Paul Giem on overlapping genetic codes

_{Denyse O'Leary

December 24, 2014

Genetics, News}

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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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Comments

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.Zachriel_{December 27, 2014
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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.Joe_{December 27, 2014
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Zachriel: Has Sanford ever corrected the bug concerning selection in his Mendel’s Accountant? Why don't you download the source code and look?Mung_{December 27, 2014
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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.Dionisio_{December 27, 2014
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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/doi/10.1002/dvdy.24235/abstract
Dionisio_{December 27, 2014
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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/calvinbeisner/2014/07/23/the-threat-to-the-scientific-method-that-explains-the-spate-of-fraudulent-science-publications-n1865201/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/2014/12/in_nature_two_c092311.html
bornagain77_{December 27, 2014
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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/doi/10.1002/dvdy.24228/abstract
Dionisio_{December 27, 2014
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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.Dionisio_{December 27, 2014
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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/content/342/6164/1367.abstract?sid=10ce3b98-d907-4d26-be90-89ffa3a245fb
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.Dionisio_{December 27, 2014
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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.
Dionisio_{December 27, 2014
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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]?Zachriel_{December 27, 2014
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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.Joe_{December 27, 2014
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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?Box_{December 27, 2014
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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.hrun0815_{December 27, 2014
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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."Box_{December 27, 2014
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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?hrun0815_{December 27, 2014
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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.Box_{December 27, 2014
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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.hrun0815_{December 27, 2014
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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.hrun0815_{December 27, 2014
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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.Dionisio_{December 27, 2014
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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).gpuccio_{December 26, 2014
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gpuccio Thank you for the insightful comments that you wrote in posts #30 and #33.Dionisio_{December 26, 2014
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#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.Dionisio_{December 26, 2014
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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.Steve_{December 26, 2014
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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.hrun0815_{December 26, 2014
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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".gpuccio_{December 26, 2014
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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.Joe_{December 26, 2014
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Dionisio, I guess You live by the credo of 'any publicity is good publicity'. In that case you are right and welcome.hrun0815_{December 26, 2014
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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.gpuccio_{December 26, 2014
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#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! :)Dionisio_{December 26, 2014
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