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DNA has hidden code for making new gene pieces

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From Jernej Ule at RealClearScience, where he explains his team’s findings, then reflects,

We’ve known for decades that evolution needs to tinker with genetic elements so they can accumulate mutations while minimising disruption to the fitness of a species. Our most recent research, published in the journal eLife, looked at over 6,000 Alu elements to show that our code does exactly this.

The two forces are tightly coupled in evolution, so that as soon as any mutations make the ying stronger, the yang catches up and stops them. This allows the Alu elements to remain in a harmless state in our DNA over long evolutionary periods, during which they accumulate a lot of change via mutations. As a result, they become less harmful and gradually start escaping the repressive force. Eventually, some of them take on an important function and became indispensable pieces of human genes.

To put it another way, the balanced forces buy the time needed for mutations to make beneficial changes, rather than disruptive ones, to a species. And this is why evolution proceeds in such small steps – it only works if the two forces remain balanced by complementary mutations, which takes time. Eventually, important new molecular functions can emerge from randomness. More.

Evolution, it seems, is an intelligent being. It can “tinker” like one busy little dwarf (illus). And “buy the time” like a financier. And, poof! “Eventually, important new molecular functions can emerge from randomness.”

Of course! The same way, when a jar falls and breaks, the shards arrange themselves in a neat pattern on the floor, then put themselves back together again. As we all know.

The practical problem, one that is becoming more evident with each succeeding wave of science thinkpieces, is this: Such a sequence could be random only in a universe where it is meaningless to talk about humans’ ability to perceive reality. And that is the universe naturalists now seek to impose on science, to its ruin.

See also: In search of a road to reality

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13 Replies to “DNA has hidden code for making new gene pieces

  1. 1
    Tom Robbins says:

    One problem – nothing supports the notion that evolution occurs in small tiny steps, not the fossil record or genetic research – I fully believe DNA has this capability, but this makes randomness even MORE silly to talk about, especially with organic matter.. it somehow learned through randomness to make the hidden CODE, to make new CODE?? It’s like the traditional evolutionists trying to say evolution evolved the ability to create epigenetics – it’s lunacy.

  2. 2
    bornagain77 says:

    as to:

    “Eventually, important new molecular functions can emerge from randomness.”

    Actually, no it can’t. Despite the authors ‘ying/yang’ just so story, the authors, nor any other Darwinists, have yet to empirically demonstrate the origin of a single functional protein by unguided Darwinian processes.

    Behe examined laboratory evolution experiments of microbes going back four decades and found no new functional proteins generated by Darwinian processes:

    “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.
    http://behe.uncommondescent.co.....evolution/

    Of note to the preceding paper, all gain of function mutations that Behe found were first preceded by a deletion of a gene by the experimenters, and then the compensation that the programming of the cell produced for the missing gene was counted as a gain of function. Slightly misleading for Behe and the experimenters to call them ‘gain of function’ mutations when in fact they are more properly thought of as ‘replacement of function’ mutations. And again, no new functional proteins were produced that were not already present before.

    And in Lenski’s Long Term Evolution Experiment, 58,000 generations and counting, which is equivalent to somewhere around 1,000,000 years of human evolution, we find, again, that no new functional proteins originated:

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

    Moreover, the citrate hype surrounding Lenski’s bacteria was found to be a repeatable, i.e. non-Darwinian, adaptation

    Richard Lenski and Citrate Hype — Now Deflated – Michael Behe – May 12, 2016
    Excerpt: In 2008 Lenski’s group reported that after more than 15 years and 30,000 generations of growth one of the E. coli cell lines suddenly developed the ability to consume citrate,,,
    the authors argued it might be pretty important.,,,
    They also remarked that,,, perhaps the mutation marked the beginning of the evolution of a brand new species.,,
    One scientist who thought the results were seriously overblown was Scott Minnich, professor of microbiology at the University of Idaho ,,,
    So Minnich’s lab re-did the work under conditions he thought would be more effective. The bottom line is that they were able to repeatedly isolate the same mutants Lenski’s lab did as easily as falling off a log — within weeks, not decades.,,,
    Richard Lenski was not pleased.,,,
    http://www.evolutionnews.org/2.....02839.html

    The reason why no one has been able to empirically demonstrate the origin of new functional proteins by unguided Darwinian processes is because functional proteins are now found, by experiment, to be exceedingly rare:

    Stephen Meyer (and Doug Axe) Critique Richard Dawkins’s “Mount Improbable” Illustration – video
    https://www.youtube.com/watch?v=7rgainpMXa8

    Conversations with Douglas Axe: What is the Search Problem? (10^40 cells that have existed on earth, 1 in 10^74 chance for finding a functional protein fold)
    https://www.youtube.com/watch?list=PLR8eQzfCOiS3-MQT4SEaLNloU5v2poZKf&v=qwFi_2YZa_c

    And when we add the ‘context dependency’ that quantum entanglement requires along the entirety of protein chains, and along the entirety of other molecules, we find that even Axe’s experimentally derived estimate for the rarity of functional proteins is far too generous:

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....Myers_.pdf

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”
    https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

    It is also important to note that their claim that “important new molecular functions can emerge from randomness” is patently false. Randomness cannot even explain how a protein achieves its final folded form. Thus, obviously, much less can randomness explain how the protein originated in the first place.

    To be clear, in order to explain how protein folding is achieved it is necessary to appeal to the world of quantum mechanics and not to the ‘random thermodynamic jostling’ of atoms that Darwinists appeal to in their worldview:

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Today, Luo and Lo say these curves can be easily explained if the process of folding is a quantum affair. By conventional thinking, a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between.
    But Luo and Lo say that if this process were a quantum one, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

    Moreover, even if Darwinists could demonstrate the generation of a single protein by unguided Darwinian processes, that still would not go one micro-meter towards explaining how the approx. billion-trillion protein molecules of the human body know where, how, and when to do the many things they do in their part in keeping the human body alive.
    The following article gives us a small glimpse of the huge ‘elephant in the living room’ problem that is never really honestly addressed by most Internet atheists or by Darwinists in general:

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

  3. 3
    bornagain77 says:

    Simply put, the ‘form’ that any particular organism may take simply is not reducible to any material particulars.
    “Form” is not even, to the consternation of Darwinists, reducible to DNA as Darwinists hold in the ‘central dogma’ of the modern synthesis, i.e. the central dogma is “DNA makes RNA makes protein makes us.”

    These following examples are also particularly good for demonstrating that ‘form’ is simply not reducible to DNA, or to any other material particulars within a organism that Darwinists may appeal to:

    DNA doesn’t even tell teeth what they should look like – April 3, 2014
    Excerpt: A friend writes to mention a mouse experiment where developing tooth buds were moved so that the incisors and the molars were switched. The tooth buds became the tooth appropriate to the switched location, not the original one, in direct contrast to what we would expect from a gene’centric view.
    http://www.uncommondescent.com.....look-like/

    If DNA really rules (morphology), why did THIS happen? – April 2014
    Excerpt: Researchers implanted human embryonic neuronal cells into a mouse embryo. Mouse and human neurons have distinct morphologies (shapes). Because the human neurons feature human DNA, they should be easy to identify.
    Which raises a question: Would the human neurons implanted in developing mouse brain have a mouse or a human morphology?
    Well, the answer is, the human neurons had a mouse morphology. They could be distinguished from the mouse ones only by their human genetic markers.
    If DNA really ruled, we would expect a human morphology.
    http://www.uncommondescent.com.....is-happen/

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.”
    leodp – UD blogger

    Here is a podcast by Dr. Jonathan Well discussing the fact that the ‘central dogma’ of Darwinian evolution, “DNA makes RNA makes protein makes us”, is shown to be “incorrect at every step”

    podcast – Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains.
    http://www.discovery.org/multi.....evolution/

    Here is a recently uploaded powerpoint presentation by Dr. Wells, starting around the 15:00 minute mark of the following video, showing that the central dogma of Darwinian evolution, i.e. “DNA makes RNA makes protein makes us”, is incorrect at every step.

    Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video (14:36 minute mark) – January 2017
    https://youtu.be/ASAaANVBoiE?t=876

    Here is the paper and article that Dr. Wells referenced at the end of his talk, as well as a podcast, that speak of spatial information in the cell that simply is not reducible to DNA sequences as is held by Darwinists:

    Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA – Jonathan Wells – 2014
    http://bio-complexity.org/ojs/.....O-C.2014.2

    Life Exponential: DNA Is Only Part of Life’s Multidimensional Design – Jonathan Wells (Fall 2016)
    Excerpt: The Need for Spatial Information (Outside of DNA),,
    Other Carriers of Spatial Information,,,
    The Membrane Code,,,
    Beyond DNA,,,
    “DNA makes RNA makes protein makes us,” which has been called the Central Dogma of molecular biology.,,,
    But the existence of the membrane code shows that the Central Dogma is false.
    http://www.salvomag.com/new/ar.....ential.php

    podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes outside DNA are discussed) – Oct. 2015
    http://www.discovery.org/multi.....more-31141

    Of particular interest, at about the 42:00 minute mark of the “Design Beyond DNA” video, Dr. Wells demonstrated that, during embryological development, information must somehow be added to the developing embryo, ‘from the outside’, by some ‘non-material’ method.

    I suggest that recent findings in ‘quantum biology’ mesh very well with Dr. Wells’s observation that spatial information must, somehow, be ‘added from the outside’ by some non-material method in order to explain what we are seeing in the developing embryo

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://youtu.be/rCs3WXHqOv8?list=PLtAP1KN7ahiYxgYCc-0xiUAhNWjT4q6LD&t=541

    Verse:

    Jeremiah 1:5
    “Before I formed you in the womb I knew you, before you were born I set you apart; I appointed you as a prophet to the nations.”

  4. 4
    Dionisio says:

    is the paper referenced in the OP taken from the 4th or the 5th way of evolution?
    🙂

  5. 5
    Dionisio says:

    maybe that paper is about a new Disney World ride? 🙂

  6. 6
    Dionisio says:

    hey, why not? 🙂

  7. 7
    Dionisio says:

    Disney’s stories were more entertaining

    or at least less boring:

    While Cinderella was working, the mice and birds fixed her dress. They added ribbons and beads that the two stepsisters had thrown away.
    Working together, the animals turned a simple dress into a fabulous gown!
    Cinderella was overjoyed when she saw the dress. Now she could go to the ball!

    [oops, that didn’t work]
    [let’s give it another try]

    Cinderella ran away to the garden to cry. Suddenly, her fairy godmother appeared.
    With a wave of her wand, she turned a pumpkin into an elegant coach. Cinderella could now go to the ball, but her dress was still ruined.
    “Bibbidi-bobbidi-boo!” said the Fairy Godmother[*], waving her wand again. Cinderella was now wearing a beautiful gown and sparkling glass slippers.

    that worked!!!

    (*) actually in the original story referenced in the OP there were two nice fairies known as Ran Mut and Nat Sel (they worked together, along with the mice, the talking cricket, the pumpkins and the whole nine yard). 🙂

  8. 8
    Dionisio says:

    wrong! the talking cricket was not in that evolutionary story. it goes with the wooden Lego(RM) boy (or something like that).
    🙂

  9. 9
    Dionisio says:

    have they gotten to the 7th way of evolution yet?

    🙂

  10. 10
    Dionisio says:

    Here’s a brief reference to the original paper:

    http://www.uncommondescent.com.....ent-624214

  11. 11
    REW says:

    Thanks for posting this. I’ve got the paper and I’m going to read several of the references within. Very interesting topic.

    You guys often post very interesting papers that I wouldnt come across otherwise!

  12. 12
    Silver Asiatic says:

    To put it another way, the balanced forces buy the time needed for mutations to make beneficial changes, rather than disruptive ones, to a species.

    It’s good that evolution plans ahead like that, buying enough time for beneficial mutations to come along in the future, otherwise disruptive ones could come along, and evolution really wouldn’t like that to happen to anyone.

  13. 13
    bornagain77 says:

    Evolution as Carpenter: Scientist Concludes Repetitive Elements “Are an Important Toolkit” – Cornelius Hunter – January 24, 2017
    Excerpt:”Imagine a car factory that uses highly complex machines, such as drill presses and lathes, to build the cars. Now imagine the factory first creating those machines by random chance, so that then the cars could be built by yet more random chance events. This violates the very basics of science. It is just silly.”
    – Cornelus Hunter
    http://www.evolutionnews.org/2.....03452.html

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