Friday, July 12, 2013

Dan Graur Gave a Great Talk This Week

But There is One Glaring Error

Evolution has always had a love-hate relationship with biological junk. When scientists discover something new in biology but don’t understand it, evolutionists—who believe everything in the universe just happened to form by chance—decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Is not our useless and dangerous appendix yet another proof text of Darwinism? Later, when the function is eventually uncovered, evolutionists begrudgingly admit to it while maintaining that its clumsiness still proves evolution. As Richard Dawkins explained, in response to the growing knowledge of how well our “backward” retina works, “it is the principle of the thing that would offend any tidy-minded engineer!” Just because it works doesn’t mean it isn’t junk. And whatever function it luckily has is claimed as an evolutionary achievement—an obvious example of the power of natural selection.

Dan Graur’s entertaining talk on junk DNA, at the Society for Molecular Biology and Evolution this week, reminds us of this dynamic. The human genome must be full of junk DNA, indifferent DNA, garbage DNA and yes, Lazarus DNA (junk DNA that has gained some kind of function).

For our genome is small, low on genes, unoriginal and repetitive. Sure it is bigger than the genome of a bacteria and of the pufferfish, but it’s ten to a hundred times smaller than the lungfish and canopy plant genome.

If recent claims from the ENCODE project, that the human genome is mostly functional, turns out to be true, Graur points out, then the human genome would be the Goldilocks of biology. Not too hot, and not too cold (or in this case, not too small, and not too large). Just right.

ENCODE’s interpretation of the evidence must be wrong. In fact, if ENCODE isn’t wrong, then evolution is.

But ENCODE is wrong, the University of Houston molecular evolution expert concludes. Junk DNA is a known known.

And what is this evidence from ENCODE that our genome is mostly functional? It is that the cell’s copying machine, RNA polymerase, makes copies of it. But so what? Just because it is copied doesn’t mean it isn’t junk. What we have is not functional DNA but an over active, out-of-control copy machine. Apparently evolution’s natural selection didn’t mind this massive waste of cellular energy.

Perhaps so, but there is one glaring error in Graur’s otherwise excellent presentation. I assure you that the truth of evolution is not vulnerable to the status of junk DNA. Contrary to Graur, if ENCODE is right, that most assuredly will not mean that evolution is wrong.

If evolution can sustain the long history of false predictions that it has, then it will not be harmed by one more; namely, that there is more functional DNA than evolutionists would like. What is yet one more just-so story to a narrative so full of them?

Surely it won’t be a problem to explain that “Science has provided yet another surprise as we continue to learn how evolution worked. It turns out that most of the genome performs useful cellular functions, though as evolutionists point out, they are backwards and inefficient.”

Graur may or may not be correct that junk DNA is a known known, but for evolutionists, evolution is definitely a known known.


  1. Among many problems with the Junk DNA scenario, if the genome was mostly junk as Darwinists contend, then it seems rather strange that there would be multiple overlapping DNA repair mechanism dedicated to preventing any 'random' changes from happening to this supposedly 'junk' DNA:

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011
    Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation."

    Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution)

    Proof reading of DNA polymerase (Reduces error rate to 1 in 100 million) - video

    The multiple overlapping repair mechanisms in DNA include:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass

    1. A Look at the Quality Control System in the Protein Factory - JonathanM - March 2012
      Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.

      More DNA Repair Wonders Found - October 2010
      Excerpt: This specialized enzyme may attract other repair enzymes to the site, and “speeds up the process by about 100 times.” The enzyme “uses several rod-like helical structures... to grab hold of DNA.”,,, On another DNA-repair front, today’s Nature described a “protein giant” named BRCA2 that is critically involved in DNA repair, specifically targeting the dangerous double-stranded breaks that can lead to serious health consequences

      Extreme Genome Repair - 20 March 2009
      Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.

      The most spectacular example for DNA repair I have seen thus far is this:

      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.

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

      NP-hard problem – Examples

      Since it is readily apparent that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers (crunching bits) to this monster logistic problem, in a purely ‘material’ fashion, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by the ‘non-local’ quantum information inherent within the cell; And indeed we have evidence that quantum information can accomplish exactly this type of extremely difficult computational problem:

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

      For those who think Quantum computation is not possible within the cell, I remind that 'non-local', beyond space and time, quantum entanglement/information has been found within molecular biology on a massive scale.:

      Quantum Information/Entanglement In DNA - Elisabeth Rieper - short video

      Quantum entanglement between the electron clouds of nucleic acids in DNA - Elisabeth Rieper, Janet Anders and Vlatko Vedral - February 2011

      Supplemental notes:

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

      Looking Beyond Space and Time to Cope With Quantum Theory - (Oct. 28, 2012)
      Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed.
      Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can't stay hidden, or they must have infinite speed.,,,
      The remaining option is to accept that (quantum) influences must be infinitely fast,,,
      "Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them," says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,


      Celtic Woman - The last Rose of Summer

    3. BA, this could be fascinating for you

      An excerpt from the New Yorker written by John McPhee
      "The Mississippi River, with its sand and silt, has created most of Louisiana, and it could not have done so by remaining in one channel. If it had, southern Louisiana would be a long narrow peninsula reaching into the Gulf of Mexico. Southern Louisiana exists in its present form because the Mississippi River has jumped here and there within an arc about two hundred miles wide, like a pianist playing with one hand—frequently and radically changing course, surging over the left or the right bank to go off in utterly new directions. Always it is the river’s purpose to get to the Gulf by the shortest and steepest gradient. As the mouth advances southward and the river lengthens, the gradient declines, the current slows, and sediment builds up the bed. Eventually, it builds up so much that the river spills to one side. Major shifts of that nature have tended to occur roughly once a millennium. The Mississippi’s main channel of three thousand years ago is now the quiet water of Bayou Teche, which mimics the shape of the Mississippi. Along Bayou Teche, on the high ground of ancient natural levees, are Jeanerette, Breaux Bridge, Broussard, Olivier—arcuate strings of Cajun towns. Eight hundred years before the birth of Christ, the channel was captured from the east. It shifted abruptly and flowed in that direction for about a thousand years. In the second century a.d., it was captured again, and taken south, by the now unprepossessing Bayou Lafourche, which, by the year 1000, was losing its hegemony to the river’s present course, through the region that would be known as Plaquemines. By the nineteen-fifties, the Mississippi River had advanced so far past New Orleans and out into the Gulf that it was about to shift again, and its offspring Atchafalaya was ready to receive it. By the route of the Atchafalaya, the distance across the delta plain was a hundred and forty-five miles—well under half the length of the route of the master stream.

  2. Q. What do you get when you read a batspit77 post backwards?

    A. Another batspit77 post!

  3. Just the term, 'natural selection' makes me LOL, since 'selection' is kind of code for 'design' (design in nature). It signifies choice, option, the exercise of volition and implicitly mind. It is the antithesis of randomness.

    There is truly no abyss of folly atheists will not plumb, in order to avoid conceding to themselves, never mind others, pellucidly obvious truths, which would 'distort' their preferred worldview.

    1. Paul, I think they are sincere. In their beliefs. Atleast many of the atheists/ materialists, I think, are. The "science" from which they draw, is so encapsulated in unabated conjecture and rhetoric. These people have been improperly educated in what science really is. It is obvious. They have a "position" to defend. And pop culture (and the "profit an any cost" predominant media that drives pop culture) allows them to "ripsaw" certain perspectives to support the conjecture without allowing any significant pushback from serious important counterpoint. This is dangerous.

      You get confident, arrogant feedback on any point of contention to their point of view. Behind which is the proclomation that, "it is obvious that your criticisms have been demonstrated false" and "science" supports our speculations as being "demonstrated" so that believing differently, makes anyone who does, deserving of ridicule and condescending comment.

      Paul, I have said it before, and will again. Anybody who says they have anywhere near sufficient "scientific" evidence to proclaim that "intelligent input" is not required to explain the origination, and development of currently "observed" phenomena, is FULL OF SHIT! (To simply draw from a pop-culture sanctioned utilization of slang that makes a point)

  4. Here is evidence for 'top down' control of the genome that neo-Darwinists will ignore because of their a-priori philosophical commitment to reductive materialism (i.e. their commitment to atheism):

    Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells - published online May 2013
    Conclusion:,, Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein-coding regions alone. Yet biological information is not limited to the genome. Even at the level of gene expression - transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA.,, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism - the genotype-phenotype mapping = cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life.

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)

    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.

    1. BA, this seems relevant
      Lyrics from one of the greatest albums

      "Long, Lonesome Highway Blues
      (Steve Earle)

      Bound down that long, lonesome highway just as far as I can go
      ‘Til I outrun your memory
      I can't go home ‘cause I can't face another day alone
      Now that you're gone this ain't no place for me
      I want to start all over new
      But I can't lose these lonesome highway blues
      Down that long, lonesome highway just as far as I can go
      ‘Til I outrun your memory

      Bound down that long, lonesome highway just as fast as I can fly
      Just wanna go to someplace you won't be
      I'm movin' on to a new place and hold my head up high
      Where no one knows what you done to me
      A thousand miles between us now
      And still some how
      These blues'll track me down
      Down that long, lonesome highway just as far as I can go
      ‘Til I outrun your memory

      I'm bound down that long lonesome highway ‘cause it's the only place I know
      Where there ain't no clouds hangin' over me
      Leave me alone ‘cause it's a long way no matter where I go
      Nothin' but blues as far as I can see
      I wish I had you back again
      But I know I can't
      So here I go again
      Down that long, lonesome highway just as far as I can go
      ‘Til I outrun your memory

      (Steve Earle)

      I am just a pilgrim on this road, boys
      This ain't never been my home
      Sometimes the road was rocky ‘long the way, boys
      But I was never travelin' alone

      We'll meet again on some bright highway
      Songs to sing and tales to tell
      But I am just a pilgrim on this road, boys
      Until I see you fare thee well

      Ain't no need to cry for me, boys
      Somewhere down the road you'll understand
      ‘Cause I expect to touch his hand, boys
      Put a word in for you if I can

  5. Dna fractionate time with a fractal. A fractal is burly,gnarly and surly like human body. Time is relative so evolution doesn't have to happen in order or life too hard to plan. Darwinism has to happen in order so require junk dna to support it.

  6. An empty that is nothing is solid. That how you create universe out of nothing. A black hole is an anarchy computer designed to make you social and intelligent. Water is liberal anarchy that increase energy and conservative anarchy that decrease energy. I made creative letter with anarchy on tv and made circle with black hole called an anarchy tail. That why mermaids have tails. My wife is aquamarine movie.

    The texture of tranquility printed first life form in abiogenisis and molecular friction aggravation upset that. The texture of mellow printed life in the womb and molecular friction tribulation upset that. Apes are texture of pleasant and molecular friction agitation upset that. Authority think a happy person is a healthy person and treat mentally I'll like apes for agitation to treat violence. Aggravation is what makes mentally I'll violent. Aggravation is bucking horse that why I'm horseman of the apocalypse.

    Curiosity is what defines animals and a skull is an inclination.
    Neanderthal is " I am sure I am".
    Cromagnum is " you will a be"
    Homosapien is " will I am"
    Missing link is " man I can"
    The future of mankind is " good will"
    Artists make adjective. Scientists make nouns. Evolution is a whole sentence. Natural selection doesn't happen because the only thing being selected is the character flaw in evil that is " integrety more important than life".

  7. Waves are conservation of anarchy. Theory of relator is anarchy and violence of energy. With theory of anarchy waves can evolve and you can make love on the guitar instead of crying. That is purpose of new song churches. Good gene,bad gene and nuetral gene don't make anarchy intelligent for evolution. A black hole is an anarchy computer. String theory is anarchy poems for imagination so I mapped black hole with anarchy poems and made theory of relator but its only in surveillance and secret service is using it to fight organized crime because an anarchy computer was meant for police not scientists by gods intelligent design.

  8. You live in a hell of beauty. Beauty is a relativity detector that primitive abiogenisis microbe. That why einstein write poems about capitolism being beautiful but stupid. Light is beautiful so its relative. Fire is schizophrenia. A rocket tune schizophrenia with a composition. A rock band is a schizophrenic computer. So when you dance to music your dancing in fire. Hell is sometimes superior to heaven. Heaven is glass stars in van gogh painting " starry night" . I make aggravation hurricanes like van gogh paintings,solar flares,killer bees and violins. The physics of violins and solar flares are the same. That why beatles song elanor rigby is crying star to cure psoriasis because supernatural is diseased and that why we are cursed. That what movie " sunshine" is about. I am flying spaggetti monster because I make aggravation hurricanes like van gogh paintings. Demon in sunshine movie is jesus that cursed. We are all cursed and must share the sacrifice for evolution to work. The purpose of hell is to make paranoia beautiful not to punish sins. That very nice gift from god.

  9. This proof of end of time. Jesus made time resolute. I made time distinct. Satan made time definition.
    Resolute is a gas
    Distinct is a liquid
    Definition is a solid
    Time is marching now and clocks starting to tick with quality.
    Decay is a function of time and jesus will fix that now we made it possible.
    Integrety is apparant and don't require proof.

  10. Stellar black holes clash. Supermassive black holes at center of galaxies clang. Clash and clang are two forms of violence that god wants to evolve. Artistic qualities of light is weight and temperature. Weight is clang. Temperature is clash. I believe that make light relative but I haven't resolved it much because I'm only an artist with suspicions.