger.
    http://phys.org/news/2012-04-q.....ction.html

    “Thus one decides the photon shall have come by one route or by both routes after it has already done its travel”
    John A. Wheeler

    Alain Aspect speaks on John Wheeler’s Delayed Choice Experiment – video
    http://vimeo.com/38508798

    Time travel theory avoids grandfather paradox – July 2010
    Excerpt: “In the new paper, the scientists explore a particular version of CTCs based on combining quantum teleportation with post-selection, resulting in a theory of post-selected CTCs (P-CTCs). ,,,The formalism of P-CTCs shows that such quantum time travel can be thought of as a kind of quantum tunneling backwards in time, which can take place even in the absence of a classical path from future to past,,, “P-CTCs might also allow time travel in spacetimes without general-relativistic closed timelike curves,” they conclude. “If nature somehow provides the nonlinear dynamics afforded by final-state projection, then it is possible for particles (and, in principle, people) to tunnel from the future to the past.”
    http://www.physorg.com/news198948917.html

    Physicists describe method to observe timelike entanglement – January 2011
    Excerpt: In “ordinary” quantum entanglement, two particles possess properties that are inherently linked with each other, even though the particles may be spatially separated by a large distance. Now, physicists S. Jay Olson and Timothy C. Ralph from the University of Queensland have shown that it’s possible to create entanglement between regions of spacetime that are separated in time but not in space, and then to convert the timelike entanglement into normal spacelike entanglement. They also discuss the possibility of using this timelike entanglement from the quantum vacuum for a process they call “teleportation in time.” “To me, the exciting aspect of this result (that entanglement exists between the future and past) is that it is quite a general property of nature and opens the door to new creativity, since we know that entanglement can be viewed as a resource for quantum technology,” Olson told PhysOrg.com.
    http://www.physorg.com/news/20.....ement.html

    “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass.”
    Richard Swenson – More Than Meets The Eye, Chpt. 12

    ‘In the ‘spirit world,,, instantly, there was no sense of time. See, everything on earth is related to time. You got up this morning, you are going to go to bed tonight. Something is new, it will get old. Something is born, it’s going to die. Everything on the physical plane is relative to time, but everything in the spiritual plane is relative to eternity. Instantly I was in total consciousness and awareness of eternity, and you and I as we live in this earth cannot even comprehend it, because everything that we have here is filled within the veil of the temporal life. In the spirit life that is more real than anything else and it is awesome. Eternity as a concept is awesome. There is no such thing as time. I knew that whatever happened was going to go on and on.’
    Mickey Robinson – Near Death Experience testimony

    It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as a ‘hypothetical’ observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video was made by two Australian University Physics Professors with a supercomputer.)

    Approaching The Speed Of Light – Optical Effects – video
    http://www.metacafe.com/watch/5733303/

    Verse and music:

    1 Corinthians 15:55-57
    “Where, O death, is your victory? Where, O death, is your sting?” The sting of death is sin, and the power of sin is the law. But thanks be to God! He gives us the victory through our Lord Jesus Christ.

    Empty (Empty Cross Empty Tomb) with Dan Haseltine Matt Hammitt (Music Inspired by The Story)
    http://www.godtube.com/watch/?v=F22MCCNU

    The Center Of The Universe Is Life – General Relativity, Quantum Mechanics, Entropy and The Shroud Of Turin – video
    http://vimeo.com/34084462

    Condensed notes on The Authenticity of the Shroud of Turin
    https://docs.google.com/document/d/15IGs-5nupAmTdE5V-_uPjz25ViXbQKi9-TyhnLpaC9U/edit

  116. Are you a YEC or OEC? If you are an OEC then natural evil was already in the world prior to the fall. Man’s sin didn’t bring it in. If you think that’s the case, please provide some citations that test the effects of sin on tornadoes, floods, disease etc.

    Also, I think I hijacked this thread which I fully admit. I would like to continue this discussion but off thread if you are interested. Despite my tone, I am seeking answers to these questions but I don’t find pat answers satisfying. I’m not saying that’s what you’re giving but that’s what I’m finding.

  117. So instead of focusing on the science, and the complete bankruptcy of Darwinism to explain the complexity we find in life, you decide to go full bore into a theological argument??? Oh well, so much for you being objective,, you ask,,

    “Are you a YEC or OEC?”

    I hold closely to what Dr. Dembski has laid out here in this book,,,

    The End Of Christianity – Finding a Good God in an Evil World
    William Dembski PhD. Theology and Mathematics
    http://www.designinference.com.....of_xty.pdf

    you then state:

    “If you are an OEC then natural evil was already in the world prior to the fall.”

    That’s not the proper Theological view when taking into account, in the fall of man, that we sinned against almighty God who is timeless, eternal, outside of time spoace matter and energy, knowing the beginning from the end,, etc… etc…, i.e. our sequential, temporal, frame of reference is completely useless as a frame of reference for time in dealing with the issue of our complete separation from God! If you still hold that such ‘retrograde action in time’ for death entering the world is impossible, well I’ve already cited empirical proof from quantum mechanics, as well as noted the ‘eternity’ of special relativity, that shows such retrograde action is not impossible as far as physics is concerned, and that there is, in fact, a higher ‘eternal’ dimension that really is above this 3-D material dimension, just as theism has always resolutely held!

    You then go full bore into theological argumentation and state:

    ‘provide some citations that test the effects of sin on tornadoes, floods, disease etc.’

    Incredible Parallels Between Israel and the U.S. Evacuations – Bill Koenig (the precise timing of the Katrina hurricane and America’s actions against Israel)
    http://www.watch.org/showart.p.....38;mcat=24

    Jonathan Cahn, author of The Harbinger, shares nine omens that spell judgment for America on this edition of Jewish Voice with Jonathan Bernis. – video
    http://www.youtube.com/watch?v=H13DPkb6kjQ

    you then state:

    ‘Also, I think I hijacked this thread which I fully admit. I would like to continue this discussion but off thread if you are interested.’

    I’m not.

    Despite my tone, I am seeking answers to these questions but I don’t find pat answers satisfying. I’m not saying that’s what you’re giving but that’s what I’m finding.

    I don’t believe you.

  118. To bring it back to the science, ENV has another article up highlighting the desperate situation Darwinists are in with this entire junk DNA dogma of theirs:

    Why the Case for Junk DNA 2.0 Still Fails – September 27, 2012
    Excerpt: if anything, ENCODE uses too narrow a definition of function — by limiting it to “biochemical” function. For this reason, the functionality reported by ENCODE surely underestimates the total.,,,
    The Darwinist bloggers are defending a ragged flag on a rapidly shrinking ice floe, insisting that the vast ocean around them is nothing to worry about. But if trends continue, as ENCODE gives us excellent reason to expect they will, then before long those defenders of junk DNA will be planting their flag in open water.
    http://www.evolutionnews.org/2.....64771.html

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