Genetics Genomics Intelligent Design

Deplorable words?: DNA is NOT the blueprint for life?

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Remember the guy who showed us a CD of his genome and said this is me? Naw, we didn’t think so at the time either, but read on:

The common view of heredity is that all information passed down from one generation to the next is stored in an organism’s DNA. But Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, disagrees.

In two new papers, Jose argues that DNA is just the ingredient list, not the set of instructions used to build and maintain a living organism. The instructions, he says, are much more complicated, and they’re stored in the molecules that regulate a cell’s DNA and other functioning systems.

Jose outlined a new theoretical framework for heredity, which was developed through 20 years of research on genetics and epigenetics, in peer-reviewed papers in the Journal of the Royal Society Interface and the journal BioEssays. Both papers were published on April 22, 2020. Jose’s argument suggests that scientists may be overlooking important avenues for studying and treating hereditary diseases, and current beliefs about evolution may be overly focused on the role of the genome, which contains all of an organism’s DNA.

Kimbra Cutlip, University of Maryland, “DNA may not be life’s instruction book—just a jumbled list of ingredients” at Phys.org

Papers:

Antony M. Jose, A framework for parsing heritable information, Journal of The Royal Society Interface (2020). DOI: 10.1098/rsif.2020.0154 (open access)

Antony M. Jose. Heritable Epigenetic Changes Alter Transgenerational Waveforms Maintained by Cycling Stores of Information, BioEssays (2020). DOI: 10.1002/bies.201900254 (paywall)

If this kind of stuff holds up and continues, our splintered lectern recycling sideline is going to be keeping us pretty busy. Cruel people say that’s what we’re really in this for. But you, loyal readers, know that that’s not true. Sure, we care about the environment. But the world of ideas… the world of ideas …

Hat tip: Philip Cunningham

56 Replies to “Deplorable words?: DNA is NOT the blueprint for life?

  1. 1
    AaronS1978 says:

    Awesome

  2. 2
    bornagain77 says:

    As to:

    “DNA cannot be seen as the ‘blueprint’ for life,” Jose said.,,,,
    ,,,, scientists are unable to determine the complex shape of an organ such as an eye, or that a creature will have eyes at all, by reading the creature’s DNA. These fundamental aspects of anatomy are dictated by something outside of the DNA.
    – per physorg

    So far so good, but, after basically destroying the foundation upon which the entire modern synthesis of Darwinian evolution rests, Jose goes on to ‘hope’ that,,,

    ,,, organisms could evolve through changes in the arrangement of molecules (outside of DNA) without changes in their DNA sequence.,,,

    Although Jose hopes to preserve Darwinian materialism, i.e. reductive materialism, by saying that Darwinian evolution could be driven by changes to the arrangement of molecules outside of the DNA, the fact of the matter is that the basic form that any organism may take, i.e. the ‘blueprint’ of an organism, besides not being reducible to DNA, is also not reducible to any other material particulars in the cell that Darwinists may wish to appeal to.

    As the following study found, “even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour”.,,, The researchers further commented that their findings “challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”

    Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics – December 9, 2015
    Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,,
    It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,,
    “We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s,” added Co-author Professor Michael Wolf from Technical University of Munich. “So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”
    – per physorg

    In fact, instead of molecules dictating what shape an organism may take, it is now found that it is the organism dictating what shape the molecules will take,

    In fact, up to one third of proteins, which are termed “Intrinsically Disordered Proteins”, assume different shapes when they interact with other molecules in different ‘contexts’,,,

    Biology’s Quiet Revolution – Jonathan Wells – September 8, 2014
    Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called “intrinsically disordered proteins,” or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,,
    So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific “fact,” as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that “DNA makes RNA makes protein makes us.”
    – per evolution news

    podcast – Dr. Jonathan Wells: Biology’s Quiet Revolution – September 17, 2014
    “We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)” – Jonathan Wells
    http://www.discovery.org/multi.....evolution/

    As well, the following article reveals that, contrary to Darwinian expectations, RNAs with the same shape could vary very widely in sequence:

    The Strange Inevitability of Evolution – Philip Ball – Jan. 2015
    Excerpt: Naively, you might expect RNAs with a similar shape, and thus presumably phenotype, to share a similar sequence, so that a map of the possible sequences—the sequence space, which can be represented as a many-dimensional space where each grid point corresponds to a particular sequence—is divided up into various “shape kingdoms” (See Not a Patch, a). But that wasn’t what Schuster found. Instead, RNAs with the same shape could vary very widely in sequence: You could get the same shape, and therefore potentially the same kind of catalytic function, from very different sequences.
    http://nautil.us/issue/20/crea.....-evolution

    As well, the following studies reveal that the three-dimensional arrangements of membrane-associated proteins, lipids and carbohydrates, cannot be reduced to sequence information in DNA and that the three-dimensional arrangement of the molecular components constitutes an independent source of information in the developing embryo.

    Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms – Casey Luskin – June 2, 2014
    Excerpt: So membrane patterns — the three-dimensional arrangements of membrane-associated proteins, lipids and carbohydrates, as they change over time — carry essential ontogenetic information. Yet (as I demonstrate below) the information carried by membrane patterns cannot be reduced to sequence information in DNA, for at least two reasons. First, the vast majority of proteins in eukaryotes are not completely specified by DNA sequences. Second, even if DNA sequences completely specified all proteins, DNA would not specify their spatiotemporal arrangements in membranes.
    – per evolution news

    To further drive to point home that the basic form of any particular organism is not reducible to the material particulars of the cells of an organism, in the following article it is noted that, “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.”

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

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

    To repeat, “the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern.”

    And although Jose may ‘hope’ to preserve Darwinian evolution by appealing to “changes in the arrangement of molecules (outside of DNA) without changes in their DNA sequence”, the fact of the matter is that even when taking into consideration the entirety of the ‘positional information’ of a embryo, (as opposed to just the sequential information of DNA), is still not nearly enough positional information to explain why any organism may take any particular shape.

    At about the 41:00 minute mark of the following video, Dr. Wells, using a branch of mathematics called category theory, demonstrates that, during embryological development, ‘positional’ information must somehow be coming into the developing embryo, ‘from the outside’, by some ‘non-material’ method.

    Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video (41:00 minute mark) – January 2017
    https://youtu.be/ASAaANVBoiE?t=2484

    And the following article states that: “the process of development should be thought of as being controlled by an “algebraic structure outside space-time itself”

    Intelligent Design and the Advancement of Science – Brian Miller – December 11, 2017
    Excerpt: DNA was expected to be the primary source of causality behind the operation and development of life. Such beliefs have previously raised concerns from leading scientists and mathematicians. For instance, physicist Walter Elsasser argued that the unfathomable complexity of the chemical and physically processes in life was “transcomputational” — beyond the realm of any theoretical means of computation. Moreover, the development of the embryo is not solely directed by DNA. Instead, it requires new “biotonic” principles. As a result, life cannot be reduced to chemistry and physics. An unbridgeable gap separates life from non-life.
    Similarly, mathematician René Thom argued that the 3D patterns of tissues in an organism’s development from egg to birth and their continuous transformation cannot be understood in terms of isolating the individual proteins generated by DNA and other molecules produced in cells. The problem is that the individual “parts” composing tissues and organs only take on the right form and function in the environment of those tissues and organs. More recent work by Denis Noble further has elucidated how every level of the biological hierarchy affects every other level, from DNA to tissues to the entire organism. Based partly on these insights, Thom concluded in his book Structural Stability and Morphogenesis that the process of development should be thought of as being controlled by an “algebraic structure outside space-time itself” (p. 119). Likewise, Robert Rosen argued that life can only be understood as a mathematical abstraction consisting of functional relationships, irreducible to mechanistic processes. He observed that life is fundamentally different from simple physics and chemistry. It embodies the Aristotelian category of final causation, which is closely related to the idea of purpose. The conclusions of these scholars challenge materialistic philosophy at its core.
    – per evolution news

    Moreover, there is a huge disparity in the amount of ‘positional information’ that is present in an embryo as compared to an adult organism.

    The ‘positional’ information content that is found to be in a one cell bacterium, when working from the thermodynamic perspective, is found to be 10 to the 12 bits,,,

    Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley
    Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
    http://www.astroscu.unam.mx/~a.....ecular.htm

    ,,, Which is equivalent of 100 million pages of Encyclopedia Britannica. ‘In comparison,,, the largest libraries in the world,, have about 10 million volumes or 10^12 bits.”

    “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.”
    – R. C. Wysong

    ‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.”
    Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894

    Thus since Bacterial cells are about 10 times smaller than most plant and animal cells.

    Size Comparisons of Bacteria, Amoeba, Animal & Plant Cells
    Excerpt: Bacterial cells are very small – about 10 times smaller than most plant and animal cells.
    https://education.seattlepi.com/size-comparisons-bacteria-amoeba-animal-plant-cells-4966.html

    And since there are conservatively estimated to be around 30 trillion cells within the average human body,

    Revised Estimates for the Number of Human and Bacteria Cells in the Body – 2016
    Abstract: Reported values in the literature on the number of cells in the body differ by orders of magnitude and are very seldom supported by any measurements or calculations. Here, we integrate the most up-to-date information on the number of human and bacterial cells in the body. We estimate the total number of bacteria in the 70 kg “reference man” to be 3.8·10^13. For human cells, we identify the dominant role of the hematopoietic lineage to the total count (?90%) and revise past estimates to 3.0·10^13 human cells. Our analysis also updates the widely-cited 10:1 ratio, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and their total mass is about 0.2 kg.
    https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533

    Then that gives us a rough ballpark estimate of around 300 trillion times 100 million pages of Encyclopedia Britannica. Or about 300 trillion times the information content contained within the books of all the largest libraries in the world. Needless to say, that is a massive amount of positional information that is somehow coming into a developing embryo from the outside by some non-material method.

    And as the following article states, the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000.

    In a TED Talk, (the Question You May Not Ask,,, Where did the information come from?) – November 29, 2017
    Excerpt: Sabatini is charming.,,, he deploys some memorable images. He points out that the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000. Later he wheels out the entire genome, in printed form, of a human being,,,,:
    [F]or the first time in history, this is the genome of a specific human, printed page-by-page, letter-by-letter: 262,000 pages of information, 450 kilograms.,,,
    – per evolution news

    Darwinists, with their reductive materialistic framework, simply have no clue where this massive amount of positional information is coming from that is dictating what final shape an organism may take.

    Whereas advances in quantum information theory and quantum biology both support the contention that it is an ‘outside observer’ who is imparting this massive amount of information into a developing embryo.

    Darwinian Materialism vs. Quantum Biology – Part II – video
    https://www.youtube.com/watch?v=oSig2CsjKbg

    In fact, as far as quantum information theory itself is concerned, this positional information that is somehow coming into the developing embryo from the outside, by some non-material method, to bring the developing embryo to be so far out of thermodynamic equilibrium, is found to be “a property of an observer who describes a system.”

    The Quantum Thermodynamics Revolution – May 2017
    Excerpt: “Now in (quantum) information theory, we wouldn’t say entropy is a property of a system, but a property of an observer who describes a system.”,,,
    – per quanta magazine

    The preceding finding from quantum information theory is simply devastating to the reductive materialistic foundation of Darwinian evolution.

    Whereas Darwinists, because of their reductive materialistic framework, deny the existence of anything beyond space and time, especially denying that an ‘outside observer’, i.e. God, could possibly be directing embryological development, on the other hand, Christianity just so happens to give us an adequate causal account for exactly Who this outside observer might be Who is imparting this massive amount of positional information into developing embryos. As Hebrews chapter 4 verse 13 states, “And no creature is hidden from his sight, but all are naked and exposed to the eyes of him to whom we must give account.”

    Hebrews 4:13
    And no creature is hidden from his sight, but all are naked and exposed to the eyes of him to whom we must give account.

    And as Psalm 139:13-14 states, “For You formed my inward parts; You covered me in my mother’s womb. I will praise You, for I am fearfully and wonderfully made;”

    Psalm 139:13-14
    For You formed my inward parts;
    You covered me in my mother’s womb.
    I will praise You, for I am fearfully and wonderfully made;
    Marvelous are Your works,
    And that my soul knows very well.

    And let’s not forget John 1:4

    John 1:4
    In him was life, and that life was the light of all mankind.

  3. 3
    Seversky says:

    That “blueprint” is a poor analogy for our genome is not a new idea. It has been recognized for a long time. For example, there’s this pop-sci piece from 2012:

    DNA Is Not a Blueprint: How Genes Really Work

    Sequencing of a fetal genome from parental samples demonstrates how we have advanced in genetic analyses, but the title of a June 6 article in The New York Times, “DNA Blueprint for Fetus Built Using Tests of Parents,” gives me pause. While the content does reflect a few interviews where researchers caution against overemphasizing what DNA sequences can tell us, the majority of the public reading the headline will see, yet again, an oversimplified and potentially damaging version of what we actually know about genetics.

    Genes play an important role in our development and functioning, not as directors but as parts of a complex system. “Blueprints” is a poor way to describe genes. It is misleading to talk about genes as doing things by themselves. There are very few instances of direct gene-to-trait scenarios, even in well known “genetic” disorders. Traits emerge from the interactions of genes and a range of developmental and environmental influences, and similar DNA sequences often produce slightly different outcomes. Our DNA influences who we are, but not in a linear or easily described manner. (See here for more.)

    DNA contains basic information that, when combined with the appropriate organic structures (in the egg) and context (the mother’s uterus), will facilitate the growth of a single cell (the combined sperm and egg) into a multibillion-cell person. Note that I say “facilitate,” not “determine.” The DNA is not the blueprint of life; rather, it contains many of the basic codes and signals for the development of an organism. At its core DNA contains the basic information needed to assemble molecules called “proteins,” which are the building blocks of our bodies, and it also acts to regulate how and where different proteins are made and used.

    Genes contain information, but the actual relationship between genes and our bodies and behavior is complicated. Chemical interactions inside our cells, interactions between cells, and developmental processes above the level of DNA occur throughout the life span. Most one-gene-to-one-trait analogies are unrealistic. For example, although your hands are composed of numerous proteins that emerge from information in your DNA, hands themselves are not the product of a “hand gene.” Hands are the product of a developmental program in which DNA plays an important, but not exclusive, role.

  4. 4
    ET says:

    seversky doesn’t grasp the fact that if the DNA is NOT a blueprint then changes to the DNA cannot produce the diversity of life starting from some unknown populations of prokaryotes.

  5. 5
    jawa says:

    At a meeting of the physiology elite of the world Denis Noble was asked the first question: what is a gene? His initial response was straightforward: nobody really knows.

  6. 6
    Seversky says:

    Bornagain77 @ 2

    Then that gives us a rough ballpark estimate of around 300 trillion times 100 million pages of Encyclopedia Britannica. Or about 300 trillion times the information content contained within the books of all the largest libraries in the world. Needless to say, that is a massive amount of positional information that is somehow coming into a developing embryo from the outside by some non-material method.

    … the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000.

    Yes, that’s an astronomical amount of information. The chances of such entities ‘poofing’ into existence fully-formed are hugely improbable.

    Just as well nobody is suggesting that they did – apart from believers, that is.

  7. 7
    bornagain77 says:

    Seversky I did not claim that embryos developing into adult organisms magically ‘poofed’ into existence,

    I claimed, via thermodynamic considerations, that a massive amount of information must be coming into a developing embryo during development, in order to give the adult organism its final shape, and I also claimed that the reductive materialism of Darwinian evolution is a complete loss to explain where that massive amount of information might be coming from. Whereas, on the other hand, recent advances in quantum information theory which show that “entropy is not a property of a system, but a property of an observer who describes a system.”, gives the Theist in general, and ID advocate in particular, empirical support for his claim that Intelligence is necessary in order to explain where this massive amount of information is coming from.

    It is simple science Seversky. Not ‘magic’

    But then again, I can easily see where Darwinists would confuse simple science with magic.

    Darwin’s Magic Evolutionary Ideology – April 2019
    Excerpt: At almost every step in Darwin’s theory of evolution someone has to pull a rabbit out of a black box. Darwin’s theory of evolution might as well be called Merlin’s theory of evolution. It is long on fantastic narrative and magic tricks and short on empirical evidence.
    https://www.timesexaminer.com/mike-scruggs/4926-darwin-s-magic-evolutionary-ideology

  8. 8
    jawa says:

    Seversky @3:
    From the article you cited:

    The DNA is not the blueprint of life; rather, it contains many of the basic codes and signals for the development of an organism. At its core DNA contains the basic information needed to assemble molecules called “proteins,” which are the building blocks of our bodies, and it also acts to regulate how and where different proteins are made and used.

    That text is inaccurate at best.   

    The DNA contains information that is used in order to make RNA molecules through a highly regulated process known as transcription.   That’s it.   

    The DNA information includes -besides the actual sequences that make the transcribed RNA molecules- control codes known as promoters, enhancers, TF binding sites (landing pads), etc.  BTW, the transcription is done by cellular machines that operate on the DNA. The DNA by itself couldn’t do much, if anything at all.

    Those transcribed RNA molecules are used in order to make proteins or to serve as regulatory signals. or as components of cellular machines.

    A substantial amount of information that is needed for the cells to work resides outside the DNA.

    They should be careful using “the” in their statements. When one says: this is THE medicine needed to cure the CoViD-19, it’s understood that this is it. We should use either “a” or “some” instead of “the”.

    Some basic English grammar knowledge could help that author to write his pop-sci articles.

    🙂

  9. 9
    JVL says:

    ET: seversky doesn’t grasp the fact that if the DNA is NOT a blueprint then changes to the DNA cannot produce the diversity of life starting from some unknown populations of prokaryotes.

    DNA is more of a recipe than a blueprint; i.e. it’s not a schematic for building a body with each part and area mapped out in some plan. Rather it’s a procedure to follow wherein certain sections are triggered by situations, most likely chemical triggers. This is why epigenetic factors can affect development without affecting the genome.

    So, yes, changes to the DNA will affect morphology because the ‘recipe’ has been changed.

    Here is a fairly accessible article: https://blogs.scientificamerican.com/observations/dna-is-not-a-blueprint/

    From the article:

    DNA is not a blueprint: it’s a recipe coding for thousands of different proteins that interact with each other and with the environment, just like the ingredients of a cake in an oven. Whereas a blueprint is an exact, drawn-to-scale copy of the final product, a recipe is just a loose plot that leaves much more room to uncertainty. Open a packet of cookies: each one was made from the same recipe and baked in the same conditions, but there are no two that are identical. Look closely, and you’ll spot hundreds of little differences: a burn here, a chocolate chip there, bumps and lumps appearing in distinct places, all because of chaotic interactions between the ingredients and the environment.

    And

    We do not inherit specific instructions on how to build a cell or an organ. Our DNA contains a list of biochemical ingredients (the proteins coded in the genes) and the basic rules for their assembly (some proteins are labeled as “master” and can control the activity of others, while others can start a dominolike cascade of events) but the pieces self-organize into biochemical pathways, cells and tissues without reading a manual. The genetic recipe for a cat will not give an elephant, but you can’t read the DNA of an individual and see a Mini-Me of his features.

    Bornagain77: I claimed, via thermodynamic considerations, that a massive amount of information must be coming into a developing embryo during development, in order to give the adult organism its final shape, and I also claimed that the reductive materialism of Darwinian evolution is a complete loss to explain where that massive amount of information might be coming from.

    What information needs to be ‘coming in’? Different parts of the DNA ‘recipe’ are triggered based on chemical considerations in the developing embryo. So, yes, a mother’s body chemistry can affect development but merely in triggering which proteins are produced and when.

  10. 10
    jawa says:

    JVL @9:

    In the article you cited, I see this text right at the start:

    “When I was a young student in Paris, the City of Love, girls at parties would what I did for a living. I still recall their unsettled looks when I answered “molecular biologist,” which would send them running to powder their noses. They never came back.”

    “…girls at parties would what I did for a living.”

    Is that statement correct? 🙂

    Also, this text:

    Make a Google search, and you’ll find hundreds of sources (including textbooks and leading scientists) describing DNA as the blueprint of life. It would be a great, easy-to-understand analogy, if it wasn’t wrong and outdated.

    Outdated? Does that mean that there was a time, not so long ago, when many thought that “blueprint of life” was correct? What changed since then that rendered “blueprint of life” outdated?
    More research discoveries, thank to advanced technology?
    Something else?

  11. 11
    ET says:

    DNA isn’t a recipe, either. There isn’t a genetic recipe for a cat. DNA does contain the coding for biologically relevant macromolecules.

  12. 12
    jawa says:

    The DNA binding sites for TFs contain codes for activator/inhibitor logical combinations associated with either transduction signal pathways that link the extra-cellular environmental signals to transcription regulation in the cell nucleus. Also relate to the intrinsic cell fate determinants that are segregated according to the symmetry breaking process that takes place before the stem cells divide. As we can see, there’s much outside the DNA per se.
    In addition wee still have the histone codes and all the epigenetic paraphernalia associated with the chromatin remodeling and the whole nine yards.
    The DNA contains information used for making RNA molecules. Some of those RNA molecules are spliced, sent to the cytoplasm and translated to proteins, using other complex cellular machinery.
    Code-wise, the DNA structure is more complex than they thought. But it seems like all that functional complexity is just the built-in paradigm for environmental adaptation and robustness.
    However, ongoing research should reveal more details of the multi-level controls for transcriptional regulation.
    We ain’t seen nothing yet.

  13. 13
    jawa says:

    Perhaps this helps to clarify what a recipe is:

    Paella Valenciana recipe:

    Ingredients:

    1 tablespoon olive oil 
    ½ (4 pound) whole chicken, cut into 6 pieces
    ½ (2 pound) rabbit, cleaned and cut into pieces
    1 head garlic, cloves separated and peeled
    1 tomato, finely chopped
    1 (15.5 ounce) can butter beans
    ½ (10 ounce) package frozen green peas
    ½ (10 ounce) package frozen green beans
    salt to taste
    1 teaspoon mild paprika, or to taste
    1 pinch saffron threads
    dried thyme to taste (optional)
    dried rosemary to taste (optional)
    4 cups uncooked white rice, or as needed

    Instructions:

    Step 1

    Heat a paella pan over medium-high heat, and coat with olive oil. Add the chicken, rabbit and garlic; cook and stir until nicely browned. Move the browned meat to the sides of the pan, and add the tomato, butter beans, peas, and green beans. Season with paprika, and mix well.

    Step 2

    Fill the paella pan almost to the top with water, measuring the water as you put it in. This is to help you to determine how much rice to add, as paella pans come in different sizes. Bring to a boil. Simmer for about 1 hour to make a nice broth.

    Step 3

    Season with a generous amount of salt, and just enough saffron to make a nice yellow color. Season with thyme and rosemary if desired. The goal is to make a rich tasting broth that will soak into the rice to make it delicious. Stir in half as much rice as the amount of water in the pan. Cover, reduce heat to low, and simmer until all of the liquid has been absorbed, about 20 minutes.

    Please, note that even someone like me, who only knows how to wash dishes in the kitchen, could make a paella just by carefully following this recipe.   

    With the information stored in the DNA the cell couldn’t do much, if anything at all, without additional extra-DNA information.   

    https://www.allrecipes.com/recipe/73337/authentic-paella-valenciana/

  14. 14
    JVL says:

    Jawa: Is that statement correct?

    What about when you said: “In addition wee still have the histone codes . . . ” and “Also relate to the intrinsic cell fate determinants that are segregated according to the symmetry breaking process . . . ” Everyone makes mistakes.

    Outdated? Does that mean that there was a time, not so long ago, when many thought that “blueprint of life” was correct? What changed since then that rendered “blueprint of life” outdated?
    More research discoveries, thank to advanced technology? Something else?

    I don’t know but I’m happy to concentrate on what is correct rather than on past misrepresentations by some writers.

    With the information stored in the DNA the cell couldn’t do much, if anything at all, without additional extra-DNA information.

    As I said, triggers outside of DNA activate certain regions while others are always active.

    DNA as a ‘recipe’ is just an analogy, like trying to understand electricity by comparing it to water flow. It’s not going to hold 100%, no one said it does. But it’s definitely NOT a ‘blueprint’. That was my main point.

  15. 15
    JVL says:

    ET: DNA isn’t a recipe, either. There isn’t a genetic recipe for a cat. DNA does contain the coding for biologically relevant macromolecules.

    Yes, referring to it as a recipe is just an analogy. The main thing I wanted to dispute was that DNA is NOT a blueprint. I think we agree on that.

  16. 16
    bornagain77 says:

    At 9 JVL falls back on the old Darwinian claim that.

    DNA is more of a recipe than a blueprint;

    JVL even referenced an article which states,

    “DNA is not a blueprint: it’s a recipe coding for thousands of different proteins that interact with each other and with the environment, just like the ingredients of a cake in an oven.”

    Yet as Jawa and ET pointed out, even the analogy that DNA is a recipe, i.e. a dedicated set of instructions, fails to tell us how an organism might achieve its final form.

    As Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy, states, “Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.”

    The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disordered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy
    http://darwins-god.blogspot.co.....rt-ii.html

    Indeed far from DNA being a recipe, i.e. a dedicated set of instructions, and as Ken Richardson, formerly Senior Lecturer in Human Development at the Open University (U.K.). states, “Instructions are created on the hoof, far more intelligently than is possible from dumb DNA. That is why today’s molecular biologists are reporting “cognitive resources” in cells; “bio-information intelligence”; “cell intelligence”; “metabolic memory”; and “cell knowledge”—all terms appearing in recent literature.1,2 “Do cells think?” is the title of a 2007 paper in the journal Cellular and Molecular Life Sciences.3 On the other hand the assumed developmental “program” coded in a genotype has never been described.”

    Is The Age Of The Gene Finally Over? – January 5, 2019
    Excerpt: So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA. That is why today’s molecular biologists are reporting “cognitive resources” in cells; “bio-information intelligence”; “cell intelligence”; “metabolic memory”; and “cell knowledge”—all terms appearing in recent literature.1,2 “Do cells think?” is the title of a 2007 paper in the journal Cellular and Molecular Life Sciences.3 On the other hand the assumed developmental “program” coded in a genotype has never been described.
    It is such discoveries that are turning our ideas of genetic causation inside out. We have traditionally thought of cell contents as servants to the DNA instructions. But, as the British biologist Denis Noble insists, “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.” …
    – Ken Richardson, formerly Senior Lecturer in Human Development at the Open University (U.K.)
    https://uncommondescent.com/genetics/is-the-age-of-the-gene-finally-over/

    Thus JVL’s analogy that DNA is a ‘recipe’, i.e. a set of instructions, is, as Wolfgang Pauli would have put it, “Not Even Wrong!”

    JVL then goes on to quote me,,,

    Bornagain77: I claimed, via thermodynamic considerations, that a massive amount of information must be coming into a developing embryo during development, in order to give the adult organism its final shape, and I also claimed that the reductive materialism of Darwinian evolution is a complete loss to explain where that massive amount of information might be coming from.

    JVL then states,

    What information needs to be ‘coming in’? Different parts of the DNA ‘recipe’ are triggered based on chemical considerations in the developing embryo. So, yes, a mother’s body chemistry can affect development but merely in triggering which proteins are produced and when.

    LOL, “What information needs to be ‘coming in’?” Oh, I don’t know JVL, could it possibly be “the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000” which I referenced at post 2?

    In a TED Talk, (the Question You May Not Ask,,, Where did the information come from?) – November 29, 2017
    Excerpt: Sabatini is charming.,,, he deploys some memorable images. He points out that the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000. Later he wheels out the entire genome, in printed form, of a human being,,,,:
    [F]or the first time in history, this is the genome of a specific human, printed page-by-page, letter-by-letter: 262,000 pages of information, 450 kilograms.,,,
    – per evolution news

    Then, after feigning ignorance as to exactly what type of information I was talking about, JVL falls back to that old Darwinian canard that ‘life is just complicated chemistry’.

    Different parts of the DNA ‘recipe’ are triggered based on chemical considerations in the developing embryo.

    As should be needless to say, appealing to ‘chemical considerations’ does not even begin to tell us how an organism might achieve its basic form. As the following article studying morphogenesis in fruit flies stated, “It is hard not to be impressed how a repeatable form reliably emerges despite considerable variation in both genes and environment.”

    Criticality in morphogenesis – September 17, 2013
    Excerpt: In many regards, a brief time-lapse video can teach more about embryonic development than any amount of reading. It is hard not to be impressed how a repeatable form reliably emerges despite considerable variation in both genes and environment. While it had been hoped that concepts borrowed from statistical mechanics or the ideas of self-organized criticality could help to create some kind of physics-based theory of development, much of what has been done lies only at the level of metaphor. In a paper just released to ArXiv, William Bialek and his colleagues from Princeton University, have taken their search for the signature of criticality in a more specific direction. They looked at a particular set of transcription factors in Drosophila embryos which control spatiotemporal development. By analyzing fluctuations in the expression levels of these so-called gap genes, they found evidence for critical (fine) tuning in this particular network.
    http://phys.org/news/2013-09-c.....nesis.html

    And as the following article stated, ,,,”Organoid formation itself demonstrates that cells can become organized in the absence of predetermined long-range external patterning influences such as morphogen gradients or mechanical forces, which are a cornerstone of classic developmental biology.”

    From Genome to Body Plan: A Mystery – January 24, 2017
    Excerpt: Decoding genomes has been one of the most important advances of the last sixty years, but it’s really just a start of a far larger mystery: the mystery of development.,,,
    “A long-term aim of the life sciences is to understand how organismal shape is encoded by the genome. An important challenge is to identify mechanistic links between the genes that control cell-fate decisions and the cellular machines that generate shape, therefore closing the gap between genotype and phenotype. “,,,
    The authors marvel at how “organoids” emerge from induced pluripotent stem cells.,,, After thinking about it, they admit that more must be going on.
    ,,,”Organoid formation itself demonstrates that cells can become organized in the absence of predetermined long-range external patterning influences such as morphogen gradients or mechanical forces, which are a cornerstone of classic developmental biology. This unexpected lack of requirement for long-range pre-patterning has led to organoid formation being described as an example of ‘self-organization’, which is defined classically as the spontaneous emergence of order through the interaction of initially homogeneous components.”,,,
    http://www.evolutionnews.org/2.....03451.html

    In fact, ‘chemical considerations’ can’t even explain how proteins achieve their final folded form, much less can ‘chemical considerations’ explain how an organism might achieve its final form:

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: 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.
    http://www.evolutionnews.org/2.....65521.html

    In fact, in order to explain how a protein achieves its final folded form, (far from appealing to ‘chemical considerations’ as JVL did), it is instead necessary to appeal to quantum principles

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

  17. 17
    bornagain77 says:

    And indeed, quantum coherence is now found in proteins, DNA, as well as in a wide range of other important biomolecules

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    “What happens is this classical information (of DNA) is embedded, sandwiched, into the quantum information (of DNA). And most likely this classical information is never accessed because it is inside all the quantum information. You can only access the quantum information or the electron clouds and the protons. So mathematically you can describe that as a quantum/classical state.”
    Elisabeth Rieper – Classical and Quantum Information in DNA – video (Longitudinal Quantum Information resides along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

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

    Of note, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, effect:

    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

    Coherence and nonlocality
    Usually quantum nonlocality is discussed in terms of correlated multiparticle systems such as those discussed by John Bell in his famous 1964 theorem and then later clarified by GHZ, David Mermin and others.
    But more striking and significant is the qualitative nonlocal phenomena associated with coherent states,,,,
    In fact, theoretically these two kinds of nonlocality have precisely the same basis: the unmeasured singlet state uncovered by EPR is a coherent ‘pure state’ despite its spatial extension, and when the parts are realized in a measurement (a la Bell) this coherence is harvested or cashed in.
    Whereas the “EPR” connections are ephemeral and fragile, some forms of nonlocal coherence are robust.
    http://www.nonlocal.com/hbar/n.....rence.html

    In fact, “the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles.”

    Physicists find extreme violation of local realism in quantum hypergraph states – Lisa Zyga – March 4, 2016
    Excerpt: Many quantum technologies rely on quantum states that violate local realism, which means that they either violate locality (such as when entangled particles influence each other from far away) or realism (the assumption that quantum states have well-defined properties, independent of measurement), or possibly both. Violation of local realism is one of the many counterintuitive, yet experimentally supported, characteristics of the quantum world.
    Determining whether or not multiparticle quantum states violate local realism can be challenging. Now in a new paper, physicists have shown that a large family of multiparticle quantum states called hypergraph states violates local realism in many ways. The results suggest that these states may serve as useful resources for quantum technologies, such as quantum computers and detecting gravitational waves.,,,
    The physicists also showed that the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles. In addition, even if a quantum hypergraph state loses one of its particles, it continues to violate local realism. This robustness to particle loss is in stark contrast to other types of quantum states, which no longer violate local realism if they lose a particle. This property is particularly appealing for applications, since it might allow for more noise in experiments.
    http://phys.org/news/2016-03-p.....alism.html

    “Non-local”, beyond space and time effects, dictating what final form a protein may take, is about as far removed from ‘chemical considerations’ as one can get.

    Indeed, advances in quantum biology have now falsified the entire reductive materialistic foundation that Darwinian evolution is built upon:

    Darwinian Materialism vs. Quantum Biology – Part II – video
    https://www.youtube.com/watch?v=oSig2CsjKbg

    Whereas on the other hand, and as should be needless to say, finding “non-local”, beyond space and time quantum effects,, (i,e, quantum entanglement and coherence), on a massive scale within molecular biology, is VERY friendly to Theistic, even to Christian, considerations, For instance Colossians 1:17,,,

    Colossians 1:17
    He is before all things, and in him all things hold together.

  18. 18
    JVL says:

    Bornagain77:

    DNA as a ‘recipe’ is just an analogy so the comparison is not all that tight in ways. What I was really trying to get across was that DNA is NOT a blueprint. That is very, very clear.

    LOL, “What information needs to be ‘coming in’?” Oh, I don’t know JVL, could it possibly be “the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000” which I referenced at post 2?

    Umm . . . DNA ‘codes’ for certain proteins and their production is controlled by other parts of the DNA and the triggers are environmental conditions in the developing embryo. There’s no need for DNA to record how to build an ‘infant’ atom by atom. It builds an ‘infant’ protein by protein.

    Look, forget the recipe analogy if you don’t like it. But can we all agree that DNA is NOT a blueprint?

  19. 19
    jawa says:

    JVL @14,

    “Everyone makes mistakes.”

    Are you joking?

    Are you comparing mistakes made in comments posted in this blog to errors left in an article published in the Scientific American online magazine?

    Really?

    Are you serious?

    I’ll assume you’re joking.

    🙂

  20. 20
    jawa says:

    JVL @14:

    “I don’t know but I’m happy to concentrate on what is correct rather than on past misrepresentations by some writers.”

    By some writers? Are you joking again?

    This is (again) from the article you cited:

    Make a Google search, and you’ll find hundreds of sources (including textbooks and leading scientists) describing DNA as the blueprint of life. It would be a great, easy-to-understand analogy, if it wasn’t wrong and outdated.

    Did you read it well?

    “hundreds of sources (including textbooks and leading scientists)”

    Do you call that “some writers”?

    Please, let’s be serious.

  21. 21
    bornagain77 says:

    JVL states,

    There’s no need for DNA to record how to build an ‘infant’ atom by atom. It builds an ‘infant’ protein by protein.

    Apparently JVL did not bother to read my posts where I commented on the inability of Darwinian materialism to even be able to explain how a single protein folds into its final shape, or else he would not have made such an unsupported claim.

    Moreover, DNA certainly does not tell proteins how to build “an ‘infant’ protein by protein.” So you are either grossly ignorant or purposely lying.

    “Since the 1980s, developmental and cell biologists such as Brian Goodwin, Wallace Arthur, Stuart Newman, Fred Nijhout, and Harold Franklin have discovered or analyzed many sources of epigenetic information.
    Even molecular biologists such as Sidney Brenner, who pioneered the idea that genetic programs direct animal development, now insist that the information needed to code for complex biological systems vastly outstrips the information in DNA.
    DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. Genes and proteins are made from simple building blocks—nucleotide bases and amino acids, respectively—arranged in specific ways. Similarly, distinctive cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans.”
    [S.Meyer, ‘Darwin’s Doubt’, Ch.14]

  22. 22
    jawa says:

    JVL @14:

    “DNA as a ‘recipe’ is just an analogy, like trying to understand electricity by comparing it to water flow. It’s not going to hold 100%, no one said it does.”

    DNA as a recipe seems like a poor analogy at best. See the example of “recipe” @13.

    It’s a criteria library used in many cellular processes in order to perform a multitude of functions.

    Different cellular processes may access parts of that huge sophisticated criteria library known as DNA to get specific information to be applied downstream in the same or other processes: RNA molecules (both pro-mRNAs and/or RNA transcripts to be used as regulatory signals or mechanism components), by setting up promoter keys according to logic conditions previously established within the binding sites or the enhancers and the epigenetic settings (histone codes, etc).

    Rather than a recipe, I would call the DNA a criteria library. DNA doesn’t seem to contain the chronological steps that are expected in a recipe. The chronology is determined by the cellular processes associated with extra-cellular events.

  23. 23
    PaV says:

    At long last–real progress!

    And, as concluded here at UD before, the answer to the question, “What came first, the chicken or the egg”? is this: the egg!!

    The upshot of this article is that the regulatory complexes operating within the cell are the true repositories of information. This is actually a revolutionary view. Darwinism will fall.

  24. 24
    Seversky says:

    Sounds like a paradigm shift to me. Better alert Susan Mazur.

  25. 25
    JVL says:

    Jawa: Are you joking? Are you comparing mistakes made in comments posted in this blog to errors left in an article published in the Scientific American online magazine? Really? Are you serious? I’ll assume you’re joking.

    Gosh, you found a mistake in an online article which did not affect understanding of the main point of the article. So what? Everyone makes mistakes, just like you did.

    Did you read it well? “hundreds of sources (including textbooks and leading scientists)” Do you call that “some writers”? Please, let’s be serious.

    Good thing someone is working to correct past mistakes isn’t it? Is your real point that the wrong impression has been given out in the past or shall we discuss what is correct? I’d rather spend my time discussing what is correct. If you want to spend your time complaining about incorrect interpretations then complain to the authors and publishers; they should be told!

  26. 26
    jawa says:

    JVL @25,

    Everyone makes mistakes, that’s why they have proofreaders that detect errors before the text goes public.

    Yours is a cheap excuse that doesn’t work in this case.

    Try again.

    🙂

  27. 27
    jawa says:

    JVL @25,

    “Is your real point that the wrong impression has been given out in the past or shall we discuss what is correct? “

    No, you didn’t get it yet.

    The real point (not only mine) is to highlight errors that have been made in the past because many scientists have been narrow minded, lacking humility to search for answers instead of jumping into conclusions before verifying them.

    In some cases that narrow mindedness has caused delays in scientific research that could have been prevented otherwise. It’s a pathetic reality nobody can honestly deny.

    Barking up the wrong tree is not a scientific attitude.

    Do you understand this now?

    Herd mentality consensus may not work in science.

    Do you want to understand it?

    Give it a try.

    As IBM used to remind many years ago: think.

    🙂

  28. 28
    jawa says:

    DNA may not be life’s instruction book—just a jumbled list of ingredients
    by Kimbra Cutlip, University of Maryland

    For example, the gene for eye color exists in every cell of the body, but the process that produces the protein for eye color only occurs during a specific stage of development and only in the cells that constitute the colored portion of the eyes. That information is not stored in the DNA.

    Actually, it’s much more interesting than that.

    Part of the information for the given example is stored in the DNA: the actual “gene” code to be translated to protein, the introns to be spliced out, the ncRNA transcripts that could intervene in some regulatory processes, the promoter region (TATA box, etc), the TF-binding sites (landing pads) near the promoter regions, the enhancers, the DNA bending proteins attached to the enhancers, etc.

    Other required information for the given example could be “stored” in the epigenetic markers, in the histone codes, in the extra-membrane receptor and the transduction signaling pathways (cascades) that must produce the right code to dovetail the TF-binding sites containing the patterning code, etc.

    The real deal is that all that stuff must match, which means that the whole choreography and its accompanying orchestration must have been designed to match. How else could one explain it?

    As Salieri told the catholic priest that visit him in the Oscar-winning movie “Amadeus”, referring to WA Mozart’s music, we’re staring at an absolute beauty. 🙂

    That’s why the heated discussions on multi-verse to cover the fine-tuning, Penrose’s cyclical eons, dark matter/energy, inflation, and all that paraphernalia, could be kind of entertaining, but the real issue is how do we explain the undeniable evidences of complex functionally specified information that are increasingly revealed by fascinating discoveries made by seriously dedicated biology researchers these days and in the days to come?

    At the end of the OP-cited article:

    generalization of memory and encoding via the entity-sensor-property framework sheds novel insights into evolution and biological complexity and suggests important revisions to existing paradigms in genetics, epigenetics and development

    Can someone honestly offer an alternative?

  29. 29
    jawa says:

    Did Dr Lee Cronin get the Evo2.0 $10M OOL prize yet?

    🙂

  30. 30
    ET says:

    There isn’t any analogy between DNA and a recipe. And there isn’t any need to put scare-quotes around the word code when referring to DNA coding for proteins.

    There isn’t anything in DNA that determines form. There isn’t anything in DNA that determines what type of organisms will develop. And that means neither Darwin nor anyone who accepts universal common descent has a mechanism capable of producing the diversity of life

  31. 31
    JVL says:

    Jawa: Everyone makes mistakes, that’s why they have proofreaders that detect errors before the text goes public. Yours is a cheap excuse that doesn’t work in this case. Try again.

    You are making a mountain out of a molehill. I’ve found typographical erros in printed books for as long as I can remember. Lots of websites allow the authors to publish their posts after only a cursory glance by their editor. AND, again, the mistake you pointed out was very peripheral to the main point of the post. Which was very, very clear.

    No, you didn’t get it yet. The real point (not only mine) is to highlight errors that have been made in the past because many scientists have been narrow minded, lacking humility to search for answers instead of jumping into conclusions before verifying them.

    It’s not perfect but that is exactly why reputable scientific journals have a system of peer-review. Most research papers are not just tossed onto a page without several people taking a good look at them. And there is always someone out there who would love to take someone else down a peg or two. And all results can be tested again by anyone who is interested in double checking. If you think most of recent biological research is rubbish then you are welcome to check it out yourself. Or do work you think IS pertinent and on target.

    In some cases that narrow mindedness has caused delays in scientific research that could have been prevented otherwise. It’s a pathetic reality nobody can honestly deny.

    For example?

    Barking up the wrong tree is not a scientific attitude. Do you understand this now? Herd mentality consensus may not work in science. Do you want to understand it? Give it a try. As IBM used to remind many years ago: think.

    Just out of curiosity, what scientific work have you done and published? Does your opinion come from experience doing the work?

  32. 32
    JVL says:

    ET: There isn’t anything in DNA that determines form. There isn’t anything in DNA that determines what type of organisms will develop.

    Well, what do you think the DNA does then? What’s it for? How do mutations affect its function?

  33. 33
    Jim Thibodeau says:

    @JVL Do you recall when ET admitted that he’s never bothered to show his revolutionary new infinity series math to any mathematician? Or put it forth to the mathematical community in any way? That was a tacit admission that he knows he full of caca.

    When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll.

  34. 34
    ET says:

    Yes, Jimbo, and I explained why. But thanks for continuing to prove that you are willfully ignorant. You don’t know anything about science, Jim. That is why you avoid all discussions pertaining to science.

  35. 35
    JVL says:

    JimThibodeau: When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll.

    I try and treat everyone with respect and give them the benefit of the doubt. Otherwise we’re just taunting each other and not getting anywhere.

  36. 36
    ET says:

    It’s very telling that evos always try to make this personal when there unscientific ways are exposed.

    DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product.

    And guess what? Evos don’t have anything to account for any of that.

  37. 37
    ET says:

    When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll.

    You just described over 99% of all evolutionists. Nice own goal.

  38. 38
    JVL says:

    ET: DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product.

    How can mutations affect the coding sequence but have no affect on the final product? Does the coding sequence not matter then? At all? What’s it for then? You did say “DNA controls and influences development” but then you said changes don’t affect the final product.

  39. 39
    ET says:

    JVL:

    How can mutations affect the coding sequence but have no affect on the final product?

    Take a biology course. Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101.

    Andreas Wagner’s book goes over that- that proteins are robust in that they can accept changes to the sequence but not change the final protein product. But what is even stranger than that is there can be a synonymous change in the sequence that does have an effect on the protein.

  40. 40
    JVL says:

    ET: Take a biology course. Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101.

    Depends on the mutation then doesn’t it?

    Andreas Wagner’s book goes over that- that proteins are robust in that they can accept changes to the sequence but not change the final protein product. But what is even stranger than that is there can be a synonymous change in the sequence that does have an effect on the protein.

    Again, that depends on the mutation doesn’t it? Some mutations break things as you’ve pointed out many times. Which means there is a change in the final product. So, it’s a little bit more complicated.

  41. 41
    Jim Thibodeau says:

    @JVL If the DNA doesn’t matter, then that destroys one of intelligent design’s biggest arguments. I mean, it was a dumb, clueless argument to begin with, but that just wrecks it further.

  42. 42
    ET says:

    Jimmie T, strawman hunter. No one has said that DNA doesn’t matter. Evos are such a clueless lot.

  43. 43
    ET says:

    JVL:

    Depends on the mutation then doesn’t it?

    Does it? Care to try to make a case?

    Creating a broken protein doesn’t help you, duh. But it is all your side has- a mechanism that can break things.

  44. 44

    #41

    A living cell is a description-based organization. The quiescent description requires a multi-referent symbol system (I.e. discontinuous association); the onset of spatial orientation, a coordinated set of non-integrable constraints, and semantic closure in order to even begin to function — to persist over time.

    It is all just as it was predicted to be, and fully documented in the literature.

    You are whistling past the graveyard. This is regularly demonstrated among materialists by their uniform inability to attack the observations and history, instead of their opponents.

  45. 45
    JVL says:

    ET: Does it? Care to try to make a case?

    You said: DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product.

    That’s not qualified; DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product.

    Then you said: Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101.

    So some changes do make a difference, yes? But you think most do not? There are few, if any changes that affect functionality of the organism?

    What about repeats of base pairs or even whole genes or chromosomes? With repeats nothing is changed there’s just an extra copy. Does that have an effect on the organism?

    Upright BiPed: This is regularly demonstrated among materialists by their uniform inability to attack the observations and history, instead of their opponents.

    I’m attacking no one. I’m asking questions about the science. Do you agree with ET when he (?) says: Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. Is he just hedging his bets by saying potentially?

  46. 46
    ET says:

    Do you have any evidence that unguided processes can produce a protein? No. Do you have any evidence that unguided processes can produce coding DNA? No.

    Do you know what determines form? No.

    Mutations don’t have to occur in coding sequences. hence the word “potentially”. It would be better to discuss biology with people who know and understand the subject.

  47. 47

    .
    JVL, as you can see, my comment wasn’t addressed to you. You have already suggested that you don’t know enough to carry on a conversation about the evidence for design in biology (and apparently dis-interested in learning anything), and I have agreed with you.

  48. 48
    JVL says:

    ET: Do you have any evidence that unguided processes can produce a protein? No. Do you have any evidence that unguided processes can produce coding DNA? No. Do you know what determines form? No.

    Well, I think there are answers to those questions but I’d really like to hear what you think first if that’s okay!

    Mutations don’t have to occur in coding sequences. hence the word “potentially”. It would be better to discuss biology with people who know and understand the subject.

    I’m still trying to understand how mutations can affect coding sequences but have no affect on the final product. If things are produced in a different sequence then you get a different folding of a protein at the very least I should think.

    And what kind of changes can proteins take and not be altered? Do you have any examples?

  49. 49
    JVL says:

    Upright BiPed: JVL, as you can see, my comment wasn’t addressed to you.

    Yes, I see that now, my apologies.

  50. 50
    ET says:

    As I said, take a biology course. Most proteins have more than one coding sequence that produces the same functional protein. Andreas Wagner goes over this in his book. He said that some proteins can handle over 80% change in sequence and still be the same functional protein. And some can’t take any hits without becoming useless or harmful- sickle-cell anemia is one such instance.

  51. 51
    JVL says:

    ET: And some can’t take any hits without becoming useless or harmful- sickle-cell anemia is one such instance.

    So, again, I’m asking: what kind of changes can occur which have no affect on the “final product” and what changes are important?

    And, the obvious follow-on question would be: are any of these changes directed and how can you tell which ones are?

  52. 52
    ET says:

    JVL:

    what kind of changes can occur which have no affect on the “final product”

    Synonymous changes can have either no effect or be detrimental. Then there are changes at the amino acid level, ie one hydrophobic amino acid for another. Or one hydrophilic amino acid for another.

    Opsin genes appear to be tunable. It seems that specific differences allow for vision @ different wavelengths.

    And any mutational sequence that requires more than 3 specific mutations would be a good candidate for directed mutations.

  53. 53
    JVL says:

    ET: Synonymous changes can have either no effect or be detrimental. Then there are changes at the amino acid level, ie one hydrophobic amino acid for another. Or one hydrophilic amino acid for another.

    Okay. How common are those?

    Opsin genes appear to be tunable. It seems that specific differences allow for vision @ different wavelengths.

    Hang on, does that mean some mutations do affect function? Which ones do and which ones don’t?

    And any mutational sequence that requires more than 3 specific mutations would be a good candidate for directed mutations.

    Okay. Why three? What about two? What about one? What about gene duplication? What about chromosomal duplication? With duplications you’re implying there should be no affect but I don’t think that is the case. Certainly not with chromosomes.

  54. 54
    ET says:

    JVL:

    How common are those?

    Very

    Hang on, does that mean some mutations do affect function?

    If the design allows for it.

    Why three?

    More than 3. Because waiting for two mutations is close to impossible for populations like primates. Gene duplication is useless without a new binding site. And even then it has to end up on the proper part of the spool to be of any use. After all that all you are doing is getting more of an existing protein. One that is free to float around and get in the way.

    With duplications you’re implying there should be no affect but I don’t think that is the case.

    You don’t get to tell me what I am implying. I was talking specifically about changes in the sequence of an existing protein. A gene duplication will bring on the same existing protein, if it gets regulated at all.

    Chromosomes never change the end product. You get a deformed human or sterile mules. The same body plan as the original.

  55. 55
    JVL says:

    ET: Chromosomes never change the end product. You get a deformed human or sterile mules. The same body plan as the original.

    I would call that a different end product but seeing how you are using the term clears up some of my questions to you.

    That’s it, thanks.

  56. 56
    bornagain77 says:

    Previously at post 9, JVL claimed that DNA being “triggered based on chemical considerations” was enough, in and of itself, to explain how an adult organism might achieve its basic form and or shape during embryological development.

    “Different parts of the DNA ‘recipe’ are triggered based on chemical considerations in the developing embryo.”
    – JVL

    Here is a video that shows JVL’s claim is patently false,

    The (Electric) Face of a Frog – video
    https://www.youtube.com/watch?v=0VULjzX__OM

    As the researcher stated, “I would never have predicted anything like it. It’s a jaw dropper.”

    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

    In fact, altering the bio-electric field without altering the underlying molecules, affects the three-dimensional shape of the developing embryo.

    podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes outside of DNA are discussed) – Oct. 2015 – 4:45 minute mark
    5.Bio-electric code – altering the bio-electric field without altering the underlying molecules affects the three-dimensional shape of the developing embryo
    http://www.discovery.org/multi.....more-31141

    In the case of frog embryos, “artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm.

    Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation – January 2013
    Excerpt: A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes.
    http://www.ncbi.nlm.nih.gov/pubmed/23802040

    To date, no one knows how the ‘bioelectric code’ is supposedly encoded within the developing embryo’s molecules, as is presupposed with Darwinian materialism, and although there is great interest in understanding exactly how such a ‘jaw dropper’ happens

    The bioelectric code: An ancient computational medium for dynamic control of growth and form. – 2017
    Excerpt: We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.
    https://www.ncbi.nlm.nih.gov/pubmed/28855098

    As the following article states, “such manipulations have produced conflicting outcomes experimentally, which poses a substantial barrier to understanding the fundamentals of bioelectrical reprogramming.”

    The Bioelectric Code: Reprogramming Cancer and Aging From the Interface of Mechanical and Chemical Microenvironments – March 2018
    Excerpt: there is considerable interest in manipulating Vm both to treat cancer as well as to regenerate organs damaged or deteriorated during aging. However, such manipulations have produced conflicting outcomes experimentally, which poses a substantial barrier to understanding the fundamentals of bioelectrical reprogramming.
    https://www.frontiersin.org/articles/10.3389/fcell.2018.00021/full

    To say that all of this is antagonistic towards the presuppositions of Darwinian materialism and favorable towards ID presuppositions would be an understatement.

    Verse:

    John 1:4
    In him was life, and that life was the light of all mankind.

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