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Kirk Durston: Information decrease falsifies essential Darwinian prediction

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From Kirk Durston,

Mounting evidence that the digital information that encodes all of life is steadily degrading, falsifies a key prediction of the theory of neo-Darwinian macroevolution and verifies a prediction of intelligent design science.

Longer:

I was struck, but not surprised, by a statement made a few days ago by Neil Turok, Director of the Perimeter Institute for Theoretical Physics here in Waterloo, Ontario. Speaking of the apparent collapse of evidence for a critical component of the Big Bang theory, he responded, ‘even though hundreds or thousands of people are working on an idea, it may still be wrong.’

His statement is a harbinger of a much greater collapse looming on the scientific horizon, also involving thousands of scientists. There is mounting evidence that most, if not all the key predictions of the neo-Darwinian theory of macroevolution are being consistently falsified by advances in science, several of which I will discuss in later posts. Here, we look at a fundamental prediction Darwinism makes regarding the increase of genetic information.

Computer information is digitally encoded using just two symbols (‘1’ and ‘0’). We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things using a four-symbol alphabet. In more technical terms, this is referred to as functional information.

In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.

An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.

Interestingly enough, a prediction of intelligent design science is quite the opposite. Since information always degrades over time for any storage media and replication system, intelligent design science postulates that the digital information of life was initially downloaded into the genomes of life. It predicts that, on average, genetic information is steadily being corrupted by natural processes. The beauty of these two mutually incompatible predictions in science is that the falsification of one entails verification of the other. So, which prediction does science falsify, and which one does science verify? More.

Actually, it no longer matters whether Darwinian evolution has any relationship to fact. Airheads believe it, judges enforce it, union teachers spout it, students know they had better absorb it—a combo like that doesn’t need facts or evidence, and is in fact hostile to them. They are unwelcome intruders into a System That Works for its proponents.

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Comments
@ jerry: I didn't mean you. @bornagain77: Did you read the full paper?Roy
June 28, 2015
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jerry, when I asked if you Disagree with me on the state of empirical evidence you are the one who brought up Juergen Brosius as if he had some empirical evidence that would counter my claim that Darwinists have no real time empirical evidence to support their grandiose claims. You have suggested I read him twice as a matter of fact. And sent a flurry of links insinuating that the evidence would be in those links. You are the one insinuating that he had some actual real time evidence that counters my claim as to the state of empirical evidence. Plain and simple, he does not. Thus why did you bring him up in the first place? The only person who went along with you was roy for crying out loud. You told roy you read him. Twice in some places, and you also mentioned that you disagree with him, but commented no further as to the fact that he has no actual real time evidence to support his claims. Which is what you originally insinuated against my claim for the actual state of the empirical evidence. I happen to be able to read myself https://uncommondescent.com/intelligent-design/kirk-durston-information-decrease-falsifies-essential-darwinian-prediction/#comment-570052 https://uncommondescent.com/intelligent-design/kirk-durston-information-decrease-falsifies-essential-darwinian-prediction/#comment-570056bornagain77
June 28, 2015
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BA, I have read everything I wrote on this page. I suggest you point out where you disagree with me. You may disagree with Juergen Brosius, and that is fine, because I do too and I say so more than once. But what did I say that was wrong?jerry
June 28, 2015
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BTW guys, it was Wells, not Meyer, who talked about information in the egg-cell wall and cytoskeleton. Wells is the developmental biologist, not Meyer.
If you want to split hairs, maybe. We learned about it from Meyer's book and Meyer gives full credit to his introduction to the topic by Wells in Chapter 14 of his book. He includes a photograph of Wells at this point. See this in Meyer's book
ABOVE AND BEYOND: EPIGENETIC INFORMATION
In 2003, MIT Press published a groundbreaking collection of scientific essays titled Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by two distinguished developmental and evolutionary biologists, Gerd Muller, of the University of Vienna, and Stuart Newman, of New York Medical College. In their volume, Muller and Newman included a number of scientific articles describing recent discoveries in genetics and developmental biology—discoveries suggesting that genes alone do not determine the three-dimensional form and structure of an animal. Instead, many of the scientists in their volume reported that so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means "above" or "beyond," so epigenetics refers to a source of information that lies beyond the genes. As Muller and Newman explain in their introduction, "Detailed information at the level of the gene does not serve to explain form."s Instead, as Newman explains, "epigenetic" or "contextual information" plays a crucial role in the formation of animal "body assemblies" during embryological development. Muller and Newman not only highlighted the importance of epigenetic information to the formation of body plans during development; they also argued that it must have played a similarly important role in the origin and evolution of animal body plans in the first place. They concluded that recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all. In the introductory essay to their volume, Miiller and Newman list a number of "open questions" in evolutionary biology, including the question of the origin of Cambrian-era animal body plans and the origin of organismal form generally, the latter being the central topic of their book. They note that though "the neo-Darwinian paradigm still represents the central explanatory framework of evolution," it has "no theory of the generative."? In their view, neo-Darwinism "completely avoids [the question of] the origination of phenotypic traits and of organismal form."s As they and others in their volume maintain, neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information. I first learned about the problem of epigenetic information and the Spemann and Mangold experiment while driving to a private meeting of Darwin-doubting scientists on the central coast of California in 1993. In the car with me was Jonathan Wells (see Fig. 14.1), who was then finishing a Ph.D. in developmental biology at the University of California at Berkeley. Like some others in his field, Wells had come to reject the (exclusively) "gene-centric" view of animal development and to recognize the importance of nongenetic sources of information. By that time, I had studied many questions and challenges to standard evolutionary theories arising out of molecular biology. But epigenetics was new to me. On our drive, I asked Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I'll never forget his reply. "Because" he said, "that's where the whole theory is going to unravel." In the years since, Wells has developed a powerful argument against the adequacy of the neo-Darwinian mechanism as an explanation for the origin of animal body plans. His argument turns on the importance of epigenetic information to animal development.
jerry
June 28, 2015
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Besides being a lead player in morphogenesis during embryological development, biophotons are also heavily involved in the cellular communication of an organism throughout an organism’s entire life. https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/#comment-569470bornagain77
June 28, 2015
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Stephen Meyer on electromagnetic fields; “Darwin’s Doubt”, ch.14, ‘Epigenetic Revolution’, ‘Beyond Genes’, ‘Ion Channels and Electromagnetic Fields’.
Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.22 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.23 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influences the development of the animal.
Here an interesting article by Richard H. W. Funk.Box
June 28, 2015
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Mapou:
I see no reason to change my mind that genes (DNA) are the primary determinants of the wide ranging diversity of life on earth.
When you find the evidence that supports that view please share it with us. Thank you. BTW guys, it was Wells, not Meyer, who talked about information in the egg-cell wall and cytoskeleton. Wells is the developmental biologist, not Meyer.Virgil Cain
June 28, 2015
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jerry, "I read the paper a few times and parts of it additional times." And the real time experimental evidence of a gene/protein being generated by unguided material processes is where exactly? That's the whole thing jerry. Darwinists are notorious for making up elaborate far fetched just so stories based on little more than their unconstrained imagination, but when push comes to shove, they NEVER deliver on the real time empirical evidence that would give their just so story credibility. Moreover, they consistently ignore insurmountable empirical difficulties with their theory. Dr. Behe states: "Grand Darwinian claims rest on undisciplined imagination" Dr. Michael Behe - 29:24 mark of following video http://www.youtube.com/watch?feature=player_detailpage&v=s6XAXjiyRfM#t=1762s and Finally, a Detailed, Stepwise Proposal for a Major Evolutionary Change? - Michael Behe - March 10, 2015 Excerpt: I would say its (Nick Matzke's 2004 proposal for the evolution of the flagellum) chief problem is that it's terminally fuzzy, bases most of its speculation on sequence comparisons, and glides over difficulties that would have to be dealt with in nature.,,, That's one reason I wrote The Edge of Evolution -- to say that we no longer have to rely on our imaginations, that we have good evidence to show what Darwinian processes are capable of doing. When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage. http://www.evolutionnews.org/2015/03/finally_a_detai094271.htmlbornagain77
June 28, 2015
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Did you read the full paper, or only the abstract? I read the paper a few times and parts of it additional times. I have the book in which it appeared as well as a pdf of the journal article. It was the lead article in a book that was a tribute to Stephen Gould. I have commented on it several times here over the years. It was first recommended by Allen MacNeill over 6 years ago.jerry
June 28, 2015
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Jerry, do you actually believe, in all the links you cited, that he has ANY real time experimental evidence showing unguided material processes generating a single gene/protein? If so, I have a bridge for you! You asked me to pick one. OK how about the this one?: [abstract omitted] All I see is one big romp through imagination, (i.e. just so stories), with no empirical support whatsoever.
Did you read the full paper, or only the abstract?Roy
June 28, 2015
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New tools developed to unveil mystery of the 'glycome' - June 10, 2012 Excerpt: One of the Least Understood Domains of Biology: The "glycome"—the full set of sugar molecules in living things and even viruses—has been one of the least understood domains of biology. While the glycome encodes key information that regulates things such as cell trafficking events and cell signaling, this information has been relatively difficult to "decode." Unlike proteins, which are relatively straightforward translations of genetic information, functional sugars have no clear counterparts or "templates" in the genome. Their building blocks are simple, diet-derived sugar molecules, and their builders are a set of about 250 enzymes known broadly as glycosyltransferases.,,, http://phys.org/news/2012-06-tools-unveil-mystery-glycome.html Glycans rival DNA and proteins in terms of complexity; Glycans: What Makes Them So Special? - The Complexity Of Glycans - short video http://www.youtube.com/watch?v=WXez_OyNBQA The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It - Jonathan Wells - published online May 2013 Excerpt: ,,In 1985 Ronald Schnaar wrote, “There appears to be a code on the surface of each cell that specifies its function and directs its interactions with other cells, a code in some ways comparable to the genetic code carried on the DNA molecules inside each cell.” The “letters” of the cell surface code to which Schnaar was referring are sugar molecules. A few monosaccharide building blocks can produce the enormous diversity of “words” needed to identify the many different kinds of cells in a complex organism, Schnaar explained, because “each building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters. (This alphabet is even more efficient than the genetic code: the four nucleic acids that constitute DNA — guanine, adenine, thymine, and cytosine — can be connected only front to back, like roller coaster cars.) So, not only are sugars in the right place to serve as the alphabet for the cell-surface code, they have the requisite structural flexibility too.” Schnaar concluded, “It may be that as much control over the cell’s fate, and as much of the language of life’s unfolding, reside on the cell’s surface as in its nucleus” [63].,, Membrane patterns in ciliates are known to be heritable independently of the information in DNA sequences, and there is evidence that some cytoskeletal and membrane patterns in the cells of multicellular organisms can also be inherited apart from the DNA. Taken together, the data suggest that embryo development is not controlled by DNA alone, and thus that DNA mutations are not sufficient to provide raw materials for evolution. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0021 Yet Glycans, despite their complexity and importance to cell function, are, like DNA and Proteins, now being found to be 'rather uncooperative' with neo-Darwinian evolution; This Non Scientific Claim Regularly Appears in Evolutionary Peer Reviewed Papers - Cornelius Hunter - April 2012 Excerpt: Indeed these polysaccharides, or glycans, would become rather uncooperative with evolution. As one recent paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. In other words, the evidence is not what evolution expected. Here is how another paper described early glycan findings: There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages. It appears that closely related species may not necessarily share close similarities in their glycan diversity, and that more derived species may have simpler as well as more complex structures. Intraspecies diversity can also be quite extensive, often without obvious functional relevance. http://darwins-god.blogspot.com/2012/04/this-non-scientific-claim-regularly.htmlbornagain77
June 27, 2015
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Jerry @49, I don't get it. You are insinuating something that is simply not there. I don't see any evidence where Meyer claims that the information that is responsible for the full diversity of life on earth is in the egg cell wall. You're making this up, IMO. In fact, it's a good bet that the proteins that make up the cell wall are manufactured according to genetic information prescribed in the gene, just like every other protein.Mapou
June 27, 2015
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Jerry, do you actually believe, in all the links you cited, that he has ANY real time experimental evidence showing unguided material processes generating a single gene/protein? If so, I have a bridge for you! You asked me to pick one. OK how about the this one?:
Gene duplication and other evolutionary strategies: from the RNA world to the future - 2003 Abstract Beginning with a hypothetical RNA world, it is apparent that many evolutionary transitions led to the complexity of extant species. The duplication of genetic material is rooted in the RNA world. One of two major routes of gene amplification, retroposition, originated from mechanisms that facilitated the transition to DNA as hereditary material. Even in modern genomes the process of retroposition leads to genetic novelties including the duplication of protein and RNA coding genes, as well as regulatory elements and their juxtapositon. We examine whether and to what extent known evolutionary principles can be applied to an RNA-based world. We conclude that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds. In this hypothetical RNA world there were few restrictions on the exchange of genetic material and principles that acted as borders at later stages, such as Weismann's Barrier, the Central Dogma of Molecular Biology, or the Darwinian Threshold were absent or rudimentary. RNA was more than a gene: it had a dual role harboring, genotypic and phenotypic capabilities, often in the same molecule. Nuons, any discrete nucleic acid sequences, were selected on an individual basis as well as in groups. The performance and success of an individual nuon was markedly dependent on the type of other nuons in a given cell. In the RNA world the transition may already have begun towards the linkage of nuons to yield a composite linear RNA genome, an arrangement necessitating the origin of RNA processing. A concatenated genome may have curbed unlimited exchange of genetic material; concomitantly, selfish nuons were more difficult to purge. A linked genome may also have constituted the beginning of the phenotype/genotype separation. This division of tasks was expanded when templated protein biosynthesis led to the RNP world, and more so when DNA took over as genetic material. The aforementioned barriers and thresholds increased and the significance and extent of horizontal gene transfer fluctuated over major evolutionary transitions. At the dawn of the most recent transformation, a fast evolutionary transition that we will be witnessing in our life times, a form of Lamarckism is raising its head. http://link.springer.com/article/10.1023%2FA%3A1022627311114
All I see is one big romp through imagination, (i.e. just so stories), with no empirical support whatsoever. Remember I said Disagree? If so, then provide direct empirical evidence to back up their claims and not just sequence comparisons that assume the conclusion into the premise. and then you said "I suggest you read Jurgen Brosius." and, after you asked me to 'pick one' of his papers, I am still waiting for that real time empirical evidence that you insinuated existed in his writings. i.e. The emperor Brosius has no clothes on!bornagain77
June 27, 2015
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jerry, please cite the specific experimental data requested of a single gene and/or protein being generated by unguided material processes in real time.
I gave you a reference for a review article. In it he discusses his ideas and lists his research. Pick one. Several look good for what he says.
Brosius, J. 1991. Retroposons—seeds of evolution. Science 251:753. Brosius, J. 1999a. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107:209–238. Brosius, J. 1999b. Many G-protein-coupled receptors are encoded by retrogenes. Trends in Genetics 15:304–305. Brosius, J. 1999c. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115–134. Brosius, J. 1999d. Transmutation of tRNA over time. Nature Genetics 22:8–9. Brosius, J. 2001. tRNAs in the spotlight during protein biosynthesis. Trends in Biochemical Sciences 26:653–656. Brosius, J. 2003a. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118:99–116. Brosius, J. 2003c. Gene duplication and other evolutionary strategies: from the RNA world to the future. Journal of Structural and Functional Genomics 3:1–17. Brosius, J. 2005a. Echoes from the past—are we still in an RNP world? Cytogenetic and Genome Research (in press). Brosius, J. 2005b. Waste not, want not—transcript excess in multicellular Eukaryotes. Trends in Genetics 21:287–288. Brosius, J. and S. J. Gould. 1992. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA.”. Proceedings of the National Academy of Sciences USA 89:10706–10710. CrossRef, PubMed Brosius, J. and H. Tiedge. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11:163–179. Brosius, J. and H. Tiedge. 2004. RNomenclature. RNA Biology 1:81–83.
From the footnotes of his review
An extension of Wally Gilbert's metaphor “exons in a sea of introns” (Gilbert 1978). Functional nuons are islands in a sea of nonfunctional (nonaptive) sequences. Nevertheless, any of those sequences has the potential to be exapted into novel functions (Brosius and Gould 1992; Balakirev and Ayala 2003). Balakirev, E. S. and F. J. Ayala. 2003. Pseudogenes: are they “junk” or functional DNA? Annual Review of Genetics 37:123–151. While “plate tectonics,” or exon shuffling, occasionally leads to rearrangements of existing functional nuons (Gilbert 1978), retroposition, the major force in the plasticity of genomes, which in our analogy is more akin to volcanic eruptions, frequently creates new nuons. Initially, most nuons (islands) are barren (nonfunctional, nonaptive) but have the potential to be fertilized by some microevolutionary base changes or short indels and exapted as functional nuons. Nonfunctional nuons erode over time and the islands disappear in the sea of anonymous sequences. An interesting example is the recruitment of part of an Alu retronuon as an alternative exon in an isoform of the cytokine tumor necrosis factor receptor. Insertion of the Alu element occurred after Anthropoidea split from prosimians and a subsequent point mutation generated an ATG start codon. This base substitution alone, however, was not sufficient for exaptation of the Alu element as a protein-coding exon, as this sequence is nonaptive (not used as part of an alternative mRNA) in Platyrrhini. Only two additional small changes in the lineage leading to Catarrhini including apes, a C?T transition to generate a GT 5? splice site and a 7-bp deletion to provide translation into the next exon in the correct reading frame, led to generation and exaptation of this alternative exon (Singer et al. 2004). Singer, S. S., D. N. Männel, T. Hehlgans, J. Brosius, and J. Schmitz. 2004. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. Journal of Molecular Biology 341:883–886.
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You are more than welcome to try to prove me, Behe, Meyer, Axe, Guager, Luskin, Sanford, etc.. etc.. wrong.
You completely misunderstand what is happening here. I am not trying to prove you wrong. I am saying that one of the most prestigious researchers today in evolutionary biology says that new information is no big deal. As such he carries a lot more weight with the scientific community than you and all the others combined. And because of this his ideas should be examined. I have never endorsed Brosius, just the opposite. But he has never been dealt with.jerry
June 27, 2015
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jerry, please cite the specific experimental data requested of a single gene and/or protein being generated by unguided material processes in real time. You made the claim. YOU need to support it with real time evidence! It is not up to me to dig through your myriad of links to try to find some evidence for a gene/protein being generated by unguided material processes when I KNOW for a fact that the evidence does not exist! You are more than welcome to try to prove me, Durston, Behe, Meyer, Axe, Gauger, Luskin, Sanford, etc.. etc.. wrong.bornagain77
June 27, 2015
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BA, Here is a thread from last year which has information about Brosius, including more links to his ideas. https://uncommondescent.com/design-inference/on-fscoi-vs-needles-and-haystacks-as-well-as-elephants-in-rooms/ Here is a major review (just abstract and footnotes) http://www.bioone.org/doi/abs/10.1666/0094-8373%282005%29031%5B0001%3ADAEBAC%5D2.0.CO%3B2 I have the full pdf and this was a chapter in a book about macro evolution by Vrba which I also have. You might be able to get it from your library if they have JSTOR service. You will notice that I do not believe he has really solved the problem but points to a few coding areas that have come into being through the exaptation of mutated DNA sequences. He is a major player and not a clown like Coyne or PZ Myers. Brosius came up because of Allen MacNeil over 6 years ago. He pointed out Vrba's book as a discussion of macro-evolution and Brosius was given the honor of authoring a long introduction in the book. He had been a co-author with Stephen Gould and his ideas provides some basis for punctuated equilibrium because they hypothesize a sudden appearance of genes.jerry
June 27, 2015
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where is the information that is responsible for the full diversity of life, if it’s not in DNA
As I said earlier, Meyer thinks it is in the egg cell wall. See Ch 14 of his book, Darwin's Doubt, especially the Sugar Code.
Biologists know of an additional source of epigenetic information stored in the arrangement of sugar molecules on the exterior surface of the cell membrane. Sugars can be attached to the lipid molecules that make up the membrane itself (in which case they are called “glycolipids”), or they can be attached to the proteins embedded in the membrane (in which case they are called “glycoproteins”). Since simple sugars can be combined in many more ways than amino acids, which make up proteins, the resulting cell surface patterns can be enormously complex. As biologist Ronald Schnaar explains, “Each [sugar] building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters.”
There is a lot more there on other epigenetic information.
Where is the information difference between human and chimp? Is it in the 1% difference in DNA?
Most of the difference are in control mechanisms that affect expression of proteins in the brain. See Wilcox http://www.asa3.org/ASA/meetings/belmont2013/papers/ASA2013Wilcox.pdf for a discussion. From Wilcox
We and chimps share 96% to 99% of our protein coding sequences. Why are we different? Not the 1.5% of our genome that codes for proteins but the 98.5% that controls their production. Literally, no other primate lineage has evolved as fast as our lineage has during the last 1.5 million years, and it’s all due to unique changes in our control genome.
jerry
June 27, 2015
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Well, ladies and gentlemen. I'm not convinced at all by the arguments I have seen so far. I see no reason to change my mind that genes (DNA) are the primary determinants of the wide ranging diversity of life on earth. One more thing. I put YEC in the same crap basket as Darwinism. I'm just voicing an opinion, BTW. So don't get bent out of shape.Mapou
June 27, 2015
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Mapou, I personally don't think this is an argument for intelligent design. It might be an argument for young earth creationism, or what Salvador has taken to calling "young life." I have no idea though what Durston's position is on the age of the earth.Mung
June 27, 2015
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SA, I am going to go with a no on that one. :)Mung
June 27, 2015
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where is the information that is responsible for the full diversity of life, if it’s not in DNA
Where is the information difference between human and chimp? Is it in the 1% difference in DNA?Silver Asiatic
June 27, 2015
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Building materials influence what type of building you can build. They do not determine the building.Virgil Cain
June 27, 2015
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Virgil Cain, I read your reply and I still see no reason to believe that genes are not the primary cause of the full diversity of lifeforms on earth. Even if environmental pressure modifies an organism (adaptation via epigenetics) in a way that changes the form and fitness of its offsprings, the new information that is inherited by the offsprings is still in the genes. Your software/hardware metaphor either went over my head or it's inappropriate. The medium in which the information is stored and interpreted is irrelevant. What's important if whether the information can be used by some “bootstrapping” mechanism to build, not only the organism, but a major portion of the mechanism itself. One more thing, why is this issue important to IDists?Mapou
June 27, 2015
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Virgil Cain, here are a few more notes to go with yours that show 'form' is not reducible to DNA:
The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism - Michael J. Denton - 2013 Excerpt: Cell form ,,,Karsenti comments that despite the attraction of the (genetic) blueprint model there are no “simple linear chains of causal events that link genes to phenotypes” [77: p. 255]. And wherever there is no simple linear causal chain linking genes with phenotypes,,,—at any level in the organic hierarchy, from cells to body plans—the resulting form is bound to be to a degree epigenetic and emergent, and cannot be inferred from even the most exhaustive analysis of the genes.,,, To this author’s knowledge, to date the form of no individual cell has been shown to be specified in detail in a genomic blueprint. As mentioned above, between genes and mature cell form there is a complex hierarchy of self-organization and emergent phenomena, rendering cell form profoundly epigenetic. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.3/BIO-C.2013.3 Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - 2014 - Jonathan Wells Excerpt Page 11: Most proteins are not completely specified by DNA sequences: The central dogma (which here includes Crick’s sequence hypothesis) claims that (1) DNA specifies RNA and (2) RNA specifies protein. Yet this claim fails at both steps, because most RNAs are not uniquely specified by DNA sequences, and many proteins are not uniquely specified by RNAs—either in their amino acid sequences or in their final folded forms. After transcription, RNAs from many eukaryotic genes undergo alternative splicing. Recent studies estimate that transcripts from approximately 95% of multi-exon human genes are spliced in more than one way [289?291]. By intervening between transcription and translation, alternative splicing generates RNAs with sequences that differ from DNA sequences [292]. The differences are functionally significant.,,, Page 12 In addition to alternative splicing, many metazoan transcripts undergo RNA editing, which can (a) modify cytidine to uridine; (b) modify adenosine to inosine; or (c) insert additional nucleotides. Several recent analyses have demonstrated extensive RNA editing in the human transcriptome [303?305]. The editing of an mRNA often alters the amino acid sequence of the encoded protein so that it differs from the sequence predicted by the DNA [306,307]. References: 289. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476. doi: 10.1038/nature07509 290. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415. doi: 10.1038/ng.259 291. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, et al. (2010) Deciphering the splicing code. Nature 465:53-59. doi: 10.1038/nature09000 292. Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, et al. (2013) Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153-165. doi: 10.1038/nrm3525 303. Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253-260. doi: 10.1038/nbt.2122 304. Bahn JH, Lee JH, Li G, Greer C, Peng G, et al. (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 22:142-150. doi: 10.1101/gr.124107.111 305. Sakurai M, Ueda H, Yano T, Okada S, Terajima H (2014) A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res (January 9, 2014). doi: 10.1101/gr.162537.113 306. Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23:297-316. doi: 10.1111/j.1574-6976.1999.tb00401.x 307. Eisenberg E, Li JB, Levanon EY (2010) Sequence based identification of RNA editing sites. RNA Biol 7:248-252. doi: 10.4161/rna.7.2.11565 http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2 In Embryo Development, Non-DNA Information Is at Least as Important as DNA - Jonathan Wells - May 2012 Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns. http://www.evolutionnews.org/2012/05/in_embryo_devel060031.html “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 podcast - Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 - Bioelectric code http://intelligentdesign.podomatic.com/entry/2014-06-11T16_35_52-07_00 Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern - July 2011 Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,",,, "We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It's a jaw dropper.",,, http://www.physorg.com/news/2011-07-frog-time-lapse-video-reveals-never-before-seen.html Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/
bornagain77
June 27, 2015
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Hi Mapou- Please check out the following from Dr Denton. Also read "Why is a Fly Not a Horse?" by geneticist Giuseppe Sermonti. And finally read what Dr Wells has to say about it. First Dr Denton in his chapter from "Dissent from Darwin":
To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment. Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes. Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene
Now a snippet from Sermonti,Chapter VI “Why is a Fly not a horse?” (same as the book’s title)
”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”
Do computer application programs make the computer? Does the OS make the computer? Does the combination of all programs make the computer? We can figure out where the software is by synthesizing an organism one piece at a time. Venter did the DNA so we can cross that off.Virgil Cain
June 27, 2015
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Seversky, I can't really think of any good reason to think that humans are so utterly different from other living organisms that they are the only ones capable of storing, communicating and transferring information. Can you? Oh, and the nucleic acids are symbols which just might give us pause and lead us to think there is language involved within the cell as well as outside. Or are you a dualist?Mung
June 27, 2015
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harry @12
... the non coding regions of DNA probably contain much functional information that we just have deciphered yet, but is probably just as organized and ordered as the regions of DNA memory that code for protein machines.
Should have been
... the non coding regions of DNA probably contain much functional information that we just have NOT deciphered yet, but is probably just as organized and ordered as the regions of DNA memory that code for protein machines.
harry
June 27, 2015
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So, Virgil Cain, where is the information that is responsible for the full diversity of life, if it's not in DNA according to you? Enquiring minds and all that.Mapou
June 27, 2015
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Umm, Seversky, Crick is the one who discussed information with respect to biology.Virgil Cain
June 27, 2015
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To start with, I think that using the word “information” as if it is describing a property of the genome could be misleading. In popular usage, “information” refers to something like what we are exchanging through these comments. It is transferring meaningful data from the mind of one intelligent agent to another through the medium of a shared language, although the process of being informed occurs at the recipient’s end. I am informed if you tell me something I didn’t know before. You are not informed by telling me something you already knew. This doesn’t mean you can’t use the word “information” to label what happens in the genome - you can use whatever word you like - but if you are going to call it “information” you have an obligation to provide the specialized definition you are using in this context to avoid any confusion. Because what happens in the genome is not what is happening here. As far as we can tell, there are no intelligent agents talking to each other using a language made up of four chemical bases, saying things like “This is an arm. Grow it here!” As for the so-called degradation of genetic information, who gets to decide whether a mutation is detrimental or beneficial? In the classic illustration, a mutation which causes a brown bear to grow a white coat could put it at a disadvantage if it lived in a landscape that was mostly brown and green. The unfortunate individual could been seen more easily by prey compared with his brown fellows and would have a harder time surviving and raising offspring. A white coat in predominantly snow-covered terrain, on the other hand, could give him an advantage over other brown bears. Same mutation, in one situation detrimental, in another beneficial. The environment decides. Current thinking holds that the majority of mutations are neutral or nearly neutral in effect. A smaller number are detrimental - there are more ways for something to go wrong than than go right - and a much smaller number still are beneficial. So why don’t the greater number of harmful mutations simply swamp the good ones and cause species to go extinct? Simple answer one, if they were to happen at such a rate that the species couldn’t cope with, then that’s exactly what would happen. There are no guarantees under evolution. We could go extinct just as easily as the next species if things went wrong. Simple answer two, detrimental mutations are harmful, by definition, because they impair the capacity to survive in a given environment. Those so afflicted, in the words of the philosopher W V O Quine in another context, “ have a pathetic but praiseworthy tendency to die before reproducing their kind”. In other words, natural selection tends to filter out the harmful mutations and only the beneficial are left. If you want to put it in information terms, harmful information has been lost and good information has replaced it. What’s the big deal about losing bad information?Seversky
June 27, 2015
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