'Junk DNA' Intelligent Design

“Junk DNA” can really matter

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Rick Sternberg explains:

… what may be “junk” at one level may be of the utmost significance at another level. This happens I think by way of a top-down causal process that Paul Davies (2012) has alluded to, explainable in part by the augmentation of

“the normal terms referring to local forces contained in the Hamiltonian for chromatin with additional (presumably small) non-local terms representing functional (i.e. semantic or contextual) information. By coupling the mechanical and informational dynamics in this manner, the dynamical laws describing chromatin behaviour would become time-dependent and change according to the informational state of the system. Information would then possess direct, albeit subtle, traction over matter and permit epigenetic control to be exercised directly on the chromatin itself.”

Such would involve an “explicit coupling between dynamical laws and information-rich states, thus endowing higher level entities, such as contextual information, with direct causal efficacy on matter alongside intermolecular forces.”

If we take such “contextual information” to be resident at all tiers of the meiosis I network, from the spindle as whole to (say) each and every centromeric locus, then “with direct causal efficacy” retroelement and satellite DNAs can be endowed with information-bearing states. Of course, “such a proposal represents a decisive break with the normal formulation of the theory of dynamical systems,” as Davies notes, which means that “theories of this sort remain largely unexplored.” But explore it we should…and especially where cytology meets “junk” DNA.

Richard Sternberg, “DNA May Be “Junk” at One Level But of Utmost Significance at Another” at Evolution News and Science Today

If there were a prize for the Darwinian idea that has proven least helpful to Darwinism, would junk DNA be the winner?

26 Replies to ““Junk DNA” can really matter

  1. 1
    BobRyan says:

    We are just starting to scratch the surface of understanding DNA. To call any part junk is nothing more than refusing to accept just how complex it is. In Darwin’s time, a single celled organism was considered simple and nothing complex about it. Without the simplicity of the organism, Darwinism fails. The organism is vastly more complex than anything he believed was possible.

  2. 2
    Pater Kimbridge says:

    We know some DNA is junk because we can see exactly what it USED to do, and we know exactly in what way it got broken.
    https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060063

  3. 3
    ET says:

    Yes, Pater, that’s about all Darwinian evolution is good for- breaking things. But even that is moot as DNA can have a function beyond being a code for proteins.

  4. 4
    bornagain77 says:

    Pater Kambridge claims that

    We know some DNA is junk because we can see exactly what it USED to do, and we know exactly in what way it got broken.

    PK cites this article from 2008 as proof for what is referred to as ‘common ancestry’, not for junk DNA per se as he falsely implied

    Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation
    Abstract: Embryonic development in nonmammalian vertebrates depends entirely on nutritional reserves that are predominantly derived from vitellogenin proteins and stored in egg yolk. Mammals have evolved new resources, such as lactation and placentation, to nourish their developing and early offspring. However, the evolutionary timing and molecular events associated with this major phenotypic transition are not known. By means of sensitive comparative genomics analyses and evolutionary simulations, we here show that the three ancestral vitellogenin-encoding genes were progressively lost during mammalian evolution (until around 30–70 million years ago, Mya) in all but the egg-laying monotremes, which have retained a functional vitellogenin gene. Our analyses also provide evidence that the major milk resource genes, caseins, which have similar functional properties as vitellogenins, appeared in the common mammalian ancestor ?200–310 Mya. Together, our data are compatible with the hypothesis that the emergence of lactation in the common mammalian ancestor and the development of placentation in eutherian and marsupial mammals allowed for the gradual loss of yolk-dependent nourishment during mammalian evolution.
    https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060063

    Moreover, Pater Kimbridge’s supposed proof for ‘common ancestry’ is not nearly as strong as he has, apparently, been falsely led to believe:

    Challenging the BioLogos Claim that a Vitellogenin (Egg-Laying) Pseudogene Exists in the Human Genome · January 2015 – Jeffrey Tomkins
    Abstract: An evolutionary argument heavily promoted by the BioLogos organization as evidence of broad-scale vertebrate macroevolution is the idea that the human genome contains the 150 base remnant of an egg-yolk related vitellogenin (vtg) gene acquired through descent from a common ancestor shared with chicken. However, research described in this report shows that the alleged vtg fragment in human is not a pseudogene remnant at all, but a functional enhancer element in the fifth intron of a “genomic address messenger” (GAM) gene. This GAM gene produces long noncoding RNAs that have been experimentally shown to selectively inhibit the translation of known target genes, a majority of which are implicated in a variety of human diseases. Messenger RNAs from this gene are also expressed in a variety of human brain tissues. The alleged 150 base vtg sequence contains a variety of highly conserved mammalian transcription factor binding domains, nucleosome depleted open-active chromatin, is hypo-methylated, associates with RNA polymerase 2 in long-range chromatin interactions, and binds the Mafk transcriptional regulator. These combinatorial data clearly show that it is a functional enhancer element in a GAM gene expressed in the human brain-strongly challenging the idea that this sequence is an egg-laying pseudogene genomic fossil.
    https://www.researchgate.net/publication/321342938_Challenging_the_BioLogos_Claim_that_a_Vitellogenin_Egg-Laying_Pseudogene_Exists_in_the_Human_Genome

    Moreover, the supposed evidence for common ancestry from sequence comparisons gets worse for Darwinists. Much Worse!

    New Paper by Winston Ewert Demonstrates Superiority of Design Model – Cornelius Hunter – July 20, 2018
    Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data.
    Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model.,,,
    Where It Counts
    Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous.
    Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.
    Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other.
    We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.
    Ten thousand is a big number. But it gets worse, much worse.
    Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division.
    The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division.
    Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth?
    Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models!
    By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent.
    10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence.
    This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits.
    But It Gets Worse
    The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450.
    In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450.
    We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.
    https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/

    Such a ‘over the top’ falsification is simply completely devastating to the Darwinist’s assumption of ‘common descent’.

    Will Pater Kimbridge ever honestly admit that his Darwinian worldview is falsified? I would hope that he would, but I seriously doubt it.

    It has been my experience over the past two decades or so that most hard core Darwinists believe in Darwinian Evolution IN SPITE of the scientific evidence against it overwhelming not because of any supposed scientific evidence supporting it.

    There simply is no falsification from empirical evidence that most hard core Darwinists will ever accept.

    The falsification of Junk DNA by ENCODE, in and of itself, proves this point:

    Moreover, these leading Darwinists insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from other sources
    https://uncommondescent.com/intelligent-design/encode-produces-a-genomic-encyclopedia/#comment-708788

  5. 5
    Querius says:

    We know some DNA is junk because we can see exactly what it USED to do, and we know exactly in what way it got broken.

    And what about all the DNA that’s in the process of evolving and just needs a few more mutations to make it functional?

    There must be dozens of examples of human DNA evolution in progress, right?

    -Q

  6. 6
    AaronS1978 says:

    Pater “exactly” is a strong and power Assertion that can easily be proven wrong

    As the replies have shown

    I wouldn’t of use the word “exactly”

    And I don’t think “exactly” helped your point exactly the way you wanted it to do

  7. 7
    Seversky says:

    From Professor Laurence A Moran’s blog Sandwalk:

    Five Things You Should Know if You Want to Participate in the Junk DNA Debate

    Here are five things you should know if you want to engage in a legitimate scientific discussion about the amount of junk DNA in a genome.

    Genetic Load

    Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.

    C-Value Paradox

    A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.

    Modern Evolutionary Theory

    Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.

    Pseudogenes and broken genes are junk

    More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.

    Most of the genome is not conserved

    Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can’t rule out some unknown function that doesn’t depend on sequence.

    If you want to argue against junk DNA then you need to refute or rationalize all five of these observations.

    Posted by Laurence A. Moran at Thursday, July 04, 2013

  8. 8
    bornagain77 says:

    Seversky, I addressed Moran’s, and Graur’s, refusal to ever accept the ENCODE findings against junk DNA in this post:

    Moreover, these leading Darwinists insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from other sources
    https://uncommondescent.com/intelligent-design/encode-produces-a-genomic-encyclopedia/#comment-708788

    As I stated previously, “There simply is no falsification from empirical evidence that most hard core Darwinists will ever accept.”

  9. 9
    EugeneS says:

    The only reasonable explanation is that

    I like that. The same Darwinist myopia as over the past 150 years. They somehow inherit it from their spiritual leader.

    https://uncommondescent.com/evolution/gamblers-ruin-is-darwins-ruin/

  10. 10
    ET says:

    The junk DNA argument is based solely on ignorance. It’s beyond stupid to think that the histone octamer spools just happened to evolve to collect and organize long strands of DNA, that owe their length to an accumulation of junk.

    Larry Moran, et al., ignore that and prattle on. If you want to argue for a prevalence of junk DNA then you need to refute or rationalize the histone octamer spooling observation.

  11. 11
    EDTA says:

    >”If most of our genome contained functional sequence information, then this would be an intolerable genetic load.”
    But as discussed here many times before, nobody is saying all that “junk” is coding for proteins. It might be error-correcting or modulating information, where mutations have an order of magnitude less visible effect on the organism.

    >”Pseudogenes and broken genes are junk”
    Unless they had more than one reading frame to begin with. And only one reading frame happens to be broken at the moment.

    >”Most of the DNA sequences in large genomes is not conserved.”
    This presumes the evolutionary tree of life to begin with, in order to conclude that most DNA sequences are not conserved.

  12. 12
    ET says:

    Exactly.

  13. 13
    bornagain77 says:

    Sternberg comments that,

    … what may be “junk” at one level may be of the utmost significance at another level. This happens I think by way of a top-down causal process that Paul Davies (2012) has alluded to, explainable in part by the augmentation of

    “the normal terms referring to local forces contained in the Hamiltonian for chromatin with additional (presumably small) non-local terms representing functional (i.e. semantic or contextual) information. By coupling the mechanical and informational dynamics in this manner, the dynamical laws describing chromatin behaviour would become time-dependent and change according to the informational state of the system. Information would then possess direct, albeit subtle, traction over matter and permit epigenetic control to be exercised directly on the chromatin itself.”

    I commented on ‘bottom up’ vs. ‘top down’ explanations yesterday.

    ,,, Atheistic materialists believe that the finely tuned laws and/or universal constants of nature arise via bottom up physical processes. In the following comment Origenes clearly explains why such a ‘bottom up’ scenario is logically impossible,

    “There cannot be, in principle, a naturalistic bottom-up explanation for immutable physical laws — which are themselves an ‘expression’ of top-down causation. A bottom-up explanation, from the level of e.g. bosons, should be expected to give rise to innumerable different ever-changing laws. By analogy, particles give rise to innumerable different conglomerations.
    Moreover a bottom-up process from bosons to physical laws is in need of constraints (laws) in order to produce a limited set of universal laws.
    Paul Davies: “Physical processes, however violent or complex, are thought to have absolutely no effect on the laws. There is thus a curious asymmetry: physical processes depend on laws but the laws do not depend on physical processes. Although this statement cannot be proved, it is widely accepted.”
    Saying that laws do not depend on physical processes, is another way of saying that laws cannot be explained by physical processes.”
    – Origenes

    ,,,The same logical impossibility faces Darwinian materialists. Darwinian materialists believe that all life can, ultimately, be explained solely by reference to ‘bottom up’ physical processes. As George Ellis stated, “A key assumption underlying most present day physical thought is the idea that causation is bottom up all the way:”,,, “However there are many topics that one cannot understand by assuming this one-way flow of causation.”,,, “living systems are highly structured modular hierarchical systems”,,, “The lower level interactions are constrained by network connections, thereby creating possibilities of truly complex behaviour. Top-down causation is prevalent at all levels in the brain: for example it is crucial to vision”,,,

    Recognising Top-Down Causation
    George Ellis, University of Cape Town
    1: The Theme
    A key assumption underlying most present day physical thought is the idea that causation is bottom up all the way: particle physics underlies nuclear physics, nuclear physics underlies atomic physics, atomic physics underlies chemistry, and so on. Thus all the higher level subjects are at least in principle reducible to particle physics, which is therefore the only fundamental science; as famously claimed by Dirac, chemistry is just an application of quantum physics [1].
    However there are many topics that one cannot understand by assuming this one-way flow of causation.,,,
    ,,, living systems are highly structured modular hierarchical systems,,,,The lower level interactions are constrained by network connections, thereby creating possibilities of truly complex behaviour. Top-down causation is prevalent at all levels in the brain: for example it is crucial to vision [24,25]
    https://fqxi.org/data/essay-contest-files/Ellis_FQXI_Essay_Ellis_2012.pdf

    George Ellis goes on to state,

    A: Causal Efficacy of Non Physical entities:
    Both the program and the data are non-physical entities, indeed so is all software. A program is not a physical thing you can point to, but by Definition 2 it certainly exists. You can point to a CD or flashdrive where it is stored, but that is not the thing in itself: it is a medium in which it is stored. The program itself is an abstract entity, shaped by abstract logic. Is the software “nothing but” its realisation through a specific set of stored electronic states in the computer memory banks? No it is not because it is the precise pattern in those states that matters: a higher level relation that is not apparent at the scale of the electrons themselves. It’s a relational thing (and if you get the relations between the symbols wrong, so you have a syntax error, it will all come to a grinding halt). This abstract nature of software is realised in the concept of virtual machines, which occur at every level in the computer hierarchy except the bottom one [17]. But this tower of virtual machines causes physical effects in the real world, for example when a computer controls a robot in an assembly line to create physical artefacts.,,,
    ,,, The mind is not a physical entity, but it certainly is causally effective: proof is the existence of the computer on which you are reading this text. It could not exist if it had not been designed and manufactured according to someone’s plans, thereby proving the causal efficacy of thoughts, which like computer programs and data are not physical entities.
    https://fqxi.org/data/essay-contest-files/Ellis_FQXI_Essay_Ellis_2012.pdf

    Why are Atheistic materialists so intent on denying the ‘top down’ causation of immaterial minds?, (so intent on denying a ‘real’ top-down effect that is right before their very eyes every time they type on a computer?), Well, as Michael Egnor explained, Darwinists are forced into this untenable position of denying what is right before their very eyes since they are intent on denying design. As he states, “eliminative materialism is necessary if a materialist is to maintain a non-teleological Darwinian metaphysical perspective. It is purpose that must be denied in order to deny design in nature. So the mind, as well as teleology, must be denied. Eliminative materialism is just Darwinian metaphysics carried to its logical end and applied to man. If there is no teleology, there is no intentionality, and there is no purpose in nature nor in man’s thoughts.”

    Teleology and the Mind – Michael Egnor – August 16, 2016
    Excerpt: From the hylemorphic perspective, there is an intimate link between the mind and teleology. The 19th-century philosopher Franz Brentano pointed out that the hallmark of the mind is that it is directed to something other than itself. That is, the mind has intentionality, which is the ability of a mental process to be about something, rather than to just be itself. Physical processes alone (understood without teleology) are not inherently about things. The mind is always about things. Stated another way, physical processes (understood without teleology) have no purpose. Mental processes always have purpose. In fact, purpose (aboutness-intentionality-teleology) is what defines the mind. And we see the same purpose (aboutness-intentionality-teleology) in nature.
    Intentionality is a form of teleology. Both intentionality and teleology are goal-directedness — intentionality is directedness in thought, and teleology is directedness in nature. Mind and teleology are both manifestations of purpose in nature. The mind is, within nature, the same kind of process that directs nature.
    In this sense, eliminative materialism is necessary if a materialist is to maintain a non-teleological Darwinian metaphysical perspective. It is purpose that must be denied in order to deny design in nature. So the mind, as well as teleology, must be denied. Eliminative materialism is just Darwinian metaphysics carried to its logical end and applied to man. If there is no teleology, there is no intentionality, and there is no purpose in nature nor in man’s thoughts.
    The link between intentionality and teleology, and the undeniability of teleology, is even more clear if we consider our inescapable belief that other people have minds. The inference that other people have minds based on their purposeful (intentional-teleological) behavior, which is obviously correct and is essential to living a sane life, can be applied to our understanding of nature as well. Just as we know that other people have purposes (intentionality), we know just as certainly that nature has purposes (teleology). In a sense, intelligent design is the recognition of the same purpose-teleology-intentionality in nature that we recognize in ourselves and others.
    Teleology and intentionality are certainly the inferences to be drawn from the obvious purposeful arrangement of parts in nature, but I (as a loyal Thomist!) believe that teleology and intentionality are manifest in an even more fundamental way in nature. Any goal-directed natural change is teleological, even if purpose and arrangement of parts is not clearly manifest. The behavior of a single electron orbiting a proton is teleological, because the motion of the electron hews to specific ends (according to quantum mechanics). A pencil falling to the floor behaves teleologically (it does not fall up, or burst into flame, etc.). Purposeful arrangement of parts is teleology on an even more sophisticated scale, but teleology exists in even the most basic processes in nature. Physics is no less teleological than biology.
    https://evolutionnews.org/2016/08/teleology_and_t/

    Of supplemental note, it is impossible for biologists to describe the complexities of life for any length of time without using words that directly imply ‘top-down’ control, i.e. teleology, goal directed purpose,…

    “Teleology is like a mistress to the biologist; he dare not be seen with her in public but cannot live without her.”
    J. B. S. Haldane

    “the most striking thing about living things, in comparison with non-living systems, is their teleological organization—meaning the way in which all of the local physical and chemical interactions cohere in such a way as to maintain the overall system in existence.
    Moreover, it is virtually impossible to speak of living beings for any length of time without using teleological and normative language—words like “goal,” “purpose,” “meaning,” “correct/incorrect,” “success/failure,” etc.”
    – Denis Noble – Emeritus Professor of Cardiovascular Physiology in the Department of Physiology, Anatomy, and Genetics of the Medical Sciences Division of the University of Oxford.

    The ‘Mental Cell’: Let’s Loosen Up Biological Thinking! – Stephen L. Talbott – September 9, 2014
    Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”.
    Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness 1.
    One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself.
    http://natureinstitute.org/txt.....ell_23.htm

    Thus, not only are Darwinists forced to deny the ‘top down’ causation of immaterial minds, (A ‘real’ top-down effect that is right before their very eyes every time they type on a computer), but Darwinian biologists are also forced to deny the very words that are coming out of their own mouths when they are doing their research.

    As should be needless to say, denying the reality of what you are seeing and what you are saying is NOT a sane position to be in.

    Matthew 12:37
    “For by your words you will be acquitted, and by your words you will be condemned.”

  14. 14
    DATCG says:

    Only thing I see from Darwinist are more blind assertions.

    The reason Darwinist need 98% of our DNA to be “Junk” is due to their failed construct of blind, random generation to create functions. If they do not have enough “Junk” they run out of time for their random, blind fairy tale. Ask Graur, if I remember correctly he admitted they need a certain percentage of JUNK DNA for Darwinist beliefs to work.

    Every hour of every day around the world, in every developed nation more useful function is being discovered in “JUNK” DNA.

    Without a large amount of “Junk”, the Darwinist religion fails. And it is a religion.

    What JUNK DNA

    According to these authors, genome-wide association studies have identified many noncoding variants associated with common diseases and traits. In their own study, the investigators showed that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs).

    Eighty-eight percent of such DHSs are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes. They further identified distant gene targets for hundreds of variant-containing DHSs that may explain phenotype associations. Disease-associated variants, they noted, systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks.

    These scientist researched “JUNK” DNA precisely because of ENCODE’s findings. Darwinist will one day go down as making one of the biggest blunders in scientific history. To write off 98% of our DNA as Junk.
    from the link…

    And, as John Stamatoyannopoulos, M.D., associate professor of genome sciences and medicine at the University of Washington, points out, while only about 2% of the human genome codes for proteins, “Hidden in the remaining 98 percent are instructions that basically tell the genes how to switch on and off.” His laboratory focuses on disease-associated variants in regulatory regions of DNA

    Yes, our DNA behaves like an Operating System that copies itself for future use. It has regulatory code to maintain the genes, to store, compress, call them, suppress them and in some cases modify them. And it’s time dependent. It appears certain regulatory code is only used at specific times. So, like any good operating system used for replication, it copies segments of data it knows it must use in the future, stores them for when the data must be utilized again. There is a “replication” phase and a “growth” phase of life. Not all proteins or regulatory code are utilized for all steps of life at all times.
    But at specific times, these essential data types are utilized and necessary – not JUNK.

    It’s more efficient to copy/store and utilize data-types as Switches for conditional processing to turn on/off genes and perform other functions, than to rebuild code from scratch for each new generation. A blind, random process would never get off the ground.

    These conditional data-types are stored, marked for location and retrieved as required. It takes planning and foresight to build such a system.

    More discoveries show “Junk” DNA is critical.

    Our DNA contains a sophisticated system of codes, programs, sub-programs, branching calls, conditional processing, switches and more, that any structural engineer or systems programmer looks at an marvels. Then questions how in the world can we copy this living, breathing, programmable, replicating system?

    What is the percentage of Introns in our Genome?

    “How does introns affect gene expression?”
    “While the role of exons in gene expression, transcription and translation into proteins is clear, introns play a more subtle role. Introns can influence gene expression through their presence at the start of an exon, and they can create different proteins from a single coding sequence through alternative splicing.”

    And here’s one of many instances of finding functionality in “JUNK” DNA…
    Junk DNA plays a crucial role in holding the genome together.

    There’s gold in “JUNK” DNA and most scientist know it today.
    Only blind Darwinist refuse to see.

  15. 15
    Pater Kimbridge says:

    The Tomkins paper that BA77 references was shown to be full of gross errors: https://biologos.org/articles/vitellogenin-and-common-ancestry

  16. 16
    bornagain77 says:

    Pater Kimbridge’s article from Venema supposedly refuting Tomkins has been refuted here,

    Functional Pseuodogenes and Common Descent – May 23, 2016
    Excerpt: Tomkins has presented evidence that the VIT1 pseudogene sits in part of an intron that is transcribed and produces long non-coding RNAs of the type we know often have function. What does Venema say next? Does he contest this evidence for functionality? No. According to Venema the “major problem” with Tomkins’s argument isn’t the evidence for functionality in the VIT1 pseudogene. Rather, he focuses on critiquing a false dichotomy that Tomkins has supposedly advanced:,,,
    Of course Venema is correct that finding function for this pseudogene is no refutation of Darwinian evolution. But his focus on this point distracts from the main issue here. And what’s that?
    The main issue is that evolutionists have commonly argued that non-functionality in shared pseudogenes is what provides evidence for common ancestry. They argue that God would not put “broken” shared DNA in multiple species and thus this must be evidence for common ancestry over intelligent design (or special creation, or whatever). We’ve seen many theistic and atheistic evolutionists treat pseudogenes in precisely this manner:,,
    * (Several quotes from evolutionists treating them exactly as such are given)
    https://evolutionnews.org/2016/05/functional_pseu/

    As you can see, the only ‘gross errors’ were in Venema’s response to Tomkins. The pseudogene is functionless whenever Darwinists think it will help their case, and yet when we find function for a pseudogene, well, they say it still does not refute Darwinian evolution per se. Basically, it is heads I win, tails you lose with Darwinists.

    Darwinism is not a scientific theory. It is a joke!

  17. 17
    EDTA says:

    “Teleology is like a mistress to the biologist; he dare not be seen with her in public but cannot live without her.”
    J. B. S. Haldane

    That is an awesome quote! Thanks for including it, BA77.

  18. 18
    DATCG says:

    Functions found in Pseudogenes…

    Another mechanism through which pseudogenes can function is by influencing chromatin or genomic architecture. HBBP1, a pseudogene residing within the haemoglobin locus, enables the dynamic chromatin changes that regulate expression of fetal and adult globin genes during development. Notably, although inhibiting HBBP1 transcription has no effect, deletion of the genomic locus reactivates fetal globin expression. HBBP1 DNA contacts, but not transcription, are required for suppressing the expression of fetal globin genes in adult erythroid cells.

    Problem is Darwinist declared pseudogenes junk for the simple reason a pseudogene may not translate into a protein.

    They were selfish for the selfish gene. Blinded, they wrote off 98% of DNA as junk. Thus their close-minded approach limited discovery.

    Quote at Evolution News from a recent paper dated December 2019. Finding function in

    Pseudogenes and the lack of curiosity by Darwinist:
    Pseudogene Function is Prematurely Dismissed

    Evidence that Darwinist dogma led to blindness for years…

    Because of the junk DNA paradigm, a lot of our biochemical techniques and technologies are set up only to identify standard protein-coding genes. They ignore and dismiss DNA that doesn’t fit that mold. Only by updating our technology to detect functional DNA elements that don’t necessarily fit the standard definition of a “gene” can be we begin to understand what pseudogenes really do.
    The paper explains that technical limitations, informed by our biases and assumptions, demotivate the study of pseudogene functions:

    In addition to the demotivation into exploring pseudogene function by the a priori assumption that they are functionless, their systematic study has also been hindered by a lack of robust methodologies capable of distinguishing the biological activities of pseudogenes from the functions of the genes from which they are derived.

    Then….

    They compare the situation to that of long non-coding RNAs (lncRNAs), which “were similarly dismissed initially as emanating from ‘junk DNA’ or as transcriptional noise, largely by virtue of their definition as non-protein-coding.” But as technology developed, lncRNAs are now widely recognized as functional and we regularly screen for their functions:

    Following a combination of technology developments, genome-wide studies and detailed biochemical studies, lncRNAs are now routinely included in genome-wide analyses, and their functional potential as cellular regulators is widely recognized.

    By naming convention, Darwinist wrote off entire regions of our DNA. If we’re to use the word, “pseudo” for any reason, the problem is the dogma and failure of closed-minded Darwinist belief systems that led them away from scientific discovery and towards pseudo-scientific beliefs.

    The blind faithful of Darwinist believers wrote off 98% of our DNA w/o actually confirming their dogmatic assertions. And thus stymied research for years in colleges, teaching young minds to ignore vast regions of DNA that in fact do have function.

    Nature Reviews Genetics, referenced by Evolution News…
    Overcoming challenges and dogmas to understand the functions of pseudogenes

    Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution.

  19. 19
    ET says:

    EDTA- over on Peaceful “Science” they are saying that teleology doesn’t imply a designer. That nature can produce a purposeful arrangement of parts, and so on. Of course they just say it and never present any evidence for it. But that is the nature of that forum- saying crap is enough.

  20. 20

    Wow. It was worth coming back to UD just to find and read Ewert’s paper. How long have ID critics insisted that there’s no testable ID theory, and have been using “nested hierarchy” as evidence for evolution? Yikes!

  21. 21
    ET says:

    William, evos still say that evolution is the only way to get a nested hierarchy. And that proves they do not understand the concept. When told that Linnaean taxonomy is the observed nested hierarchy and it has nothing to do with evolution, they just attack and prattle on.

    When told that the expected innumerable transitional forms would ruin any attempt to create a nested hierarchy, again they attack and prattle on.

    Facts and reality don’t mean anything to evolutionists.

  22. 22
    Pater Kimbridge says:

    BA77: No, Tomkin’s “paper” is pure garbage. Apparently the ICR pays him to come up with pseudoscientific gobbledygook to fool the ignorant masses.

    1) He bases his argument on a tiny 150bp sequence, while ignoring the 3100+bp sequence that comprises the vitellogenin gene.

    Talk about cherry-picking!

    2) He seems to conveniently get protein-coding genes mixed up with non-coding RNA genes.

    Talk about slight-of-hand!

    3) His “evidence of function” turns out to be way more noise than signal.

    Talk about non-sequiturs !

    Even a lowly graduate student saw through his subterfuge:

    https://evograd.wordpress.com/2019/07/30/tomkins-on-the-human-vitellogenin-pseudogene-who-needs-signal-when-you-have-noise/

  23. 23
    ET says:

    Earth to Pater- Your side can only explain the noise. That isn’t a ringing endorsement.

  24. 24
    bornagain77 says:

    Pater Kimbridge, who is a Darwinist who believes that the unfathomable complexity of living organisms is, basically, a complete accident, has the audacity to say this,

    BA77: No, Tomkin’s “paper” is pure garbage. Apparently the ICR pays him to come up with pseudoscientific gobbledygook to fool the ignorant masses.

    First, since you believe in Darwinism, then it is safe to say that you would not know real science if it bit you in the rear end, and secondly, that you have also, essentially, “lost your mind,”

    “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. It strikes me as urgent to insist that you not allow your mind to surrender the absolute clarity that all complex and magnificent things were made that way. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.””
    – Jay Homnick – 2005 – American Spectator

    As to this claim,

    1) He (Tomkins) bases his argument on a tiny 150bp sequence, while ignoring the 3100+bp sequence that comprises the vitellogenin gene.

    Unsurprisingly, like the vast majority of other claims from Darwinists, that too is a false claim

    Finding Adam in the Genome: A BioLogos cover-up? by Dr. Nathaniel T. Jeanson – August 17, 2017
    Excerpt: Had Venema carefully read Tomkins’ paper, Venema would not have made this mistake. Tomkins clearly analyzed more than the 150-letter vitellogenin fragment:

    “When the human vtg pseudogene fragment [the 150 nucleotide fragment] was aligned using very liberal gapping parameters (see Materials and Methods) to the chicken genomic sequence, sequence identity was only 62%. Genomic DNA surrounding this fragment was sequentially increased three-fold in size (symmetrically) and each fragment aligned up to 36,450 bases of human genomic DNA. Sequence identity dropped as the fragment size increased, eventually leveling off to about 39% identity for a region of 36,450 bases.12”

    Venema missed the fact that Tomkins analyzed the 150-letter fragment—and tens of thousands of DNA letters surrounding this fragment. The 150-letter fragment is not the only sequence that Tomkins analyzed; Tomkins did indeed investigate the supposed vit1 sequence remnants surrounding this fragment.

    After this egregious error in scholarship, Venema’s attacks only get worse.,,

    etc.. etc.. etc..
    https://answersingenesis.org/genetics/dna-similarities/biologos-cover-up/

    To repeat, “After this egregious error in scholarship, Venema’s attacks only get worse.” You can read the rest of the article at your leisure. It is an excellent refutation of Venema’s ‘sloppy’ scholarship.

    And please note that Pater Kimbridge hung his hat on this one piece of evidence whilst completely ignoring the Ewert paper that I listed at post 4 as well as ignoring DATCG’s post on pseudogenes at 18, which completely blows the entire foundation of his argument out from under him.

    Thus Pater Kimbridge’s scholarship turns out to be much worse than Venema’s ‘sloppy’ scholarship. PK’s scholarship is downright willfully ignorant of facts that are in play on this very thread!

    Such willful blindness and/or willful ignorance is simply pathetic! There is no excuse for it!

  25. 25
    DATCG says:

    BA77 @24,

    Because Darwinist live in the past, straining at gnats while the camel stares them in the face…
    http://pseudogene.org/psicube/

    Good rebuttal to misleading attempts to cloud the truth. And good review of Ewert’s paper on Dependency Graphs @ #4 – a fascinating paper and good direction for ID!

    Have a good day guys.

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