Evolutionary biology Intelligent Design Orphan genes

At Phys.org: Uncharted genetic territory offers insight into human-specific proteins

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When researchers working on the Human Genome Project completely mapped the genetic blueprint of humans in 2001, they were surprised to find only around 20,000 genes that produce proteins. Could it be that humans have only about twice as many genes as a common fly? Scientists had expected considerably more.

Now, researchers from 20 institutions worldwide bring together more than 7,200 unrecognized gene segments that potentially code for new proteins. For the first time, the study makes use of a new technology to find possible proteins in humans—looking in detail at the protein-producing machinery in cells. The new study suggests the gene discovery efforts of the Human Genome Project were just the beginning, and the research consortium aims to encourage the scientific community to integrate the data into the major human genome databases.

Note that so-called orphan genes have been discussed in-depth at Evolution News:

Orphan genes (sometimes called ORFan genes in bacteria) are those open reading frames that lack identifiable sequence similarity to other protein-coding genes. Lack of similarity is hard to prove, given the size of the genomic universe. Methods vary from researcher to researcher, so each study needs to be evaluated carefully. There is also always the possibility that any given ORF has no function. No doubt some orphan genes will prove to be artifacts of incomplete evidence (see below). But orphan genes are a reality, nonetheless, based on numerous and substantial studies.

Thus, the existence and prevalence of orphan genes raises a number of significant questions.

Then there is the elephant in the room that evolutionary biologists don’t want to acknowledge. Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent.

Continuing with the Phys.org article…

New gene sequences remained out of reach

In the past few years, thousands of frequently very small open reading frames (ORFs) have been discovered in the human genome. These are spans of DNA sequence that may contain instructions for building proteins.

Traditionally, protein-coding regions in genes have been identified by comparing DNA sequences from multiple species: the most important coding regions have been preserved during animal evolution. But this method has a drawback: coding regions that are relatively young, i.e., that arose during the evolution of primates, fall through the cracks and are therefore missing from the databases.

So now the task is to integrate the largely ignored ORFs into the largest reference databases, because researchers have so far had to specifically search for them in the literature if they wanted to study them.

ORFs likely play a role in common diseases

Dr. Sebastiaan van Heesch, group leader at the Princess Máxima Center for pediatric oncology, says that their “research marks a huge step forward in understanding the genetic make-up and complete number of proteins in humans. It’s tremendously exciting to enable the research community with our new catalog. It’s too soon to say whether all of the unexplored sections of DNA truly represent proteins, but we can clearly see that something unexplored is happening across the human genome and that the world should be paying attention.”

“It is especially remarkable that most of these 7,200 ORFs are exclusive to primates and might represent evolutionary innovations unique to our species,” reports Jorge Ruiz-Orera, an evolutionary biologist working in Hübner’s lab at the MDC. “This shows how these elements can provide important hints of what makes us humans.”

Read the complete article at Phys.org.

Another “elephant in the room” is the question of how did the significant amount of information needed for novel protein-coding regions arise without intelligent design?

84 Replies to “At Phys.org: Uncharted genetic territory offers insight into human-specific proteins

  1. 1
    bornagain77 says:

    as to:

    “the most important coding regions have been preserved during animal evolution. But this method has a drawback: coding regions that are relatively young, i.e., that arose during the evolution of primates, fall through the cracks and are therefore missing from the databases.”

    There is a small problem with this Darwinian narrative. Specifically, “young” coding regions are found to be just as essential as the “important” older coding regions that have been supposedly ‘preserved’.

    A survey of orphan enzyme activities – 2007
    Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles.
    http://www.biomedcentral.com/1471-2105/8/244

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    – per science daily

    New genes in Drosophila quickly become essential. – December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/cont.....2.abstract

    Scientists Find Vital Genes Evolving in Genome’s Junkyard – Nov. 2020
    Excerpt:,,, Essential genes are often thought to be frozen in evolutionary time — evolving only very slowly if at all, because changing or dying would lead to the death of the organism.,,,
    This remarkable evolutionary conservation is a foundational concept in genome research.,,,
    “Not only is this (research) questioning the dogma, it is blowing the dogma out of the water,”,,,
    Long was so surprised in 2010, when he and his students “knocked down” 200 young, novel genes in Drosophila using a technique called RNA interference. Almost 30% of those young genes turned out to be essential; the flies died without them. Even more surprisingly, though, roughly the same percentage of old genes were essential — only about 25%-35% of them. Young genes were just as likely as old ones to encode essential functions.
    “I was really shocked and very excited,” Long said. “The old ideas of the field, we felt, were not right, not correct.” Because their discovery seemed so iconoclastic, Long says he decided to gather data carefully and use new technologies like CRISPR to test it further. His team updated their 2010 study in a recent preprint, which addressed some methodological challenges from the earlier study and expanded their analysis to 702 new Drosophila genes. The new paper reached the same general conclusions,,,
    “you really begin to question everything you think about in terms of biology, because you’re like, ‘Wait a minute. What is this?’,,,
    https://www.quantamagazine.org/scientists-find-vital-genes-evolving-in-genomes-junkyard-20201116/

    As to:

    “When researchers working on the Human Genome Project completely mapped the genetic blueprint of humans in 2001, they were surprised to find only around 20,000 genes that produce proteins. Could it be that humans have only about twice as many genes as a common fly? Scientists had expected considerably more.
    Now, researchers from 20 institutions worldwide bring together more than 7,200 unrecognized gene segments that potentially code for new proteins.,,,
    “It is especially remarkable that most of these 7,200 ORFs are exclusive to primates and might represent evolutionary innovations unique to our species,”

    First off, 7,200 Orphan genes roughly matches previous findings which found that up to a third of genes in a genome were Orphans.

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    https://www.newscientist.com/article/mg21729002-200-genes-from-nowhere-orphans-with-a-surprising-story/

    Mechanisms and dynamics of orphan gene emergence in insect genomes – January 2013
    Excerpt: Orphans are an enigmatic portion of the genome since their origin and function are mostly unknown and they typically make up 10 to 30% of all genes in a genome.
    http://gbe.oxfordjournals.org/.....l.pdf+html?

    Secondly, even though Orphan genes, in and of themselves, are enough to falsify Darwinian claims. That falsification from Orphan genes pales in comparison to the fatal blow that ‘alternative splicing’ does to Darwinian claims.

    Specifically, where differences are greatest between chimps and humans, (and between all other creatures), are not in the genetic sequences, (as great as those differences are turning out to be), but the greatest differences are instead found in alternative splicing patterns.

    As the following paper states, “A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,”

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    In fact, due to alternative splicing, “Alternatively spliced isoforms,,, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,” and “As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms,,”

    Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing – 2016
    In Brief
    Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,
    Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013).
    http://iakouchevalab.ucsd.edu/.....M_2016.pdf

    As should be needless to say, finding “perhaps a million distinct polypeptides obtained by post-translational modification” is simply completely devastating to the ‘bottom up’ reductive materialistic explanations of Darwinists.

    As Stephen Meyer stated in the following interview, “it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species.,,, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates,”

    An Interview with Stephen C. Meyer
    TT: Is the idea of an original human couple (Adam and Eve) in conflict with science? Does DNA tell us anything about the existence of Adam and Eve?
    SM: Readers have probably heard that the 98 percent similarity of human DNA to chimp DNA establishes that humans and chimps had a common ancestor. Recent studies show that number dropping significantly. More important, it turns out that previous measures of human and chimp genetic similarity were based upon an analysis of only 2 to 3 percent of the genome, the small portion that codes for proteins. This limited comparison was justified based upon the assumption that the rest of the genome was non-functional “junk.” Since the publication of the results of something called the “Encode Project,” however, it has become clear that the noncoding regions of the genome perform many important functions and that, overall, the non-coding regions of the genome function much like an operating system in a computer by regulating the timing and expression of the information stored in the “data files” or coding regions of the genome. Significantly, it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species. Yet, if alleged genetic similarity suggests common ancestry, then, by the same logic, this new evidence of significant genetic disparity suggests independent separate origins. For this reason, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates,
    http://www.ligonier.org/learn/.....-conflict/

    In short, the evidence from genetics, (and from many other lines of evidence), directly contrary to what Darwinists repeatedly claim, simply does not support the Atheist’s Darwinian ‘narrative’ that humans evolved from apes, but instead supports the Christian’s belief that God created humans uniquely, apart from the other creatures.

    Verse:

    Genesis 1:26-27
    Then God said, “Let Us make man in Our image, after Our likeness, to rule over the fish of the sea and the birds of the air, over the livestock, and over all the earth itself and every creature that crawls upon it.” So God created man in His own image; in the image of God He created him; male and female He created them.…

  2. 2
    EDTA says:

    So the number of protein-coding genes found in 2001 was a minimum, not the maximum. Hmm. Nobody in the ID world predicted that! [sarcasm]

  3. 3
    relatd says:

    EDTA at 2,

    Those looking at a Darwinian explanation are finding more and more surprises and therefore, fewer and fewer reasons to believe that these surprises happened through blind, unguided chance. And scientists are still finding new things to study.

    https://www.nature.com/articles/s41467-022-30207-9

  4. 4
    jerry says:

    How difficult is it to sequence a complete genome?

    I’m sure 20-30 years ago such a thing was daunting but with computers doing millions of calculations a second, could a data base be constructed containing a half dozen or more of genomes of the same species.

    Then, it should be easy to pick out what percentage is identical and what percentage is not. It should also be easy to identify if a specific protein has a gene sequence that is compatible even if that gene sequence is in several places.

    Such a project would answer once and for all if naturalistic processes could have produced the gene sequences. Several of the papers that BA77 referenced in #1 indicate it is definitely possible and being done by the evolutionary biologist community.

    I would not start with humans but with a species with a smaller genome.

              The debate would be over.

    Aside: it might answer the questions about non-coding parts of a genome and what percentage have function. The above knockout studies indicated that certain protein eliminations ended up with dead entities.

  5. 5
    relatd says:

    The Human Genome Project completed the job.

    https://www.genome.gov/about-nhgri/Director/genomics-landscape/april-7-2022-the-human-genome-sequence-is-now-complete

    The current problem is figuring out what everything does, so scientists are working on the Human Genome Reference Program.

    https://www.genome.gov/Funded-Programs-Projects/Human-Genome-Reference-Program

  6. 6
    Lieutenant Commander Data says:

    Relatd
    The Human Genome Project completed the job.

    https://www.genome.gov/about-nhgri/Director/genomics-landscape/april-7-2022-the-human-genome-sequence-is-now-complete

    The current problem is figuring out what everything does, so scientists are working on the Human Genome Reference Program.

    https://www.genome.gov/Funded-Programs-Projects/Human-Genome-Reference-Program

    Flash News: Genetic code is the simplest code found in the cell but somehow we have a distorted image about genetic code[as the most complex and important in the cell :which is false] because darwinist birocracy control the flux of informations (schools and mass-media) so they have the power to mold public opinions.

    Glycome(sugar code):Nucleotides and proteins are linear polymers that can each contain only one basic type of linkage between monomers. In contrast, each monosaccharide can theoretically generate either an ? or a ? linkage to any one of several positions on another monosaccharide in a chain or to another type of molecule. Thus, it has been pointed out that although three different nucleotides or amino acids can only generate six trimers, three different hexoses could produce (depending on which of their forms are considered) anywhere from 1,056 to 27,648 unique trisaccharides. This difference in complexity becomes even greater as the number of monosaccharide units in the glycan increases. For example, a hexasaccharide with six different hexoses could have more than 1 trillion possible combinations.Nucleotides and proteins are linear polymers that can each contain only one basic type of linkage between monomers. In contrast, each monosaccharide can theoretically generate either an ? or a ? linkage to any one of several positions on another monosaccharide in a chain or to another type of molecule. Thus, it has been pointed out that although three different nucleotides or amino acids can only generate six trimers, three different hexoses could produce (depending on which of their forms are considered) anywhere from 1,056 to 27,648 unique trisaccharides. This difference in complexity becomes even greater as the number of monosaccharide units in the glycan increases. For example, a hexasaccharide with six different hexoses could have more than 1 trillion possible combinations.

    https://www.ncbi.nlm.nih.gov/books/NBK1931/ (Essentials of Glycobiology. 2nd edition.)

  7. 7
    relatd says:

    LCD at 6,

    Do you think the average person discusses this? Ever? “Hey Bob. You know those hexoses?”

    The what?

  8. 8
    Alan Fox says:

    Seconded. Can anyone explain the glycan code? Is it a real thing in living organisms?

  9. 9
  10. 10
  11. 11
    jerry says:

    Can anyone explain the glycan code? Is it a real thing in living organisms?

    Seconded!

    It is apparently very real but reading about it is not enlightening. There has to be a short hand version somewhere. Certainly not in Wikipedia. Something like what has been done for transcription and translation.

    The other question is are these codes part of OOL or part of evolution? It seems that glycans what ever they are/do are more prevalent in multicellular organisms which definitely points to Evolution.

    One of the realizations is that cellular activity is so complex that the original proponents of naturalized evolution would have thrown in the towel. There are just too many complications to explain away by just chance.

    Prediction: there will be too much complexity for naturalized Evolution to explain as just happening by any methodology they can propose.

    There will also be too many inexplicable events to explain away as a coherent design of an all powerful creator.

    The latter is the real basis for adhering to naturalized Evolution and is why they cannot really defend any mechanism because one does not exist no matter how desperately they want one.

    Also they essentially want to eliminate a creator, the concept of they basically abhor. But the irony is that Evolution is a side show and as Denton’s recent book illustrates, Earth is exquisitely designed for complex life to go along with the fine tuning of the universe.

  12. 12
    Alan Fox says:

    So sugars, in the form of monosaccharides, oligosaccharides, polysaccharides, glycolipids, glycoproteins (glycan is a synonym for polysaccharide) are a very important group of molecules. Examples are cellulose and chitin, essential structural components of plants and invertebrates respectively. Glycogen is a glycan that animals use as an energy reserve. Glycolipids are associated with cell membranes and are important in cell recognition and immune reactions. It’s a big field with suggestions it’s under-researched.

    However, I can’t find anything substantive about a glycan code.

  13. 13
    Lieutenant Commander Data says:

    Jerry
    There will also be too many inexplicable events to explain away as a coherent design of an all powerful creator.

    Your ignorance is not an argument.

    Alan Fox
    However, I can’t find anything substantive about a glycan code.

    It has long been known(1952) that carbohydrates encode biological information
    :variation of blood group determinants is a consequence of glycosylation, that is, the addition of complex carbohydrates to proteins and lipids. Today is 2022 and still are people who don’t find anything substantive about glycan code. Ok.

  14. 14
    Alan Fox says:

    @LCD

    OK? Not really. Not seeing anything about codes.

    https://www.nature.com/articles/s41435-020-0105-9

    A recent review paper covers the subject without mentioning codes.

  15. 15
    jerry says:

    Your ignorance is not an argument.

    I guess you don’t believe in ID from this comment.

    I am one of biggest advocates of ID on this site, have been for over 16 years. So I guess my arguments have been from ignorance.

  16. 16
    jerry says:

    Once a frequent visitor to ID, Allen MacNeill, has been incommunicado for about 8 years.

    While retired from teaching evolutionary biology at Cornell, he had health problems and is now 71. His personal blog on evolution hasn’t been updated since 2014. But it is still available even if 8 years old. It is

    http://evolutionlist.blogspot.com/

    The posts on that page only go back to 2010 though it’s possible to find earlier post by searching. For example here is a post on HGT from 2009

    Horizontal Gene Transfer and Intelligent Design Theory

    http://evolutionlist.blogspot......r-and.html

    It is Allen’s ideas that have to be refuted if there ever was a civil discussion. I personally don’t see that they won’t but one has to deal with the fact that a greater number of young people are being taught natural Evolution as gospel and are believing in it.

    For example, does this describe modern evolutionary biology.

    The Modern Synthesis is Dead – Long Live the Evolving Synthesis!

    http://evolutionlist.blogspot......-live.html

    We can pontificate/lament all we want but I doubt it will make much difference given that the trend is definitely the other way.

    https://www.sciencedaily.com/releases/2021/08/210820111042.htm

  17. 17
    kairosfocus says:

    AF,

    That’s odd, I readily see:

    https://pubmed.ncbi.nlm.nih.gov/15939591/

    The glycan code of the endoplasmic reticulum: asparagine-linked carbohydrates as protein maturation and quality-control tags
    Daniel N Hebert 1 , Scott C Garman, Maurizio Molinari
    Affiliations

    PMID: 15939591 DOI: 10.1016/j.tcb.2005.05.007

    Abstract

    The majority of proteins that traverse the secretory pathway receive asparagine (Asn)-linked glycosylations. Glycans are bulky hydrophilic modifications that serve a variety of structural and functional roles within the cell. Here, we review the recent growing knowledge on the role of Asn-linked glycans as maturation and quality-control protein tags in the early secretory pathway. The carbohydrate composition encodes crucial information about the structure, localization and age of glycoproteins. The “glycan code” is encoded by a series of glycosidases and carbohydrate transferases that line the secretory pathway. This code is deciphered by carbohydrate-binding proteins that possess distinct carbohydrate binding properties and act as molecular chaperones or sorting receptors. These glycosidases and transferases work in concert with resident secretory pathway carbohydrate-binding proteins to form a network that assists in the maturation and trafficking of both native and aberrant glycoproteins within the cell.

    KF

    PS, that is off on a side branch, we all must know about the multiple Nobel Prize winning work that elucidated the genetic code and how it works in protein synthesis, complete with transcription, editing and translation. Where the anticodons of tRNAs are at opposite ends of the L to the CCA universal tool tip that is loaded with a code specific AA, when chemically it could load with any one. Where the aaRS carries out the double matching of AA and tRNA effecting encoding.

    As a handy summary:

    https://www.genome.gov/genetics-glossary/Genetic-Code

    Genetic code refers to the instructions contained in a gene that tell a cell how to make a specific protein. Each gene’s code uses the four nucleotide bases of DNA: adenine (A), cytosine (C), guanine (G) and thymine (T) — in various ways to spell out three-letter “codons” that specify which amino acid is needed at each position within a protein . . . .

    Genetic code. The story of the genetic code is the story of biology and genetics in the 19th, 20th, and 21st centuries, as well as its promises and its perils. Oswald Avery in 1944, for example, proved that the genetic code — that DNA —was indeed the carrier of hereditary information, ending more than 80 years of productive speculation. But as important as DNA was to the so-called heroic era of molecular biology, spanning the generation of scientific discovery after the Second World War, and as important as DNA is to the revolutionary sciences of genetics and genomics, neither genes nor DNA determine who you are or what you shall do.
    Christopher R. Donohue
    Christopher Donohue, Ph.D.

    Historian

    NHGRI History of Genomics Program

    Similarly, Wikipedia concedes:

    The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
    A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually corresponding to a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code.

    The codons specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in mitochondria) exist.

    By all rights, this should be a commonplace and utterly non controversial. That the circles of objectors keep trying to suggest this is a weak and dubious analogy and the like, likely reflects how decisive it is to see machine code algorithms with halting that carry out a key part of a central matter in the cell, formation of proteins. As, that is language used to effect stepwise, goal directed processes. And language as well as goal directedness are known strong signs of rational, free, intentional designers and designs.

    At this point, I do not let such objections constrain what I confidently conclude is well warranted.

  18. 18
    relatd says:

    Jerry at 16,

    Truth is truth. Once Leftists/Liberals infiltrated the schools, they had to convince young people that they came from nowhere. That no one made them. “Getting the poll numbers up” means nothing. ID is the correct answer.

    I was reading so-called reviews about a book about Intelligent Design. Guess what? The primary concern was “if this gets into the schools.” That’s not a real book review. So now that Leftists/Liberals control education, they will not prevail. “If this gets into the schools” then Atheists will have a hard time dealing with an established science that points to a designer. Example: Did your computer design and build itself? Yes or no.

  19. 19
    Alan Fox says:

    KF

    This code is deciphered by carbohydrate-binding proteins that possess distinct carbohydrate binding properties and act as molecular chaperones or sorting receptors.

    In other words physical binding, not codes.

  20. 20
    kairosfocus says:

    AF, your quarrel is with the authors not me. And of course, there is the primary case. KF

  21. 21
    Fasteddious says:

    Along with the genetic code and the glycan code, there must also be a code for the lipids that make up cell walls and other membranes of the cell. Those are by no means simple in that some different cell types have different fat molecules and the inner and outer membranes use different molecules as well. Those phospholipids, and other fats also need to be assembled, sorted, connected, moved around, etc.

  22. 22
    bornagain77 says:

    Of related note:

    Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA
    Jonathan Wells* – 2014
    Excerpt page 7: THE SUGAR CODE
    The plasma membranes of all living cells studied to date are covered by arrays of carbohydrates called “glycans” [162]. Glycans can be attached to lipid molecules (glycolipids) or to proteins (glycoproteins), and many of them are quite complex [163]. In living cells, nucleotides in DNA are covalently linked to each other in linear chains; with some exceptions, the same is true for amino acids in proteins. But monosaccharides can be covalently linked to each other through one or more of their hydroxyl groups. Since D-glucose (for example) has five hydroxyl groups, one of which can assume two different positions, it can be covalently linked to other monosaccharides in six different ways (Fig. 4). As a result, carbohydrates can form branching chains that are far more elaborate than linear chains of nucleotides and amino acids (Fig. 5) [164].
    While the four nucleotides in the genome can form a maximum of 46 ? 4 x 10^3 hexanucleotides, and the twenty amino acids in the proteome can form a maximum of 206 ? 6 x 10^7 hexapeptides, the dozen or so monosaccharides in the “glycome” can theoretically form more than 10^12 hexasaccharides. Clearly, the information-carrying capacity of the “glycome” far exceeds the combined capacities of the genome and the proteome. The information carried by the glycome has been called the “glycocode” or “sugar code” [165?169].
    Glycosaminoglycans (GAGs) are unbranched polysaccharides composed of disaccharide subunits containing an amino group. Yet although they are unbranched, they can be assembled from dozens of different subunits, and sulfate groups can be attached to them in a wide variety of patterns. For example, a sulfate group can be attached to a trisaccharide in ten different positions, increasing its information-carrying capacity tenfold [170]. This makes GAGs some of the most information- dense molecules in biology [171?173]. Of the five types of glycosaminoglycans, four are covalently attached to proteins to form proteoglycans (PGs). Like glycolipids and glycoproteins, PGs are common in the plasma membranes of many cells.
    https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2

    Life Exponential: Life Exhibits Intelligent Design at Many Levels – Jonathan Wells – June 1, 2018
    Excerpt: The Membrane Code
    So localized RNAs in the cortex, glycan patterns on the membrane, and bioelectric fields generated by ion channels in the membrane all carry spatial information. Although individual molecules may be specified by DNA, their three-dimensional patterns are not. Taken together, these patterns constitute a “membrane code” that is independent of DNA sequences.,,,
    ,,, the existence of the membrane code shows that the Central Dogma is false. And the materialistic idea that evolution is unguided cannot account for the complex specified information in DNA, much less for the extensive complex specified information in the membrane code. Just as the information in DNA points to design, so does the information beyond DNA.
    https://evolutionnews.org/2018/06/life-exponential-life-exhibits-intelligent-design-at-many-levels/

    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
    1. Epigenetic Code – modifies DNA molecule
    2. RNA (Alternative) Splicing Code – modifies RNA sequences to produce many different proteins from same DNA sequence
    3. Sugar Code – almost every protein is further modified by the addition of complex sugar molecules
    4. Membrane Code – membrane patterns are inherited independently of DNA, and yet determine the spatial arrangement in the cell.
    5. Bio-electric code – altering the bio-electric field without altering the underlying molecules affects the three-dimensional shape of the developing embryo
    https://idthefuture.com/887/

    Moreover, there have now been found multiple overlapping codes within DNA itself.

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].

    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.

    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

  23. 23
    Silver Asiatic says:

    Horizontal Gene Transfer and Intelligent Design Theory

    Here’s Allen MacNeill’s argument:

    But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an “intelligent designer”.

    The designer wouldn’t do it that way.

    Such an entity would (as several of the commentators in this thread have suggested) tailor HGTs to produce adaptive (i.e. beneficial) changes in the phenotypes of the recipients of its HGTs.

    What the designer would do ( according to unnamed IDists from 13 years ago) is “tailor HGTs” to make them beneficial.

    Either that, or the “intelligent designer” doesn’t “tailor” its HGTs at all, but rather produces them randomly, rather like a dealer in a card game. But in that case, the actions of a soi dissant “intelligent designer” would be indistinguishable from Darwinian evolution, and including any reference to its actions (and/or inferring its existence) would be unnecessary (and would therefore violate Occam’s razor).

    Or, instead of tailoring HGTs, the designer would produce random gene transfers – Just like Darwinian evolution claims – because as everyone already knows, evolution is random and therefore there would be no need for a designer (and no evidence of design).

    a relatively small number produce phenotypic effects that are correlated with increased survival and/or reproductive success. Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. That is, they are preserved and passed on (while deleterious HGTs are eliminated), and thereby become more common over time among the populations in which they occur.

    And there we have it. A relatively small number of beneficial HGTs turned bacteria into human beings without need for a designer at all.

  24. 24
    Alan Fox says:

    AF, your quarrel is with the authors not me.

    I’m not quarreling with anyone. I’m just wondering how much concrete evidence there is for a glycan code. In my enquiries so far, I have found none.

  25. 25
    jerry says:

    We need an interpreter.

    The sugar code: Why glycans are so important

    The cell surface is the platform for presentation of biochemical signals that are required for intercellular communication. Their profile necessarily needs to be responsive to internal and external factors in a highly dynamic manner. The structural features of the signals must meet the criterion of high-density information coding in a minimum of space. Thus, only biomolecules that can generate many different oligomers (‘words’) from few building blocks (‘letters’) qualify to meet this challenge. Examining the respective properties of common biocompounds that form natural oligo- and polymers comparatively, starting with nucleotides and amino acids (the first and second alphabets of life), comes up with sugars as clear frontrunner. The enzymatic machinery for the biosynthesis of sugar chains can indeed link monosaccharides, the letters of the third alphabet of life, in a manner to reach an unsurpassed number of oligomers (complex carbohydrates or glycans). Fittingly, the resulting glycome of a cell can be likened to a fingerprint. Conjugates of glycans with proteins and sphingolipids (glycoproteins and glycolipids) are ubiquitous in Nature. This implies a broad (patho)physiologic significance. By looking at the signals, at the writers and the erasers of this information as well as its readers and ensuing consequences, this review intends to introduce a broad readership to the principles of the concept of the sugar code.

    https://pubmed.ncbi.nlm.nih.gov/28709806/

    An introduction to the sugar code

    Carbohydrates have physiological importance far beyond their roles as source of energy (glycolysis) and activated hydrogen for synthesis (pentosephosphate pathway) or as constituent of the backbone of nucleic acids and of cell wall polysaccharides. The extent of compositional and structural variability of their oligomers (glycans) is unsurpassed in Nature due to the unique property of independently combining the following parameters with sequence: anomeric status, linkage positions, ring size, addition of branches and site-specific introduction of substitutions. The monosaccharides (letters of the third alphabet of life) thus generate ‘words’ (signals) of high-density coding capacity. These ‘words’ are part of the glycans on proteins and lipids, and the glycome represented by these ‘words’ in their entirety has cell type-dependent features. The often limited intramolecular flexibility of oligosaccharides along with an abundance of contact points for intermolecular interactions is ideal for binding processes. Glycan-based ‘words’ can thus be ‘read,’ and their message translated into cellular effects by receptors called lectins. This journal’s special issue covers central aspects of the concept of the sugar code.

    https://pubmed.ncbi.nlm.nih.gov/27975142/

    Maybe we can make sense of it.

  26. 26
    ET says:

    Alan Fox:

    I’m just wondering how much concrete evidence there is for a glycan code. In my enquiries so far, I have found none.

    Then you are willfully ignorant.

  27. 27
    kairosfocus says:

    AF, for reasons as seen, you likely never will. Start with this, is there a genetic code that is part of protein synthesis? Y/N _____ Why/why not _______ KF

  28. 28
    Silver Asiatic says:

    Jerry @ 16

    Evolution now accepted by majority of Americans – ScienceDaily
    “Almost twice as many Americans held a college degree in 2018 as in 1988,” said co-author Mark Ackerman, a researcher at Michigan Engineering, the U-M School of Information and Michigan Medicine. “It’s hard to earn a college degree without acquiring at least a little respect for the success of science.”

    That’s a good reference, thanks. The anti-ID crowd will claim it as a victory. “See, ID is dying!”
    At the same time, some IDists will say that evolution has little to do with ID, and that ID fully accepts evolution as it is.
    For me, I consider the survey evidence of the spread of evil ideology. Call it “evolution” or not, when someone has to tell lies about their belief system, then I consider that evil manipulation. What lies? you may ask …?
    Well, when a person equivocates on the use of the very term that defines their belief (“evolution”) having it mean one thing to get a buy-in from ignorant students, and then mean another thing after people think that “all educated people accept evolution” – that’s propaganda and manipulation.
    But that’s what they’ve done.
    And how do evil ideas spread through society like that?
    Weirdly, it’s explained by the author of the survey:

    Almost twice as many Americans held a college degree in 2018 as in 1988,”

    So, its the colleges and universities that are indoctrinating students into the evolutionary cult. Given the philosophical consensus among the professorial caste, that kind of indoctrination is not surprising. Students can gain a degree in English literature without ever having read Shakespeare. Other professors (as our own Caspian can attest) will be fired merely for mentioning that “ultimate verities such as God could be considered in the origin of the universe”.

    said co-author Mark Ackerman, a researcher at Michigan Engineering, the U-M School of Information and Michigan Medicine. “It’s hard to earn a college degree without acquiring at least a little respect for the success of science.”

    The last phrase says it. They give “respect for the success of science”. That’s why they buy-into Darwin. It’s not that evolutionary theory is successful at all – it’s the fact that it is taught and propagandized against all counter-evidence that indicates that evolution is “successful”.
    So again, if you want to be part of the intellectual elite, accept Darwin has a hero and that his theory is unquestionable.

    ID is either true or not. If it’s true, it remains true even if the entire human race denies it.

  29. 29
    relatd says:

    The ongoing attempt to create an Atheist-Communist America.

  30. 30
  31. 31
    Alan Fox says:

    @ LCD

    Did you follow any of those links and read what I found there? Because I found nothing about how the “sugar code” is supposed to work.

  32. 32
    Alan Fox says:

    ID is either true or not.

    Well, it could have aspects of accuracy and other aspects of inaccuracy. Is there an accepted consensus of what “Intelligent Design” is as a philosophy or science?

  33. 33
    Lieutenant Commander Data says:

    Alan Fox
    @ LCD

    Did you follow any of those links and read what I found there? Because I found nothing about how the “sugar code” is supposed to work.

    🙂 Maybe is time to change your glasses or ask one of your grand-grandsons to read to you.

  34. 34
    kairosfocus says:

    AF, attn LCD, perhaps, some substantial matters can be on the table. Here, LCD’s first link:

    Review Article
    The sugar code: letters and vocabulary, writers,
    editors and readers and biosignificance of
    functional glycan – lectin pairing
    Herbert Kaltner
    1
    , José Abad-Rodríguez
    2
    , Anthony P. Corfield
    3
    , Jürgen Kopitz
    4
    and Hans-Joachim Gabius
    1
    1
    Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinaerstr. 13, 80539 Munich, Germany;
    2
    Membrane Biology and
    Axonal Repair Laboratory, Hospital Nacional de Parapléjicos (SESCAM), Finca La Peraleda s/n, 45071 Toledo, Spain;
    3
    School of Clinical Sciences, Bristol Royal Infirmatory, Mucin
    Research Group, University of Bristol, Bristol BS2 8HW, U.K.;
    4
    Institute of Pathology, Department of Applied Tumor Biology, Faculty of Medicine, Ruprecht-Karls-University
    Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
    Correspondence: Jürgen Kopitz (Juergen.kopitz@med.uni-heidelberg.de) or Hans-Joachim Gabius (gabius@tiph.vetmed.uni-muenchen.de or gabius lectins.de)
    Rceived: 11 July 2019
    Revised: 31 August 2019
    Accepted: 4 September 2019
    © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2623
    Biochemical Journal (2019) 476 2623 – 2655
    https://doi.org/10.1042/BCJ20170853 [ . . . ]

    Ubiquitous in Nature, even constituting the most abundant compounds on the Earth, namely the polymers, cellulose and chitin [3], and also prominently positioned on cell surfaces [4], carbohydrates qualify as more than being the biochemical fuel and molecular concrete of cell walls. Terminologically, the common presence of glycans as part of glycoproteins and glycosphingolipids was an incentive for coining the term ‘glycobiology’ [5] (or more general: glycosciences). It implies fundamental functionality. Conceptually, the term gave research work on glycans a clear direction. As a consequence, carbohydrates, like amino acids and nucleotides, gained the status of an alphabet of life [6]: ‘letters’ of this alphabet are shown in Figure 1. Chemical modi?cations, such as the derivatization of glucose (Glc) or galactose (Gal) to their 2-amino sugars and then to N-acetylated products (GlcNAc, GalNAc), can be likened to Umlaut formation in the German language. This process is especially frequent in the case of N-acetylneuraminic acid (Figure 1, bottom row — center). Its modification yields more than 80 different sialic acids, in mammals prominently O-acetylation and hydroxylation to N-glycolylneuraminic acid [7,8]. Thus, the ‘letters’ of an alphabet are available. By having a close look at the meaning of the term ‘carbohydrates’ and the structures shown in Figure 1, the fundamental potential of sugars to store (in ‘words’) and to transfer biological information (by molecular recognition) will become evident . . . .

    Figure 1. Letters of the sugar language.

    Illustration of the main letters of the third alphabet of life. In each case, the structure, name and symbol as well as known acceptor positions (by arrows) in glycoconjugates are presented. Four sugars have L -con fi guration: fucose (6-deoxy- L -galactose), rhamnose (6-deoxy- L -mannose) and arabinose are introduced during chain elongation or at branch positions, whereas L -iduronic acid (IdoA) results from the enzymatic epimerization of GlcA (at C5) in glycosaminoglycans that is sandwiched between the N-deacetylase/N-sulfotransferase and the O-sulfotransferase reactions. Its 1 C 4 conformer (left) is in dynamic equilibrium with the 2 S 0 form (right) that has the appropriate stereochemical arrangement for glycosaminoglycan (heparin/heparan sulfate)-receptor binding (please see also Figure 3d). Xylose is part of the GlcA-(Gal) 2 -Xyl linker between the proteoglycan core protein and the disaccharide repeat section of O-linked glycosaminoglycans (chondroitin, dermatan and heparan sulfates). Neu5Ac, one of more than 80 sialic acids, is a common constituent of glycoprotein and ganglioside glycans. Its presence and the ? 2-linkage to 3-, 6- or 8-positions of acceptors give the respective oligosaccharide a speci fi c meaning. Kdo is a building block of lipopolysaccharides in the cell wall of Gram-negative bacteria and is also found in cell wall polysaccharides of green algae and higher plants. Here, polysaccharides, such as arabinoxylans or pectins (such as rhamnogalacturonans), are abundant (from [248], extended; with permission).

    In case someone wants to dismiss as templates for reactions, templates by definition are information rich structures, here is Merriam Webster:

    Definition of template

    1a(1) : a gauge, pattern, or mold (such as a thin plate or board) used as a guide to the form of a piece being made
    (2) : a molecule (as of DNA) that serves as a pattern for the generation of another macromolecule (such as messenger RNA) [–> which is edited and spliced to issue protein assembly algorithms.]
    b : overlay sense c
    2 : something that establishes or serves as a pattern

    KF

    PS, the more basic question still stands, from 27:

    is there a genetic code that is part of protein synthesis? Y/N _____ Why/why not _______

  35. 35
    jerry says:

    Is there an accepted consensus of what “Intelligent Design” is as a philosophy or science

    ID is logic on top of science.

    Is that philosophy?

    Many here want to say ID is science. I personally don’t believe it’s science but others will go through the wall that it is.

    At a minimum, ID concludes the universe was created by an intelligence. Some will also point to the Earth and say it was created by an intelligence. Some will point to OOL and say life was created by an intelligence. Some will point to Evolution and say an intelligence created most of the life form changes. Some will say an intelligence created life forms with consciousness.

    ID doesn’t say how or why or who did all the creating. Could it be more than one entity? ID does not say that just that it was an intelligence.

    Now people here will express their beliefs on who are the creators. But that is not ID. That includes a substantial amount of non scientific material.

    I’m sure this assessment will get a lot of pushback from some.

  36. 36
    kairosfocus says:

    Jerry, empirically anchored explanatory inference. Similar to many other scientific causal inferences. Again, Title of Vol 3 of Lyell, principles of Geology . . . is Geology Science?:

    PRINCIPLES OF GEOLOGY:

    BEING

    AN INQUIRY HOW FAR THE FORMER CHANGES OF THE EARTH’S SURFACE ARE REFERABLE TO CAUSES NOW IN OPERATION. [–> appeal to Newton’s Rules, in the title of the work]

    BY

    CHARLES LYELL, Esq, F.R.S.

    PRESIDENT OF THE GEOLOGICAL SOCIETY OE LONDON . . . JOHN MURRAY , , , 1835 [–> later, publisher of Origin]

    The Sciences make modern form inductive inferences to best explanation all the time. In this case, with codes and algorithms in the cell: language and goal directed process, it should long since have been acknowledged.

    KF

  37. 37
    Alan Fox says:

    @KF
    Gabius died recently. There doesn’t appear to be anyone developing his ideas. The fact is there is no substance to a glycan code, only wishful thinking. That may change some day but here is where we are now.

  38. 38
    Alan Fox says:

    Jerry at 35

    That seems a reasonable assessment.

  39. 39
    Alan Fox says:

    LCD

    Maybe is time to change your glasses or ask one of your grand-grandsons to read to you.

    You didn’t bother to read what was at those links, did you? The Gabius one is a classic example of speculation.

  40. 40
    Silver Asiatic says:

    Alan

    Well, it could have aspects of accuracy and other aspects of inaccuracy.

    There is confusion about what ID is really saying. Some people think it’s a worldview, others think that it’s an entire parallel field of science (the ID way of doing science) others think that it’s a religious phenomenon.
    But in my understanding, from Behe, Meyer and most of the scientists at the DI, ID is only one thing:

    “There is scientific evidence that some features of the universe and of living things are best explained by an intelligent cause rather than an undirected, unintelligent process.”

    There is evidence that some things in nature have been designed by intelligence.

    That’s it.

    And therefore, if so, then there really couldn’t be “aspects of accuracy and aspects of inaccuracy”.
    There either is evidence of intelligent design in nature or there is not.
    ID is either true or false.

    I’m open to correction and I accept that some people view differently than I do.

  41. 41
    kairosfocus says:

    AF, we notice, first your continued side-stepping of the pivotal case, R/DNA. Accordingly, I ask again:

    Start with this, is there a genetic code that is part of protein synthesis? Y/N _____ Why/why not _______

    This is the primary case, driven by multiple Nobel Prize winning work. Your answer to this will tell us whether any amount of observational evidence and reasoning would move you. My bet is, none. Prove me wrong.

    On the secondary case, there is something fairly serious on the table, but it is not the pivot of argument. To try to ignore a primary case while going after a secondary one tells us a lot.

    KF

  42. 42
    kairosfocus says:

    SA, attn AF: In the OP here, I noted that there are three distinct considerations and themes:

    It seems, despite UD’s resources tab, some still struggle to understand ID in the three distinct senses: inference, theory/research programme, movement . . . .

    [I:] . Observed tested, reliable signs such as FSCO/I [= functionally specific, complex organisation and/or associated information, “fun-skee”] beyond 500 – 1,000 bits point to design as cause for cases we have not observed. This is the design INFERENCE . . . .

    [II:] we can identify ID Theory as a [small] research programme that explores whether there are such observable, testable, reliable signs, whether they appear in the world of life and in the cosmos, whether we may responsibly — notice, how duties of reason pop up naturally — use them to infer that cell based life, body plans, the cosmos etc are credibly the result of intelligently directed configuration . . . and that’s a definition of design. This, in a context where the proposed “scientific” alternative, blind chance and/or mechanical necessity has not been observed to actually produce things exhibiting FSCO/I etc . . . .

    [III:] Beyond the theory, there is a movement, comprising supporters and friendly critics as well as practitioners consciously researching design theory or extending thinking on it and applying same to society or civilisation, including history of ideas . . .

    Those three senses are longstanding, and it is clear that senses I and II are scientific. Even were it to be falsified at a future date (just like the second law of thermodynamics) the design inference would remain as part of the history of inferences to best current explanation common in science. And of course, on trillions of observed cases it is a reliable explanation. The second, is little more than saying that there is a movement in science that supports and discusses ID, which gives a theoretical programme of research and analysis.

    KF

  43. 43
    kairosfocus says:

    PS: We can expand postulates:

    [First, Evidence-backed Programmatic Postulate:] certain features of the universe and of living things are best explained [–> explicit reference to logic of abductive reasoning] by an intelligent cause rather than an undirected process such as natural selection.

    [2nd, Operational Postulate:] Intelligent Design is simply the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose.

    [3rd, Empirical Warrant/Point of test or potential falsification postulate:] An inference that certain biological information may be the product of an intelligent cause can be tested or evaluated in the same manner as scientists daily test for design in other sciences.

    [Evidence Corollary:] Positive evidence of design in living systems consists of the semantic, meaningful or functional nature of biological information, the lack of any known law that can explain the sequence of symbols that carry the “messages,” and statistical and experimental evidence that tends to rule out chance as a plausible explanation. Other evidence challenges the adequacy of natural or material causes to explain both the origin and diversity of life . . . .

    [4th, Designs and Signs Postulate:] as we ourselves instantiate [thus exemplify as opposed to “exhaust”], intelligent designers act into the world, and create artifacts. When such agents act, there are certain characteristics that commonly appear, and that – per massive experience — reliably mark such artifacts. It it therefore a reasonable and useful scientific project to study such signs and identify how we may credibly reliably infer from empirical sign to the signified causal factor: purposefully directed contingency or intelligent design. [–> definition of design, note, abductive inference from observed sign to signified cause.]

    Where:

    [Supplement, on evidence:] [a] FSCI — function-specifying complex information [e.g. blog posts in English text that take in more than 143 ASCII characters, and/or — as was highlighted by Yockey and Wickens by the mid-1980s — as a distinguishing marker of the macromolecules in the heart of cell-based life forms], or more broadly

    [b] CSI — complex, independently specified information [e.g. Mt Rushmore vs New Hampshire’s former Old Man of the mountain, or — as was highlighted by Orgel in 1973 — a distinguishing feature of the cell’s information-rich organized aperiodic macromolecules that are neither simply orderly like crystals nor random like chance-polymerized peptide chains], or

    [c] IC — multi-part functionality that relies on an irreducible core of mutually co-adapted, interacting components. [e.g. the hardware parts of a PC or more simply of a mousetrap; or – as was highlighted by Behe in the mid 1990’s — the bacterial flagellum and many other cell-based bodily features and functions.], or

    [d] “Oracular” active information – in some cases, e.g. many Genetic Algorithms, successful performance of a system traces to built-in information or organisation that guides algorithmicsearch processes and/or performance so that the system significantly outperforms random search. Such guidance may include oracles that, step by step, inform a search process that the iterations are “warmer/ colder” relative to a performance target zone. (A classic example is the Weasel phrase search program.) Also,

    [e] Complex, algorithmically active, coded information – the complex information used in systems and processes is symbolically coded in ways that are not preset by underlying physical or chemical forces, but by encoding and decoding dynamically inert but algorithmically active information that guides step by step execution sequences, i.e. algorithms. (For instance, in hard disk drives, the stored information in bits is coded based a conventional, symbolic assignment of the N/S poles, forces and fields involved, and is impressed and used algorithmically. The physics of forces and fields does not determine or control the bit-pattern of the information – or, the drive would be useless. Similarly, in DNA, the polymer chaining chemistry is effectively unrelated to the information stored in the sequence and reading frames of the A/ G/ C/ T side-groups. It is the coded genetic information in the successive three-letter D/RNA codons that is used by the cell’s molecular nano- machines in the step by step creation of proteins. Such DNA sets from observed living organisms starts at 100,000 – 500,000 four-state elements [200 k – 1 M bits], abundantly meriting the description: function- specifying, complex information, or FSCI.)

    [(f) evidence of the fine tuned cosmos.] . . . .

    “Thus, ID can be framed on postulates, and we may draw forth from such that cells using memory structures storing coded algorithms and associated execution machinery are strong evidence of the design of cell based life. With Drexler, we are looking a bit at nanotech issues.”

    PPS: Kindly note p. 5 of Crick’s letter to his son, March 19, 1953.

  44. 44
    Lieutenant Commander Data says:

    Alan Fox Case Study:

    Alan Fox: Can anyone explain the glycan code? Is it a real thing in living organisms?
    KF:This code is deciphered by carbohydrate-binding proteins that possess distinct carbohydrate binding properties and act as molecular chaperones or sorting receptors.
    Alan Fox: In other words physical binding, not codes.
    LCD: Provide links: here here here
    Alan Fox : I found nothing about how the “sugar code” is supposed to work.
    KF Posted quotes from paper
    Alan Fox: Gabius died recently. There doesn’t appear to be anyone developing his ideas. The fact is there is no substance to a glycan code, only wishful thinking.

    Alan Fox make no case only declare that he deny sugar code 😆 .No logical argumentation, no quote presented, nothing just “Gabius died recently therefore he is wrong and I ‘m right because I say so”. If you read Gabius you would have plenty of quotes from him to present here as being wrong.

    You sound like Fred “hydrogen bond” Hickson.

    Cell is a controlled space (like a lab) where chemistry is constrained to take place at certain places/times for certain purposes . This is happening repeatedly (not randomnly)with the same succesful results that correspond to an abstract goal beyond chemistry . Darwinists know that in the moment they accept the code reality everything it’s over for them . Code mean purpose /error repair/ communication/feedback loops and chemistry can’t built meaningful complex systems randomnly and succesfully . They tried and they failed to make their case for chemistry as a designer.

  45. 45
    Alan Fox says:

    @KF

    I have no idea why you are rambling on about the genetic code, information storage and retrieval, regulation and protein synthesis. This is all well researched, well understood and well reported. It remains an active and well-funded area of research. Do I need to repeat that? Please pay attention.

    My point of contention is that I keep being referred to a “glycan code” as if it is a thing rather than a conjecture, largely by Hans-Joachim Gabius, who died in 2021. The only issue I have about the genetic code is a semantic quibble on the use of the word “code”. The issue I have with the glycan code is that it doesn’t appear to exist in biological systems..

  46. 46
    Alan Fox says:

    LCD

    Code mean purpose /error repair/ communication/feedback loops and chemistry can’t built meaningful complex systems randomnly and succesfully . They tried and they failed to make their case for chemistry as a designer.

    Oh dear! Darwinian evolution has a non-random element, don’t you know! Natural selection, survival of the fittest (in the relevant niche), proliferation of the most fecund (in the relevant niche), suck-it-and-see is not a random process.

  47. 47
    Alan Fox says:

    If you read Gabius you would have plenty of quotes from him to present here as being wrong.

    He’s not wrong, he doesn’t get that far. Gabius didn’t explain how a glycan code works. He suggested a potential for storing information simply on the theoretical possibilities for different combinations of sugar polymers. That’s it, though he pads it out with spurious examples.

    If you’ve read Gabius, you’d be able to find his proposed mechanism for storage and retrieval of information, surely? I can’t.

  48. 48
    ET says:

    Alan Fox:

    The only issue I have about the genetic code is a semantic quibble on the use of the word “code”.

    The genetic code acts like a code. It has all of the attributes of a code. And it fits the definition of a code. Even Larry Moran and Richard Dawkins say it’s a real code.

  49. 49
    ET says:

    Alan Fox:

    Darwinian evolution has a non-random element, don’t you know!

    Very trivial. The non-random aspect of natural selection is ju7st that not all variants have the same chance of being eliminated. You have to be desperate to think that actually means something beyond that.

  50. 50
    kairosfocus says:

    AF, “rambling”? Loaded language to disguise the central concession, AF: “. . . the genetic code, information storage and retrieval, regulation and protein synthesis. This is all well researched, well understood and well reported.” Yes, and so, central to the cell is string data structure, algorithmic, coded information, thus language specifying goal directed process. Those are decisive signs of design and purpose of a designer. So, the root of the world of life, the cell, reflects design. That issue is central, and you know it, belittling language like “pay attention” notwithstanding. Actually, I have paid attention enough to identify what is primary from what is secondary and might well just be a distractive strawman. Whether or not a sugar code is recognised from functional specificity and organisation thus role in the cell, whether we can discover where it came from, whether its storage is implicit in life being passed from going concern complete cells to others, whether it is widely accepted etc are in fact secondary and derivative. Indeed, i/l/o the main point where we already have codes and execution machinery in the cell it is not unlikely that there will be other cases. Including possibly cases where the protocols of information and communication are implicit, embedded in functional cell structures passed down in the chain from one cell to another; consider how protein AA sequences implicitly reflect the coded information in D/RNA. And more. KF

  51. 51
    Lieutenant Commander Data says:

    Alan Fox
    Oh dear! Darwinian evolution has a non-random element, don’t you know! Natural selection, survival of the fittest (in the relevant niche), proliferation of the most fecund (in the relevant niche), suck-it-and-see is not a random process

    😆 Oh dear! There is no Natural selection without all operating cell codes: genetic code, sugar code, lipids code, repair code ,etc. .
    There is no survival of the fittest(=survival of survivors : nonsense darwinist expression ) without functional internal systems operated by genetic code, sugar code, lipids code, repair code ,etc.
    There is no known mechanism that can prove that mutations are random.
    As of today there is no known mechanism that could prove that chemistry laws can produce meaningful functional systems/information/codes. There is only the religious belief in materialism that can do the trick. Unfortunately for atheists is not scientific to declare that matter creates coded functional information without proving it in the lab so it’s just a belief that can be rejected on the spot. 😆

  52. 52
    Alan Fox says:

    Guys.

    Focus!

    Glycan code. Exists biologically? Evidence?

  53. 53
    kairosfocus says:

    AF, the pivotal matter already having been settled, we leave you to your debate with those you disagree with. Have you published a cogent refutation or substantial dismissal, if so, where? KF

  54. 54
    JVL says:

    ET: The non-random aspect of natural selection is ju7st that not all variants have the same chance of being eliminated. You have to be desperate to think that actually means something beyond that.

    Why don’t you set up an experiment or simulation to see if that leads to anything? If you can’t create the sophisticated enough computer simulation then take a population of some easily bred creature, raise a bunch of different batches of them under different selection pressures and see what happens? That’s pretty scientific isn’t it? So why not do it?

  55. 55
    Alan Fox says:

    Have you published a cogent refutation or substantial dismissal?

    The first time I heard of the glycan code was in a comment addressed to me on this site. I’ve yet to find any substance to the idea so I don’t feel the need to rebut anything. On the contrary, it may be a new and fascinating avenue of research. Why can’t anyone tell me about it?

  56. 56
    kairosfocus says:

    Translation, hyperskeptical dismissiveness and highlighting the secondary and potentially distractive while side stepping the central and decisive on the merits.

  57. 57
    Silver Asiatic says:

    AF

    Glycan code. Exists biologically? Evidence?

    Where in nature do you accept the existence of a code? If anywhere, what evidence do you have? If nowhere, where do you accept that a code exists anywhere at all?

  58. 58
    Alan Fox says:

    @SA

    The genetic code is shorthand for the DNA storage retrieval system involving the the 64 triplet codons. I think it’s pretty amazing and conclusive evidence for common descent. There is no question that the system is present in all extant living organisms.

    On the other hand, there is no evidence I can find for a system involving polysaccharides that looks like a storage and retrieval system.

  59. 59
  60. 60
    Silver Asiatic says:

    AF

    Answering my question I believe you’re saying: Yes a code exists in nature: the DNA storage retrieval system. However, glycan structures, or as you call it “a system involving polysaccharides” are not code because they’re not a storage retrieval system.

    So, you define “code” as a storage-retrieval system.

    The paper Es58 posted will give you a lot to argue against.

  61. 61
    bornagain77 says:

    AF: “I think it’s pretty amazing and conclusive evidence for common descent.”

    Save, of course, for when it isn’t.

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011?Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.”
    (Dawkins – 2009, p. 409-10 – The Greatest Show On Earth)?OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 19 variants of the genetic code).
    Simple counting question: does “one or two” equal 19? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.?http://www.evolutionnews.org/2.....44681.html

    Universal Genetic Code? No! – January 18, 2016
    Excerpt: “To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA… “,,,
    This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal. This, of course, is often cited as evidence for evolution.,,,
    In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book.
    http://blog.drwile.com/?p=14280

    The Genetic Codes
    http://www.ncbi.nlm.nih.gov/Ta.....cgi?mode=c

    podcast 2017 – Brian Miller interviews Paul Nelson on universal common ancestry. Listen in as Nelson describes how common descent predicts one – and only one – genetic code. Yet, this is not what we find.
    https://www.podomatic.com/podcasts/intelligentdesign/episodes/2017-04-10T14_52_38-07_00

    There are now many variants of the “universal” genetic code – June 13, 2018
    Excerpt: – From Theistic Evolution (2017): “Perhaps the most common argument for universal common ancestry encountered by students in college-level biology textbooks is the universality of the genetic code- the claim that all life uses the same nucleotide triplets to encode the same amino acids. 5° However, the genetic code is not universal; many variants in the genetic code are known among various organisms. note 51 [51 For a list of known variants to the standard genetic code, see Andrzej (Anjay) Elzanowski and Jim Ostell, “The Genetic Codes,” Taxonomy Browser, National Center for Biotechnology Information (NCB!), accessed October 25, 2016, https://www.ncbi.nlm.nih.govfraxonomyltaxonomyhome.htmllindex.cgi?chapter=cgencodes. See also Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, “Rewiring the Keyboard: Evolvability of the Genetic Code,” Nature Reviews Genetics 2 (January 2001): 49- 58.]”
    https://uncommondescent.com/evolution/there-are-now-many-variants-of-the-universal-genetic-code/

    Question for you AF, is there ANY finding that could ever falsify Darwinian evolution?

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    – Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    As Denis Noble noted, “If, as the commentator seems to imply, we make neo-Darwinism so flexible as an idea that it can accept even those findings that the originators intended to be excluded by the theory it is then incumbent on modern neo-Darwinists to specify what would now falsify the theory. If nothing can do this then it is not a scientific theory.”

    Central tenets of neo-Darwinism broken. Response to ‘Neo-Darwinism is just fine’ – 2015
    Excerpt: “If, as the commentator seems to imply, we make neo-Darwinism so flexible as an idea that it can accept even those findings that the originators intended to be excluded by the theory it is then incumbent on modern neo-Darwinists to specify what would now falsify the theory. If nothing can do this then it is not a scientific theory.”
    – Denis Noble – President of International Union of Physiological Sciences
    https://jeb.biologists.org/content/218/16/2659

    Here is a short list of falsifications of Darwin’s theory that Darwinists simply refuse to ever accept as falsifications of their theory.

    1. Darwin’s theory holds mutations to the genome to be random. The vast majority of mutations to the genome are not random but are now found to be ‘directed’.

    2. Darwin’s theory holds that Natural Selection is the ‘designer substitute’ that produces the ‘appearance’ and/or illusion of design. Natural Selection, especially for multicellular organisms, is found to be grossly inadequate as the ‘designer substitute.

    3. Darwin’s theory holds that mutations to DNA will eventually change the basic biological form of any given species into a new form of a brand new species. Yet, biological form is found to be irreducible to mutations to DNA, nor is biological form reducible to any other material particulars in biology one may wish to invoke.

    4. Darwin’s theory, (via Fisher’s Theorem in population genetics), assumed there to be an equal proportion of good and bad mutations to DNA which were, ultimately, responsible for all the diversity and complexity of life we see on earth. Yet, the ratio of detrimental to beneficial mutations is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever.

    5. Charles Darwin himself held that the gradual unfolding of life would (someday) be self-evident in the fossil record. Yet, from the Cambrian Explosion onward, the fossil record is consistently characterized by the sudden appearance of a group/kind in the fossil record, (i.e. disparity), then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. Moreover, Fossils are found in the “wrong place” all the time (either too early, or too late).

    6. Darwin’s theory, due to the randomness postulate, holds that patterns will not repeat themselves in supposedly widely divergent species. Yet thousands of instances of what is ironically called ‘convergent evolution’, on both the morphological and genetic level, falsifies the Darwinian belief that patterns will not repeat themselves in widely divergent species.

    7. Charles Darwin himself stated that “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Yet as Doug Axe pointed out, “Basically every gene and every new protein fold, there is nothing of significance that we can show that can be had in that gradualistic way. It’s all a mirage. None of it happens that way.”

    8. Charles Darwin himself stated that “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.” Yet as Wolf-Ekkehard Lönnig pointed out, “in thousands of plant species often entirely new organs have been formed for the exclusive good of more than 132,930 other species, these ‘ugly facts’ have annihilated Darwin’s theory as well as modern versions of it.”

    9. Charles Darwin himself stated that, ““The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God. Yet ‘our conscious selves’ are certainly not explainable by ‘chance’ (nor is consciousness explainable by any possible reductive materialistic explanation in general), i.e. ‘the hard problem of consciousness’.

    10. Besides the mathematics of probability consistently showing that Darwinian evolution is impossible, the mathematics of population genetics itself has now shown Darwinian evolution to be impossible. Moreover, ‘immaterial’ mathematics itself, which undergirds all of science, engineering and technology, is held by most mathematicians to exist in some timeless, unchanging, immaterial, Platonic realm. Yet, the reductive materialism that Darwinian theory is based upon denies the existence of the immaterial realm that mathematics exists in. i.e. Darwinian evolution actually denies the objective reality of the one thing, i.e. mathematics, that it most needs in order to be considered scientific in the first place!

    11. Donald Hoffman has, via population genetics, shown that if Darwin’s materialistic theory were true then all our observations of reality would be illusory. Yet the scientific method itself is based on reliable observation. Moreover, Quantum Mechanics itself has now shown that conscious observation must come before material reality, i.e. falsification of ‘realism’ proves that our conscious observations are reliable!.

    12. The reductive materialism that undergirds Darwinian thought holds that immaterial information is merely ’emergent’ from a material basis. Yet immaterial Information, via experimental realization of the “Maxwell’s Demon” thought experiment, is now found to be its own distinctive physical entity that, although it can interact in a ‘top down’ manner with matter and energy, is separate from matter and energy.

    13. Darwinists hold that Darwin’s theory is true. Yet ‘Truth’ itself is an abstract property of an immaterial mind that is irreducible to the reductive materialistic explanations of Darwinian evolution. i.e. Assuming reductive materialism and/or Naturalism as the starting philosophical position of science actually precludes ‘the truth’ from ever being reached by science!

    14. Darwinists, due to their underlying naturalistic philosophy, insist that teleology (i.e. goal directed purpose) does not exist. Yet it is impossible for Biologists to do biological research without constantly invoking words that directly imply teleology. i.e. The very words that Biologists themselves are forced to use when they are doing their research falsifies Darwinian evolution.

    Verse:

    1 Thessalonians 5:21
    Test all things; hold fast what is good.

  62. 62
    ET says:

    Earth to Alan Fox:

    ” Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.”– Larry Moran. Larry also says the genetic code is a real code.

    The genetic code is evidence for a common design. There aren’t any naturalistic mechanisms capable of producing the diversity of life.

  63. 63
    ET says:

    JVL:

    Why don’t you set up an experiment or simulation to see if that leads to anything?

    Lenski has. And it hasn’t.

  64. 64
    JVL says:

    ET: Lenski has. And it hasn’t.

    So, such experiments are doomed to failure?

    So, where are we right now then: the existing biological lifeforms are not the ones designed to evolve. It may have been a long time since those lifeforms existed. (But that programming still permeates the cell? I guess it wouldn’t have just disappeared.)

    At the risk of you accusing me of being some kind of imbecile . . . do you think that whatever design was initially present has run its course and what we see now are just examples of degradation? That whatever was the goal of the designer(s) that’s been met and it’s now down to us to control what happens subsequently?

    It’s an interesting hypothesis which is why I’m asking about it.

  65. 65
    Silver Asiatic says:

    JVL

    So, where are we right now then: the existing biological lifeforms are not the ones designed to evolve.

    Yes, and that’s also assuming that the previous forms were designed to evolve – which I disagree with.

    That whatever was the goal of the designer(s) that’s been met and it’s now down to us to control what happens subsequently?

    It’s an interesting idea and I don’t see a problem with that view. It does seem to match what we observe. We find fully sophisticated organisms in the fossil record and we also know that mutations do, indeed degrade them and not build new features.
    So, with design goals met, humans now take on a new role in nature as caretakers and even innovators (artificial selection, hybrids, etc). The designer planned this transition and it’s the human task to work against degradations, and we do this because we appreciate what was designed. We also emulate and build on the original design. If it was otherwise, we wouldn’t care or pay any attention or have a sense of awe and respect for the design we observe.

  66. 66
    JVL says:

    Silver Asiatic: Yes, and that’s also assuming that the previous forms were designed to evolve – which I disagree with.

    That was directed at ET who has made such statements in the past.

    It’s an interesting idea and I don’t see a problem with that view. It does seem to match what we observe. We find fully sophisticated organisms in the fossil record and we also know that mutations do, indeed degrade them and not build new features.

    Which is why I was asking ET if that was his view. It seems a reasonable conclusion based on his previous stated views and observations.

  67. 67
    Alan Fox says:

    ” Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.”– Larry Moran. Larry also says the genetic code is a real code.

    Alan Fox agrees. Alan Fox thinks however the semantic obfuscation played over the word “code” is silly.

  68. 68
    Alan Fox says:

    JVL

    The Lenski long term experiment. Is fascinating. There are twelve separate strains of E. coli bacteria, kept and allowed to grow and reproduce in identical deliberately sparsely simple environments. The only selection that can take place is intra-species. It tests whether evolutionary change is convergent or divergent in an identical niche. One amazing result is mutation and selection producing the ability to metabolise citrate aerobically in one of the twelve strains yet not in the other eleven. There is much much more detail available if you are interested.

  69. 69
    Alan Fox says:

    The paper Es58 posted will give you a lot to argue against.

    Not seeing anything in that paper that contradicts the point I’ve been making that there is no mechanistic model for a “glycan code”.

  70. 70
    JVL says:

    Alan Fox: The Lenski long term experiment. Is fascinating.

    Yes, it is. I am quite familiar with it and have referenced it in discussions here in the past. Not that it changed anyone’s mind of course.

  71. 71
    Lieutenant Commander Data says:

    Alan Fox
    The Lenski long term experiment. Is fascinating. There are twelve separate strains of E. coli bacteria, kept and allowed to grow and reproduce in identical deliberately sparsely simple environments. The only selection that can take place is intra-species. It tests whether evolutionary change is convergent or divergent in an identical niche.

    Yep, absolutely fascinating a bacteria become bacteria.

    One amazing result is mutation and selection producing the ability to metabolise citrate aerobically in one of the twelve strains yet not in the other eleven. There is much much more detail available if you are interested.

    😆 Yep, amaaazin’ a normal bacteria transforms into (a crippled) bacteria . Another darwinist stunt.
    That “ability” is activated in only 14 days(not decades 😆 ) . It’s not about new ability it’s about losing the function of a control element in presence of oxygen(like saying that incontinence resolve the problem of going to toilet) .

    An “ability” aquired in repeated experiments only after 14 days means that no random mutation is involved but the functional code of different strains resolved the survival math problem by finding same result again and again (damaging a control element for survival purpose ) .

    The only problem is that in normal conditions this ability become a disability and this bacteria can’t compete anymore with normal bacteria.

    Van Hofwegen, Hovde, and Minnich demonstrated this through do-or-die experiments with E. coli, which led to the bacteria developing the capacity not in years or decades, as in the Lenski experiment, but in 14 days, in as little as 100 generations.

    Long-term evolution experiments (LTEE) performed by Blount et al. (Z. D. Blount, J. E. Barrick, C. J. Davidson, and R. E. Lenski, Nature 489:513–518, 2012, http://dx.doi.org/10.1038/nature11514) found a single aerobic, citrate-utilizing E. coli strain after 33,000 generations (15 years). This was interpreted as a speciation event. Here we show why it probably was not a speciation event. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are members of the same class of mutations identified by the LTEE. We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.
    https://evolutionnews.org/2021/06/biologist-dustin-van-hofwegen-punctures-claims-for-lenskis-long-term-evolution-experiment/

  72. 72
    ET says:

    Lenski’s LTEE shows the severe limits of evolutionary processes. The E coli already had the ability to digest citrate. It’s just that in an aerobic environment the gene for transporting the citrate across the cell membrane was not expressed. O2 switched it off. What happened was that gene for the citrate transport protein was duplicated and put under the control of a promoter that was not switched off in the presence of O2.

    No new genes were formed in the LTEE. No new proteins were formed. No new multi-protein complexes were formed.

  73. 73
    ET says:

    Alan Fox:

    Alan Fox thinks however the semantic obfuscation played over the word “code” is silly.

    Please explain this alleged “semantic obfuscation”. The only people I see doing that are evolutionists. It’s as if they can’t stand it that life is ruled by coded information processing systems.

  74. 74
    ET says:

    JVL:

    So, such experiments are doomed to failure?

    What failure?

    At the risk of you accusing me of being some kind of imbecile . . . do you think that whatever design was initially present has run its course and what we see now are just examples of degradation? That whatever was the goal of the designer(s) that’s been met and it’s now down to us to control what happens subsequently?

    No. Humans can still think, plan and react. Nylonase was less than 100 years ago. Epigenetics still holds sway.

  75. 75
    JVL says:

    ET: No. Humans can still think, plan and react. Nylonase was less than 100 years ago. Epigenetics still holds sway.

    Okay. But lots of big changes (new body plans, new families or orders) are unlikely?

  76. 76
    Seversky says:

    Alan Fox/68

    The Lenski long term experiment. Is fascinating. There are twelve separate strains of E. coli bacteria, kept and allowed to grow and reproduce in identical deliberately sparsely simple environments. The only selection that can take place is intra-species. It tests whether evolutionary change is convergent or divergent in an identical niche. One amazing result is mutation and selection producing the ability to metabolise citrate aerobically in one of the twelve strains yet not in the other eleven. There is much much more detail available if you are interested.

    I wonder how many UDs we’d have to set up and how long they’d have to run before one of them “mutated” to become tolerant of evolution?

  77. 77
    bornagain77 says:

    Lenski’s e-coli provided evidence alright. It provided clear evidence that Darwinists are desperately dishonest. (see LCD at 71).

  78. 78
    Seversky says:

    Bornagain77/61
    “Once more unto the breach … ”

    Darwin’s theory holds mutations to the genome to be random. The vast majority of mutations to the genome are not random but are now found to be ‘directed’.

    You should at least try to understand the basics. Darwin knew nothing about the genome so had nothing to say about whether mutations were random or directed. And, no, the vast majority of mutations in the genome are not found to be “directed”, certainly not in the sense you are implying, they are neutral.

    Darwin’s theory holds that Natural Selection is the ‘designer substitute’ that produces the ‘appearance’ and/or illusion of design. Natural Selection, especially for multicellular organisms, is found to grossly inadequate as the ‘designer substitute.

    Darwin’s theory of natural selection offered a naturalistic alternative to creationism which was the only credible explanation for the appearance of design up to that point. It may well be that natural selection is no longer considered to be the primary engine of variation but the much bigger problem for ID/creationists is why we should observe any variation at all in what should be the perfect creations of a perfect creator.

    Darwin’s theory holds that mutations to DNA will eventually change the basic biological form of any given species into a new form of a brand new species. Yet, biological form is found to be irreducible to mutations to DNA, nor is biological form reducible to any other material particulars in biology one may wish to invoke.

    Once again, Darwin knew nothing about DNA. He did not propose that “brand new” species would arise just from mutations. He simply argued that descendent species could arise from natural selection acting on variations in the parent species. That said, plenty of experimental evidence has accumulated subsequently for mutations in DNA having dramatic effects on the phenotype.

    Darwin’s theory holds there to be an extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever

    Whether or not you agree with it, you should at least be aware that current thinking holds that the majority of mutations are neutral or nearly-neutral in effect, a much smaller number are detrimental and an even smaller number still are beneficial. The theory argues that natural selection will tend to filter out the detrimental leaving only the beneficial to have any long-lasting effect, the neutral mutations being effectively invisible to selection.

    Charles Darwin himself held that the gradual unfolding of life would (someday) be self-evident in the fossil record. Yet, from the Cambrian Explosion onward, the fossil record is consistently characterized by the sudden appearance of a group/kind in the fossil record(disparity), then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. Moreover, Fossils are found in the “wrong place” all the time (either too early, or too late)

    Darwin was aware that fossilization was a rare occurrence so gaps were to be expected. The sudden appearance of some species could simply be an artefact of the coarse-grained image preserved in the fossil record. On the other hand, significant environmental changes could allow life to flourish relatively rapidly which could appear as an “explosion” even though it lasted for tens of millions of years. As for transitional fossils, there are plenty to be found in the literature. You could start here if you are actually interested.

    Charles Darwin himself stated that “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Yet as Doug Axe pointed out, “Basically every gene and every new protein fold, there is nothing of significance that we can show that can be had in that gradualistic way. It’s all a mirage. None of it happens that way.”

    Axe’s case is simply another variant of the argument from incredulity. He can’t imagine genetic or protein fold pathways that could have led to complex organs so they could not have happened. But neither Axe’s knowledge nor that of any other researcher in this field is exhaustive. Put another way our ignorance is not evidence of impossibility.

    Charles Darwin himself stated that “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.” Yet as Wolf-Ekkehard Lönnig pointed out, “in thousands of plant species often entirely new organs have been formed for the exclusive good of more than 132,930 other species, these ‘ugly facts’ have annihilated Darwin’s theory as well as modern versions of it.”

    Do you have any examples of an organ formed by one species that is exclusively for the benefit of another species and confers no benefit whatsoever on the species which evolved it. How does Loennig show that all these plant species generated organs purely for the benefit of other species rather than for themselves?

    Charles Darwin himself stated that, ““The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God. Yet ‘our conscious selves’ are certainly not explainable by ‘chance’ (nor is consciousness explainable by any possible reductive materialistic explanation in general), i.e. ‘the hard problem of consciousness’.

    Red herring. Darwin’s theory was about how living things could have varied and diversified over time through natural processes, it says nothing about the origins of “life, the Universe and everything”.

    David Chalmers referred to the hard problem of consciousness not the insoluble problem of consciousness. No, we do not have a materialistic explanation for consciousness – yet – but our ignorance does not mean that there isn’t one. Abd the “ugly fact” remains that when the brain stops working the associated consciousness disappears irretrievably.

    Besides the mathematics of probability consistently showing that Darwinian evolution is impossible, the mathematics of population genetics itself has now shown Darwinian evolution to be impossible. Moreover, ‘immaterial’ mathematics itself, which undergirds all of science, engineering and technology, is held by most mathematicians to exist in some timeless, unchanging, immaterial, Platonic realm. Yet, the reductive materialism that Darwinian theory is based upon denies the existence of the immaterial realm that mathematics exists in. i.e. Darwinian evolution actually denies the objective reality of the one thing, i.e. mathematics, that it most needs in order to be considered scientific in the first place!

    The theory of evolution is about living organisms. It says nothing at all about the ontology of mathematics or Platonic realms. Another red herring.

    Donald Hoffman has, via population genetics, shown that if Darwin’s materialistic theory were true then all our observations of reality would be illusory. Yet the scientific method itself is based on reliable observation. Moreover, Quantum Mechanics itself has now shown that conscious observation must come before material reality, i.e. falsification of ‘realism’ proves that our conscious observations are reliable!.

    Is a map an illusion? It is certainly not a one-to-one representation of all the features of a landscape but, as a model created from the abstraction of salient features, it is nonetheless a very useful tool for navigating around it. As for the existence of objective reality being observer-dependent, that is but one interpretation. And you still haven’t answered the obvious objection of, if nothing exists before it is observed, what is being observed in the first place? In those terms, the idea is absurd.

    The reductive materialism that undergirds Darwinian thought holds that immaterial information is merely ’emergent’ from a material basis. Yet immaterial Information, via experimental realization of the “Maxwell’s Demon” thought experiment, is now found to be its own distinctive physical entity that, although it can interact in a ‘top down’ manner with matter and energy, is separate from matter and energy.

    What is meant by “information” here because it sounds very much like you are equivocating between different usages? What version is being used? You also need to explain how information can be both “immaterial” and a “distinctive physical entity” at one and the same time with out it being a contradiction.

    Darwinists hold that Darwin’s theory is true. Yet ‘Truth’ itself is an abstract property of an immaterial mind that is irreducible to the reductive materialistic explanations of Darwinian evolution. i.e. Assuming reductive materialism and/or Naturalism as the starting philosophical position of science actually precludes ‘the truth’ from ever being reached by science!

    Science does not deal in “truth” but in explanations. In the correspondence theory of “truth” the truth-value of an explanation lies in the extent to which it is observed to correspond to the phenomena for which it is intended to provide an account. If you are working with a different theory of truth you need to explain it.

    Darwinists, due to their underlying naturalistic philosophy, insist that teleology (i.e. goal directed purpose) does not exist. Yet it is impossible for Biologists to do biological research without constantly invoking words that directly imply teleology. i.e. The very words that Biologists themselves use when they are doing their research falsifies Darwinian evolution.

    The difficulty of explaining scientific concepts in non-teleological terms most probably arises from humans, being social animals, having evolved languages originally to explain and describe the activities of purposive agents like human beings and other animals. The need for non-teleological terminology is a much more recent requirement. While it is possible, with some difficulty, to formulate accounts using a non-teleological vocabulary, it is all to easy to revert to default teleological forms.

    Your problem is that, while there are still a lot of questions that need to be answered, none of the objections listed above, especially those of more tangential relevance, taken either singly or together, amount to anything like irrefutable falsification of the theory of evolution.

  79. 79
    bornagain77 says:

    Defense of each claim

    1. Darwin’s theory holds mutations to the genome to be random. The vast majority of mutations to the genome are not random but are now found to be ‘directed’.
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734315

    2. Darwin’s theory holds that Natural Selection is the ‘designer substitute’ that produces the ‘appearance’ and/or illusion of design. Natural Selection, especially for multicellular organisms, is found to be grossly inadequate as the ‘designer substitute.
    Dec. 2021
    https://uncommondescent.com/evolution/could-newly-hatched-pterosaurs-fly/#comment-743728

    3. Darwin’s theory holds that mutations to DNA will eventually change the basic biological form of any given species into a new form of a brand new species. Yet, biological form is found to be irreducible to mutations to DNA, nor is biological form reducible to any other material particulars in biology one may wish to invoke.
    Dec. 2021 –
    https://uncommondescent.com/evolution/could-newly-hatched-pterosaurs-fly/#comment-743732

    4. Darwin’s theory, (via Fisher’s Theorem in population genetics), assumed there to be an equal proportion of good and bad mutations to DNA which were, ultimately, responsible for all the diversity and complexity of life we see on earth. Yet, the ratio of detrimental to beneficial mutations is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever.
    Dec. 2021
    https://uncommondescent.com/evolution/could-newly-hatched-pterosaurs-fly/#comment-743740

    5. Charles Darwin himself held that the gradual unfolding of life would (someday) be self-evident in the fossil record. Yet, from the Cambrian Explosion onward, the fossil record is consistently characterized by the sudden appearance of a group/kind in the fossil record(disparity), then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. Moreover, Fossils are found in the “wrong place” all the time (either too early, or too late).
    Dec. 2021
    https://uncommondescent.com/evolution/could-newly-hatched-pterosaurs-fly/#comment-743796

    6. Darwin’s theory, due to the randomness postulate, holds that patterns will not repeat themselves in supposedly widely divergent species. Yet thousands of instances of what is ironically called ‘convergent evolution’, on both the morphological and genetic level, falsifies the Darwinian belief that patterns will not repeat themselves in widely divergent species.
    (partial defense)
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734735

    7. Charles Darwin himself stated that “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Yet as Doug Axe pointed out, “Basically every gene and every new protein fold, there is nothing of significance that we can show that can be had in that gradualistic way. It’s all a mirage. None of it happens that way.”
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734506

  80. 80
    bornagain77 says:

    8. Charles Darwin himself stated that “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.” Yet as Wolf-Ekkehard Lönnig pointed out, “in thousands of plant species often entirely new organs have been formed for the exclusive good of more than 132,930 other species, these ‘ugly facts’ have annihilated Darwin’s theory as well as modern versions of it.”
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734509

    9. Charles Darwin himself stated that, “The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God.” Yet ‘our conscious selves’ are certainly not explainable by ‘chance’ (nor is consciousness explainable by any possible reductive materialistic explanation in general), i.e. ‘the hard problem of consciousness’.
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734512

    10. Besides the mathematics of probability consistently showing that Darwinian evolution is impossible, the mathematics of population genetics itself has now shown Darwinian evolution to be impossible. Moreover, ‘immaterial’ mathematics itself, which undergirds all of science, engineering and technology, is held by most mathematicians to exist in some timeless, unchanging, immaterial, Platonic realm. Yet, the reductive materialism that Darwinian theory is based upon denies the existence of the immaterial realm that mathematics exists in. i.e. Darwinian evolution actually denies the objective reality of the one thing, i.e. mathematics, that it most needs in order to be considered scientific in the first place!
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734527

    11. Donald Hoffman has, via population genetics, shown that if Darwin’s materialistic theory were true then all our observations of reality would be illusory. Yet the scientific method itself is based on reliable observation. Moreover, Quantum Mechanics itself has now shown that conscious observation must come before material reality, i.e. falsification of ‘realism’ proves that our conscious observations are reliable!.
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734569

    12. The reductive materialism that undergirds Darwinian thought holds that immaterial information is merely ’emergent’ from a material basis. Yet immaterial Information, via experimental realization of the “Maxwell’s Demon” thought experiment, is now found to be its own distinctive physical entity that, although it can interact in a ‘top down’ manner with matter and energy, is separate from matter and energy.
    https://uncommondescent.com/intelligent-design/asked-at-reason-magazine-how-much-science-research-is-fraudulent/#comment-734622

    13. Darwinists hold that Darwin’s theory is true. Yet ‘Truth’ itself is an abstract property of an immaterial mind that is irreducible to the reductive materialistic explanations of Darwinian evolution. i.e. Assuming reductive materialism and/or Naturalism as the starting philosophical position of science actually precludes ‘the truth’ from ever being reached by science!
    Dec. 2021
    https://uncommondescent.com/intelligent-design/maori-creationism-is-okay-in-new-zealand-schools-objectors-could-be-booted-from-nzs-royal-society/#comment-741814

    14. Darwinists, due to their underlying naturalistic philosophy, insist that teleology (i.e. goal directed purpose) does not exist. Yet it is impossible for Biologists to do biological research without constantly invoking words that directly imply teleology. i.e. The very words that Biologists themselves use when they are doing their research falsifies Darwinian evolution.
    December 2021 –
    https://uncommondescent.com/intelligent-design/at-mind-matters-news-jonathan-bartlett-will-the-sokal-hoaxes-worsen-the-academic-echo-chamber/#comment-742455

  81. 81
    relatd says:

    Seversky at 76,

    The more I read – here – the less plausible “evolution” becomes. Do you believe your computer was designed and built by nobody? How about living cells?

  82. 82
    Silver Asiatic says:

    Seversky

    the much bigger problem for ID/creationists is why we should observe any variation at all in what should be the perfect creations of a perfect creator

    ID does evaluate evidence of whether the creator is perfect or imperfect.
    To me your argument reveals that you don’t have a scientific rebuttal but you have to turn to an anti-religious one.

  83. 83
    Silver Asiatic says:

    That is “ID does not evaluate evidence of whether the creator is perfect …”

  84. 84
    Alan Fox says:

    LCD

    The only problem is that in normal conditions this ability become a disability and this bacteria can’t compete anymore with normal bacteria.

    That’s not a problem; that is a fact. Glad you are beginning to grasp how adaptive evolution works. The niche is everything.

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