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Junk DNA hires a PR firm

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Fights back.

Well, that seems to be what’s happening. Further to: New York Times science writer defends junk DNA (Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism), one of the conundrums on which the junk DNA folk rely heavily is the “onion test” (why does the onion have such a large genome?). Without waiting to answer the question, the junk DNA folk assume that that’s because most of it is junk.

But let’s face it, when even Francis Collins, the original Christian Nobelist for Darwin, is abandoning ship, they really need to double down on that junk.

From Evolution News & Views:

What’s so striking about Zimmer’s current piece is his explicit worry that — should “junk” DNA turn out to be functional — the “creationists” (as he calls the baddies) would be vindicated. At least twice in this long article, Zimmer raises the alarm that genomes had BETTER be junky, OR…the bad guys will win. It’s the same anxiety driving Dan Graur and Lawrence Moran into their fits of rage about ENCODE.

Hence in a not-so-subtle way, project ENCODE researchers are put on notice that, should they continue looking for function in non-coding DNA, they will be traitors to evolution and science.

Doubtless, the ENCODE guys have already begun to stammer and splutter. That’s what tends to happen when Darwin’s boys arrive (except here). For ENCODE, when they could afford to be open, see, for example:

Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Junk DNA’s defender doesn’t “do” politeness (No, we bet not.)

and

At least Forbes.com’s John Farrell, while trashing Jonathan Wells’ The Myth of Junk DNA, doesn’t threaten to actually read the book, the way some do.

For free highlights of the junk DNA uproar, see:

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

Hey, by the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening.

Plus, pass the chocs, will you?

File:A small cup of coffee.JPG Anyone else for the myth of junk DNA? Richard Dawkins, for one (Reliable Source Central 😉 )

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121 Replies to “Junk DNA hires a PR firm

  1. 1
    Piotr says:

    Sigh… News, why don’t you just present your back-of-envelope calculation of what fraction of the human genome is known to be functional in any way (having regulatory functions, producing useful RNAs, etc.)? Can you make the total more than 10%? Even with generous allowance for functional elements not discovered as yet, something like 20% would probably be a gross overestimate.

  2. 2
    Joe says:

    Piotr, your position can’t account for any genomes. Perhaps you should focus on that.

  3. 3
    harry says:

    A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.
    — Max Planck

    There is truth in Planck’s observation, but more to the point is the fact that the Truth has its own power and is irrepressible; it is an anvil that has worn out many hammers; it is Someone, not something.

    The discoveries of modern science have made words of St. Paul ring truer than ever:

    For what can be known about God is perfectly plain to them since God himself has made it plain. Ever since God created the world his everlasting power and deity – however invisible – have been there for the mind to see in the things he has made. That is why such people are without excuse: they knew God and yet refused to honour him as God or to thank him; instead, they made nonsense out of logic and their empty minds were darkened.
    — Rom 1:19-21

    Those who deny the Truth have been reduced to arguing that the Universe popped into existence out of nothingness without a cause; reduced to arguing that the digital-information-based nanotechnology of life, the functional complexity of which we now know to be light years beyond anything modern science knows how to build from scratch, is a mindless accident; reduced to arguing that there are countless other universes that are all tuned differently, so one of them had to end up like ours, fine-tuned for life — an incredibly lame response to the overwhelming evidence of the fine-tuning of the Universe for life, intended to make the notion that that fine-tuning was a mindless accident seem more plausible.

    A huge, irrational, blind faith is required to embrace modern atheism. Only a relatively small, and very reasonable faith is required to believe in one God instead of countless other universes; to believe ultra-sophisticated, digital-information-based nanotechnology does not emerge mindlessly and accidentally; and to believe things don’t pop into existence, uncaused, out of nothingness.

  4. 4
    Diogenes says:

    Joe, your side lost the argument on Junk DNA so now you seek to change the subject to “where did DNA come from?”– which, besides being irrelevant to the subject at hand, and a calculated Gish Gallop, is a question your side cannot answer. “God made genomes by sorcery” is not supported by evidence; it can’t be tested or falsified unless you assume you know the purposes of God in creating genomes. Which means the ID answer is not a scientific answer as it is not supported by evidence; it is a religious answer.

    To recap: some ENCODE scientists said IN A PRESS RELEASE in 2013 (NOT in a peer reviewed scientific article) that Junk DNA had been disproven; many other ENCODE scientists said that ENCODE could not disprove Junk DNA because ENCODE did NO functional assays OOPS. Those ENCODE scientists who said IN A PRESS RELEASE that junk DNA had been disproven, walked back their claims in a peer reviewed article (Kellis et all. 2014) and now claim they never said what they said in a 2013 PRESS RELEASE. The ENCODE scientists who said ENCODE never disproved Junk DNA because there’s positive evidence there’s a lot of it, never changed their story.

    But tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Is it not true that to attempt to answer this question, you must know the purposes of God? And if your hypothesis depends on your beliefs about God’s purposes, doesn’t that make ID dependent on religion?

  5. 5
    Joe says:

    Diogenes, Your side cannot explain the existence of DNA. Your position doesn’t have anything that can be tested. It is useless and barren. You don’t even have a mechanism capable of getting beyond populations of prokaryotes and that is given starting populations of prokaryotes.

    Also the junk DNA was never my argument and you need to define “junk” in a context-specific and meaningful way.

  6. 6
    Diogenes says:

    And Joe proves my point. Gish Gallop, change the subject to a different question no IDer can answer anyway. “God made genomes by sorcery” is not a scientific answer. You have no answer to EITHER question, not the topic of this thread NOR the subject you tried to change to. You change the subject consistently, every single time, because you lost the argument over Junk DNA. Gish gallop + evasion = you lose both arguments, the old one and the new one.

    I repeat my question that you evaded, and dare not answer:

    Tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Is it not true that to attempt to answer this question, you must know the purposes of God? And if your hypothesis depends on your beliefs about God’s purposes, doesn’t that make ID dependent on religion?

  7. 7
    wd400 says:

    Leaving this strange fantasy of “Darwin’s boys” strong-arming the scientific community to lie about their findings to one side for now.

    Can anyone explain why they are so sure most of the genome is not junk? Or answer Diogenes questions? Or mine from the other thread on this topic (if genomes are nearly 100% functional why aren’t mutations mutations devastating to us)

  8. 8
    Bob O'H says:

    What’s the ID explanation for the size of the onion genome? I mean beyond “it must all be functional”. Why would an onion be so much more functional than, say, a human, or why would wheat be more functional than rice?

  9. 9
    bornagain77 says:

    Onion Exposé: Carl Zimmer on Why “Junk DNA” Had Better Be Real – March 6, 2015
    Excerpt: For another take on the cherished onion, see the relevant section in Jonathan Wells’s book, The Myth of Junk DNA, and Jonathan M.’s article at ENV, “Why the ‘Onion Test’ Fails as an Argument for ‘Junk DNA.'” Casey Luskin took Carl’s measure here, “Already Outdated: Will Carl Zimmer Update His New Evolution Textbook on Junk DNA?”
    http://www.evolutionnews.org/2.....94161.html
    of note: the papers are linked on the site.

  10. 10
    Joe says:

    Diogenes:

    Tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish,

    Your position can’t explain any of that. And ID doesn’t have anything to do with God.

    Your desperation, while amusing, is not an argument.

  11. 11
    Diogenes says:

    So the answer would be no, as BA77 proves by linking to ancient debunked crap from IDers, no, no IDer can explain why the onion genome is 5x the size of the human genome… or why the VARIATION in genome sizes within the genus Allium is several times larger than the whole human genome.

    Why is it that within some genera of frogs, where all the species look equally complex, some species have far less DNA than humans, while other species in the same genus, distinguishable only by experts, have far more DNA than humans? Why?

    And excluding frogs, all amphibians that have been studied, including caecilians that have no legs nor eyes, have much, much more DNA than humans. Why?

    Nor can any of you answer Wd400’s frequently repeated question: if every baby born has ~ 100 more mutations than its parents, ~200 more than its grandparents etc. etc., and if all that DNA is functional, and mutations are “catastrophic” as IDcreationists always say, why don’t all babies die?

    And nobody tried to answer my question:

    Tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Is it not true that to attempt to answer this question, you must know the purposes of God? And if your hypothesis depends on your beliefs about God’s purposes, doesn’t that make ID dependent on religion?

  12. 12
    Joe says:

    Diogenes- You don’t have an answer either. So perhaps you should just shut up.

  13. 13
    wd400 says:

    Evolutionary biology actually has some pretty good answers about the evolution of genome size, Joe. You should read about them

  14. 14
    Diogenes says:

    Joe Security Clearance says:

    Your position can’t explain any of that. And ID doesn’t have anything to do with God.

    Really? ID doesn’t have anything to do with God? But Phillip Johnson, who founded ID as a political movement and the DI as a think tank, said Intelligent Design was simply ”the reality of God.” Why do you not criticize him for saying that?

    If Phillip Johnson said that at UD, would you ban him, the way UD has banned evolutionists for saying the same thing– by quoting Johnson?

    William Dembski didn’t say that ID has nothing to do with God. He said Intelligent Design starts with the Gospel of John, and that ID was the bridge between science and theology.

    ID doesn’t have anything to do with God? That’s not what the Wedge Document says. It’s not what the DI says to millionaire prospective donors when the DI needs money. Maybe ID has nothing to do with God when you have money, and is “the reality of God” when you don’t?

    I repeat my question: How do you know how much junk DNA there can be or can’t be, unless you assume you know the purposes of God? You IDers predicted NO Junk DNA because the God you believe in wouldn’t do it that way. You were wrong. So either your God doesn’t exist, or else your beliefs about him were wrong.

  15. 15
    bornagain77 says:

    Actually, far from debunking the ‘crap from IDers’ refuting the infamous Onion test, the fact of the matter is that the case against neo-Darwinism’s insistence on widespread junk DNA has gotten far worse for neo-Darwinists. For instance, we now know that the genome, much contrary to neo-Darwinian thought, is an ‘organ of the cell, not its dictator’:

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences
    http://musicoflife.co.uk/

    Disagree that the genome is merely a organ of the cell and not its dictator? Well, then you have to deal with the fact that ‘the spatial organization of genomes is tissue-specific’,,,

    Tissue-specific spatial organization of genomes – 2004
    Excerpt: Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence.
    Conclusion: Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues.
    http://genomebiology.com/content/5/7/R44

    “Three-Dimensional Connections Across the Genome“ Keith Dunaway – ENCODE 2012
    Excerpt: These analyses portray a complex landscape of long-range gene-element connectivity across ranges of hundreds of kb to several Mb, including interactions among unrelated genes (Supplementary Figure Y1). Furthermore, in the 5C results, 50-60% of long-range interactions occurred in only one of the four cell lines, indicative of a high degree of tissue specificity for gene-element connectivity
    http://www.nature.com/encode/t.....the-genome

    Further evidence that the genome is subservient to the overall needs of the cell and organism that it is in is found in this recent article by Dr. Jonathan Wells on ‘genetic mosaicism’:

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,,
    The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism.
    In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,,
    ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view.
    I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.
    http://www.evolutionnews.org/2.....93851.html

    Further evidence that DNA is subservient to needs of the entire organism is found here:

    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

    Timelapse Video Reveals Electric Face in Embryonic Tadpole – July 2011
    Excerpt: “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo. We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”
    http://www.sciencespacerobots......ole-718111

    podcast – Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 – Bioelectric code
    http://intelligentdesign.podom.....5_52-07_00

    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.
    http://www.evolutionnews.org/2.....54071.html

    Body Plans Are Not Mapped-Out by the DNA – Jonathan Wells – video
    http://www.youtube.com/watch?v=meR8Hk5q_EM

    etc.. etc..

  16. 16
    CHartsil says:

    So still no thoughts of your own to contribute huh BA77?

    How’s that SITC channel doing?

  17. 17
    PaV says:

    Piotr:

    A recent study is out where they show that the Alu portions of the genome—what you might call “classic” “junk-DNA”—is actually involved in the cell and organism’s immune system response.

    Alu portions account, they say in the study, for 10% of the genome. Isn’t this a double-whammy for you?

  18. 18
    PaV says:

    Bob O’H:

    About the onion:

    (1) Isn’t it common for plants to have a high C-number?
    (2) If this is so, then there should be some ‘reason’ for this,
    (3) And probably it’s because they are generally sessile organisms. I.e., they can’t go scavenge for their food, so they might need duplicate copies of genes so as to ‘multiply’ the amount of certain gene products when the right moment comes—like when it rains, or when its fed plant food, or when some detritus comes its way.

  19. 19
    Diogenes says:

    BA77, none of you IDers have attempted to answer either the Onion test, the C value paradox, the huge variations in genome size within single genera, the genetic load argument (every baby gets ~100 new mutations but doesn’t die)– or how IDers can predict how much junk DNA there is unless you assume you know the purposes of God.

    Instead, BA77 does the usual UD “response” of posting a list of canned creationist arglebargle IRRELEVANT TO THE QUESTION. YOU DID NOT ANSWER THE QUESTION. NO IDER CAN.

    Do you not see that these long, disorganized gabble of irrelevant creationist religious blurts make you, Kairosfocus, Wallstreeter etc. look insane? Do you think this arglebargle will persuade scientists that ID is a real theory? Who are you trying to persuade? What is the logic or rationale behind these long lists of irrelevant links? Just “God of the Gaps” times infinity? “Look at how complex science is. I can’t understand it, so it must be magic”? Will this win over scientists, you think?

  20. 20
    Diogenes says:

    PaV, you did not link to any study on Alu elements.

    But how many nucleotides within the Alu’s were found to be functional? Ten, I’d guess. 100, if you’re lucky.

    Now divide by 3.2 billion. How much of the genome are we talking about, percentage-wise? 0.001%? As usual.

  21. 21
    bornagain77 says:

    Diogenes, contrary to what you seem to believe, finding that “The genome is an ‘organ of the cell’, not its dictator” is in fact a direct falsification of the modern synthesis i.e. of neo-Darwinism,

    You being a neo-Darwinist, having your base position falsified IS NOT A MINOR PROBLEM FOR YOU!!!

    Why does your response remind me of the Black Knight’s response?

    “It’s just a flesh wound!”
    Monty Python-The Black Knight
    https://www.youtube.com/watch?v=zKhEw7nD9C4

  22. 22
    Diogenes says:

    PaV, as for your hypothesis about plants, note that you incorrectly assume plants have many duplicates of genes. Some do, some don’t. Some are polyploid. The onion is not polyploid. In the C value paradox, the C is divided by ploidy.

    The bladderwort Utricularia has a very tiny genome, but it is a complex plant that eats animals. This would seem to falsify your hypothesis. The bladderwort has almost no non-coding DNA, but has slightly more genes than humans. This falsifies ENCODE’s hypothesis that complexity is produced by “millions of switches” in non-coding DNA that greatly outweigh the size of all genes.

    As for being sessile, I just listed many animals that have far more DNA than humans but are NOT sessile.

  23. 23
    bornagain77 says:

    More Functions Discovered for “Jumping Genes” – March 2015
    Excerpt: News from the University of Geneva shows that geneticists have changed their minds about these jumping genes. The “junk DNA” label is in their rear-view mirror:

    “Alu” sequences are small repetitive elements representing about 10% of our genome. Because of their ability to move around the genome, these “jumping genes” are considered as real motors of evolution. However, they were considered for a long time as “junk” DNA, because, although they are transcribed into RNA, they encode no proteins and do not seem to participate actively in the cell’s functions. Now, the group of Katharina Strub, professor at the Faculty of Science of the University of Geneva (UNIGE), Switzerland, has uncovered two key functions of Alu RNAs in human cells, which are the subject of two different articles published in Nucleic Acids Research. Alu RNA can bind to specific proteins forming a complex called Alu RNP. On the one hand, this complex allows the cells to adapt to stress caused for example by chemical poisoning or viral infection. On the other hand, the same complex plays a role in protein synthesis by regulating the number of active ribosomes, suggesting that it could be part of the innate system of cellular defense against certain viruses.
    http://www.evolutionnews.org/2.....94091.html

  24. 24
    Diogenes says:

    BA77, the links you compiled are irrelevant to the topic at hand as always. Claims about how the genome is an organ of the cell etc. do not mean much and do not explain why organisms with the same complexity have widely varying amounts of DNA or why genetic load is tolerated.

    You cannot answer any of the questions, so you attempt Gish Gallop. IDers’ predictions about junk DNA were falsified.

    However, now I see that your rationale for compiling irrelevant links is that you believe that, if ANY gap in science exists, then this vindicates ALL other claims of gaps– the facts be damned– and you fill all these gaps, imaginary or not, with God. A science stopper.

    BA77, donn’t you claims about the genome not being the dictator of the organism constitute an admission that most DNA is non-functional? You IDiots were just saying all of the DNA is functional. Now none of it is functional? Which is it?

  25. 25
    bornagain77 says:

    Diogenes, instead of just insisting that most of genomes are junk without any real time evidence, (other than your ‘hunch’ that it must be that way because if you were god you would not do it that way), I suggest you actually prove your claim to be true for junk DNA by removing a large percentage of the DNA of a genome from an egg cell and see what you get! When that has been done thus far, the results are not consistent with your ‘hunch’:

    Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011
    Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA and that they could “see no effect in them.”
    But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
    In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.
    http://www.uncommondescent.com.....-junk-dna/

  26. 26
    Diogenes says:

    And BA77 is now back to saying DNA is functional and the genome is again the dictator of the organism. A minute ago, DNA was not functional and not the dictator of the organism. Ahblblbllblbl.

    For Alu elements, BA77 links to ENV, a creationist website. Admission that BA77 learned all his science from creationist websites. I did not ask for creationist distortions.

    Here is what I asked, again:

    But how many nucleotides within the Alu’s were found to be functional? Ten, I’d guess. 100, if you’re lucky.

    Now divide by 3.2 billion. How much of the genome are we talking about, percentage-wise? 0.001%? As usual.

  27. 27
    bornagain77 says:

    Diogenes, so falsification of the modern synthesis means nothing to you as a neo-Darwinist? And having the genome be a organ instead of a dictator has no implications for how a genome can vary depending on the specific needs of an organism?

    Well, seeing as reason has completely left the building, and looney tunes has now entered, that all folks.

    Thats All Folks
    https://www.youtube.com/watch?v=Q3bbsDJWlXQ

  28. 28
    Diogenes says:

    BA77, copying from creationist the Reverend Wells.

    So scientists removed more than 1 million bp’s from the mouse and nothing bad happened. Looks like junk.

    Some other scientists removed 58,000 bp’s and the mouse died. We are back to DNA being functional and the genome is the dictator. A minute ago, it wasn’t.

    How many of those base pairs were functional? Ten, I’d guess. 100, if you’re lucky.

    Now divide by 3.2 billion– or let’s say, 58,000. What fraction of the genome is functional, as shown by this experiment?

  29. 29
    Mapou says:

    OH:

    What’s the ID explanation for the size of the onion genome? I mean beyond “it must all be functional”. Why would an onion be so much more functional than, say, a human, or why would wheat be more functional than rice?

    It all has to do with intelligent design, IMO. Some of the designers obviously were highly advanced chefs. The onion and its cousins can probably be bred into an amazing variety of flavors, shapes and appearances. It’s all locked inside the onion genome, waiting to be discovered by future chefs.

    The advanced designers who designed life on earth seemed to have had an eye for beauty, taste and the good life. It could not have been evolution since evolution doesn’t care about such things.

  30. 30
    Mapou says:

    Diogenes talking to Joe:

    But tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Intelligent designers work in mysterious ways. Fish make excellent tasting food, if you’re into seafood. It’s all about the taste. Obviously, humans were not designed to be eaten. 😀

    And, BTW, what does sorcery have to do with intelligence? Enjoy playing with yourself much?

  31. 31
    Quest says:

    Diogenes,

    Why don’t you remind us all how the genetic load is calculated…

  32. 32
    Quest says:

    The distribution of deleterious genetic variation in human populations

    Population genetic studies suggest that most amino-acid changing mutations are deleterious. Such mutations are of tremendous interest in human population genetics as they are important for the evolutionary process and may contribute risk to common disease. Genomic studies over the past 5 years have documented differences across populations in the number of heterozygous deleterious genotypes, number of homozygous derived deleterious genotypes, number of deleterious segregating sites and proportion of sites that are potentially deleterious. These differences have been attributed to population history affecting the ability of natural selection to remove deleterious variants from the population. However, recent studies have suggested that the genetic load is the same across populations and that the efficacy of natural selection has not differed across human populations. Here I show that these observations are not incompatible with each other and that the apparent differences are due to examining different features of the genetic data and differing definitions of terms.

  33. 33
    Diogenes says:

    Pest,

    what in Heaven’s name is your source, and who is the “I” referred to?

  34. 34
    Diogenes says:

    Mapou says:

    But tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Intelligent designers work in mysterious ways.

    If intelligent designers are mysterious, how did IDers know that God didn’t make junk DNA? God didn’t work in mysterious ways when IDers said ID predicts there will be NO Junk DNA. Then God was not so mysterious, but rather, his purposes were known.

    Why were IDers so sure? How do you know that God didn’t make us as vectors for carrying around Junk DNA? Or that Junk DNA will have a front-loaded function that will only be revealed in a more advanced successor species to Homo sapiens 1 billion years from now?
    God didn’t work in mysterious ways when IDers said ID predicts there will be NO Junk DNA. Then God was not so mysterious, but rather, his purposes were known.

    Why were IDers so sure? How do you know that God didn’t make us as vectors for carrying around Junk DNA? Or that Junk DNA will have a front-loaded function that will only be revealed in a more advanced successor species to Homo sapiens 1 billion years from now?

  35. 35
    Diogenes says:

    Mapou, A minute ago you said Intelligent Designers were mysterious.

    Intelligent designers work in mysterious ways.

    Now you say they’re not mysterious, you know the purposes of God.

    The onion and its cousins can probably be bred into an amazing variety of flavors, shapes and appearances… The advanced designers who designed life on earth seemed to have had an eye for beauty, taste and the good life.

    They’re not mysterious now. Now you DO know the purposes of God: to make food that tastes good… to those people who like onions.

    Now many people hate the taste of onions, but they are not like God, huh? God’s taste is similar to that of people who like onions. You sure know a lot about the purposes of God– this minute. The next minute you’ll know nothing.

    If your above hypothesis were true, the variations in taste between onions would track to the regions that are variable within the genus Allium. The variations between the species within Allium are 10 times larger than the entire human genome. Is it necessary to have a variation in genome size 10x larger than that of the whole human genome to create a nearly imperceptible change in taste?

    Now to the frogs. Within some genera of frogs, some frogs have much more DNA than humans and some species, looking nearly identical, have far less DNA than humans. What was God’s purpose there? Since you know his Infinite Mind now.

    And lastly, consider humans. Consider all our Junk DNA. How do you know that Junk DNA is not beautiful to God? How do you know what is beautiful to an Infinite Mind? Since you allow that God created onions to taste good, how do you know that God didn’t create humans as vectors just to carry around beautiful (to Him) broken transposons?

  36. 36
    Diogenes says:

    BA77, as I have already pointed out, you IDers started out arguing that all DNA was functional and that the genome was the dictator controlling the organism, and that this falsifies evolution, which means that according to you, evolution predicts non-functional DNA.

    Now your argument has flipped. Now you argue that DNA is non-functional and that the genome is NOT the dictator controlling the organism, and that this also falsifies evolution, which means that according to you, evolution predicts *FUNCTIONAL* DNA.

    So which is it? Which prediction is entailed by evolution, according to you? They’re opposites.

    I will return to my still-unanswered questions.

    No, no IDer can explain why the onion genome is 5x the size of the human genome… or why the VARIATION in genome sizes within the genus Allium is several times larger than the whole human genome.

    Why is it that within some genera of frogs, where all the species look equally complex, some species have far less DNA than humans, while other species in the same genus, distinguishable only by experts, have far more DNA than humans? Why?

    And excluding frogs, all amphibians that have been studied, including caecilians that have no legs nor eyes, have much, much more DNA than humans. Why?

    Nor can any of you answer Wd400?s frequently repeated question: if every baby born has ~ 100 more mutations than its parents, ~200 more than its grandparents etc. etc., and if all that DNA is functional, and mutations are “catastrophic” as IDcreationists always say, why don’t all babies die?

    Tell me how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”

    Is it not true that to attempt to answer this question, you must know the purposes of God? And if your hypothesis depends on your beliefs about God’s purposes, doesn’t that make ID dependent on religion?

  37. 37
    Mapou says:

    Diogenes,

    Man, give it a rest. First, I was giving plausible reasons for the onion’s huge genome. Second, intelligent designers do work in mysterious ways (of course, since we don’t yet know exactly who they are and what their goals were) but not in stupid ways. Intelligence is the key word here. Whoever designed life on earth were not a bunch of goofballs or buttheads. They were extremely disciplined, knowledgeable and methodical with a highly advanced sense of beauty. Creating truckloads of junk DNA just for silly grins and giggles would not be one of their goals, IMO.

  38. 38
    Diogenes says:

    Mapou:

    Creating truckloads of junk DNA just for silly grins and giggles would not be one of their goals, IMO.

    Oh. Now God’s back to not being mysterious, and now you DO know God’s purposes again.

  39. 39
    Mapou says:

    Man, go fly a kite or mow the lawn or something.

  40. 40
    Joe says:

    ID doesn’t have anything to do with God:

    in “The Design Revolution”, page 25, Dembski writes:

    Intelligent Design has theological implications, but it is not a theological enterprise. Theology does not own intelligent design. Intelligent design is not a evangelical Christian thing, or a generally Christian thing or even a generally theistic thing. Anyone willing to set aside naturalistic prejudices and consider the possibility of evidence for intelligence in the natural world is a friend of intelligent design.

    He goes on to say:

    Intelligent design requires neither a meddling God nor a meddled world. For that matter, it doesn’t even require there be a God.

    In his book “Signature in the Cell” Stephen C. Meyer addresses the issue of Intelligent Design and religion:

    First, by any reasonable definition of the term, intelligent design is not “religion”.- page 441 under the heading Not Religion

    He goes on say pretty much the same thing I hve been saying for years- ID doesn’t say anything about worship- nothing about who, how, why, when, where to worship- nothing about any service- nothing about any faith nor beliefs except the belief we (humans) can properly assess evidence and data and properly process information. After all the design inference is based on our knowledge of cause and effect relationships.

  41. 41
    Mapou says:

    Joe, it really does not matter that ID says nothing about the who or the when. There is no harm in analyzing all available evidence (the designed objects) to see what it can tell us about the designers. This, too, should be a scientific field of enquiry in its own right. Design detection as envisioned by Dembsky et al is not the be-all of the entire field of intelligent design.

  42. 42
    Joe says:

    Exactly, Mapou, exactly. ID isn’t a scientific dead end for tat simple fact- it forces us to ask questions we will try to answer.

  43. 43
    Box says:

    Bacterium deinococcus radiodurans carries many copies of its genome – resulting in a 3.3 mb genome – and utilizes that in an amazing way.

    Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the DNA double helix. The familiar bacterium, E.coli, not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans,by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting task, to say the least.

    “D. radiodurans survives 7 kGy of ionizing radiation with marginal lethality (10%). This dose shatters its 3.28 Mb genome into 20–30 kb fragments (…)”

    All the copies are shattered, but as the breakage is random (i.e., it doesn’t occur on both copies at the same place), repair by homologous recombination can occur between the copies.

    The unsolved mystery is how the homologous fragments are brought together in the correct sequence.

  44. 44
    Cross says:

    Diogenes

    “Look Diogenes, I can see you’re really upset about this. I honestly think you ought to sit down calmly, take a stress pill, and think things over. ” HAL 9000 Computer

    “If it helps, I could sing you a song, would you like to here it?”

    https://www.youtube.com/watch?v=OuEN5TjYRCE

    Cheers

  45. 45
    Quest says:

    Dionogenesis,
    You haven’t answered my very important question; how is genetic load calculated…? I’m going to skip the rest of your embarrassment… You are just too low ball for me…

  46. 46
    Quest says:

    Dionogenesis,

    Here is the link you couldn’t find:http://www.sciencedirect.com/s.....7X14001002

    There is more to come…. lol

  47. 47
    Curly Howard says:

    Box, did you actually read the paper you have cited?
    It’s not as much of an unsolved mystery as you seem to think.

  48. 48
    wd400 says:

    There are several different ways to calculate or estimate genetic load, Quest. What has this to do with anything?

  49. 49
    Box says:

    Curly Howard #47,

    I did. I even had some correspondence with one of the researchers at the time. She explicitly stated that this was exactly the unsolved mystery.
    I know that the paper doesn’t make this clear at first glance, but you can trust me on this one.

  50. 50
    wd400 says:

    Curly,

    Unfortunately, I’ve been down this path with Box before. (S)he doesn’t seem to want to accept the pedestrian answer.

    I’ve no idea how this is meant to relate to junk DNA.

  51. 51
    Quest says:

    WU40,

    How accurate are the calculations of the genetic load…?

  52. 52
    Box says:

    WD400 #50 (and Curly Howard),

    the mystery is really easy to explain, but probably I have been unclear. Allow me to try again:

    “D. radiodurans survives 7 kGy of ionizing radiation with marginal lethality (10%). This dose shatters its 3.28 Mb genome into 20–30 kb fragments (…)”

    Those fragments are “stitched” back together. The paper describes the mechanism by which the fragments are stitched back together.
    The remaining question is: how are the DNA-fragments reordered in the correct sequence before they are stitched back together.
    The researcher doesn’t know and told me: “Yes, that’s exactly the biggest remaining mystery”.
    Something in the cell knows the correct sequence, is capable of solving the puzzle and reorders the many fragments before reconstruction. But what?

    WD400: I’ve no idea how this is meant to relate to junk DNA.

    Just an example of a large genome (with a lot of apparent redundancy) that pays off in an unexpected way.

  53. 53
    Curly Howard says:

    Quite frankly Box, I don’t believe you. Homologous recombination relies on the complementarity between homologous chromosomes. Sequences finding each other is driven by the fact that they are virtually identical. Also a paper out of their own lab in 2006 showed that realignment of the genome through ESDSA occurs through annealing of complementary 20-30 kilobase single-strand DNA ends. Lastly, you should look up some of the more recent work that’s been done as well.

  54. 54
    wd400 says:

    Quest,

    Different methods (and even definitions of load), and different kinds of data make for better or worse estimates, it’s not really possible to answer your question in the abstract.

    If you have a point, please make it.

  55. 55
    Diogenes says:

    Wd400,

    As you know, in the C value paradox, C is divided by number of duplicates of genome. So Box’s story of bacteria with duplicate genomes is irrelevant.

    But in their mind, any gap in scientific knowledge vindicates ALL claims of gaps in scientific knowledge, facts be damned– and then they fill all the gaps with God. Even those which are already, uncomfortably filled with Science.

  56. 56
    rvb8 says:

    Of course in some perverse experiments scientists have turned on non-coding DNA in chickens and produced teeth. So the birds have the DNA for teeth but it is not functional. If it were removed the bird would be none the worse off; sounds like pointless junk to me.

    Then again maybe god did design a chicken to have teeth and after the arc landing they micro-devolved away; that god chap, what a joker.

    Alternatively birds evolved from land animals that used to have teeth, and as an evolved answer to the problems of weight and aerodynamics in flight, teeth were selected against. Thus the DNA remained, but in junk non-coding form. One of these answers is rational, can you guess which?

  57. 57
    Andre says:

    Diogenes….

    Have all the other sites you stalk banned you and now you’re pulling your creepy wares here at UD?

    Junk DNA, aka Darwin style has been falsified, your religion is in tatters rather go do some PR work around the fact that your entire movement is drenched in sex scandals, just like the priests…….

    Go clean-up your own house!

  58. 58
    Andre says:

    Headshot!

    More function less junk!

    http://www.nature.com/nsmb/jou......2799.html

    Diogenes the official materialist snake oil salesman…..

  59. 59
    Andre says:

    Bet you 50 bucks Diogenes have never thought about it like this,

    Perhaps we see junk and clutter in the DNA because over time it behaves just like a windows registry?

    The Registry clutter is a condition in which disorganized data stuffs up over time. In a freshly installed copy of Windows, the clutter is not considerable enough to affect performance. As most of the systems today are protected by Antivirus and Antispyware, complete corruption of Windows to warrant re-installation is less frequent. Hence the same Windows is used for years and therefore accumulates broken links and leftover files in the registry. The more the registry is cluttered, the more loss in speed will be observed. Following is the list of reasons that cause registry clutter:

    1.When multiple software are installed and removed over time, they leave some amount of redundant, useless links and files behind. As uninstallations increase, clutter spreads.
    2.An incomplete installation (one that is done without an uninstaller) will leave more traces of broken and unwanted files in the registry.
    3.A fragmented registry will also bring down a computer’s performance. Empty spaces and sectors will increase the time taken to address the registry (Similar to how a fragmented disk slows down performance, read the article The path to performance loss; How a computer loses speed)
    4.Viruses, malware, trojans generate embedded keys. These will cause registry errors and reduce performance.

    The undesirable clutter and errors in the registry will cause crashes, error messages and screen freezes. At the end of the day we know its software that drives us…….

    So I have a hypotheses, just like a brand new install of windows we started out pristine but over time even with some maintenance system junk builds up due to frequent use.

  60. 60
    Bob O'H says:

    PaV @ 18 –
    (sorry for coming in after another 40 comments, but the time zones are not favourable)

    (3) And probably it’s because they are generally sessile organisms. I.e., they can’t go scavenge for their food, so they might need duplicate copies of genes so as to ‘multiply’ the amount of certain gene products when the right moment comes—like when it rains, or when its fed plant food, or when some detritus comes its way.

    This hypothesis would suggest that all plants would have large genomes, which would mostly be non-coding DNA. But then why would rice have such a small genome compared to wheat?

    There’s a nice figure here showing variation in genome size amongst taxonomic groups. Note, for example, that sessile fungi tend to have small genomes, as do a lot of angiosperm plants.

    EDIT: I wonder how large the genome is of a triffid.

  61. 61
    Joe says:

    rvb8:

    Alternatively birds evolved from land animals that used to have teeth,…

    How can that be tested? No one knows what makes a bird a bird…

  62. 62
    Box says:

    Curly Howard #53,

    “D. radiodurans survives 7 kGy of ionizing radiation with marginal lethality (10%). This dose shatters its 3.28 Mb genome into 20–30 kb fragments (…)”

    Get the picture: all of the DNA is shattered in small fragments. Next Drad will

    (1) Align the fragments in the correct order

    (2) Stitch the DNA fragments together again by a process termed “homologous recombination”

    Now the mystery rests in (1). Remember that Drad carries multiple copies of its genome, however these copies are also shattered in tiny fragments; making the “puzzle” even more difficult.
    From this tangle of short DNA-fragments Drad needs to select usable fragments and align them in the CORRECT (original) sequence.

    Question: How does Drad know the correct sequence? With so many fragments available Drad can align the DNA in many wrong sequences.

    Curly Howard: Sequences finding each other is driven by the fact that they are virtually identical.

    How is that an answer to the question? What do you even mean? Identical fragments are not socializing at any stage of the repair process. Why would they?

    Curly Howard: Also a paper out of their own lab in 2006 showed that realignment of the genome through ESDSA occurs through annealing of complementary 20-30 kilobase single-strand DNA ends.

    I know it’s complicated, but that is part of the not mysterious phase (2) – stitching DNA fragments together again. You need to address (1) – align the fragments in the correct order.

    Curly Howard: Lastly, you should look up some of the more recent work that’s been done as well.

    I suppose that you refer to Kisko and Radman, however they don’t address the mystery as layed out in (1).

  63. 63
    harry says:

    Diogenes @36

    All your “why” questions miss the point. What we have is a device the purpose of which is obviously to store digital information, some of which contains the assembly instructions for various functional protein machines. Knowing that, it is reasonable to assume the rest of it will either be functional in some other way not yet understood, or just be unused memory capacity. In a given instance, regardless of how much of the total memory is extra capacity the contents of which are functionally insignificant, and how much memory is functionally significant, what is of major consequence is that a biological digital-information storage device exists at all. Such a device was absolutely necessary, since without the assembly instructions it is obvious that the protein machines required for metabolism and reproduction would have as much chance of getting slopped together accidentally as one would have at arriving at Margaret Mitchell’s Gone with the Wind by continually dumping out crates of Scrabble pieces on empty parking lots until the pieces happened to fall such that they were neatly arranged that way.

    When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? Yet how would its contents evolve into such functional information without machinery exterior to it that could read and write the memory? And why would such machinery evolve while the contents of the storage device’s memory were still gibberish, and reading and writing it was just a waste of energy? Mindless evolutionary processes can arrive at neither the functional information nor the machinery to access it in the absence of the other. In other words, life just isn’t going to happen mindlessly and accidentally. Or did Margaret Mitchell actually come up with Gone with the Wind by randomly selecting letters of the alphabet?

  64. 64
    PaV says:

    Diogenes:

    Now divide by 3.2 billion. How much of the genome are we talking about, percentage-wise? 0.001%? As usual.

    Nice speculation. Just look up the paper. The 10% figure comes from there.

    (Here’s the link.)

  65. 65
    PaV says:

    Diogenes:

    As for being sessile, I just listed many animals that have far more DNA than humans but are NOT sessile.

    If they are not sessile, then the hypothesis wouldn’t apply. And how many “plants” are NOT sessile? I don’t there’s many.

    I find it interesting that none of this has been thought about before. Evolutionary biologists, I guess, reach the conclusion that the polyploidy is just “junk-DNA,” and they stop asking questions, since this fits their narrative so well.

    BTW, as I thought a little bit further about this “onion” problem, it came to me that the plants would respond more to the presence and absence of water than simply ‘food,’ although needing both. I would think, however, that ‘water’ would be the prime requirement based simply on my experiences in the garden.

    Interestgingly, the bladderwort has no problem with ‘finding’ water, since it lives on water. This might be exactly why its genome is so relatively short.

  66. 66
    wd400 says:

    I find it interesting that none of this has been thought about before. Evolutionary biologists, I guess, reach the conclusion that the polyploidy is just “junk-DNA,” and they stop asking questions, since this fits their narrative so well.

    This is getting comical. There are loads of papers that actually test hypotheses about the evolution of junky genomes, you should read some.

  67. 67
    Mapou says:

    wd400 proudly declares:

    There are loads of papers that actually test hypotenuses

    How does one test a hypotenuse? Why are so many atheists and Darwinists so insufferably pompous? It’s the same refrain: We know something you don’t and if you knew what we knew, then you too would believe that living organisms evolve all by themselves into what they are and that life arose from dirt all by itself. What utter crap!

  68. 68
    PaV says:

    Bob O’H:

    This hypothesis would suggest that all plants would have large genomes, which would mostly be non-coding DNA. But then why would rice have such a small genome compared to wheat?

    It suggests that duplicating the entire genome is an adaptive measure for plants.

    As to rice, aren’t they grown in areas where the ground is flooded with water? This isn’t the case for wheat. If my thesis has some merit, then, because the plant has to actually respond more to presence of water than that of ‘food,’ then the rice would have possibly “lost” its duplicated form, being that it is grown in a flooded state.

  69. 69
    Curly Howard says:

    Box, it seems you don’t have a very good understanding of homologous recombination. Both 1 and 2 are processes within homologous recombination. The sequences are aligned based on the homology between DNA molecules. This is the same reason why crossing over exchanges precise fragments between homologous chromosomes in us.
    “Tiny” fragments is not a good description in my opinion. 20-30kb is quite large and with the ssDNA overhangs, allows for complementary base pairing between homologous strands that are not fragmented in the same place. Having fragments that overlap allow for reconstruction of the genome based on complementary base pairing of sections of the fragments in a way similar to how a genome would be realigned during shotgun sequencing.

    When I say recent work, I am referring to:
    Cox et al. 2010 PLoS Genetics
    Sugiman-Marangos & Junop. 2010 Nucleic Acids Res.
    Bent chilly et al. 2010 PLoS Genetics
    Hickman et al. 2010 EMBO J
    Motors et al. 2010 J Nucleic Acids
    Bouthier de la tour et al. 2011 DNA Repair Amst
    Subhuman-Marangos et al. 2013 Nucleic Acids Res
    George et al. 2012 J Biol Chem

  70. 70
    PaV says:

    wd400:

    This is getting comical. There are loads of papers that actually test hypotheses about the evolution of junky genomes, you should read some.

    Glad to add to your merriment. However, I was not talking about “junk-DNA” in general, but to genome duplication events and increased genome size in plants, specifically. Also, look at my comment to Bob O’H.

    Finally, do you really believe that the idea of Darwinism—in your case neo-Darwinism—doesn’t drive your decisions about what to look further into, and what not?

    Being self-critical can help. The physicist Feynman cautioned: “The first principle is that you must not fool yourself and you are the easiest person to fool.”

    And that’s a physicist who has all kinds of repeatable experimental evidence.

  71. 71
    Box says:

    Curly Howard,

    Curly Howard: Box, it seems you don’t have a very good understanding of homologous recombination.

    If that is the case, maybe you can help me out here.

    Curly Howard: Both 1 and 2 are processes within homologous recombination. The sequences are aligned based on the homology between DNA molecules.

    How does homology help sequencing the fragments into an obviously non-homologous DNA molecule? I can understand that homology helps explaining that homologous DNA-fragments face each other during homologous recombination. But I certainly don’t understand that fragments are sequenced in the right (non-homologous) order of an entire DNA-molecule. Homology is of help in one dimension (direction) but not in another, so to speak.

    edit: is this an atheist thing? WD400 also failed to see the mystery. Am I being unclear or what?

  72. 72
    wd400 says:

    However, I was not talking about “junk-DNA” in general, but to genome duplication events and increased genome size in plants, specifically

    Onions are diploid.

  73. 73
    Curly Howard says:

    “Obviously non-homologous DNA molecule,” Box?
    I don’t think you understand the words you are using.

  74. 74
    Piotr says:

    #64 PaV,

    They say that Alu elements make up more than 10% of the human genome. They don’t say that all of them are (or can be) functional.

  75. 75
    Box says:

    follow up #71 //

    The problem is simple. A comparison:

    Hamlet’s Sililoquy (and several copies of this work) is fragmented into thousand of words and parts of words. We now have something like:

    sleep Arms or Whether Aye against
    Arrows outrag eams That Flesh
    consummation question Slings
    To die Sea To be, not mind
    against to eous be, that is the question
    Sea shuffled mind Whether
    To be, sleep Aye To b Slings

    [and so forth]

    Now how do we repair things? (just like Drad repairs its shattered genome; see #43)

    To be, or not to be, that is the question—
    Whether ’tis Nobler in the mind to suffer
    The Slings and Arrows of outrageous Fortune,
    Or to take Arms against a Sea of troubles,
    And by opposing, end them? To die, to sleep—
    No more; and by a sleep, to say we end
    The Heart-ache, and the thousand Natural shocks
    [and so forth]

    Okay the stitching things back together ONCE THEY HAVE BEEN SEQUENCED IN THE RIGHT ORDER has been explained and part of that stitching process has to do with homology. But homology between the fragments doesn’t help finding the correct sequence at all.

    Am I being clear this time?

  76. 76
    Curly Howard says:

    Well, you are certainly being clear about what it is you don’t understand!

    Here’s a better, more simple example with the numbers representing the original chromosome.

    1. the quick brown fox jumped over the lazy dog
    2. the quick brown fox jumped over the lazy dog

    Fragmented:

    1. the quick
    1. brown fox jumped
    1. over the lazy
    1. dog

    2. the quick brown
    2. fox jumped over the
    2. lazy dog

    Now sequence alignment by complementary base pairing allows you to realign the original sequence based on the different fragments of homologous chromosomes.

    1. brown fox jumped over the lazy dog
    2. ———-fox jumped over the————

    Do you see how 2 fragments originally from chromosome 1 were rejoined in the correct order based on the homologous sequence of a fragment from chromosome 2?
    And now another fragment from chromosome 2 can be added in correct sequence based on the homology in the chromosome 1 fragment:

    1. ————–brown fox jumped over the lazy dog
    2. the quick brown fox jumped over the————

    I don’t know how much simpler I can make it. You simply don’t know what you are talking about. Homology is always between 2 separate DNA molecules (or their fragments in this case) whereas complementary base pairing doesn’t care whether it’s within a single DNA molecule or between two different molecules. This is why complementary base pairing can be used to reorder fragments from homologous chromosomes.
    I know it’s complicated, but try to stay with me.

  77. 77
    RodW says:

    Hey IDers,

    You should reply to the onion test by saying that the wildly varying amounts of DNA in onion and other species can be accounted for by whole genome duplications. These are random events that occur in many species, especially plants, and to a non-biologist it might sound like a valid explanation. Of course it doesn’t answer the onion test, but explaining why could be difficult and confound some of the science folks…..and that’s all that really matters

  78. 78
    Box says:

    Curly Howard,

    Thank you for the explanation. Somehow I didn’t get that mechanism you have spelled out. If what you describe is indeed the explanation then I must have misinterpreted the words of one the researchers during my e-mail correspondence.
    On my question “Am I correct when I say that one of the unanswered questions is how the hundreds of overlapping genomic fragments are reordered in the correct sequence? This seems like a miracle to me.” the following response:

    Yes, that’s exactly the biggest remaining mystery, how are the homologous fragments brought together. We know that there is no pre-alignment of the genomic copies, but perhaps alignment occurs before repair takes place. How this happens is a mystery. We wanted to test the possibility of ‘post-alignment’ (after IR) by tagging a certain locus with GFP and looking at whether we see two dots side by side or fart apart, but the resolution of light microscopy doesn’t allow for the GFP foci to be visualized separately.

    Of course the selecting and placement still remains mysterious. Something (similar to RNA polymerase?) reads the code of a DNA-fragment (how does it find the “first one”?), remembers it and then starts a search for an overlapping homologue piece and then maneuvers it in the correct position. I don’t expect an explanation for that any time soon.

    Weird that the researcher writes “but perhaps alignment occurs before repair takes place”, I mean logic dictates that this must happen. The “post-alignment” idea I did not get.

    Another perhaps relevant fact is that there are many DNA repeat elements in Drad’s genome. That may or may not complicate homologous recombination.
    In 1999 researchers write:

    Another important component may be the presence of DNA repeat elements scattered throughout the genome.These repeats satisfy several expected requirements for involvement in recombinational repair including that they are intergenic, they are ubiquitous in the chromosomes and the megaplasmid, and they occur at a frequency that is comparable to the number of double stranded DNA breaks that can be tolerated by D. radiodurans. A possible function of the repeats may be in regulating DNA degradation after damage. DNA degradation following the introduction of double stranded breaks is an integral part of the DNA repair process in D. radiodurans;

  79. 79
    PaV says:

    If you duplicate a diploid chromosome, you get TWO diploid chromosomes.

  80. 80
    PaV says:

    They say that Alu elements make up more than 10% of the human genome. They don’t say that all of them are (or can be) functional.

    Sounds like you’re in a state of denial.

  81. 81
    wd400 says:

    If you duplicate a diploid chromosome, you get TWO diploid chromosomes.

    … I don’t even… what?

  82. 82
    Piotr says:

    #80 PaV,

    Denial of what?

  83. 83
    PaV says:

    That what has been hailed as classic examples of “junk-DNA” are now being found to have function: an omen that the neo-Darwinist evo-bios are losing the battle to ID.

    It seems a bit odd that if you have an Alu sequence that is shown to have function, and there are loads of other such sequences, that you would think that this entire class of similar Alu sequences would only be limited to a handful of cases.

    What about pseudogenes? Classic “junk-DNA,” and now known to be intimately involved in the developing embryo.

  84. 84
    Curly Howard says:

    Something seems fishy Box because as I said, in their 2006 paper they describe the mechanism by which fragments realign.
    They outline the mechanism in the abstract:
    “…’extended synthesis-dependent strand annealing’ (ESDSA), followed and completed by crossovers. At least two genome copies and random DNA breakage are requirements for effective ESDSA. In ESDSA, chromosomal fragments with overlapping homologies are used both as primers and as templates for massive synthesis of complementary single strands, as occurs in a single-round multiplex polymerase chain reaction. This synthesis depends on DNA polymerase I and incorporates more nucleotides than does normal replication in intact cells. Newly synthesized complementary single-stranded extensions become ‘sticky ends’ that anneal with high precision, joining together contiguous DNA fragments into long, linear, double-stranded intermediates. These intermediates require RecA-dependent crossovers to mature into circular chromosomes that comprise double-stranded patchworks of numerous DNA blocks synthesized before radiation, connected by DNA blocks synthesized after radiation.”

    Also PaV, everywhere your statement about duplicating chromosomes could have been wrong, it was wrong.
    Chromosomes are not diploid, genomes are.
    Duplication of homologous chromosomes (2 independent, single DNA molecules) in eukaryotes still gives you only 2 chromosomes. Only now each chromosome consists of two DNA molecules. You should’ve paid more attention in bio class.

  85. 85
    PaV says:

    wd400:

    Stop being pedantic. It’s irritating.

  86. 86
    Box says:

    CH #84,

    What exactly seems fishy, Howard? What you quote seems consistent with “Yes, that’s exactly the biggest remaining mystery, how are the homologous fragments brought together.” Your quote doesn’t say how the fragments are selected and how they are transported.

  87. 87
    bornagain77 says:

    Inferring functionality for virtually 100% of the genome, even though we do not know the precise function of all of the sequences of all the elements of the genome, is relatively easy. One way to infer widespread functionality, despite not having knowledge of precise function, is to note that the entire genome, contrary to Darwinian presuppositions, is subject to multiple layers of DNA repair thus raising the obvious question of ‘why is the cell so jealously protecting so much dead weight junk?’

    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
    http://www.newgeology.us/presentation32.html

    The following repair mechanism is my favorite since it indicates, (due to the traveling salesman problem which is a notoriously difficult problem in classical computation), that quantum computation is somehow involved in the repair process:

    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

    Moreover sophisticated repair mechanism in place for DNA are incompatible with Darwinism in principle:

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Another way to infer widespread functionality across the entire genome, despite not having knowledge of precise function, is empirically. In the following study the entire genome is transformed into a optical device:

    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.....ellig.html

    In the following study, what was thought to be junk DNA was cut out but, contrary to Darwinian thought, it had a negative effect:

    Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011
    Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.”
    But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
    In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.
    http://www.uncommondescent.com.....-junk-dna/

    Another way to infer widespread functionality across the entire genome, despite lacking knowledge of precise function, is to note the trend in evidence. Every element that Darwinists have insisted to be junk in the past has been now shown to have function of one kind or the other. i.e. There has only been an increase in the amount of the genome known to functional, never a decrease!

    Reference Notes For Jonathan Wells’ Book – The Myth Of Junk DNA – Hundreds of Studies Outlining Function for various elements of supposed ‘Junk’ DNA
    http://www.discovery.org/f/7651

    another way to infer widespread functionality across the entire genome is to look at the ‘polyfunctionality’ of the genome:

    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.
    http://www.sciencedaily.com/re.....142957.htm

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

  88. 88
    bornagain77 says:

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://vimeo.com/81930637
    Concluding powerpoint of the lecture (at the 1 hour mark):
    “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
    Edward N. Trifonov – 2010

    Astonishing DNA complexity update
    Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
    https://creation.com/images/pdfs/tj/j21_3/j21_3_111-117.pdf

    Multidimensional Genome – Dr. Robert Carter – video
    http://www.metacafe.com/watch/8905048/

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

    Duality in the human genome – Nov. 28, 2014
    Excerpt: The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,”,,,
    “Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms.,,,
    http://medicalxpress.com/news/.....enome.html

    Towards the latter half of the following podcast, Dr Sternberg, who has a PhD in evolutionary biology, elucidates how the overturning/loss of the ‘gene’ as the central unit of inheritance turns the modern synthesis of neo-Darwinism from a science into no better than the discarded alchemy or Ptolemy astronomy of yesteryear.

    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 5
    (emphasis on ENCODE and the loss of the term ‘gene’ as a accurate description in biology and how that loss undermines the modern synthesis of neo-Darwinism)
    http://www.discovery.org/multi.....-dna-pt-5/

    etc.. etc.. etc..

  89. 89
    Curly Howard says:

    Box, I guess you’re still not getting it. The “selection” of fragments relies on complementary base pairing and is aided by RecA. The entire mechanism is pretty well explained in the 2006 paper and by studies done in the 1990s-early 2000s and summed up in a mini review by Frenkiel-Krispin & Minsky (2006).

    Andddd here comes a BA77 regurgitation.
    Just looking at your first point BA, the cell protects all DNA because the repair systems can’t differentiate between protein coding regions, regulatory regions or junk regions. They only recognize broken DNA and fix it as best they can.
    Molecules can’t think, can you?

    PS-I don’t think “quantum computation” is involved at all in the repair process. You didn’t just see the word “quantum dots” and immediately go into one of your quantum physics frenzies did you?

  90. 90
    Piotr says:

    #83 PaV

    Is there a difference between “Some Alu elements, pseudogenes, ERVs, TEs, etc., have been co-opted for a function” and “Most/all DNA has a function”? For what percentage of those elements has any kind of functionality been demonstrated?

  91. 91
    Box says:

    Well Curly,

    I gather that you hold that I fabricate e-mail correspondence. I do not. However I’m the only one who knows this for a fact. Consequently I also know for a fact that you are the one who is still not getting it.

  92. 92
    Curly Howard says:

    Right. I’m not getting it, I’m just sitting here explaining things to you, Box.

  93. 93
    Quest says:

    It looks like Dan Graur finally removed his embarrassing rhetoric on Junk DNA: If @ENCODE_NIH is right, each of us should have 7 x 10^45 children…

    http://judgestarling.tumblr.co.....hould-have

    I guess he finally updated his total lack of knowledge on genetic load….

  94. 94
    Cross says:

    harry @ 63

    “When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? Yet how would its contents evolve into such functional information without machinery exterior to it that could read and write the memory? And why would such machinery evolve while the contents of the storage device’s memory were still gibberish, and reading and writing it was just a waste of energy? Mindless evolutionary processes can arrive at neither the functional information nor the machinery to access it in the absence of the other. In other words, life just isn’t going to happen mindlessly and accidentally.”

    Exactly, but you note that the materialists posting here will ignore the hard bits they can’t explain.

    Cheers

  95. 95
    bornagain77 says:

    Curly at 89 asks:

    “Molecules can’t think, can you?”

    I wish you, and other Darwinists, would honestly ask yourself that question Curly:

    Why Evolutionary Theory Cannot Survive Itself – Nancy Pearcey – March 8, 2015
    Excerpt: Steven Pinker writes, “Our brains were shaped for fitness, not for truth. Sometimes the truth is adaptive, but sometimes it is not.” The upshot is that survival is no guarantee of truth. If survival is the only standard, we can never know which ideas are true and which are adaptive but false.
    To make the dilemma even more puzzling, evolutionists tell us that natural selection has produced all sorts of false concepts in the human mind. Many evolutionary materialists maintain that free will is an illusion, consciousness is an illusion, even our sense of self is an illusion — and that all these false ideas were selected for their survival value.
    So how can we know whether the theory of evolution itself is one of those false ideas? The theory undercuts itself.,,,
    Of course, the atheist pursuing his research has no choice but to rely on rationality, just as everyone else does. The point is that he has no philosophical basis for doing so. Only those who affirm a rational Creator have a basis for trusting human rationality.
    The reason so few atheists and materialists seem to recognize the problem is that, like Darwin, they apply their skepticism selectively. They apply it to undercut only ideas they reject, especially ideas about God. They make a tacit exception for their own worldview commitments.
    http://www.evolutionnews.org/2.....94171.html

  96. 96
    Quest says:

    For those who want to do some reading on genetic load… how accurate the calculations are…and how lucky we really are to have junk DNA or else we’d have been extinct millions of years ago…

    agrawal.eeb.utoronto.ca/files/2013/06/afa_mcw_2012.pdf

  97. 97
    Curly Howard says:

    Have you figured out why you think “quantum computation is somehow involved in the repair process,” BA?

    It’s not just because you saw “quantum dots” is it?

    How are things over at the funny-farm anyways?

  98. 98
    bornagain77 says:

    Curly Howard, the reason why quantum computation is implicated in this particular DNA repair process,,,

    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

    ,,, is not because of quantum dots, but is because of the traveling salesman problem. First off, to show how quantum computation is possible in DNA, lets back up a bit and learn that DNA has now been shown to have quantum entanglement within it:

    Quantum Information/Entanglement In DNA – short video
    https://vimeo.com/92405752

    Moreover, it is important to also learn that ‘non-local’, beyond space and time, quantum entanglement (A. Aspect, A. Zeilinger, etc..) can be used as a ‘quantum information channel’,,,

    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.
    http://plato.stanford.edu/entries/qt-entangle/

    Thus it is possible, since DNA has quantum entanglement lengthwise along its entire axis, that entire DNA molecule is performing quantum computation of some sort. But how do we verify if it is? Well, back to our example. 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
    Excerpt: Another example of an NP-hard problem is the optimization problem of finding the least-cost cyclic route through all nodes of a weighted graph. This is commonly known as the traveling salesman problem.
    – per wikipedia

    Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:

    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.”
    http://www.sciencedaily.com/re.....122828.htm

    Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, must somehow be solved by ‘non-local’ quantum computation within the cell and/or within DNA itself;
    Moreover, we also have evidence of quantum computation solving the ‘travelling salesman problem’ within protein folding:

    It is known that proteins do not find their final folded form by random processes:

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are.
    http://www.evolutionnews.org/2.....65521.html

    Confronting Science’s Logical Limits – John L. Casti – 1996
    Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard.
    http://www.cs.virginia.edu/~ro.....Limits.pdf

    That no one really has a firm clue how proteins are finding their final folded form is made clear by the immense time (a few weeks) it takes for a few hundred thousand computers, which are linked together, to find the final folded form of a single protein:

    A Few Hundred Thousand Computers vs. (The Folding Of) A Single Protein Molecule – video
    https://www.youtube.com/watch?v=lHqi3ih0GrI

  99. 99
    bornagain77 says:

    The reason why finding the final form of a folded protein is so hard for supercomputers is that it is like the ‘traveling salesman’ problem, which are ‘Just about the meanest problems you can set a computer (on) ‘.

    DNA computer helps traveling salesman – Philip Ball – 2000
    Excerpt: Just about the meanest problems you can set a computer belong to the class called ‘NP-complete’. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the ‘travelling salesman’ puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,,
    Solving the traveling-salesman problem is a little like finding the most stable folded shape of a protein’s chain-like molecular structure — in which the number of ‘cities’ can run to hundreds or even thousands.
    http://www.nature.com/news/200.....13-10.html

    And protein folding is found to be ‘NP-complete’

    Combinatorial Algorithms for Protein Folding in Lattice
    Models: A Survey of Mathematical Results – 2009
    Excerpt: Protein Folding: Computational Complexity
    4.1
    NP-completeness: from 10^300 to 2 Amino Acid Types
    4.2
    NP-completeness: Protein Folding in Ad-Hoc Models
    4.3
    NP-completeness: Protein Folding in the HP-Model
    http://www.cs.brown.edu/~sorin.....survey.pdf

    Thus we have very good circumstantial evidence that proteins are very likely finding their final folded form by some method of quantum computation. ,,,, If so, as seems very reasonable to believe at this point, then this far exceeds anything man has yet accomplished in regards to quantum computation, although billions of dollars have been spent trying to build better quantum computers!
    Of related note: Here is the paper that proved that protein folding belongs to the physics of the quantum world and that protein folding does not belong to the physics of the classical world:

    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: 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, the fact that ‘non-local’ quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger, etc..), should be found in molecular biology on such a massive scale, in every DNA and protein molecule, is a direct empirical falsification of Darwinian claims, for how can the ‘non-local’ quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) cause when the quantum entanglement effect falsified material particles as its own causation in the first place? Appealing to the probability of various ‘random’ configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “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,”
    http://www.quantumlah.org/high.....uences.php

    etc.. etc..

    In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, one cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    And although Naturalists have proposed various, far fetched, naturalistic scenarios to try to get around the Theistic implications of quantum non-locality, none of the ‘far fetched’ naturalistic solutions, in themselves, are compatible with the reductive materialism that undergirds neo-Darwinian thought.

    “[while a number of philosophical ideas] may be logically consistent with present quantum mechanics, …materialism is not.”
    Eugene Wigner
    Quantum Physics Debunks Materialism – video playlist
    https://www.youtube.com/watch?list=PL1mr9ZTZb3TViAqtowpvZy5PZpn-MoSK_&v=4C5pq7W5yRM

    Why Quantum Theory Does Not Support Materialism By Bruce L Gordon, Ph.D
    Excerpt: The underlying problem is this: there are correlations in nature that require a causal explanation but for which no physical explanation is in principle possible. Furthermore, the nonlocalizability of field quanta entails that these entities, whatever they are, fail the criterion of material individuality. So, paradoxically and ironically, the most fundamental constituents and relations of the material world cannot, in principle, be understood in terms of material substances. Since there must be some explanation for these things, the correct explanation will have to be one which is non-physical – and this is plainly incompatible with any and all varieties of materialism.
    http://www.4truth.net/fourtrut.....8589952939

    Thus, as far as empirical science itself is concerned, Neo-Darwinism is falsified in its claim that information is ‘emergent’ from a material basis.

    Verse and Music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men.

    Michael W. Smith – You Won’t Let Go (Lyric Video)
    https://www.youtube.com/watch?v=MRb_NIQTzyA

  100. 100
    Curly Howard says:

    Congratulations BA, you can copy/paste from Wikipedia. The problem with your analogy is that in the DNA repair system there are multiple salesmen. There’s no need for any of your quantum computation crap. The repair enzymes diffuse around the cell and recognize DNA errors. You are off your rocker. I don’t even know why I bother. Banging my head against a wall would be more productive than talking to you, Joe, Mapou, etc.

    Enjoy your time on cloud nine!

  101. 101
    wd400 says:

    I can assure you, PaV, that I’m very genuine in my ability to extract anything of meaning from that sentence. Pedantry has nothing to do with it.

    All I can do is encourage you to remove yourself from your armchair and learn a little about what biologists have done on the evolution of genome size.

  102. 102
    bornagain77 says:

    as to: “The repair enzymes diffuse around the cell and recognize DNA errors.”

    actually:

    No, Scientists in Darwin’s Day Did Not Grasp the Complexity of the Cell; Not Even Close – Casey Luskin – June 6, 2013
    Excerpt: We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB — and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM,which is only one substrate molecule for every 105 water molecules, the enzyme’s active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second.
    But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”
    (Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294)
    http://www.evolutionnews.org/2.....72871.html

    and:

    Protein Researchers Unravel the Molecular Dance of DNA Repair – March 2012
    Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, “We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications,” Petra Beli says.
    “This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works.”
    The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways.
    http://www.sciencedaily.com/re.....123022.htm

    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.
    http://www.evolutionnews.org/2.....57791.html

  103. 103
    Zachriel says:

    harry: When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible?

    The self-replicating units, possibly RNA or kin, are posited to be both the “digital-information storage device” and the replicator.

  104. 104
    PaV says:

    Pedantry has nothing to do with it.

    Oh, but it does.

    You’re trying to say that an onion is allopolyploid, and not polyploid, without actually coming out and saying so. You’re playing games.

    Where are we in all of this?

    Well, the Darwinist’s point in all of this is to announce that there is an excessive amount of DNA in the onion—as compared to humans, e.g.—thus demonstrating the truth that huge amounts of ncDNA in the genome “proves” that ID is wrong and that neo-Darwinism is right.

    Well, this Darwinian perspective is completely unfounded.

    First, it’s not a lot of ncDNA; it is copied chromosomes, which have regulatory regions and coding regions throughout. So, it demonstrates nothing of the kind when it comes to the fundamental point neo-Darwinists want to make.

    IOW, why should the fact that chromosomes can, and are, duplicated, have anything to do with the Mendelian inheritance of traits,per se? There is no correlation between the two. That is, chromosomes are not producing or eliminating ‘traits,’ they’re simply being duplicated. There’s more of them—but it’s the same “them.”

    So, this means that some other explanation must be found for this polyploidy (allopolyploidy) since were dealing with things that are happening not at the nucleotide level, but at the chromosomal level.

    Accordingly, I supplied several ways of understanding what is at play here. I’ve mentioned that plants, unlike most animals, are sessile. When it comes to food and hydration, this can be a problem that plants have that many animals don’t have. So, maybe there is a need to be able to ramp up protein production quickly when conditions are favorable for the plant.

    You might disagree, but at least this makes some sense.

    Additionally, over at ENV, Jonathan Wells writes:“There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus — which affects the rate of cell growth and division. “.

    Angiosperms, flowering plants/trees, generally have much smaller genome sizes.

    Putting this all together, and especially following what Wells has written, when it comes to plants that produce “seeds” that have lots of water, it might be necessary to have cells that are filled with larger amounts of water–hence, larger sized—and so to maintain their metabolism, they duplicate their choromosomes so as to compensate for their smaller concentration in a more hydrated cell environment.

    Now, what I’ve written is plausible, and possibly correct.

    I’m sure you’re ready to dismiss all of this. But before you do, let me quote this from Wikipedia from their thread on ‘polyploidy’:

    The mechanisms leading to novel variation in newly formed allopolyploids may include gene dosage effects (resulting from more numerous copies of genome content), the reunion of divergent gene regulatory hierarchies, chromosomal rearrangements, and epigenetic remodeling, all of which affect gene content and/or expression levels.[28][29][30][31] Many of these rapid changes may contribute to reproductive isolation and speciation. However seed generated from interploidy crosses, such as between polyploids and their parent species, usually suffer from aberrant endosperm development which impairs their viability,[32][33] thus contributing to polyploid speciation.

    This is my last statement on all of this. I don’t care to respond any further to your nitpicking senselessness.

  105. 105
    wd400 says:

    What I’m saying is that onions are diploid (2n=16).

    I have no earthly idea what you are saying.

  106. 106
    Zachriel says:

    PaV: Angiosperms, flowering plants/trees, generally have much smaller genome sizes.

    Onions are angiosperms.
    http://th00.deviantart.net/fs7.....5fs0oy.jpg

  107. 107
    Curly Howard says:

    So, BA, biological function at the cellular level are generally carried out by complexes of proteins…this adds nothing to the conversation. Repair enzymes are still diffusing around the cell, they bind damaged DNA and recruit a complex of proteins to the site that actually carry out the repair function.
    Congratulations on another completely pointless post that lacks any intelligence on your part.

  108. 108
    Cross says:

    Zachriel @ 103

    “The self-replicating units, possibly RNA or kin, are posited to be both the “digital-information storage device” and the replicator.”

    Hopeful just so story, and evidence?

    “The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)”
    http://www.ncbi.nlm.nih.gov/pm.....MC3495036/

    Cheers

  109. 109
    Zachriel says:

    Cross: Hopeful just so story, and evidence?

    RNA and kin can act as both information storage and replicator. That answers harry’s objection.

    Cross: http://www.ncbi.nlm.nih.gov/pm.....MC3495036/

    We agree that proteins may have coevolved with RNA or kin. We disagree that the hypothesis is “probably unprovable”.

  110. 110
    Cross says:

    Zachriel @ 109

    His referee disagrees

    “Referee 1: Eugene Koonin

    I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World.”

    I read this as a bad hypothesis that is full of holes. Then the materialist manifesto rears its head.

    “the RNA World appears to be an outright logical inevitability. ‘Something’ had to start efficiently replicating to kick off evolution, and proteins do not have this ability”

    Something had to start replication to kick of evolution, RNA world is full of holes but it must be right because the answer must be material, can’t let a divine foot in the door.

    Just so.

    Cheers

  111. 111
    Zachriel says:

    Cross: His referee disagrees. Referee 1: Eugene Koonin

    Sure, though Koonin tends to be an outlier.

    Koonin (2012): To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World.

    Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “Amplification of 10^100-fold was achieved over a period of 37.5 hr”

    However, that doesn’t necessarily mean RNA was the original replicator. The experiment was highly contrived. The original replicator may have been a related polymer. However, the fact that RNA can act as both enzyme and genetic memory is proof of principle, answering a common objection (Koonin, harry).

    Cross: Something had to start replication to kick of evolution, RNA world is full of holes

    RNA World is certainly wrong, or at least incomplete.

  112. 112
    Piotr says:

    #104 PaV,

    Hey! You, in the hole — stop digging! There are some polyploids (including allopolyploids) among the 750 or so species of Allium, but the common onion, A. cepa, the species featured in the Onion Test, is not one of them. What made you think it was an allopolyploid? T. Ryan Gregory wanted to compare like with like, so he chose the diploid common onion for comparison with diploid Homo sapiens.

    While we are at it, polyploid plants can have really huge genomes. The current record-holder is the Japanese canopy plant, Paris japonica (almost 150 billion base pairs, 50 times more than in humans). It is an octaploid, but even if you correct for the ploidy effect, each of its sets of chromosomes is still 12 times bigger than the human set.

  113. 113
    Joe says:

    Piotr, It remains that your position cannot account for any genomes. Perhaps you chumps should focus on that.

  114. 114
    harry says:

    Zachriel @109,

    RNA and kin can act as both information storage and replicator. That answers harry’s objection.

    It doesn’t matter at all if the storage device and the replicator are one device. The problem remains: How did the replicator portion of the device evolve? There is no selectable advantage in reading and copying what is as yet still gibberish, not functional information; that only wastes energy. And how did the contents of the digital-information-storage component of the single device evolve into functional information without a mechanism to access/alter it (whether that mechanism was physically a component of same device or not), since there was as yet no selectable advantage in accessing/copying gibberish, so no such mechanism would evolve? Again: Mindless evolutionary processes can arrive at neither the functional information nor the mechanism to utilize it in the absence of the other.

    Why would matter assemble itself into digital-information storage functionality at all, regardless of whether that was a separate device or a component of another? There is a chasm that cannot crossed over mindlessly between the beginning of a natural evolutionary process lacking foresight, and the point where having such a digital-information storage device becomes a selectable advantage.

  115. 115
    harry says:

    harry @114

    Oops. “there was as yet no selectable advantage” should have been “there was no selectable advantage”.

    There was never going to be a selectable advantage in accessing/copying gibberish. ;o)

  116. 116
    Zachriel says:

    Let’s look at your original question.

    harry: what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible?

    The functional information is the function of replication.

    harry: It doesn’t matter at all if the storage device and the replicator are one device. The problem remains: How did the replicator portion of the device evolve?

    Those replicators that are best able to make use of the available raw materials and energy would tend to predominate in a population.

    harry: There is no selectable advantage in reading and copying what is as yet still gibberish, not functional information; that only wastes energy.

    It’s not gibberish. It’s a functional self-replicator.

    harry: “there was as yet no selectable advantage” should have been “there was no selectable advantage”.

    Once there is replication, there is selectable advantage.

  117. 117
    harry says:

    Zachriel @116

    Let me try to convey to you the big picture. The probabilistic resources of the entire universe are inadequate to produce even one 150 amino acid protein by chance. What will make life possible is a digital-information storage device that contains the assembly instructions for the protein machines required for metabolism and reproduction. Life just isn’t going to happen without such information being readily available.

    How do we arrive at that by chance when all matter can do is work its way towards a more probable state, which is definitely not that of a digital-information storage device? What needs to happen is that a mechanism to constructively harness the sun’s energy must spontaneously arise so our project can begin.

    So let’s assume that miraculously happens in the form of an environment that allows for, and continues to sustain, self-replicating units of chemical activity. Given that, there is still a huge gap that must be mindlessly and accidentally crossed over between replicating units of chemical activity and the arrival of a digital-information storage device.

    There is another huge gap between a digital-information storage device containing gibberish and one the contents of which are functional information. That functional information isn’t going to evolve without machinery to utilize the contents of the storage device’s memory.

    That machinery isn’t going to evolve along with the evolution of the storage device, or afterwards, because such machinery can provide no selectable advantage while the contents of memory are gibberish. We don’t have a selectable advantage until the contents of memory contain functional information and the machinery exists to constructively utilize it. That isn’t ever going to happen mindlessly because you can’t get the functional information without the machinery and the machinery can’t evolve unless it provides some selectable advantage, which it can’t because accessing/copying gibberish only wastes energy.

  118. 118
    Zachriel says:

    harry: The probabilistic resources of the entire universe are inadequate to produce even one 150 amino acid protein by chance.

    Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001.

    These proteins are only 80 in length, but they can be made as long as you like.

    harry: Given that, there is still a huge gap that must be mindlessly and accidentally crossed over between replicating units of chemical activity and the arrival of a digital-information storage device.</i.

    RNA is a digital storage device. An RNA replicator contains the information necessary to replicate itself, and can certainly include the ability to forge peptides that might aid in that replication.

  119. 119
    Louis C. Morelli says:

    “Junk DNA” is the genetic code at universal level when it is called Matrix which contains the biological code called DNA. What is called “junk DNA” is the memory of 10 billions years of universal evolutionary history before life’s origins.

    The long repetitions of same letters means that evolution at astronomical level is too much slow in relation to time of biological level and every Matrix’s evolutionary jump needs to register the changes occurring at the whole space and time.

    And the DNA is being observed by humans and their scientific instruments only at its horizontal material visible by visible light, but the DNA is built vertically by seven dimensions encompassing all seven differents vibrational states of natural light. So, the evolution of DNA at one dimension is dependable from the evolution at others dimensions, ans all evolutionary dimensions need be registered, that why sometimes the DNA is fulfilled with long repetitions of letters waiting the events at other dimensions.

    By the same motive that a human body can not exist without its bone skeleton and the code inherited from ancestors, the active regions of human DNA can not be supported without the skeleton’s DNA, mistakenly called “junk”. Disease like cancers when a cell is repetitive ad infinitum without control is also a problem about faults of dimension’s connections. That’s the nowaday state of investigation by Matrix/DNA Theory method.

    There is no “Darwinist evolution”, but a long universal process of genetic reproduction of the unknown natural system that triggered the Big Bang ( if you want call it God or Nothing, no problem, fell free) , which is accomplished by several steps of micro-evolution and that contains the mechanisms pointed out by Darwin a lot more. There is previous design for the universal natural system being developed here, but it is a natural process without the needs of a intelligent designer, like mother giraffe is able to produce a new baby giraffe without applying intelligence.

  120. 120
    harry says:

    An inexplicable fit of intellectual honesty from the abiogenesis crowd:

    A pile of bricks does not make a cathedral, and a collection of organic molecules does not make a living cell. There is presently no such thing as a “primitive” cell. There is no experiment that produces anything resembling living things. Imagine a junk yard with bits and pieces of metal of various shapes. Then think of a modern automobile with GPS and onboard computer, and a voice telling you to fasten your seat belt. That is roughly the distance between the organic matter seen in experiments simulating early-Earth conditions and the life forms now extant.
    http://earthguide.ucsd.edu/vir.....Soup.shtml

    UCSD isn’t exactly known for being a bastion of Young Earth Creationism.

    Zachriel, RNA is an unreliable storage device, used for transient, not permanent memory. It lacks error correction and detection in the copying process. That is why DNA is necessary. You don’t get life until the contents of DNA memory contains the assembly instructions for the protein machines required for cellular metabolism and reproduction.

  121. 121
    Zachriel says:

    harry: RNA is an unreliable storage device, used for transient, not permanent memory. It lacks error correction and detection in the copying process. That is why DNA is necessary.

    Apparently not. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “Amplification of 10^100-fold was achieved over a period of 37.5 hr”.

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