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Paul Giem on overlapping genetic codes

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In the book “Biological Information: New Perspectives” Chapters 6 and 9 (at least) argue that stretches of DNA can have multiple functions encoded into them. We will partially evaluate the strength of the evidence behind that argument.

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208 Replies to “Paul Giem on overlapping genetic codes

  1. 1
    bornagain77 says:

    The evidence presented in the video is simply devastating to Neo-Darwinism! As to why that would be extremely sad news for some determined nihilistic atheists, well that is a mystery that may never be figured out completely by man.

  2. 2
    hrun0815 says:

    This is yet again very amusing. Overlapping genetic encoding has been textbook knowledge since the eighties. I guess ‘Darwinists’ are just so stupid that they need more than a quarter century and sharp minds like BA77 to figure out just how devastating that news is.

    And News, could you actually mark in your posts which part is a direct quote and which one isn’t? I’m curious who is responsible for this sentence: “We will partially evaluate the strength of the evidence behind that argument.” It’s clearly another sign of a very sharp mind so I’d like to know who to attribute it to.

  3. 3
    bornagain77 says:

    hrun0815, I did not make the video, so I am not the ‘sharp mind’ behind the video nor do I pretend to be as sharp as the minds of the PhDs behind the paper that was the inspiration of the video.

    But as to your claim that ‘overlapping genetic encoding has been textbook knowledge since the eighties’, I do have a bit of knowledge in that area and it turns out when overlapping coding was first discovered in viruses a few decades ago, it created a bit of a stir but, as Dr. Bohlin explains in the following video, people wrote it off as a anomaly.

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin
    https://vimeo.com/106012299

    Thus, though is may have been ‘textbook knowledge’ back in the eighties, overlapping coding was certainly not expected on neo-Darwinian presuppositions, nor does discovering further levels of overlapping coding, several on top of each other, give comfort to the atheistic belief that such an extreme level of code crowding arose accidentally:

    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.
    http://www.worldscientific.com.....08728_0006

    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 – May 2013
    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

    Biological Information – Overlapping Codes 10-25-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene ‘inflicted an immense damage to biological sciences’, for over 30 years:

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://vimeo.com/81930637

    In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

    Concluding powerpoint of the lecture (at the 1 hour mark):

    “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
    Edward N. Trifonov – 2010

  4. 4
    hrun0815 says:

    Linkedy link link link
    Extremely selective admiration of authority
    Non-sequiturs
    False arguments

    A typically empty post by BA77.

  5. 5
    bornagain77 says:

    as to “A typically empty post by BA77.”
    Well that responce was certainly empty of anything other than usual ad hominem of dogmatic Darwinists.. but anyways,,
    What is truly EMPTY is the empirical evidence that unguided Darwinian processes can create even a single gene/protein, much less create the several layers of overlapping coding that our best computer programmers can only dream of imitating!

    ‘It’s becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can’t even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and more the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.’ –
    Dr. John Sanford – Inventor of the ‘Gene Gun’ – 31 second mark – video
    http://www.youtube.com/watch?f.....dM_s#t=31s

    In the following artcile/paper, Dr. Behe surveys four decades of laboratory evolution experiments and finds that not a single gene/protein has been created by Darwinian processes during that time. In fact, Dr. Behe points out that the overwhelming tendency of unguided Darwinian processes is to break things rather than ever build them up. He dubs it, “The First Rule of Adaptive Evolution”:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Alan H. Linton, emeritus professor of bacteriology at the University of Bristol, also notes that in 150 years of testing no one has ever seen one bacteria change into another.

    Scant search for the Maker
    Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms.
    – Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
    http://www.timeshighereducatio.....ode=159282

    In fact, as far back in time that we can revive spores of bacteria that have remained dormant for millions of years, we find no evidence for Darwinian evolution in those bacteria.

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    The fossil evidence agrees:

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
    http://bcb705.blogspot.com/200.....st_23.html

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

    Scientists find signs of life in Australia dating back 3.48 billion years – Thu November 14, 2013
    Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”… “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,”
    http://www.cnn.com/2013/11/13/.....ient-life/

  6. 6
    hrun0815 says:

    Nope, BA77. It was not an ad hominem. I did not criticize you as s person to discredit your post. Your post, no matter who made it, is a link-fest sprinkled with non-sequiturs and false arguments.

  7. 7
    bornagain77 says:

    I note, that instead of producing any counter evidence that Darwinian processes can create genes/proteins or overlapping codes, you instead want to squabble over whether or not your posts were empty of anything other than ad hominem.

    You accused my posts of being ’empty’, yet you presented no evidence whatsoever. You merely stated your personal opinion as if that mattered in science!

    Despite how highly you may value your own personal opinion that multiple overlapping genetic codes are no problem for unguided Darwinian processes to account for, and your self-declaration that any evidence, presented against Darwinian processes producing as such, are ‘non-sequiturs and false arguments’, the fact of the matter is that you are the one making ‘non-sequiturs and false arguments’ since you are in fact not addressing the evidence on its merits but are instead pretending as if your personal opinion mattered.

    Let me be the first to inform you, as far as empirical science is concerned, your personal opinion doesn’t matter one iota if you can’t back it up. You need to present counter evidence that Darwinian processes can create such extreme complexity as we see in overlapping coding and not just belittle anything are anyone who questions Darwinism!

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

  8. 8
    hrun0815 says:

    Wrong again. I did not claim that or want to discuss the content of my post. I did not pretend it was anything other than my opinion. And I certainly did not make any argument or comment about “Darwinian processes” creating overlapping codes.

    It was you who made the false argument, obviously without any reasoning or supporting evidence, that this is “devastating for Neo-Darwinism”. I guess all those biology Ph.D.s who failed to notice this since the overlapping code was discovered in the late seventies (including the guys that actually put this info into textbooks) were not “as sharp as the minds of the PhDs behind the paper that was the inspiration of the video.”

  9. 9
    bornagain77 says:

    hrun0815, since you are not even in the realm of empirical science but are instead in the realm of proclaiming whoever’s personal opinion should matter, I rest my case.

    i.e. your argument is ’empty’.

    Merry Christ-mas sir.

  10. 10
    hrun0815 says:

    “I rest my case.”

    And a devastating ‘case’ it was.

    And may your Christ’s-mass (at least I assume that’s what you were alluding to) be as filled with joyful pagan rituals as for many of us.

  11. 11
    Steve says:

    hrun0815 is reduced to spitballing in absence of an argument.

    Oh, but he has complicated narratives galore.

    Just a sec, hrun, i gotta get the popcorn. OK, hrun, go!!

    hrun: Ok, ready. in the beginning there was nothing…but then something happened, a twitch, an itchy scratch, then life….yes, it ’twas but an itch that started little round marbles movin’ about, then out of nowhere a little nub pops out of one, then another, and before you know it..they weren’t marbles anymore…they became …..jacks. yes the jacks you know so well from your childhood. some jacks stayed jacks because they liked being jacks (and thats why our kids can still play jacks see, well they used to like them anyway) but some wanted more than a jack life. but they had to wait, wait for a chance….something to trigger more change…it took a while, an excruciating long while, but in the end it happened, and some jacks slowly, slowly, morphed…..

    ….and the rest was history.

    i like those fuzzy little evolution fables. sleep like a baby every time.

    thanks hrun!!!

  12. 12
    Sebestyen says:

    Sorry hrun0815,

    they can’t earn trophies for writing the most idiotic posts here. You can go back to YouTube now…

    Sebestyen

  13. 13
    Dionisio says:

    BA77

    Ignore the whiners, specially when they’re barking up the wrong trees.

    Keep providing the information you post.

    🙂

  14. 14
    Dionisio says:

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types.

    We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites.

    Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.

    Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons.

    More than 17% of single-nucleotide variants within duons directly alter TF binding.

    Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.

    http://www.sciencemag.org/cont.....ffa3a245fb

  15. 15
    Dionisio says:

    Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge

    doi: 10.1093/bioinformatics/btu797

    Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation.

    When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression.

    However, when these data are not available, it is impossible to infer and validate such models.

    http://bioinformatics.oxfordjo.....7.abstract

  16. 16
    Dionisio says:

    Multiple roles of the coding sequence 5? end in gene expression regulation

    doi: 10.1093/nar/gku1313

    The codon composition of the coding sequence’s (ORF) 5? end first few dozen codons is known to be distinct to that of the rest of the ORF.

    Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation.

    However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging.

    Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.

    http://nar.oxfordjournals.org/.....3.abstract

  17. 17
    Dionisio says:

    Different types of secondary information in the genetic code

    doi: 10.1261/rna.044115.113

    Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code.

    Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information:
    codon-specific translational pauses that can be used by particular proteins toward their unique folding and
    biased codon patterns shared by groups of functionally related mRNAs with coordinate regulation.

    AGI is important to genetics in general and to human disease; here, we consider influences of its three major components, biased codon use itself, variations in the tRNAome, and anticodon modifications that distinguish synonymous decoding.

    AGI is plastic and can be used by different species to different extents, with tissue-specificity and in stress responses.

    Because AGI is species-specific, it is important to consider codon-sensitive experiments when using heterologous systems; for this we focus on the tRNA anticodon loop modification enzyme, CDKAL1, and its link to type 2 diabetes.

    Newly uncovered tRNAome variability among humans suggests roles in penetrance and as a genetic modifier and disease modifier.

    Development of experimental and bioinformatics methods are needed to uncover additional means of auxiliary genetic information.

    http://rnajournal.cshlp.org/co.....7.abstract

  18. 18
    Dionisio says:

    Overlapping genes and variability of the genetic code

    DOI: 10.1023/A:1026631030516

    the finding that the meanings of some codons of the mitochondrial genetic code differ from the usual ones was unexpected.

    http://www.researchgate.net/pu.....netic_code

  19. 19
    Dionisio says:

    Computation of the genetic code

    DOI: 10.1134/S1064562410040095

    The author has conducted mathematical analysis of genetic decoding for a number of years.

    Overlapping genes, discovered in 1976, were one of the main objects of the study.

    These are cases where the same segment of DNA encodes two or more protein sequences.

    Numerous cases of identified genetic overlaps allowed setting a number of mathematical problems that have been successfully solved.

    A detailed exposition of these problems is given in the author’s monograph Mathematical Analysis of Genetic Code (BINOM, Moscow, 2010).

    Such problems have made it possible to penetrate deeply enough into the structure of the genetic code and its relationship with the overlapping genes.

    As a result, a new problem was set: the computation of the genetic code on the basis of the amino acid sequences that record overlapping genes.

    One approach to this problem is described in this paper.

    http://www.researchgate.net/pu.....netic_code

  20. 20
    Dionisio says:

    Some new characteristics of large genomes

    DOI: 10.1134/S2070048213030071

    http://www.researchgate.net/pu.....ge_genomes

  21. 21
    Dionisio says:

    Scientists Discover Another Genetic Code

    Overlapping language seems to help direct DNA activity in cells, researchers report

    Another code within DNA has been discovered by scientists — a finding that the researchers say sheds light on how changes to DNA affect health.

    Since the genetic code was first deciphered in the 1960s, scientists have believed it was used solely to write information about proteins.

    But this new study from University of Washington scientists found that genomes use the genetic code to write two separate languages.

    One language describes how proteins are made, and the other helps direct genetic activity in cells. One language is written on top of the other, which is why this other language went undiscovered for so long, according to the report in the Dec. 13 issue of Science.

    “For over 40 years, we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” team leader Dr. John Stamatoyannopoulos, an associate professor of genome sciences and of medicine, said in a university news release.

    “Now we know that this basic assumption about reading the human genome missed half of the picture,” he said.

    http://health.usnews.com/healt.....netic-code

  22. 22
    Dionisio says:

    Overlapping genes referred in post #19 are not exactly the same as the overlapping languages referred in post #21.
    They seem like two different concepts, don’t they?
    The former refers to overlapping protein code, which apparently was discovered in 1976, while the latter has to do with the alleged recent discovery of another DNA-related language used for the operating logic. Is this correct?
    Can someone elaborate on this? Thank you.

  23. 23
    Dionisio says:

    Scientists discover double meaning in genetic code

    Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

    http://www.washington.edu/news.....etic-code/

  24. 24
    Dionisio says:

    gpuccio,

    Please, can you comment on post #22?

    BTW, do posts #21 & 23 somehow relate to the TAD concept that you brought up in the ‘third way’ discussion thread?

    Thank you.

  25. 25
    Dionisio says:

    Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago.

    Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes.

    Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22.

    Analyses of the locations of the 5? and 3? transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes.

    The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs.

    The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.

    Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, et al. (2012) Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE 7(1): e28213. doi:10.1371/journal.pone.0028213

    http://www.plosone.org/article.....ne.0028213

  26. 26
    Dionisio says:

    Scientists discover double meaning in genetic code

    Scientists have discovered a second code hiding within DNA.

    The second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

    Genomes use the genetic code to write two separate languages.

    One describes how proteins are made, and the other instructs the cell on how genes are controlled.

    One language is written on top of the other.

    http://www.sciencedaily.com/re.....142151.htm

  27. 27
    hrun0815 says:

    Steve, that’s impressive. Even more empty than the BA77 posts. At least he pretends to make an argument. You just put random words into other people’s mouths.

  28. 28
    hrun0815 says:

    Sebestyen, I guess I agree that “they can’t earn trophies for writing the most idiotic posts here.” But that sure doesn’t stop them from trying–check out the posts from BA77, Steve, or Dionisio (at 13).

  29. 29
    Dionisio says:

    #28 hrun0815

    Your comments seem like an underserved compliment to me. Who would have thought that anything posted by an ignorant like me could attract anyone’s attention? Thank you!

    Feliz Navidad!

    🙂

  30. 30
    gpuccio says:

    Dionisio:

    “Overlapping genes referred in post #19 are not exactly the same as the overlapping languages referred in post #21.
    They seem like two different concepts, don’t they?
    The former refers to overlapping protein code, which apparently was discovered in 1976, while the latter has to do with the alleged recent discovery of another DNA-related language used for the operating logic. Is this correct?!”

    Yes, it is correct. the first paper is about possible alternative reading frames which use the same nucleotides to code for different aminoacid sequences. While there is overlapping, the symbolic code is the same.

    The second paper is about the role of nucleotides in promoting the binding of transcription factors. That function can be found anywhere in the genome, including coding exons. So, those nucleotides in coding exons which are also involved in TF binding seem to have a double function: they retain their meaning in the traditional genetic code as symbols of AAs, and at the same time they have a role in interacting with TFs.

    Here the code is not the same: two different codons can code for the same aminoacid, but only one of them can be active in TF binding. For example, Fig. 2 A of the paper shows that both AAC and AAT code for asparagine, but AAC seems to be preferred in TF interaction, while AAT is not.

    “BTW, do posts #21 & 23 somehow relate to the TAD concept that you brought up in the ‘third way’ discussion thread?”

    Only indirectly, in a sense. TADs are divisions of the genome which are determined by specific boundaries which limit long distance interactions between genomic regions when TFs bind to DNA and generate loops. So, in a sense, all that influences TF binding has probably some relationship with TAD architecture.

  31. 31
    hrun0815 says:

    Dionisio, I guess You live by the credo of ‘any publicity is good publicity’.

    In that case you are right and welcome.

  32. 32
    Joe says:

    hrun0815:

    Overlapping genetic encoding has been textbook knowledge since the eighties.

    Right and it is still unexplainable via unguided/ blind watchmaker evolution. Just because we can observe something doesn’t make it explainable via unguided/ blind watchmaker evolution.

  33. 33
    gpuccio says:

    hrun0815:

    “the overlapping code was discovered in the late seventies”

    OK, but the epigenetic levels of regulation are being clarified only now. The contributions of DNA sequences to cell differentiation and regulation by multiple parallel and interacting “codes” (like the methylome, the histone codes, the TF networks and their combinatorial effects, all the post-transcriptional interventions by non coding RNAs, and so on) are hot new subjects of scientific research. They are new, exciting information. And the genome is at the center of those multiple, parallel interactions.

    So excuse us, poor ID fools, if we are discussing those interesting things that you apparently “failed to notice”.

  34. 34
    hrun0815 says:

    So excuse us, poor ID fools, if we are discussing those interesting things that you apparently “failed to notice”.

    Excused. Discuss away.

    And good luck on perfecting the art of mind reading. You clearly need more practice though.

  35. 35
    Steve says:

    Steve, that’s impressive. Even more empty than the BA77 posts. At least he pretends to make an argument. You just put random words into other people’s mouths.

    Im not surprised you would find that post impressive. Its emptiness sums up your position nicely.

    Yes, you can claim squatters rights if you must and noone could blame you.

    But it just drives home the point further that evolution, without design is an empty, worthless concept.

  36. 36
    Dionisio says:

    #34 hrun0815

    And good luck on perfecting the art of mind reading. You clearly need more practice though.

    What did you try to tell gpuccio with those statements?
    Can you explain it?
    Thank you.

  37. 37
    Dionisio says:

    gpuccio

    Thank you for the insightful comments that you wrote in posts #30 and #33.

  38. 38
    gpuccio says:

    hrun0815

    “And good luck on perfecting the art of mind reading. You clearly need more practice though.”

    It was simply irony.

    But maybe I need more practice in that too. Or maybe I just need to choose better interlocutors (this is serious).

  39. 39
    Dionisio says:

    hrun0815

    Do you understand what gpuccio explained so clearly in posts 30 and 33?

    In light of gpuccio’s comments, was your first post in this discussion thread a little off topic?

    BTW, if you still can’t see the post numbers on your iPhone, you may want to try looking a this UD website directly on the safari browser.

  40. 40
    hrun0815 says:

    What did you try to tell gpuccio with those statements?
    Can you explain it?
    Thank you.

    Seriously? You need help with that? You need help to understand that he was attributing something to me that he couldn’t possibly know (other than through some magical mind reading?

    In light of gpuccio’s comments, was your first post in this discussion thread a little off topic?

    How does gpuccio’s post possible show that my first post in this thread was off topic? That’s just utterly bizarre. I referenced post number one if this thread and pointed out that in the original post it is not clear what is written by news and what is written by somebody else. That’s about as on topic as it can go around here.

  41. 41
    hrun0815 says:

    But maybe I need more practice in that too. Or maybe I just need to choose better interlocutors (this is serious).

    That’s probably both true.

    Find someone who is impressed by not at all advancing the argument but simply adding another random facts. My first point was this:

    Overlapping codes have been textbook knowledge for decades. Yet, virtually nobody in biology has recognized what BA77 claimed-namely that such thing is ‘simply devastating news’.

    But I guess the answer to that can be found on his next post: biologist PhDs are really sharp minds if they write something that you agree with– but otherwise they are simply not.

  42. 42
    Box says:

    hrun0815:
    Overlapping codes have been textbook knowledge for decades. Yet, virtually nobody in biology has recognized what BA77 claimed-namely that such thing is ‘simply devastating news’.

    Which is pretty weird, since it takes only a moment of reflection to understand that this reduces the likelihood of beneficial mutations.

  43. 43
    hrun0815 says:

    Which is pretty weird, since it takes only a moment of reflection to understand that this reduces the likelihood of beneficial mutations.

    Yes. That’s pretty weird, alright. Especially if every now and then these PhDs are pretty sharp.

    I truly truly wonder what you think the explanation for this weirdness could be?

  44. 44
    Box says:

    Hrun0815: I truly truly wonder what you think the explanation for this weirdness could be?

    Other than the fact that no one likes to be the bearer of bad news? No, I have no explanation. Fortunately it doesn’t stop everyone:
    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation (PDF) George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013.

    “We conclude that beneficial mutations that are unambiguous (not deleterious at any level), and useful (subject to natural selection), should be extremely rare.”

  45. 45
    hrun0815 says:

    Other than the fact that no one likes to be the bearer of bad news? No, I have no explanation.

    I think you misunderstand incentives in science. Showing paradigm shifts is the the most sure fire way of attaining fame and continued funding.

    If I were you I would further ponder the question rather than hanging my hopes on a selected few PhDs that confirm your notion while discarding the others.

  46. 46
    Box says:

    Hrun0815,

    Pointing out the obvious – overlapping codes decrease probability of beneficial mutations – does not equal a paradigm shift.
    Moreover you are wrong about general receptiveness towards paradigm shifts. Max Planck wrote:

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

    Hrun0815: … while discarding the others

    Which others? Is there one scientist who holds that overlapping codes increase the probability of beneficial mutations?

  47. 47
    Joe says:

    hrun:

    Overlapping codes have been textbook knowledge for decades.

    And unguided evolution still can’t produce them. It is devastating news to Darwinism and neo-darwinism. When something exists that a paradigm has no chance of explaining then the paradigm is in big trouble.

  48. 48
    Zachriel says:

    Box: Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation (PDF) George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013.

    For those nucleotides that are part of a given code but are not yet the optimal nucleotide for that code, we assume that only one of the three alternative nucleotides will be an improvement relative to the existing sub-optimal nucleotide. Mutations at such sites will therefore have one-third chance of being beneficial, but will still have a two-thirds probability of being deleterious.

    No, the other mutations may be neutral. This analysis results in any beneficial mutations in one code almost certainly being deleterious for another, when it may be neutral. Furthermore, if codes co-evolved, then they would evolve in such a way that they would still maintain flexibility, or they wouldn’t persist. A second code could be opportunistic. Indeed, in evolutionary algorithms, it is very common to get overlaps of various sorts, arrangements no designer would use, but happenstance in the course of evolution.

    This means that over time large numbers of such deleterious mutations should accumulate continuously, leading to ever-increasing genetic load [29-33].

    Citing Sanford, Sanford, Sanford & Sanford [29-33].

    Has Sanford ever corrected the bug concerning selection in his Mendel’s Accountant [29]?

  49. 49
    Dionisio says:

    BA77,
    Please, read the below quotes from hrun0815 and gpuccio.
    Don’t you get the perception that someone here in this discussion is barking up the wrong tree? Perhaps I misunderstood the main point of the OP video?

    #2 hrun0815 wrote:

    This is yet again very amusing. Overlapping genetic encoding has been textbook knowledge since the eighties.

    #8 hrun0815 wrote:

    I guess all those biology Ph.D.s who failed to notice this since the overlapping code was discovered in the late seventies (including the guys that actually put this info into textbooks) were not “as sharp as the minds of the PhDs behind the paper that was the inspiration of the video.”

    #33 gpuccio clarified:

    …the epigenetic levels of regulation are being clarified only now.

    The contributions of DNA sequences to cell differentiation and regulation by multiple parallel and interacting “codes” (like the methylome, the histone codes, the TF networks and their combinatorial effects, all the post-transcriptional interventions by non coding RNAs, and so on) are hot new subjects of scientific research.

    They are new, exciting information. And the genome is at the center of those multiple, parallel interactions.

  50. 50
    Dionisio says:

    BA77

    Please, check this out:

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    http://www.sciencemag.org/cont.....ffa3a245fb

    For those of us who may have reading comprehension problems, it might be worth to clarify that the term both seems to refer to two types of codes:
    One code that was allegedly discovered in 1976, and another code that is the subject of much more recent research.

    Isn’t the main discussion about the latter?

    Doesn’t this render the comments in posts #2 and 8 off topic?

    Am I missing something in this?

    What do you think? Please, correct me if I misunderstood anything here.

    Thanks.

  51. 51
    Dionisio says:

    gpuccio,

    Your clarifying comments on posts 49 and 50 will be more than welcome, though practically you already stated the bottom line of the discussed subject.

    Is the OP video talking mainly about the genetic code specifying amino acids or a regulatory code specifying transcription factor (TF) recognition sequences, or both, or none of them, or something else?

    Thank you.

  52. 52
    Dionisio says:

    New insights in the clockwork mechanism regulating lineage specification

    DOI: 10.1002/dvdy.24228

    Powerful transcription factors called fate determinants induce robust differentiation programs in multipotent cells and trigger lineage specification.

    These factors guarantee the differentiation of specific tissues/organs/cells at the right place and the right moment to form a fully functional organism.

    Fate determinants are activated by temporal, positional, epigenetic, and post-transcriptional cues, hence integrating complex and dynamic developmental networks.

    In turn, they activate specific transcriptional/epigenetic programs that secure novel molecular landscapes.

    In this review, we use the Drosophila Gcm glial determinant as a model to discuss the mechanisms that allow lineage specification in the nervous system.

    The dynamic regulation of Gcm via interlocked loops has recently emerged as a key event in the establishment of stable identity.

    Gcm induces gliogenesis while triggering its own extinction, thus preventing the appearance of metastable states and neoplastic processes.

    Using simple animal models that allow in vivo manipulations provides a key tool to disentangle the complex regulation of cell fate determinants.

    Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc.

    http://onlinelibrary.wiley.com.....8/abstract

  53. 53
    bornagain77 says:

    Dionisio, yes I read those comments. Same ole, same ole, drivel from Darwinists. No finding, no matter how counterintuitive for Neo-Darwinian claims, is ever problematic for Neo-Darwinists because Neo-Darwinism is not even a falsifiable hard science in the first place but is a philosophical/religious belief system grounded in atheistic naturalism. A philosophical/religious belief system that had nothing to do with the founding of modern science. Moreover, it is a philosophical/religious belief system which leads to the epistemological failure of modern science:

    “Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.”
    ~ Cornelius Hunter

    “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
    http://izquotes.com/quote/147518

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    The Threat to the Scientific Method that Explains the Spate of Fraudulent Science Publications – Calvin Beisner | Jul 23, 2014
    Excerpt: It is precisely because modern science has abandoned its foundations in the Biblical worldview (which holds, among other things, that a personal, rational God designed a rational universe to be understood and controlled by rational persons made in His image) and the Biblical ethic (which holds, among other things, that we are obligated to tell the truth even when it inconveniences us) that science is collapsing.
    As such diverse historians and philosophers of science as Alfred North Whitehead, Pierre Duhem, Loren Eiseley, Rodney Stark, and many others have observed, and as I pointed out in two of my talks at the Ninth International Conference on Climate Change (ICCC), science—not an occasional flash of insight here and there, but a systematic, programmatic, ongoing way of studying and controlling the world—arose only once in history, and only in one place: medieval Europe, once known as “Christendom,” where that Biblical worldview reigned supreme. That is no accident. Science could not have arisen without that worldview.
    http://townhall.com/columnists...../page/full
    Several other resources backing up this claim are available, such as Thomas Woods, Stanley Jaki, David Linberg, Edward Grant, J.L. Heilbron, and Christopher Dawson.

    Why No One (Can) Believe Atheism/Naturalism to be True (Plantinga’s Evolutionary Argument Against Naturalism) – video
    Excerpt: “Since we are creatures of natural selection, we cannot totally trust our senses. Evolution only passes on traits that help a species survive, and not concerned with preserving traits that tell a species what is actually true about life.”
    Richard Dawkins – quoted from “The God Delusion”
    http://www.youtube.com/watch?v=N4QFsKevTXs

    Quote: “In evolutionary games we put truth (true perception) on the stage and it dies. And in genetic algorithms it (true perception) never gets on the stage”
    Donald Hoffman PhD. – Consciousness and The Interface Theory of Perception – 7:19 to 9:20 minute mark – video
    https://www.youtube.com/watch?feature=player_detailpage&v=dqDP34a-epI#t=439

    supplemental note on the non-falsifiability inherent to atheistic naturalism:

    In Nature, Two Cosmologists Chide Other Cosmologists for Lack of Testable Evidence – December 22, 2014
    Excerpt: We have frequently criticized some of the crazy ideas emerging from modern cosmology: notions like the multiverse, inflation, Everett’s “many-worlds” scenario, and other concoctions that try to escape the overwhelming evidence for design in the universe,,. Here’s what George Ellis and Joe Silk say in Nature (“Scientific Method: Defend the Integrity of Physics”):
    “This year, debates in physics circles took a worrying turn. Faced with difficulties in applying fundamental theories to the observed Universe, some researchers called for a change in how theoretical physics is done. They began to argue — explicitly — that if a theory is sufficiently elegant and explanatory, it need not be tested experimentally, breaking with centuries of philosophical tradition of defining scientific knowledge as empirical. We disagree. As the philosopher of science Karl Popper argued: a theory must be falsifiable to be scientific.”
    http://www.evolutionnews.org/2.....92311.html

  54. 54
    Dionisio says:

    Keeping an eye on SOXC proteins

    DOI: 10.1002/dvdy.24235

    The formation of a mature, functional eye requires a complex series of cell proliferation, migration, induction among different germinal layers, and cell differentiation.

    These processes are regulated by extracellular cues such as the Wnt/BMP/Hh/Fgf signaling pathways, as well as cell intrinsic transcription factors that specify cell fate.

    In this review article, we provide an overview of stages of embryonic eye morphogenesis, extrinsic and intrinsic factors that are required for each stage, and pediatric ocular diseases that are associated with defective eye development.

    In addition, we focus on recent findings about the roles of the SOXC proteins in regulating vertebrate ocular development and implicating SOXC mutations in human ocular malformations.

    Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc.

    http://onlinelibrary.wiley.com.....5/abstract

  55. 55
    Dionisio says:

    BA77

    Ok, thanks. Now I see their trick: head they win, tail we lose. Pretty clever, isn’t it? 🙂

    Really pathetic. Can’t seriously discuss anything with those folks. It’s a complete waste of time, if it weren’t for the onlookers/lurkers.

    Oh, well… whatever.

  56. 56
    Mung says:

    Zachriel: Has Sanford ever corrected the bug concerning selection in his Mendel’s Accountant?

    Why don’t you download the source code and look?

  57. 57
    Joe says:

    Indeed, in evolutionary algorithms, it is very common to get overlaps of various sorts, arrangements no designer would use, but happenstance in the course of evolution.

    All known evolutionary algorithms require an intelligent designer. Evolutionary algorithms are perfect examples of intelligent design evolution.

  58. 58
    Zachriel says:

    Mung: Why don’t you download the source code and look?

    Tried that. It made a mash of the computer, and wouldn’t run. Their FTP for the source code didn’t work either. However, the original version referenced in their paper definitely didn’t represent selection properly.

  59. 59
    Joe says:

    However, the original version referenced in their paper definitely didn’t represent selection properly.

    LoL! How would you know? We would love to see you try and make a case to support your claim.

  60. 60
    Zachriel says:

    Mung: Why don’t you download the source code and look?

    Dug around and found the source code for 2.0.2. It has the same problem. The algorithm divides the working fitness by a random number, which erases nearly the entire signal from working fitness. Rewriting the algorithm using Roulette Wheel selection, eliminates the meltdown they claim is inevitable.

    We contacted the author about this problem in 2009, but never heard back. Anyone with knowledge of how algorithms work can see the problem for themselves.

  61. 61
    Joe says:

    And what is the evidence that demonstrates “Roulette Wheel selection” simulates natural selection?

  62. 62
    Dionisio says:

    It seems like some folks that sounded so ‘convinced’ early in this thread, now have realized it’s much better for them to quietly withdraw from this discussion, after their ‘off topic’ tricky comments were caught up in the air.
    What else is new? Same ole, same ole…
    🙂

  63. 63
    gpuccio says:

    Dionisio:

    “Is the OP video talking mainly about the genetic code specifying amino acids or a regulatory code specifying transcription factor (TF) recognition sequences, or both, or none of them, or something else?”

    Well, in the video Paul Giem comments (very well, IMO) a paper by George Montañez, Robert J. Marks II, Jorge Fernandez
    and John C. Sanford. The paper is about the mathematical modeling of beneficial mutations when nucleotides are involved in multiple codes, and does not refer to specific examples. However, there are references in the bibliography. For example, this work by Trifonov:

    Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical
    Biology 51:417–432.

    The original paper is in Russian, but here is the abstract:

    “Apart from the classical RNA-protein translation code, the genomic DNA sequences carry many other, nontriplet codes of different nature. Those of them which are at least partly deciphered are discussed in this review in the order of their estimated occupancy in the eukaryotic genome. Each of the codes is degenerate, like the triplet code. This is the basis for their coexistence in one and the same sequence, so that the same base often (if not always) belongs to several different overlapping sequence patterns. The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages.”

    So, the idea is that if some nucleotides are functional at different levels and in different codes, that implies extreme functional constraint, and extreme improbability of evolving the result by random beneficial mutations. That seems to be the main point of the paper.

    The recent paper you referenced in your post:

    “Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution”

    http://www.sciencemag.org/content/342/6164/1367

    is another good example.

    I think that any multiple function at the nucleotide level is a special constraint for that position. Multicode functionality is a special kind of information compression, ad it generates extreme limitations.

    The codes can be of the protein coding type, or just regulatory: the concept remains the same.

    We can have multiple overlapping ORFs, or an ORF overlapping with non coding regulatory sequences, and so on. Look at this page, for example:

    http://www-sequence.stanford.e.....pping.html

  64. 64
    Dionisio says:

    gpuccio

    Thank you (again!) for the clarification.

  65. 65
    Dionisio says:

    At this point one could say that posts 30, 33 and 63 by gpuccio basically summarize the main ideas associated with this thread. Those three posts could wrap up this discussion. We still could provide more references to research papers as examples, but conceptually the bottom line has been explained in a very compacted manner in the mentioned 3 posts, though some interlocutors might not agree. Well, it’s hard to please everybody, isn’t it? 🙂

  66. 66
    hrun0815 says:

    It seems like some folks that sounded so ‘convinced’ early in this thread, now have realized it’s much better for them to quietly withdraw from this discussion, after their ‘off topic’ tricky comments were caught up in the air.
    What else is new? Same ole, same ole… 🙂

    I would stop digging. The OP talked about “overlapping genetic codes” as did I.

    –> on topic

    The OP seems to be quoted (or typically mangled in news style) and I asked for clarification.

    –> on topic

    Your attempts to point to multiple different functions does not invalidate what I wrote in the beginning. This is so obvious that I chose to simply ignore your statements.

    I do want to offer you one more piece of advice: Don’t automatically conclude in Internet discussions that you are right just because a counter part stopped replying. You may ‘win’ many arguments that way, but that does not increase the chances that you actually learn something or that you are in fact right.

  67. 67
    Paul Giem says:

    Hi guys,

    Sorry for the late entry. I was busy when this posted and didn’t catch up on it until today (I didn’t even realize that my video had been copied; not that I mind 🙂 ).

    hrun0815 asked (#2),

    And News, could you actually mark in your posts which part is a direct quote and which one isn’t? I’m curious who is responsible for this sentence: “We will partially evaluate the strength of the evidence behind that argument.” It’s clearly another sign of a very sharp mind so I’d like to know who to attribute it to.

    From reading the rest of hrun0815’s comments, I gather that his comment may be ironic and I may be in for some abuse, but I’m actually the “very sharp mind” that wrote “We will partially evaluate the strength of the evidence behind that argument.” I do hope hrun0815 likes the video a little better than s/he likes some of the comments here.

    The comment that was quoted actually went with this video:
    https://www.youtube.com/watch?v=3WZy0n60_ZU
    The comment that went with the above video was:

    In the book “Biological Information: New Perspectives” the chapter entitled “Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation” discusses the implications of the fact that multiple DNA codes often involve the same stretch of DNA.

    Again, that comment originated with me.

  68. 68
    Dionisio says:

    #66 hrun0815

    I do want to offer you one more piece of advice: Don’t automatically conclude in Internet discussions that you are right just because a counter part stopped replying. You may ‘win’ many arguments that way, but that does not increase the chances that you actually learn something or that you are in fact right.

    You misunderstood my comments, again.

    Did I ever say I was right? Can you point to such text written by me? If I mistakenly did it, I’m willing to correct it right away. But where is it?

    Didn’t you notice how many times I ask gpuccio and other folks in this site, who know much more than I do about the discussed subjects, to review my comments and correct them?

    What I wrote was an indirect invitation (or you could call it provocation or a bait) to bring you back into this thread. Apparently it worked! You came back and added another comment. Thank you. 🙂

    BTW, I appreciate your desire to teach me internet discussion manners. I can use any help I can get in that area, because I really don’t know much about it. 🙂

    Kind regards.

  69. 69
    Dionisio says:

    #67 Paul Giem

    Thank you for clarifying that point, which apparently confused or preoccupied some interlocutors here.

    However, apparently there are other objections to the OP in this thread. Here’s one: is the central subject of your video (shown in the OP for this thread) related to an old issue that has been in textbooks since the eighties? (see post #2).
    Could it be that it has been discussed in scientific literature since the eighties, but did not make it into actual textbooks until later?
    Or could it be that it has become a hot subject just recently?
    Some articles referenced in a few posts in this discussion thread seem to point to more recent discussions on the given subject of different types of codes within the genome. However, that could be my wrong perception. At least E.N. Trifonov pointed to some of that stuff in 1989, but was that subject explained in textbooks back then?
    To me textbooks are books that school courses explicitly indicate as the referenced literature. I think that not all scientific books are textbooks*, but maybe I’m wrong on this too.
    Can you please clarify all this for us? Thank you in advance.
    (*) some textbooks seem to contain subtle propaganda for certain not-so-clear agendas.

  70. 70
    hrun0815 says:

    Dionisio, you first suggested that I am off topic, then implied I’m barking up the wrong tree, and then suggested that I initially was so convinced I was right and then quietly dropped off the conversation.

    Now, you can claim that this does not mean you thought you were right… but that won’t be very convincing.

    But it’s good to here that rather you very provoking and baiting. So be it.

  71. 71
    Dionisio says:

    #70 hrun0815

    But it’s good to here that rather you very provoking and baiting. So be it.

    Did you mean “to hear”?

    🙂

  72. 72
    Dionisio says:

    hrun0815 @70

    But it’s good to here that rather you very provoking and baiting. So be it.

    Did you mean “to hear”?

    🙂

    You may still have a few minutes left to edit your text and repost it, if you want to.

  73. 73
    hrun0815 says:

    I also meant were instead of very.

    But I am sure you were able to figure out what I meant, right?

  74. 74
    Dionisio says:

    #70 hrun0815

    Now, you can claim that this does not mean you thought you were right… but that won’t be very convincing.

    I can’t think I’m right about a subject I’m not an expert on (and in most cases I’m very far from becoming one). That’s why I ask others, who seem to know much more than I do, so they correct my comments on the discussed subject, if that’s required.
    I could even accept a correction from you, but your comments should not contradict the known evidences. If I see a contradiction, then I could ask someone else, who seem to know more on the given subject, to clarify the issue.
    At the end of the day some of us would like to find the truth about the discussed subject, right?
    Do you see my point now?

  75. 75
    Dionisio says:

    #73 hrun0815

    But I am sure you were able to figure out what I meant, right?

    Yes, that’s right. I was just trying to tease you a little, just for fun, so we relax our discussion.
    You see, this time we have been able to maintain a serious discussion, and I thank you for that, because we have been respectfully exchanging opinions. That’s an encouraging sign, isn’t it?

    🙂

  76. 76
    DNA_Jock says:

    Box @26

    Is there one scientist who holds that overlapping codes increase the probability of beneficial mutations?

    Yes. Yes there is.
    “Synonymous” mutations have the opportunity to be mildly beneficial, or mildly deleterious. We discussed this with ericB on his “N.E.C.R.O.” thread at TSZ.

    Dionisio @50

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    [link]

    For those of us who may have reading comprehension problems, it might be worth to clarify that the term both seems to refer to two types of codes:
    One code that was allegedly discovered in 1976, and another code that is the subject of much more recent research.

    No. The “both” above refers to the original genetic code (1960’s) and the “binding factor” (1990’s – present) code. The overlapping reading frames were discovered (no allegedly about it) in 1976 by Bart Barrell.

  77. 77
    bornagain77 says:

    To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face, to actually get a proper ‘beneficial mutation’ in a polyfunctional genome we would actually be encountering something akin to this illustration found on page 141 of the book ‘Genetic Entropy’ by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Sator Square
    http://en.wikipedia.org/wiki/Sator_Square

    Which is translated ,

    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to at least 79 AD, reads the same four different ways. Thus, if we change (mutate) any letter we may get a new meaning for a single reading read any one way, (as in Dawkins’ weasel program), but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center).
    This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations (Sanford: Genetic Entropy).
    Of note to DNA_Jock’s claim that mutations ‘have the opportunity to be mildly beneficial, or mildly deleterious’ in an area of overlapping coding, I hold that, as Dr. Behe has shown, the beneficial mutations will almost always occur at the cost of breaking something, i.e. “The First Rule of Adaptive Evolution”, and that the ‘benefit’ will only be beneficial in a anomalous environment, as with antibiotic resistant bacteria.
    A few notes to that effect:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    http://www.trueorigin.org/bacteria01.asp

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    https://www.youtube.com/watch?v=rYaU4moNEBU

    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 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

    Moreover, although single mutations may seem to be beneficial in a limited environment, the constraint imposed on evolutionary processes by overlapping coding, on truly beneficial mutations ever happening, really shows its face when two coordinated mutations are required to confer an evolutionary benefit:

    Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
    Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
    http://www.discovery.org/a/9951

    Testing Evolution in the Lab With Biologic Institute’s Ann Gauger – podcast with link to peer-reviewed paper
    Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger’s paper, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,”.
    http://intelligentdesign.podom.....4_13-07_00

    Epistasis between Beneficial Mutations – July 2011
    Excerpt: We found that epistatic interactions between beneficial mutations were all antagonistic—the effects of the double mutations were less than the sums of the effects of their component single mutations. We found a number of cases of decompensatory interactions, an extreme form of antagonistic epistasis in which the second mutation is actually deleterious in the presence of the first. In the vast majority of cases, recombination uniting two beneficial mutations into the same genome would not be favored by selection, as the recombinant could not outcompete its constituent single mutations.
    http://www.uncommondescent.com.....ach-other/

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

  78. 78
    Dionisio says:

    #76 DNA_Jock

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    http://www.sciencemag.org/cont.....ffa3a245fb

    The “both” above refers to the original genetic code (1960?s) and the “binding factor” (1990?s – present) code. The overlapping reading frames were discovered (no allegedly about it) in 1976 by Bart Barrell.

    Thank you for the clarification.

  79. 79
    Dionisio says:

    DNA_Jock @76

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    http://www.sciencemag.org/cont.....ffa3a245fb

    The “both” above refers to the original genetic code (1960?s) and the “binding factor” (1990?s – present) code. The overlapping reading frames were discovered (no allegedly about it) in 1976 by Bart Barrell.

    Thank you for the clarification.

    Are the “overlapping reading frames discovered in 1976 by Bart Barrell” more related to the “genetic code specifying amino acids” or to the “regulatory code specifying transcription factor (TF) recognition sequences”, or to both, or to none of the above, or to something else?

    Can someone explain this to me? Thanks in advance.

  80. 80
    Dionisio says:

    Can someone see any relation between post #79, post #69 and posts 30, 33 and 63 by gpuccio ?

    Thanks.

  81. 81
    DNA_Jock says:

    Barrell and Sanger showed that the genetic code specifying amino acids overlaps in the genome of phage phiX174.

  82. 82
    Dionisio says:

    #81 DNA_Jock

    Barrell and Sanger showed that the genetic code specifying amino acids overlaps in the genome of phage phiX174.

    Ok, so that was not related to the “regulatory code specifying transcription factor (TF) recognition sequences”, right?

  83. 83
    DNA_Jock says:

    Correct.

  84. 84
    Dionisio says:

    DNA_Jock

    Does the OP somehow (directly or indirectly) refer to the “regulatory code specifying transcription factor (TF) recognition sequences” too?

    See insightful post #63 by gpuccio. Optionally, posts #30 and 33, also by gpuccio, shed more light on this discussion.

  85. 85
    Dionisio says:

    DNA_Jock

    Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?

    See posts #14-21, 23 and 26 for examples.

  86. 86
    wd400 says:

    Jacob and Monod won a Nobel for uncovering the prokayote system in 1965, the experiments that established the same in eukaryotes were done in the early 80s, and no doubt made into text books not long after.

    Control of gene expression is not really a code like the genetic code though. You wouldn’t normally be able to look at genomic data and see when and where a gene will be expressed. You can just look at a coding sequence and know the corresponding peptides.

  87. 87
    Dionisio says:

    #86 wd400

    You can just look at a coding sequence and know the corresponding peptides.

    Look where? in the DNA? what coding sequence? the nucleotide sequence within the DNA?

    Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?

    Does that nucleotide sequence in the DNA always translate into a sequence of amino acids?

    Do portions of the DNA nucleotide sequence get involve in regulatory or controlling mechanisms?

    Are there any portions of the DNA nucleotide sequence that may be associated with both protein coding and regulatory/controlling mechanisms?

    Is the term “overlapping” being used for the case of
    (1) DNA nucleotide sequences that code for proteins, and also in the case of (2) DNA nucleotide sequences that get associated with regulatory/controlling mechanisms, and also in the cases (3) where DNA nucleotide segments may have dual functioning (duons), and in (4) other cases?

    Which of the above mentioned cases have been in textbooks since the eighties? Which ones are more recent?

    DNA_Jock is welcome to answer these questions too.

    [Note: I may need gpuccio to jump in and give us a hand with this, because I’m in “unknown to me territory”. :)]

  88. 88
    Dionisio says:

    #87 addendum

    wd400

    Please, be aware that I’m a student (autodidact), hence I’m interested in learning many things I still don’t know about biology. Any useful information I can gather from our discussions is very appreciated. My current scientific ignorance could make me write questions that make no sense. On top of that, to make things more difficult to me, English is not my first language. Any corrections are very welcome!

    Thanks.

    [don’t worry, blogs are not the main source of information for my studying. There are free online classes provided by several universities. I’ve taken a few of those. They are pretty cool, because I can attend the same lecture multiple times, make the professor repeat any part of his lecture several times, learn at my slow pace, no peer pressure, and many other explicit or implicit benefits. Also books like “biochemistry for dummies” and others can be helpful to beginners like me. Also a number of specialized online journals are available. In the university library I can access most of their contents freely. Just need to enroll in a free course to get a temporary visitor card for the library. There are other available tools and ways to facilitate learning. In this blog gpuccio and other folks here have helped me to understand a few concepts I did not get quite well from other sources. As you can see, there are some benefits from being in this blog.]

  89. 89
    DNA_Jock says:

    Does the OP somehow (directly or indirectly) refer to the “regulatory code specifying transcription factor (TF) recognition sequences” too?

    I think so, but…

    See insightful post #63 by gpuccio. Optionally, posts #30 and 33, also by gpuccio, shed more light on this discussion.

    Post #30 is a good explanation. So is post 33, except for its asinine final sentence. However, the Sanford paper gp refers to in #63 (and the OP itself) fall into the ‘not even wrong’ category.

    Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?

    No.

    Look where? in the DNA? what coding sequence? the nucleotide sequence within the DNA?

    Yes

    Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?

    Almost always.

    Does that nucleotide sequence in the DNA always translate into a sequence of amino acids?

    More often than not.

    Do portions of the DNA nucleotide sequence get involve in regulatory or controlling mechanisms?

    Occasionally.
    Again, I would encourage you to actually enroll in a biology course at a reputable university.

  90. 90
    Dionisio says:

    #89 DNA_Jock

    You didn’t answer all the questions written in post #87, just some of them. Any particular reason why?

    BTW, post #88 could be a comment on your last statement in post #89. The online courses I took are provided by reputable universities. Since you didn’t answer all the questions, can I say you should enroll in a biology course at a reputable university? No! I don’t know why you did not answer all of my questions. But the answers to some biology questions may not be in any biology course at any reputable university. The answer my friend is blowing in the wind. 🙂

  91. 91
    Dionisio says:

    #89 DNA_Jock

    Does the OP somehow (directly or indirectly) refer to the “regulatory code specifying transcription factor (TF) recognition sequences” too?

    I think so, but…

    but what?

  92. 92
    Dionisio says:

    #89 DNA_Jock

    See insightful post #63 by gpuccio. Optionally, posts #30 and 33, also by gpuccio, shed more light on this discussion.

    Post #30 is a good explanation. So is post 33, except for its asinine final sentence. However, the Sanford paper gp refers to in #63 (and the OP itself) fall into the ‘not even wrong’ category.

    What is it that you don’t like about gpuccio’s final sentence @33?
    Why do you say that the paper gpuccio refers to @63 is ‘not even wrong’?

  93. 93
    Dionisio says:

    #89 DNA_Jock

    Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?

    No.

    Could it have been since the eighties?

    Do you know if the “regulatory code specifying transcription factor (TF) recognition sequences” sometimes may at least partially overlap with the “genetic code specifying amino acids”? Have you heard or read anything on this subject lately? When was the overlapping between two distinct codes first mentioned in textbooks? Since the eighties? Earlier? Later? It hasn’t been mentioned at all? Don’t know?

  94. 94
    Dionisio says:

    #89 DNA_Jock

    Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?

    Almost always.

    Why not always? In which case(s) the two sequences don’t correspond directly?

  95. 95
    DNA_Jock says:

    re 94, google formylglycine.

    Your other questions have been answered (except for the ‘not even wrong’ one): try reading for comprehension.
    Get a biology degree.

  96. 96
    Dionisio says:

    #89 DNA_Jock

    Please, don’t send me out to enroll in classes (posts #88 and 90 comment on that subject), let’s discuss here. I’m trying to engage in a serious discussion. If you don’t want to discuss this, then simply skip my questions or state it openly that you are not interested in this kind of discussion. I will respect your preference.
    But I’ve been told that in this and other blogs the onlookers/lurkers are important too. Hence, even if you ignore some questions, the onlookers/lurkers may still read the posts and arrive at their own conclusions.
    🙂

  97. 97
    Joe says:

    Dionsio- The DNA is transcribed into mRNA which is then processed, meaning the nucleotide sequence can change. Think of alternative splicing.

    What our opponents are not saying is that unguided evolution cannot account for any of it.

  98. 98
    Dionisio says:

    #95 DNA_Jock

    Your other questions have been answered (except for the ‘not even wrong’ one)

    No, you haven’t answered several questions. This thread is an obvious testimony. But that’s fine, you don’t have to answer all the questions. The onlookers/lurkers will have the opportunity to review this thread and arrive at their own conclusions.
    🙂

  99. 99
    Dionisio says:

    #89 DNA_Jock

    Dionisio: Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?

    DNA_Jock: Almost always.

    Dionisio: Why not always? In which case(s) the two sequences don’t correspond directly?

    #95 DNA_Jock

    DNA_Jock: re 94, google formylglycine.

    I’m not asking for specific examples at this point, just general concepts, principles. See Joe’s post #97. Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    Can you summarize general concepts, principles?

    If examples are required, they should be given upon request. Although voluntarily providing them is ok too, but after the general concepts, principles, are presented in a compacted manner. Does this make sense?

    However, many folks don’t like to engage in this kind of serious discussions. That’s fine. If you’re in that group, just say it, so those who might be interested in having such a discussion know that they have to find another interlocutor. 🙂

  100. 100
    Dionisio says:

    Ok, this is just a post to reach the #100 mark! 🙂

  101. 101
    wd400 says:

    Dionisio,

    Biology is weird, for any general rule there will be exceptions. There are a few cases in which genomic DNA doesn’t fully specify a protein, as later modifications change the mRNA or amino acid sequence.

    More generally, most of the questions you are asking are the things you’d expect to learn in the first week of a molecular biology course, if you don’t understand these you have no hope of understanding the papers you link to.

    It’s really not DNAjock’s (or anyone else’s) job to teach you elementary biology, and making snide comments about there not answering all of your many questions is not becoming.

  102. 102
    Dionisio says:

    Apparently this could be the post #101

    #89 DNA_Jock

    Dionisio: Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?

    DNA_Jock: Almost always.

    Dionisio: Why not always? In which case(s) the two sequences don’t correspond directly?

    #95 DNA_Jock

    DNA_Jock: re 94, google formylglycine.

    I’m not asking for specific examples at this point, just general concepts, principles. See Joe’s post #97.

    Can you summarize general concepts, principles?

    If examples are required, they should be given upon request. Although voluntarily providing them is ok too, but after the general concepts, principles, are presented in a compacted manner. Does this make sense?

    However, many folks don’t like to engage in this kind of serious discussions. That’s fine. If you’re in that group, just say it, so those who might be interested in having such a discussion know that they have to find another interlocutor. 🙂

  103. 103
    Dionisio says:

    #101 wd400

    Biology is weird, for any general rule there will be exceptions. There are a few cases in which genomic DNA doesn’t fully specify a protein, as later modifications change the mRNA or amino acid sequence.

    More generally, most of the questions you are asking are the things you’d expect to learn in the first week of a molecular biology course, if you don’t understand these you have no hope of understanding the papers you link to.

    It’s really not DNAjock’s (or anyone else’s) job to teach you elementary biology, and making snide comments about there not answering all of your many questions is not becoming.

    As I have stated very clearly before, I’m not trying to learn biology from DNA_Jock or from you or from any of your comrades and fellow travelers. That would be like trying to swim across the ocean nonstop without any assistance. Well, perhaps the latter is not as difficult as the former. 🙂

    There are plenty of resources to learn biology these days.
    Online courses at reputable universities is just one of the many ways to acquire the information.
    Been there, done that.

    I’m trying to make you and your comrades show your real motives in this discussion, so everyone sees them openly. Those interested in having serious discussions will try to answer all questions. If they don’t know the answer, they humbly will admit it. In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it.

    That’s all. It’s that simple.

    Relax. Cool down.

    🙂

  104. 104
    wd400 says:

    You mean you waste people’s time asking them questions you know the answers to, then claim others are not interested in a serious discussion?

  105. 105
    Dionisio says:

    Obviously some interlocutors in this blog don’t seem interested in serious discussions. Perhaps my rare ‘blitzkrieg’ interrogation approach is uncomfortable to those who just want to mock others and have fun. Some interlocutors called me ‘exorcist’ and ‘Spanish inquisitor’ in this blog, because I was asking many simple childish questions to help them reveal to me their true motives. If that’s your case, too bad. Just ignore my posts, so you go undetected to me. 🙂
    Again, I’m trying to have serious discussions, but need to know if my interlocutors are interested too. They are the only ones who can reveal their true motives. I can’t. Hence I ask simple questions, which sometimes seem kind of dumb, just to let the interlocutors react and thus reveal their own motives.
    That’s all. I rejoice when I find someone like gpuccio, who sticks to the questions I ask, and goes an extra mile for the sake of explaining to me anything I have asked that he knows. He has never told me to go out and look for that information somewhere else, except when he himself has provided the links to the papers he recommends.
    And you know what? I’m not sure if gpuccio and I are on the same page theologically speaking. Probably not exactly. But he is very respectful and always willing to share what he knows, which seems to be a lot more than I and many other folks in this blog do. Gpuccio explains things in a very respectful manner, in very simple terms, and doesn’t make fun of my lack of knowledge or my dumb-sounding questions or my sometimes repetitive style.
    Also, gpuccio has demonstrated possessing the gift of patience, which I miserably lack. He has engaged in discussions with stubborn interlocutors that obviously have little or no interest in their discussions. Definitely I was not endowed with such a virtue. I believe gpuccio is a very dedicated medical doctor, with additional extensive studies in biological sciences, but he could do very well as a professor lecturing at a university. But that’s my personal perception of his strong pedagogical skills.
    Just wanted to comment on two contrasting extremes seen in this blog.
    🙂

  106. 106
    Dionisio says:

    #104 wd400

    You mean you waste people’s time asking them questions you know the answers to, then claim others are not interested in a serious discussion?

    No, quite on the contrary. I don’t want to waste anyone’s time. I don’t have any rights nor desire to do so. That’s why I ask questions that may lead to a productive discussion or completely shutdown the whole exchange for good. It all depends on the interest shown by each party involved in the discussion.

    I don’t know the exact answer to all the questions I ask. I have studied the subject, but see contradictions between different statements written by various folks in the thread or outside the blog. So I ask for clarification on the subject, while giving the interlocutors the opportunity to easily reveal their true motives for engaging in the given discussion, before the discussion proceeds too far, trying to keep it from turning into a wasted senseless debate.

    I don’t know many details and terminology, but just enough to discuss and to collaborate in multidisciplinary teamwork approach, which is very common in research these days. Computer scientists, electrical engineers, biologists, all collaborate in multidisciplinary teams working on biology or biotechnology research. None of the members are experts in everything. They complement one another. Their union has much more knowledge and expertise than the total sum of their individual knowledge and expertise.

    I have seen excessively long debates in this blog, that ultimately have led nowhere. That’s a waste of time I prefer to avoid. My initial questioning may quickly help to reveal the true motives of both parties, before the debate extends further into waste territory. That’s saved time.
    Perhaps if others in this blog take a similar approach, many excessively long debates would have stopped much earlier than they actually did. That would have translated into saved time for everyone. But some folks in this blog don’t mind the long senseless debates, because they could benefit the onlookers/lurkers out there.

    See post #105 for more on this.

  107. 107
    fifthmonarchyman says:

    Aurelio Smith says,

    He is like a six-year-old asking “why is the sky blue, daddy,?”

    I say,

    quote:

    what do they teach at these schools?

    end quote:

    CS Lewis

    …….
    Socratic method (also known as method of elenchus, elenctic method, or Socratic debate), named after the classical Greek philosopher Socrates, is a form of inquiry and discussion between individuals, based on asking and answering questions to stimulate critical thinking and to illuminate ideas.
    ……….

    peace

  108. 108
    Dionisio says:

    #107 Aurelio Smith

    It’s pretty clear Dionisio doesn’t know the answers to many questions. He is like a six-year-old asking “why is the sky blue, daddy,?” Such questions are easy for a six-year-old to ask but the answers are impossible for him to grasp.

    Please, read posts # 99, 103, 105, 106 for my comments related to what you just wrote.

    If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote? 🙂

  109. 109
    Dionisio says:

    #108 fifthmonarchyman

    Socratic method (also known as method of elenchus, elenctic method, or Socratic debate), named after the classical Greek philosopher Socrates, is a form of inquiry and discussion between individuals, based on asking and answering questions to stimulate critical thinking and to illuminate ideas.

    Excellent point. Thank you.

    Glad to see a thinking person here!
    🙂

  110. 110
    bornagain77 says:

    Dionisio, the sky is blue because God made it that way! 🙂

    ,,,These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe’s entire range of electromagnetic emissions.

    Extreme Fine Tuning of Light for Life and Scientific Discovery – (Privileged Planet excerpt)video
    https://vimeo.com/114136732

    Fine Tuning Of Universal Constants, Particularly Light – Walter Bradley – video
    https://vimeo.com/114137127

    Fine Tuning Of Light to the Atmosphere, to Biological Life, and to Water – graphs
    http://docs.google.com/Doc?doc.....aGh4MmdnOQ

    Michael Denton: Remarkable Coincidences in Photosynthesis – podcast
    http://www.idthefuture.com/201....._coin.html

  111. 111
    Dionisio says:

    #111 bornagain77

    Yes, that’s the ultimate reason that explains the ultimate reality. But I don’t want to push the interlocutors into that area at the beginning of the discussion. I believe most evidences discussed in a serious discussions should eventually lead us all to that ultimate realization.

  112. 112
    DNA_Jock says:

    Dionisio,
    I know you think you are applying the Socratic method brilliantly, but your failure to read for comprehension and actually engage with your interlocutors on the subject matter makes you look more like an ignorant six-year-old.
    I did enjoy this:

    If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote?

    You sound very erudite, if a bit condescending. Ironically, all daddy needs to understand is “Light-scattering”, which, much to my amusement, did not make it onto your list…

    You claim that this thread is clear testimony to the fact that I have not answered all your questions (excluding the ‘not even wrong’ one).
    Here’s the problem: given that I had already answered the question

    Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?

    with the response “No” (@89), then your questions at 93

    When was the overlapping between two distinct codes first mentioned in textbooks? Since the eighties? Earlier? Later? It hasn’t been mentioned at all? Don’t know?

    have been answered before you ever asked them. And Socrates would never ask them, because he would make the effort to comprehend the answers he receives.
    In a similar vein, your other questions have already been answered. Q: “What is it that you don’t like about gpuccio’s final sentence @33?” A: “It’s asinine.” Maybe you meant to ask a different question. 🙂 I have no motivation to keep answering questions that have already been answered, merely because my inquisitor isn’t paying attention.
    Your comment 103 is the conversation-ender, however:

    As I have stated very clearly before, I’m not trying to learn biology from DNA_Jock or from you or from any of your comrades and fellow travelers

    Please provide a link to your “very clear” statement with respect to myself. I must have missed it. But if you are not interested in learning any biology, then I will stop trying to help you learn.

    I’m trying to make you and your comrades show your real motives in this discussion, so everyone sees them openly. Those interested in having serious discussions will try to answer all questions.

    Well, all relevant questions. I am happy to discuss biology with anyone who is interested in discussing biology.

    In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it.

    So, by your own definition [in bold above], you are not a sincere interlocutor.
    ‘Nuff said.

  113. 113
    Dionisio says:

    #113 DNA_Jock

    Ironically, all daddy needs to understand is “Light-scattering”,…

    Are you sure? That limited knowledge won’t help, when dealing with the questions a curious child could ask, which could cover all areas of knowledge at some point sooner than later. You see, children have a sense of wonder that gets lost as we grow older and let the mundane things of live to take over our original curiosity. Every answer may provoke new questions. The process may continue until it’s time to take a break or something (external signal, physiological need, etc.) distracts the child’s attention away from the original curiosity. Obviously, different children act differently. But generally, that’s the expected behavior. That’s the way we should approach science research too. With child-like mentality, not sparing any question, no matter how dumb it may sound.

    On the other hand, children (as well as adults) complain when required to deal with larger volumes of information in order to understand a problem. When my children were in high school, they took AP calculus. They asked me to help them to learn how to resolve the problems they had for homework. When I tried to explain to them a practical method to resolve the problems, I noticed they could not grasp it well. Every time they faced a different problem, with a slight change of conditions, they had hard time trying to figure out what was what. So I started to ask them very basic mathematical questions, going from the most elementary issues and gradually moving up to more complex concepts and principles. Then they complained that I’m asking them so many stupid questions about things they already knew well. I told them I needed to ask them those questions so that I could find what they didn’t know, in order to take it from there. Well, to make the story shorter, they reluctantly submitted to my interrogation until I detected the weak spots in their knowledge, which then I explained to them carefully, using all kinds of illustrations and examples. Apparently the method worked, because they passed those AP calculus courses. That was long ago. They are now medical doctors, which is far beyond what my wife and I reached educationally or professionally. 🙂
    Ironically, it was a human development textbook, which one of my children left at home after finishing medical school, that activated my curiosity for biology, when I tried -unsuccessfully- to read a few pages on the cellular processes that take place in the first couple of weeks after conception. The few paragraphs I barely could read blew up my mind into pieces. I have not recovered since them. The sense of wonder, which I experienced so intensively in my childhood, but had lost as I grew older, suddenly was back, even more intensive and passionate than ever before. I gradually paid less attention to my software development work, as my mind got consumed in trying to understand other arts of that book. I started to ask questions to relatives and friends in biomedical fields. But my questions had a heavy information-processing flavor, most probably influenced by my software development background, hence the scientists I consulted were not sure they understood the bottom line of my questioning (well, most probably it was also because I did not know and perhaps still don’t know how to ask questions correctly).

  114. 114
    Dionisio says:

    It’s been said that it ain’t over ’til is over.

    Well, apparently this thread is over. Well, it lasted much longer than one could have expected at its start. 🙂

    Happy New Year!

    ¡Feliz Año Nuevo!

  115. 115
    Dionisio says:

    Reminding some (not all) important information that was posted in this thread (leaving aside the distracting senseless debate that pointed nowhere):

    #14

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

    DOI: 10.1126/science.1243490

    Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences.

    We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types.

    We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites.

    Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.

    Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons.

    More than 17% of single-nucleotide variants within duons directly alter TF binding.

    Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.

    http://www.sciencemag.org/cont.....ffa3a245fb

    #15

    Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge

    doi: 10.1093/bioinformatics/btu797

    Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation.

    When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression.

    However, when these data are not available, it is impossible to infer and validate such models.

    http://bioinformatics.oxfordjo.....7.abstract

    #16

    Multiple roles of the coding sequence 5? end in gene expression regulation

    doi: 10.1093/nar/gku1313

    The codon composition of the coding sequence’s (ORF) 5? end first few dozen codons is known to be distinct to that of the rest of the ORF.

    Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation.

    However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging.

    Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.

    http://nar.oxfordjournals.org/.....3.abstract

    #17

    Different types of secondary information in the genetic code

    doi: 10.1261/rna.044115.113

    Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code.

    Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information:
    codon-specific translational pauses that can be used by particular proteins toward their unique folding and
    biased codon patterns shared by groups of functionally related mRNAs with coordinate regulation.

    AGI is important to genetics in general and to human disease; here, we consider influences of its three major components, biased codon use itself, variations in the tRNAome, and anticodon modifications that distinguish synonymous decoding.

    AGI is plastic and can be used by different species to different extents, with tissue-specificity and in stress responses.

    Because AGI is species-specific, it is important to consider codon-sensitive experiments when using heterologous systems; for this we focus on the tRNA anticodon loop modification enzyme, CDKAL1, and its link to type 2 diabetes.

    Newly uncovered tRNAome variability among humans suggests roles in penetrance and as a genetic modifier and disease modifier.

    Development of experimental and bioinformatics methods are needed to uncover additional means of auxiliary genetic information.

    http://rnajournal.cshlp.org/co.....7.abstract

    #18

    Overlapping genes and variability of the genetic code

    DOI: 10.1023/A:1026631030516

    the finding that the meanings of some codons of the mitochondrial genetic code differ from the usual ones was unexpected.

    http://www.researchgate.net/pu.....netic_code

    #19

    Computation of the genetic code

    DOI: 10.1134/S1064562410040095

    The author has conducted mathematical analysis of genetic decoding for a number of years.

    Overlapping genes, discovered in 1976, were one of the main objects of the study.

    These are cases where the same segment of DNA encodes two or more protein sequences.

    Numerous cases of identified genetic overlaps allowed setting a number of mathematical problems that have been successfully solved.

    A detailed exposition of these problems is given in the author’s monograph Mathematical Analysis of Genetic Code (BINOM, Moscow, 2010).

    Such problems have made it possible to penetrate deeply enough into the structure of the genetic code and its relationship with the overlapping genes.

    As a result, a new problem was set: the computation of the genetic code on the basis of the amino acid sequences that record overlapping genes.

    One approach to this problem is described in this paper.

    http://www.researchgate.net/pu.....netic_code

    #20

    Some new characteristics of large genomes

    DOI: 10.1134/S2070048213030071

    http://www.researchgate.net/pu.....ge_genomes

    #21

    Scientists Discover Another Genetic Code

    Overlapping language seems to help direct DNA activity in cells, researchers report

    Another code within DNA has been discovered by scientists — a finding that the researchers say sheds light on how changes to DNA affect health.

    Since the genetic code was first deciphered in the 1960s, scientists have believed it was used solely to write information about proteins.

    But this new study from University of Washington scientists found that genomes use the genetic code to write two separate languages.

    One language describes how proteins are made, and the other helps direct genetic activity in cells. One language is written on top of the other, which is why this other language went undiscovered for so long, according to the report in the Dec. 13 issue of Science.

    “For over 40 years, we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” team leader Dr. John Stamatoyannopoulos, an associate professor of genome sciences and of medicine, said in a university news release.

    “Now we know that this basic assumption about reading the human genome missed half of the picture,” he said.

    http://health.usnews.com/healt.....netic-code

    #23

    Scientists discover double meaning in genetic code

    Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

    http://www.washington.edu/news.....etic-code/

    #25

    Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago.

    Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes.

    Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22.

    Analyses of the locations of the 5? and 3? transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes.

    The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs.

    The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.

    Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, et al. (2012) Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE 7(1): e28213. doi:10.1371/journal.pone.0028213

    http://www.plosone.org/article.....ne.0028213

    #26

    Scientists discover double meaning in genetic code

    Scientists have discovered a second code hiding within DNA.

    The second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

    Genomes use the genetic code to write two separate languages.

    One describes how proteins are made, and the other instructs the cell on how genes are controlled.

    One language is written on top of the other.

    http://www.sciencedaily.com/re.....142151.htm

    #30 by gpuccio

    “Overlapping genes referred in post #19 are not exactly the same as the overlapping languages referred in post #21.
    They seem like two different concepts, don’t they?
    The former refers to overlapping protein code, which apparently was discovered in 1976, while the latter has to do with the alleged recent discovery of another DNA-related language used for the operating logic. Is this correct?!”

    Yes, it is correct. the first paper is about possible alternative reading frames which use the same nucleotides to code for different aminoacid sequences. While there is overlapping, the symbolic code is the same.

    The second paper is about the role of nucleotides in promoting the binding of transcription factors. That function can be found anywhere in the genome, including coding exons. So, those nucleotides in coding exons which are also involved in TF binding seem to have a double function: they retain their meaning in the traditional genetic code as symbols of AAs, and at the same time they have a role in interacting with TFs.

    Here the code is not the same: two different codons can code for the same aminoacid, but only one of them can be active in TF binding. For example, Fig. 2 A of the paper shows that both AAC and AAT code for asparagine, but AAC seems to be preferred in TF interaction, while AAT is not.

    “BTW, do posts #21 & 23 somehow relate to the TAD concept that you brought up in the ‘third way’ discussion thread?”

    Only indirectly, in a sense. TADs are divisions of the genome which are determined by specific boundaries which limit long distance interactions between genomic regions when TFs bind to DNA and generate loops. So, in a sense, all that influences TF binding has probably some relationship with TAD architecture.

    #33 by gpuccio

    hrun0815:

    “the overlapping code was discovered in the late seventies”

    OK, but the epigenetic levels of regulation are being clarified only now. The contributions of DNA sequences to cell differentiation and regulation by multiple parallel and interacting “codes” (like the methylome, the histone codes, the TF networks and their combinatorial effects, all the post-transcriptional interventions by non coding RNAs, and so on) are hot new subjects of scientific research. They are new, exciting information. And the genome is at the center of those multiple, parallel interactions.

    So excuse us, poor ID fools, if we are discussing those interesting things that you apparently “failed to notice”.

    #63 by gpuccio

    “Is the OP video talking mainly about the genetic code specifying amino acids or a regulatory code specifying transcription factor (TF) recognition sequences, or both, or none of them, or something else?”

    Well, in the video Paul Giem comments (very well, IMO) a paper by George Montañez, Robert J. Marks II, Jorge Fernandez
    and John C. Sanford. The paper is about the mathematical modeling of beneficial mutations when nucleotides are involved in multiple codes, and does not refer to specific examples. However, there are references in the bibliography. For example, this work by Trifonov:

    Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical
    Biology 51:417–432.

    The original paper is in Russian, but here is the abstract:

    “Apart from the classical RNA-protein translation code, the genomic DNA sequences carry many other, nontriplet codes of different nature. Those of them which are at least partly deciphered are discussed in this review in the order of their estimated occupancy in the eukaryotic genome. Each of the codes is degenerate, like the triplet code. This is the basis for their coexistence in one and the same sequence, so that the same base often (if not always) belongs to several different overlapping sequence patterns. The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages.”

    So, the idea is that if some nucleotides are functional at different levels and in different codes, that implies extreme functional constraint, and extreme improbability of evolving the result by random beneficial mutations. That seems to be the main point of the paper.

    The recent paper you referenced in your post:

    “Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution”

    http://www.sciencemag.org/content/342/6164/1367

    is another good example.

    I think that any multiple function at the nucleotide level is a special constraint for that position. Multicode functionality is a special kind of information compression, ad it generates extreme limitations.

    The codes can be of the protein coding type, or just regulatory: the concept remains the same.

    We can have multiple overlapping ORFs, or an ORF overlapping with non coding regulatory sequences, and so on. Look at this page, for example:

    http://www-sequence.stanford.e.....pping.html

  116. 116
  117. 117
    Dionisio says:

    PS. Post #113 was loaded with so much vitriolic ad hominem nonsense that it’s not worth commenting on it, besides post #114.

  118. 118
    DNA_Jock says:

    PS. Post #113 was loaded with so much vitriolic ad hominem nonsense that it’s not worth commenting on it, besides post #114.

    LOL
    Vitriol: Yes
    Ad hominem: No. That phrase does not mean what you think it means…
    Nonsense: Why are you suddenly so shy about pointing out nonsense? Isn’t that the ultimate goal of your brilliant inquisitorial method?
    But your lack of any response is noted.
    My response to 114 : “Yes, I am sure”.

    Now for the fun bit:

    Which of the following two statements are you going to retract, Dionisio?

    @88, addressing wd400:
    Please, be aware that I’m a student (autodidact), hence I’m interested in learning many things I still don’t know about biology. Any useful information I can gather from our discussions is very appreciated.

    @103, addressing wd400:
    As I have stated very clearly before, I’m not trying to learn biology from DNA_Jock or from you or from any of your comrades and fellow travelers

    Furthermore, where did you make this “very clear” statement that you allude to?
    In the same post (103) you also, very helpfully, defined a common goal of “sincere interlocutors” thus:

    In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it.

    How can one avoid the conclusion that you are, by your own definitions, insincere?
    How can one avoid the conclusion that either 88 or 103 must be a lie?

    It’s okay if you don’t want to answer these questions.
    I’ll understand.
    LMAO

  119. 119
    wd400 says:

    I’m certainly confident that onlookers will be able to understand why you won’t respond, Dionisio.

  120. 120
    Dionisio says:

    #119 DNA_Jock

    Which of the following two statements are you going to retract?

    None. Both are accurate. Your lack of understanding confirms them. 🙂

    No one can’t learn much of anything from anyone who is not interested in serious discussions.

    See gpuccio as a contrasting example of someone who patiently explains things with details and is always willing to answer all questions, even my childishly dumb ones. 🙂 You may want to learn from him too.

    where did you make this “very clear” statement that you allude to?

    In another thread. Why are you so interested in that? 🙂

    How can one avoid the conclusion that you are, by your own definitions, insincere?
    How can one avoid the conclusion that either 88 or 103 must be a lie?

    Perhaps one way to avoid that conclusion is to read carefully what I wrote and to have a desire to really understand it. However, it may take a miracle for that to occur. 🙂

    It’s okay if you don’t want to answer these questions.

    Yes, it’s ok if one doesn’t answer questions.
    You have not answered some questions in this thread, but then you claimed that you did answered them.
    That’s fine.

    ¡Feliz Año Nuevo!

    🙂

  121. 121
    DNA_Jock says:

    Oh dear. Do try to keep up.

    None. Both are accurate. Your lack of understanding confirms them.

    Unfortunately for you, Dionisio, my understanding is neither here or there, since as I pointed out to you in 119 both statements were made to wd400:
    In post 87, you asked wd400 a series of ~13 questions about basic biology. Post 88 was your ‘addendum’ to post 87, in which you stated :

    @88, addressing wd400:
    Please, be aware that I’m a student (autodidact), hence I’m interested in learning many things I still don’t know about biology. Any useful information I can gather from our discussions is very appreciated.

    So it is clear from the context that “our discussions” includes your querying of wd400 @87.

    @103, addressing wd400:

    As I have stated very clearly before, I’m not trying to learn biology from DNA_Jock or from you or from any of your comrades and fellow travelers

    where did you make this “very clear” statement that you allude to?

    In another thread. Why are you so interested in that?

    For the following reason: unless you made that “very clear” statement in the 3 hour 7 minute window between your posts 88 and 103, it represents a prior statement that you are NOT trying to learn biology from DNA_Jock or wd400.
    Therefore your lame ”No one can’t learn much of anything from anyone who is not interested in serious discussions” attempt to weasel out of being caught in a lie fails miserably.
    According to you, you stated (on another thread) that you were NOT interested in learning biology from wd400, then stated @88 that you were, then stated @103 that you were not.
    “Serious discussions”: you keep using that phrase, I do not think that it means…
    I am happy to discuss biology with anyone who is interested.

  122. 122
    Dionisio says:

    #122 DNA_Jock

    my understanding is neither here or there,…

    Yes, it’s obvious that your understanding seems to be nowhere. 🙂

    Glad to see you’re aware of that too. 🙂

  123. 123
    Dionisio says:

    #122 DNA_Jock

    So it is clear from the context that “our discussions” includes your querying of wd400 @87.

    No, that’s not accurate, you’ve misunderstood it.

    My questions were required before we could get into a serious discussion. Hence, they were not part of a serious discussion yet. Unfortunately, we never reached that desired ‘serious discussion’ level.

    For example, I have been able to reach that ‘serious discussion’ level with gpuccio on various occasions, because gpuccio is very helpful and careful about answering my questions clearly and accurately. Sometimes he has corrected my misunderstandings with refined pedagogical skills. I’ve heard he’s a medical doctor, but I won’t be surprised if I find that he’s also an academic professor.

    Apparently some folks can’t or don’t want to do the same. But that’s not my problem. If there’s anything I could do to help, I would definitely do it. 🙂

  124. 124
    5for says:

    Go home Dinisio, you’ve been shown up badly.

  125. 125
    Dionisio says:

    #122 DNA_Jock

    Why do you like to write so many personal attacks?
    Why are you so upset? Can’t you calm down?

    Obviously, older comments I posted in other threads could not refer to specific names associated with newer posts in this thread. Why have you made such a big deal of that obvious detail you have failed to understand?

    However, now looking back at my comments, I think I realize what could have caused so much confusion, itching and hype. Perhaps I should take some blame for not communicating my thoughts correctly. If that’s the case, then I apologize for that mistake.

    But please, keep in mind that, as I have stated before (yes, maybe in other threads), my reading comprehension is poor, my communication skills are almost nonexistent, English is not my first language, my mind is slow – when someone tells a joke on the weekend, I may get it by Tuesday, after my wife explains it to me. Now you have a better idea who you’re dealing with. 🙂

    All that said, below you may see a few examples of my comments in other threads, where I wrote about similar situations, that have to do with folks that get easily upset, apparently because they don’t seem to like having to answer certain number of questions (though I really don’t know the exact reason for their bad mood):

    Post #45 in this thread:

    http://www.uncommondescent.com.....ent-527201

    Post #137 in this thread:

    http://www.uncommondescent.com.....ent-527458

    Post #138 in this thread:

    http://www.uncommondescent.com.....ent-527461

    Post # 846 in this thread:

    http://www.uncommondescent.com.....ent-532823

    Perhaps there are more threads where I have posted similar comments.

    Is the situation more clear to you now?

    Relax. Calm down.

    🙂

  126. 126
    Dionisio says:

    5for @125

    Go home Dinisio, you’ve been shown up badly.

    Hmm… What do you mean? Why did you write that?

    Thank you.

  127. 127
    Dionisio says:

    Ok, let’s wrap up this discussion. Again, here’s a list of some (not all) interesting posts in this thread:

    http://www.uncommondescent.com.....ent-539425

  128. 128
    DNA_Jock says:

    Honestly, Dionisio, you don’t upset me. You crack me up.
    You wrote:

    But please, keep in mind that, as I have stated before (yes, maybe in other threads), my reading comprehension is poor, my communication skills are almost nonexistent, English is not my first language, my mind is slow…

    I am mindful of these attributes, Dionisio, since they shine through your prose. Nobody with any knowledge of the subjects under discussion could read your interactions with reality-based posters here and fail to notice your shortcomings.
    I was quite willing to help you overcome these handicaps and learn some biology, if you were interested.

    The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.

    This is revealed when you make the switch from “curious idiot” mode into “erudite and condescending” mode, e.g.

    If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote?

    The above is not the writing of someone who believes their comprehension poor, communication skills non-existent and their mind slow. It is the writing of someone trying to show off. You even changed “is blue” to “looks blue” so that you could add some superfluous tripe about biology. But you failed to mention “light scattering”. Ooops.

    I am still willing to cut you a little slack regarding English-not-your-first language – my apologies for confusing you with the colloquial phrase “my understanding is neither here nor there” – so here’s a piece of friendly advice : ending your pontification with “Do you grasp what I just wrote?” is rude.

    When it comes to biology, the gap between your level of understanding and what you think is your level of understanding is rather wide:

    Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    The above paragraph takes some really basic, introductory level biology and tries to make it sound complicated. Given that you know my background and even tried to make fun of the fact that I used to be a molecular biologist, the “Have you heard” questions are rather condescending. Before you wrote this, I was ready to discuss formylglycine and other mechanisms that might not get covered an intro to biochem course; we could have had a “serious discussion” about biology. But you would rather ask childish “Have you heard?” questions and lecture me on pedagogical technique. Your choice, I guess. And yet again, hilariously, your attempt at sounding erudite fails: there is a basic error in your paragraph.
    So when you write “I don’t know much about this” you only think you are lying.

  129. 129
    Dionisio says:

    #129 DNA_Jock

    Please, can you explain in easy to understand terms what exactly reveals an “erudite and condescending” mode in the below quoted text?

    If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote?

    Thanks.

  130. 130
    Dionisio says:

    #129 DNA_Jock

    The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.

    Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true?

    Thank you.

  131. 131
    Dionisio says:

    #129 DNA_Jock

    I am still willing to cut you a little slack regarding English-not-your-first language – my apologies for confusing you with the colloquial phrase “my understanding is neither here nor there” – so here’s a piece of friendly advice : ending your pontification with “Do you grasp what I just wrote?” is rude.

    I didn’t know that. Please, accept my apologies for saying something that was rude. Really appreciate that you have brought this up to my attention.

    I think my former boss used to say that to me, but I’m not completely certain about that. However, if he really did, I didn’t take it as offensive back then. In a way I’m glad I wasn’t aware of the correct meaning of that expression in those days. Actually, at some point my supervisor, who was the head of development, told me he was wasting time when dealing with me, because I did not understand much of what he was trying to tell me and he did not understand much of what I was trying to tell him. Eventually I learned just enough English to keep a very basic communication with my supervisor and colleagues. I guess my knowledge of English has not progressed much further from that level since then. But God is gracious and took me through a long and winding road to this point. Can’t complain at all. I’ve been blessed. 🙂

    BTW, my former supervisor is a good friend of mine now. Isn’t that great?

    Perhaps you’re familiar with this biblical passage, which I believe somehow applies to this case:

    …not many of you were wise according to worldly standards,[c] not many were powerful, not many were of noble birth. 27 But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; 28 God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, 29 so that no human being[d] might boast in the presence of God. 30 And because of him[e] you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, 31 so that, as it is written, “Let the one who boasts, boast in the Lord.”

  132. 132
    Dionisio says:

    #129 DNA_Jock

    So when you write “I don’t know much about this” you only think you are lying.

    How do you know that I think that I’m lying?

    I don’t want to lie because that’s a very sinful action. God knows when I’m lying. He does not like when I lie.

    Why don’t you want to believe me when I write that I don’t know much about something?
    How do you know what ‘much’ means to me?

    Please, would you explain all this in easy to understand terms?

    Thank you.

    PS. I’m not an ID proponent, or a YEC, or OEC, or any acronym of any kind. I’m a miserable sinner who has been saved by God, even though I don’t deserve it at all. My only identity is in Christ, my Savior and my Lord. That’s all.

    When I say I don’t know much of something, I really mean it. Specially when I read a few posts written by other folks here, perhaps including you too, and I have very little idea, if any, of what is being discussed.

    Biology has fascinated me since a few years ago. I retired early, so that I could have more tome to learn some new software development techniques for 3D interactive animation development, which I did not know, and also certain aspects of biology associated with information-processing within the bio systems.

    My mother-in-law doesn’t like when I say that I’m worse than most people I know personally. She doesn’t want to understand that I don’t compare myself with other people, but with the absolute standard of purity, Christ, and I can’t even start the comparison. That’s why Paul the apostle wrote that he is the chief of sinners.

    Likewise, I compare my knowledge with what is unknown to me, which is practically infinite.

    When I write that I don’t know much about something, I’m not comparing my knowledge level with other people’s. I’m comparing it with what I would like to know.

    Perhaps I can’t explain this in a clear way that is understandable. But I’m very interested in ensuring that you do understand me.

    I pray that we can have a serious conversation. But that’s not under my control. Actually, very little is under my control.

    I wish you a Happy New Year and many blessings in the days to come. To you and to your family and to your friends.

    Perhaps the story of my former boss and I can repeat with you and me.

  133. 133
    DNA_Jock says:

    Dionisio,
    Re 130,
    Your 132 acknowledges the condescending part. As to the “erudite” part, the text

    and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff

    can safely be omitted from your paragraph without any loss of meaning.

    So why include all this superfluous science-y stuff, unless in an attempt to appear erudite?

    Re 131,
    No, not really. All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning. Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.

    Re 133,
    What you wrote to me @99 was

    Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    Given that “ I’m not trying to learn biology from DNA_Jock”, the final sentence is obviously untrue, even if you choose to redefine “much” to mean “as much as I would like”. By your own definitions, you are not a “sincere interlocutor” (see 113).

    Now I cannot know what is in your mind, obviously, but the way you alternate between “curious idiot” mode and “erudite and condescending” mode (see 129) leads me to the conclusion that you think you are lying when you profess the depth of your ignorance.

    The idea that you are indulging in a little “role-play” for Socratic effect is the most charitable explanation for this pattern, and would explain why you are unable to keep track of whether you are interested in learning biology from wd400 or not (see 122). And the good news is that you are not, in fact, lying when you say “I don’t know much about this”.

  134. 134
    Dionisio says:

    #134 DNA_Jock

    Your 132 acknowledges the condescending part.

    Please, can you quote the specific text that supports your statement?

    Thank you.

  135. 135
    Dionisio says:

    #134 DNA_Jock

    So why include all this superfluous science-y stuff, unless in an attempt to appear erudite?

    Q1. Could there be other reasons?

    Q2. Why do you call that information superfluous?

  136. 136
    Dionisio says:

    #129 DNA_Jock

    The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.

    Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true?

    Thank you.

  137. 137
    Dionisio says:

    @129 DNA_Jock

    The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.

    Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true?

    Thank you.

  138. 138
    Dionisio says:

    DNA_Jock @129

    The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.

    Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true?

    Thank you.

  139. 139
    Dionisio says:

    #129 DNA_Jock

    Re 131,
    No, not really.

    Why couldn’t you answer the question posted @131?

  140. 140
    Dionisio says:

    #129 DNA_Jock

    All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

    (based on your behavior)

    Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?

    …it appears to me that…

    Q2. Could that be a misperception? Appearances could be deceiving, couldn’t they?

    …are insincere

    Q3. How do you know they are not sincere?

    …your “Socratic” questioning.

    Q4. Why do you use that term in reference to my simple questions?

    Thank you in advance for trying to answer my questions.

  141. 141
    Dionisio says:

    @129 DNA_Jock

    All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

    (based on your behavior)

    Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?

    …it appears to me that…

    Q2. Could that be a misperception? Appearances could be deceiving, couldn’t they?

    …are insincere

    Q3. How do you know they are not sincere?

    …your “Socratic” questioning.

    Q4. Why do you use that term in reference to my simple questions?

    Thank you in advance for trying to answer my questions.

  142. 142
    Dionisio says:

    DNA_Jock @129

    All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

    (based on your behavior)

    Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?

    …it appears to me that…

    Q2. Could that be a misperception? Appearances could be deceiving, couldn’t they?

    …are insincere

    Q3. How do you know they are not sincere?

    …your “Socratic” questioning.

    Q4. Why do you use that term in reference to my simple questions?

    Thank you in advance for trying to answer my questions.

  143. 143
    Dionisio says:

    #129 DNA_Jock

    Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.

    Q1. Then why did you make it sound as if it is true?

    Q2. Why did you make all those personal attacks based on ‘personal impression’ which you didn’t know if it was true?

    Q3. Is that the way you treat everyone, including your relatives and friends?

  144. 144
    Dionisio says:

    @129 DNA_Jock

    Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.

    Q1. Then why did you make it sound as if it is true?

    Q2. Why did you make all those personal attacks based on ‘personal impression’ which you didn’t know if it was true?

    Q3. Is that the way you treat everyone, including your relatives and friends?

  145. 145
    Dionisio says:

    DNA_Jock @129

    Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.

    Q1. Then why did you make it sound as if it is true?

    Q2. Why did you make all those personal attacks based on ‘personal impression’ which you didn’t know if it was true?

    Q3. Is that the way you treat everyone, including your relatives and friends?

  146. 146
    Dionisio says:

    #129 DNA_Jock

    I have more questions, which will try to post later.

    🙂

  147. 147
    Dionisio says:

    #129 DNA_Jock

    …the final sentence is obviously untrue,…

    Are you certain that your (above quoted) statement is true?

  148. 148
    Dionisio says:

    @129 DNA_Jock

    …the final sentence is obviously untrue,…

    Are you certain that your (above quoted) statement is true?

  149. 149
    Dionisio says:

    DNA_Jock @129

    …the final sentence is obviously untrue,…

    Are you certain that your (above quoted) statement is true?

  150. 150
    Dionisio says:

    @129 DNA_Jock

    I have more questions, which will try to post later.

    🙂

  151. 151
    wd400 says:

    Dionisio,

    Since you are interested in knowing when you appear rude:

    Asking asinine questions like the above, which are all answered in DNA_Jock’s original comments is rude, a waste to time and unlikely to generate the “serious” discussion you claim to want.

    Spamming a thread by deliberately double and triple posting those questions is rude.

    (I can assure you I’m not going to answer follow-up questions as inane as the above, so please don’t waste anyone’s time by asking them)

  152. 152
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?

  153. 153
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?
    How do you know they have been answered?

  154. 154
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?
    How do you know they have been answered?
    He has not answered several questions.

  155. 155
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?
    How do you know they have been answered?
    He has not answered several questions.
    Are you going to answer them for him?

  156. 156
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?
    How do you know they have been answered?
    He has not answered several questions.
    Are you going to answer them for him?
    Are you interested in ensuring that what you write is true?

  157. 157
    Dionisio says:

    #152 wd400

    which are all answered in DNA_Jock’s original comments

    Are you certain they have been answered?
    How do you know they have been answered?
    He has not answered several questions.
    Are you going to answer them for him?
    Are you interested in ensuring that what you write is true?
    Are you interested in ensuring that what you write is understood, at least by the person you are addressing directly?

  158. 158
    DNA_Jock says:

    Yikes, Dionisio, your reading comprehension really is dire.

    Re 135 :
    A: the first three sentences of your 132, viz:

    I didn’t know that. Please, accept my apologies for saying something that was rude. Really appreciate that you have brought this up to my attention.

    Re 136:
    Q1. Could there be other reasons?
    A: Enlighten me.

    Q2. Why do you call that information superfluous?
    A: Read the preceding sentence, viz: “can safely be omitted … without any loss of meaning.”

    Re 131, 137, 138, 139 (wtf?) and 140
    Read the rest of the paragraph:

    No, not really. All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning. Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.

    Alternatively, I could have answered your (repeated) question by saying “because I am describing my own thought processes” but that would not have moved the conversation forward, I suspect.

    Re 142, 143 (wtf?)
    Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?
    A: Gee, how about:

    Ok, let me see if I understand this: is “the Purpose” related to your work or profession?
    Does that mean you’re a molecular biology scientist and you possess some breakthrough information but can’t reveal it here?
    Is that right?
    Sorry if I got it wrong again. Please, refer to post #507 to understand my condition.
    Obviously, my guessing was wrong, because a molecular biology scientist would be too busy working on serious research, hence no spare time to squander on the blogosphere
    Would “the Purpose” allow you to answer questions like those, as long as you don’t reveal any confidential breakthrough information?
    Did you read gpuccio’s post #501 carefully enough to comment on it so fast?
    Do you understand this?
    Did you read post #516?
    Did you understand it?
    Do you agree?
    No? Why not?
    Would a passionate molecular biology scientist ever leave such a fascinating profession?
    What could be more exciting than that?
    Can you elaborate on this?
    Participating in what thread? What are you talking about?
    Did anyone ask you to participate in any thread?
    Can you explain what you meant by that statement you wrote?
    Did you understand what I wrote? Apparently you didn’t.
    Please, don’t tell me your reading comprehension is as poor as mine.

    and the entirety of this thread.

    It was an ID-proponent who called you “bratty” (I thought that was a little harsh.)

    Q2. Could that be a misperception? Appearances could be deceiving, couldn’t they?
    A: Could be. Convince me otherwise.

    Q3. How do you know they are not sincere?
    A: I cannot know, obviously, but the impression is a very strong one. Convince me otherwise, perhaps by showing an interest in learning, rather than indulging in an awesomely lame meta-discussion.

    Q4. Why do you use that term [“Socratic”] in reference to my simple questions?
    A: See your 110.

    Re 144, 145, 146 (are you feeling okay?)
    Q1: The things that I perceive to be true, I perceive to be true. If I thought I was wrong, I would change my mind! Maybe you can convince me of your sincerity. You’re not doing too well right now.
    Q2. The “attacks” (with the sole exception of that one paragraph that begins “The problem, as I see it,…”) are not based on my personal impression of your state of mind, but rather consist of calling you out on your behavior. Lying, for example.
    Q3. Absolutely. If my daughter is coming across as a bitch, I will tell her “don’t be the bitch”. It’s called honesty.

    Re 147, 151
    I’m off on vacation soon, so I may not respond. You might consider taking a break too.

    Re 148, 149, 150 (seriously, please slow down)
    Yes. Read the entire sentence.
    Please Dionisio, before you start responding to a post, read it through twice (or more), trying to understand the author’s meaning. This will, hopefully, save you from embarrassments like posts 137 – 143 and from asking infantile questions such as “Why do you call that information superfluous?“

    Your multiple posting is making Gary Gaulin appear correct, and absolutely nobody wants that. Please ease up.

  159. 159
    Dionisio says:

    #152 wd400

    I have more questions for you too, but will have to post them later.

    BTW, you don’t have to answer them. It’s up to you.

  160. 160
    Dionisio says:

    #159 DNA_Jock

    [DNA_Jock wrote:] Yikes, Dionisio, your reading comprehension really is dire.

    Re 135 :
    A: the first three sentences of your 132, viz:

    [Dionision wrote:] I didn’t know that. Please, accept my apologies for saying something that was rude. Really appreciate that you have brought this up to my attention.

    How do you relate what I wrote @132 (which you quoted @159 – see above) with your claim that I was trying to be condescending?

    BTW, the condescending term was used in your post #129, where you wrote:

    [DNA_Jock wrote:] This is revealed when you [Dionisio] make the switch from “curious idiot” mode into “erudite and condescending” mode

    Are you retracting your previous statements indicating that I was being condescending?

    Please, would you mind explaining all this in a way that I can understand it? Thank you.

  161. 161
    Dionisio says:

    DNA_Jock

    Why do you like to write so many personal attacks?

    BTW, I asked the same question @126, but don’t recall seeing your answer.

    Please, would you mind to show me where you answered that specific question, if you did? Thank you.

  162. 162
    Dionisio says:

    #159 DNA_Jock

    Re 136:
    [Dionisio asked:] Q1. Could there be other reasons?
    [DNA_Jock wrote:] A: Enlighten me.

    Are you saying that there could not be other reasons for writing what I wrote, beside the reason you assumed?

    Are you sure about that?

  163. 163
    Dionisio says:

    #159 DNA_Jock

    I have more questions, which will try to post later.

    🙂

  164. 164
    Dionisio says:

    #159 DNA_Jock

    BTW, you don’t have to answer all the questions. You may leave them unanswered. That’s fine too.

    🙂

  165. 165
    Dionisio says:

    #159 DNA_Jock

    …but that would not have moved the conversation forward, I suspect.

    Do you really care about the conversation moving forward?

    🙂

  166. 166
    Dionisio says:

    #134 DNA_Jock

    Re 133,
    What you wrote to me @99 was

    Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    Given that “ I’m not trying to learn biology from DNA_Jock”, the final sentence is obviously untrue, even if you choose to redefine “much” to mean “as much as I would like”. By your own definitions, you are not a “sincere interlocutor”

    My statement

    I don’t know much about this, hence any correction is welcome!

    was open, not personal, i.e. it was not addressed to you only, but to anyone who may read this thread and could notice a mistake in my assertions.

    In case you haven’t noticed this yet, there are other folks who write comments in this blog and could read my post and decide to correct any mistake they see in my comments. I will welcome that.

    Next time ask me first why I wrote it before rushing into premature conclusions and engaging in disgusting and shameful personal attacks. Asking questions is not bad. Many times it helps.

  167. 167
    Dionisio says:

    @134 DNA_Jock

    Re 133,
    What you wrote to me @99 was

    Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    Given that “ I’m not trying to learn biology from DNA_Jock”, the final sentence is obviously untrue, even if you choose to redefine “much” to mean “as much as I would like”. By your own definitions, you are not a “sincere interlocutor”

    My statement

    I don’t know much about this, hence any correction is welcome!

    was open, not personal, i.e. it was not addressed to you only, but to anyone who may read this thread and could notice a mistake in my assertions.

    In case you haven’t noticed this yet, there are other folks who write comments in this blog and could read my post and decide to correct any mistake they see in my comments. I will welcome that.

    Next time ask me first why I wrote it before rushing into premature conclusions and engaging in disgusting and shameful personal attacks. Asking questions is not bad. Many times it helps.

  168. 168
    Dionisio says:

    DNA_Jock @134

    Re 133,
    What you wrote to me @99 was

    Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA.
    I don’t know much about this, hence any correction is welcome!

    Given that “ I’m not trying to learn biology from DNA_Jock”, the final sentence is obviously untrue, even if you choose to redefine “much” to mean “as much as I would like”. By your own definitions, you are not a “sincere interlocutor”

    My statement

    I don’t know much about this, hence any correction is welcome!

    was open, not personal, i.e. it was not addressed to you only, but to anyone who may read this thread and could notice a mistake in my assertions.

    In case you haven’t noticed this yet, there are other folks who write comments in this blog and could read my post and decide to correct any mistake they see in my comments. I will welcome that.

    Next time ask me first why I wrote it before rushing into premature conclusions and engaging in disgusting and shameful personal attacks. Asking questions is not bad. Many times it helps.

  169. 169
    Dionisio says:

    #134 DNA_Jock

    I have more questions, which will try to post later.

    🙂

  170. 170
    Dionisio says:

    #159 DNA_Jock

    I have more questions, which will try to post later.

    🙂

  171. 171
    Dionisio says:

    @134 DNA_Jock

    Will try and comment on the rest of your post later today.

    🙂

  172. 172
    Dionisio says:

    @159 DNA_Jock

    Will try and comment on the rest of your post later today, if I find some time.

    🙂

  173. 173
    Dionisio says:

    #120 wd400

    I’m certainly confident that onlookers will be able to understand why you won’t respond, Dionisio.

    Hmm… really? Cool!

    🙂

  174. 174
    Dionisio says:

    @120 wd400

    I’m certainly confident that onlookers will be able to understand why you won’t respond, Dionisio.

    Hmm… really? Cool!

    🙂

  175. 175
    Dionisio says:

    wd400 @120

    I’m certainly confident that onlookers will be able to understand why you won’t respond, Dionisio.

    Hmm… really? Cool!

    🙂

  176. 176
    Dionisio says:

    #119 DNA_Jock

    It’s okay if you don’t want to answer these questions.
    I’ll understand.
    LMAO

    Alright. That’s fine. Have fun! 🙂

  177. 177
    Dionisio says:

    @119 DNA_Jock

    It’s okay if you don’t want to answer these questions.
    I’ll understand.
    LMAO

    Alright. That’s fine. Have fun! 🙂

  178. 178
    Dionisio says:

    DNA_Jock @119

    It’s okay if you don’t want to answer these questions.
    I’ll understand.
    LMAO

    Alright. That’s fine. Have fun! 🙂

  179. 179
    Dionisio says:

    Onlookers/lurkers:
    Here’s a list of some (not all) serious posts in this thread:
    http://www.uncommondescent.com.....ent-539425

  180. 180
    Dionisio says:

    Onlookers/lurkers:
    If you’d prefer to skip the ongoing chat with wd400 and DNA_Jock, here’s a list of some (not all) serious posts in this thread:
    http://www.uncommondescent.com.....ent-539425

  181. 181
    Dionisio says:

    Onlookers/lurkers:
    If you’d prefer to skip the ongoing chat, here’s a list of some (not all) serious posts in this thread:
    http://www.uncommondescent.com.....ent-539425

  182. 182
    Dionisio says:

    wd400 & DNA_Jock

    My recent postings are intended to show you and your comrades along with your fellow travelers how bad your own medicine tastes. I don’t like it.

    Maybe you’ll finally realize that it’s better to get serious.

    It would be more pleasant.

    Let’s be nice. It’ll make difficult discussions a little easier.

  183. 183
    Dionisio says:

    If you want, we can all agree to stop it here. Or you may continue the old rotten style, if that’s what you prefer.
    Let’s make a deal?
    If we agree, we’ll try to refrain from commenting on anything we all write from now on.
    At this point one of my main interests is to gather references to research papers for review using Zotero + Mind Meister + private WordPress web logs, some of which I share here in this blog.

  184. 184
    Dionisio says:

    DNA_Jock

    You have called me a liar but have not been able to produce a proof to support your accusation.
    It was just based on your own misperceptions.
    Can’t you understand that I admit to my lack of knowledge and my slow thinking sincerely?
    Still you haven’t been able to explain your position clearly.
    Can any directed explanation be considered effective if the addressed audience doesn’t understands it?
    Can you make it more understandable to me?
    If you can’t, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards?

    Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect?

    Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I’m lying, just because you don’t want to accept my sincere explanation?

    Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?

    …not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.”
    [1 Corinthians 1:26-31]

    How many times should I repeat this post so that you consider it seriously? 3? 7?

  185. 185
    Dionisio says:

    DNA_Jock,

    You have called me a liar but have not been able to produce a proof to support your accusation.
    It was just based on your own misperceptions.
    Can’t you understand that I admit to my lack of knowledge and my slow thinking sincerely?
    Still you haven’t been able to explain your position clearly.
    Can any directed explanation be considered effective if the addressed audience doesn’t understands it?
    Can you make it more understandable to me?
    If you can’t, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards?

    Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect?

    Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I’m lying, just because you don’t want to accept my sincere explanation?

    Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?

    …not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.”
    [1 Corinthians 1:26-31]

    How many times should I repeat this post so that you consider it seriously? 3? 7?

  186. 186
    Dionisio says:

    DNA_Jock:

    You have called me a liar but have not been able to produce a proof to support your accusation.
    It was just based on your own misperceptions.
    Can’t you understand that I admit to my lack of knowledge and my slow thinking sincerely?
    Still you haven’t been able to explain your position clearly.
    Can any directed explanation be considered effective if the addressed audience doesn’t understands it?
    Can you make it more understandable to me?
    If you can’t, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards?

    Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect?

    Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I’m lying, just because you don’t want to accept my sincere explanation?

    Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?

    …not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.”
    [1 Corinthians 1:26-31]

    How many times should I repeat this post so that you consider it seriously? 3? 7?

  187. 187
    Dionisio says:

    DNA_Jock

    If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it’s just related to old history.

    It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness.

    Most probably you already knew this. But perhaps some onlookers/lurkers don’t know it.

    BTW, it’s possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. 🙂

  188. 188
    Dionisio says:

    DNA_Jock,

    If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it’s just related to old history.

    It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness.

    Most probably you already knew this. But perhaps some onlookers/lurkers don’t know it.

    BTW, it’s possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. 🙂

  189. 189
    Dionisio says:

    DNA_Jock:

    If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it’s just related to old history.

    It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness.

    Most probably you already knew this. But perhaps some onlookers/lurkers don’t know it.

    BTW, it’s possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. 🙂

  190. 190
    Dionisio says:

    #159 DNA_Jock

    Re 147, 151
    I’m off on vacation soon, so I may not respond. You might consider taking a break too.

    Glad you’re off on vacation soon. It’s good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.

  191. 191
    Dionisio says:

    #159 DNA_Jock,

    Re 147, 151
    I’m off on vacation soon, so I may not respond. You might consider taking a break too.

    Glad you’re off on vacation soon. It’s good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.

  192. 192
    Dionisio says:

    #159 DNA_Jock:

    Re 147, 151
    I’m off on vacation soon, so I may not respond. You might consider taking a break too.

    Glad you’re off on vacation soon. It’s good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.

  193. 193
    Dionisio says:

    DNA_Jock:

    Did you respond my questions posted @161 yet?

    I don’t recall seeing it, but perhaps it was posted after you left on vacation?

    Anyway, in case you have time, here’s a link to post #161 in this thread:

    http://www.uncommondescent.com.....ent-539935

  194. 194
    Dionisio says:

    DNA_Jock,

    Did you respond my questions posted @161 yet?

    I don’t recall seeing it, but perhaps it was posted after you left on vacation?

    Anyway, in case you have time, here’s a link to post #161 in this thread:

    http://www.uncommondescent.com.....ent-539935

  195. 195
    Dionisio says:

    DNA_Jock, RE: #161

    Did you respond my questions posted @161 yet?

    I don’t recall seeing it, but perhaps it was posted after you left on vacation?

    Anyway, in case you have time, here’s a link to post #161 in this thread:

    http://www.uncommondescent.com.....ent-539935

  196. 196
    Dionisio says:

    DNA_Jock

    Why do you like to write so many personal attacks?

    BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail?
    You may want to try to make your explanation more understandable to people who are not as sharp and don’t think as fast as you do. Make it understandable to a 6-yo child. 🙂

    @162 I asked this:

    Please, would you mind to show me where you answered that specific question, if you did? Thank you.

  197. 197
    Dionisio says:

    DNA_Jock,

    Why do you like to write so many personal attacks?

    BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail?
    You may want to try to make your explanation more understandable to people who are not as sharp and don’t think as fast as you do. Make it understandable to a 6-yo child. 🙂

    @162 I asked this:

    Please, would you mind to show me where you answered that specific question, if you did? Thank you.

  198. 198
    Dionisio says:

    DNA_Jock:

    Why do you like to write so many personal attacks?

    BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail?
    You may want to try to make your explanation more understandable to people who are not as sharp and don’t think as fast as you do. Make it understandable to a 6-yo child. 🙂

    @162 I asked this:

    Please, would you mind to show me where you answered that specific question, if you did? Thank you.

  199. 199
    Upright BiPed says:

    Dio, you’ve now posted 60 of the last 62 posts on this thread, including the last 37 posts straight. Many of your posts are seemingly repeats (or almost identical to) adjacent posts you’ve made. You are effectively killing the threads.

    This is ineffective. Please consider altering your approach.

  200. 200
    Dionisio says:

    DNA_Jock,

    Did you respond my questions posted @163 yet?

    I don’t recall seeing it, but perhaps it was posted after you left on vacation?

    Anyway, in case you have time, here’s a link to post #163 in this thread:

    http://www.uncommondescent.com.....ent-539937

  201. 201
    Dionisio says:

    DNA_Jock:

    Did you respond my questions posted @163 yet?

    I don’t recall seeing it, but perhaps it was posted after you left on vacation?

    Anyway, in case you have time, here’s a link to post #163 in this thread:

    http://www.uncommondescent.com.....ent-539937

  202. 202
    Dionisio says:

    #200 Upright BiPed

    Dio, you’ve now posted 60 of the last 62 posts on this thread, including the last 37 posts straight. Many of your posts are seemingly repeats (or almost identical to) adjacent posts you’ve made. You are effectively killing the threads.

    This is ineffective. Please consider altering your approach.

    Ok, will change the posting approach. Didn’t know this affected the thread so badly. The ‘third way’ thread is much larger than this and no one has mentioned this kind of critical problem.
    Thank you for bringing this up to my attention.
    Happy New Year!

  203. 203
    wd400 says:

    Are the mods on holiday?

    What value does Dinisio’s spam add to this thread, or indeed this site? How long would an pro-evolutionary biology poster last here if they spammed threads with the same sort of inane questions repeated so many times?

  204. 204
    Dionisio says:

    #204 wd400
    Whining?
    You, your comrades and fellow travelers do the same all the time, but in a more subtle manner, scattering your nonsense comments through the threads, in order to get away with it by flying under the radar.
    What I did was more obvious, kind of like a short-timed blitzkrieg offensive. I gave you your own medicine, but on larger dose, so you knew how bad it tastes. Now you know.

    But I have good news for you. UB nicely asked me to stop it and I immediately did it. You see? It works when people talk nicely. You may want to try learning that style too, though it’s probably unknown to you.
    Now run and tell your comrades the good news! But don’t think you’re off the hook. Questions will keep coming your way, but not in an unnecessary ‘Dresden bombardment’ style. Just one at a time. 🙂
    Just be careful and don’t try to setup another money exchanging business in the main portal. Someone could come and overturn your tables again. 🙂

    Anyway, a more effective way to collaborate here is to provide references to research papers that show how quickly the magic ‘n-D e’ formula RV+NS+HGT+T=E is failing to explain the origin of the elaborate cellular and molecular choreographies orchestrated within the biological systems.

    In a way now think that I wasted too much time trying to play by your dirty rules. Looking back I have to admit that I didn’t enjoy it. Another lesson learned.
    I should learn to ignore y’all. 🙂

  205. 205
    wd400 says:

    Not whining, Dio. What you’ve done is exceedingly childish and rude and your questions are inane. I fail to see how having you spam these threads serves any purpose, let alone gets you the the “serious discussion” you started out claiming to seek.

    You can’t behave as you have and expect others to treat you with respect or politeness. The best I can offer is to add you the BA/Joe class and scroll past your comments, but I still question why your spam should clog up these threads at all.

  206. 206
    Dionisio says:

    #206 Aurelio Smith

    Don’t let UB bully you.

    UB asked me very nicely to change my approach, giving me clear to understand reasons.
    You may want to try learning from UB. It won’t hurt you to know how to present information in a nice and easy to understand manner.
    Perhaps UB can teach you that. I should learn that too. 🙂

  207. 207
    Dionisio says:

    #207 wd400
    Normally I don’t post comments for you or your comrades, except when I mistakenly get engaged in senseless debates with y’all, which become a tremendous waste of time I later regret.
    You and your fellow travelers have not been in the main list of intended recipients of my posts.
    Actually, most of my posts are simply references to research papers I find interesting enough to share with others here. They are not mine. I don’t qualify to write anything worth reading.
    🙂

  208. 208
    Dionisio says:

    Anyway, a more effective way to collaborate here is to provide references to research papers that show how quickly the magic ‘n-D e’ formula RV+NS+HGT+T=E is failing to explain the origin of the elaborate cellular and molecular choreographies orchestrated within the biological systems.

    Here’s one fish from the oven:

    unexpected mechanism of protein synthesis, in which a protein—not an mRNA—determines tRNA recruitment

    Science 2 January 2015:
    Vol. 347 no. 6217 pp. 75-78
    DOI: 10.1126/science.1259724

    Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

    In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation.

    Here we report cryo–electron microscopy structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S subunit at sites exposed after 40S dissociation, placing the Ltn1p RING (Really Interesting New Gene) domain near the exit channel and Rqc2p over the P-site transfer RNA (tRNA).

    We further demonstrate that Rqc2p recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits.

    Our work uncovers an unexpected mechanism of protein synthesis, in which a protein—not an mRNA—determines tRNA recruitment and the tagging of nascent chains with carboxy-terminal Ala and Thr extensions (“CAT tails”).

    http://www.sciencemag.org/cont.....0c68795868

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