tag:blogger.com,1999:blog-37148773.post9171896392223824487..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: Revisiting the Central Dogma in the 21st CenturyLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger544125tag:blogger.com,1999:blog-37148773.post-79648199808539715892013-10-30T12:29:05.894-04:002013-10-30T12:29:05.894-04:00is the central dogma of molecular biology acceptab...is the central dogma of molecular biology acceptable in the 21st century??<br />Anonymoushttps://www.blogger.com/profile/03608752866760994013noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48511888144470562312011-10-13T03:30:35.909-04:002011-10-13T03:30:35.909-04:00Over there, the ad hominem-s still rage around the...Over there, the <i>ad hominem</i>-s still rage around the "Myth of Junk DNA", but finally Ohno's "non-genic, therefore Junk DNA" nonsense is dead as a doornail. <br /><br />Central Dogmatist still plays his solitary shell-game (where hides the "right" version of the Dogma to fit the occasion), but his Junk-conclusion melted into clarity: <i>"Nobody questions the fact that lots of non-protein-coding DNA has a function."</i> <br /><br />A guessing game of percentages (by one who can't even produce properly rounded percentages) can go on <i>ad nauseam</i>, but who cares?<br /><br />The task that really matters is to explain genome regulation by those whatever percentages of intergenic and intronic segments that most mistakenly called "Junk" - but now the many bits of function must be put in a larger (and mathematical) frame. <br /><br />If the algos are not palatable to computers, solution will not be attained.Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22284024630323964852011-10-11T01:43:35.270-04:002011-10-11T01:43:35.270-04:00@ Allan Miller:
Yes, a number of Alus appear to d...@ Allan Miller:<br /><br /><i>Yes, a number of Alus appear to do something.</i><br /><br />Since we absolutely agree in this basic scientific conclusion, I do not think that there is an issue of "logic".<br /><br />Fact is that absolutely nobody can claim knowledge of the unknown; exactly what percent (properly rounded or not) will be the "final" result for newly found functionality in what formerly was non-genic, "therefore Junk". <br /><br />True scientists could do what makes sense: (1) continue on the new path of exploring function where - according to the old school - could not be any. (2) wanting to play a "numbers'game" do what Birney and Mattick did for fun (made a bet for a case of vintage champagne around a fictive magic number). <br /><br />(3) I am stepping into the direction of advancing genome informatics <b>how</b> whatever percent that is found at any given time functional could regulate the genome-epigenome system (yes, use fractal geometry for reasons showing that recursion used is best characterized as fractal iteration). <br /><br />I am not requiring anyone to follow my choice - though welcome all who sooner or later will. I am absolutely comfortable and happy for all doing choice 1. <br /><br />As for choice 2., I don't do it, because I don't like betting (I never liked Vegas and don't even like champagne). I don't mind at all if some do that - but would not call them scientists for that entertainment alone.<br /><br />So where do we (or our logic) disagree?Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7589011482535240442011-10-10T09:49:08.024-04:002011-10-10T09:49:08.024-04:00It is absolutely astonishing to see Pellionisz'...It is absolutely astonishing to see Pellionisz' citing abilities, next to his grasp of fact.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24143880039534427362011-10-10T08:25:20.608-04:002011-10-10T08:25:20.608-04:00Allan Miller wrote
My point is not that no Alus d...Allan Miller wrote<br /><br /><i>My point is not that no Alus do anything […] you have trouble with the distinctions between approximate quantities such as “some”, “many” or “all”.</i><br /><br />Pellionsz responded<br /><br /><i>“It is great that within three short years since The Principle of Recursive Genome Function we succeeded to eliminate the very issues of "Central Dogma" and"Junk DNA". <br /><br />As for Alus (the "junkiest of all junks") it is nice to agree to an agenda of finding out what (any percentage, rounded properly or not) is actually doing.”</i><br /><br />Your PhDs appear to have been obtained without a facility in basic logic.<br /><br /><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461783/pdf/11560904.pdf" rel="nofollow">Alu Insertion Polymorphisms for the Study of Human Genomic Diversity</a><br /><br />“The old Alu subfamilies (Sx, J, and Sg1), which comprise the vast majority (>1,000,000 copies) of the Alu elements present in the human genome, appear completely inactive as none of their members have been associated with de novo Alu inserts”<br /><br />Yes, a number of Alus appear to do something. But over a million Alu’s can’t jump, don’t jump, won’t jump. Half of those just there sit untouched in intergenic space, buried in heterochromatin; the consequence of historic infections, like smallpox scars or a polio limp. They are nonfunctional; they are ex-elements. They are junk.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70429273047868699392011-10-10T02:34:22.237-04:002011-10-10T02:34:22.237-04:00Anonymous said Aug. 26. (it is likely to be denied...Anonymous said Aug. 26. (it is likely to be denied that he was banned for this lucid message …):<br /><br /><i><b>Moran goes to great lengths to denigrate the integrity of the person…This is absolutely part of the Moran shtick and he does it again and again.</b></i><br /><br />Cabbagesofdoom concluded:<br /><i><b>I don't really care what "The Central Dogma" is. I care about the reality of biology...</b></i><br /><br />Allan Miller concluded:<br /><i><b>My point is not that no Alus do anything...</b></i><br /><br />Larry Moran: <br /><i><b>… some sort of message … is sinking in nicely.</b></i> <br /><br />I say: <br /><br /><i>From the 12,304 views of my <a href="http://www.youtube.com/watch?v=WJMFuc75V_w" rel="nofollow">YouTube</a> - (he would probably have to view it not three, but a dozen more times to barely start understanding informatics, lessons sank in for all): <br /><br />True scientists work hard all over the World towards an algorithmic (software enabling) understanding of hologenome regulation, to save millions, if not hundreds of millions from "Junk DNA diseases". <br /><br />Dogmas are swept to the side, to share the appropriate company of <b>The Flat Earth Society</b>.<br /><br />Detractors of breakthrough principles joke around, but are unable, even through 554 posts, to formulate any scientific argument pertaining to mathematics, as they admitted to their daughter's judgement (of inability to comprehend math). Instead, detractors engage in <b>ad hominem</b>-s, again and again.<br /><br /><b>Evolution is probably correct in natural selection. The DNA of the Central Dogmatist may well be 98.7% Junk.</b> <br /><br />Not so for the rest of us.</i>Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30714271054494049292011-10-09T08:32:09.190-04:002011-10-09T08:32:09.190-04:00Pellionisz says,
The peer-reviewed science paper ...Pellionisz says,<br /><br /><i>The peer-reviewed science paper of The Principle of Recursive Genome Function may be too difficult for some novices to understand fractals.<br /><br />However, the 12,296 views of the popular YouTube and so many gigabytes of downloads from my sites document that the message is sinking in nicely.</i><br /><br />I've viewed that video at least three times and I've sent many of my readers to the YouTube site [<a href="http://sandwalk.blogspot.com/2008/11/is-andras-pellionisz-kook.html" rel="nofollow">Is Andras Pellionisz a Kook?</a>].<br /><br />Those 12,296 views may not mean what you think they mean.<br /><br />On the other hand, you're probably correct to assume that some sort of message about you is sinking in nicely.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16635647971978028962011-10-09T08:12:28.686-04:002011-10-09T08:12:28.686-04:00Pellionisz said...
It is great that within three s...Pellionisz said...<br /><i>It is great that within three short years since The Principle of Recursive Genome Function we succeeded to eliminate the very issues of "Central Dogma" and"Junk DNA". </i><br /><br />Given that both the 'Central Dogma' and 'Junk DNA' are doing very well thank you, it seems if any eilimation was don, it was the Principle of Recursive Genome Function - that no one but Pellionisz has recognized as a principle.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82560914033979421192011-10-09T02:16:57.534-04:002011-10-09T02:16:57.534-04:00@ some no-name
It is absolutely astonishing to se...@ some no-name<br /><br /><b><i>It is absolutely astonishing to see Pellionisz' grasp of fact.</i></b><br /><br />The peer-reviewed science paper of <a href="http://ww.junkdna.com/pellionisz_principle_of_recursive_genome_function.pdf" rel="nofollow"><b>The Principle of Recursive Genome Function</b></a> may be too difficult for some novices to understand fractals. <br /><br />However, the 12,296 views of the popular <a href="http://www.youtube.com/watch?v=WJMFuc75V_w" rel="nofollow"><b>YouTube</b></a> and so many gigabytes of downloads from my sites document that the message is sinking in nicely. <br /><br />By the way, how many times was Gregor Mendel's seminal work cited in the first 35 years after publication? (The answer is 7).Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42547383727501431232011-10-08T05:24:56.505-04:002011-10-08T05:24:56.505-04:00Pellionisz said...
It is great that within three s...Pellionisz said...<br /><i>It is great that within three short years since The Principle of Recursive Genome Function we succeeded to eliminate the very issues of "Central Dogma" and"Junk DNA". </i><br />It is absolutely astonishing to see Pellionisz' grasp of fact.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30400054172734684712011-10-08T01:57:11.332-04:002011-10-08T01:57:11.332-04:00@Pellionisz: please explain what the (repetitive e...@Pellionisz: please explain what the (repetitive element) "fractal" adds to your last comment? It makes much more sense without using that word. (And also nicely sums up the efforts of bioscientists all over the world.)Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83307969465958765302011-10-07T21:19:43.167-04:002011-10-07T21:19:43.167-04:00@ Allan Miller
My point is not that no Alus do an...@ Allan Miller<br /><br /><i><b>My point is not that no Alus do anything</b></i><br /><br />It is great that within three short years since The Principle of Recursive Genome Function we succeeded to eliminate the very issues of "Central Dogma" <b>and</b>"Junk DNA". <br /><br />As for Alus (the "junkiest of all junks") it is nice to agree to an agenda of finding out what (any percentage, rounded properly or not) is actually doing. While Victoria needs no help for interpretation of their findings, I am happy that we are on the right course of looking at them (instead of overlooking them).<br /><br />I don't think the role of those "non-coding DNA" that are already found to be functional is a "numbers game" (but is a theory-game). I let you and Victoria to fight her thesis out.<br /><br />In my Cold Spring Harbor presentation (2009) I showed that the known "run" that causes Friedreich Spinoceebellar Ataxia (often a lethal disease) is in the middle of an intronic Alu-segment. The "run" is a fractal defect that disrupts regulation. <br /><br />Anyone should be free to publish their theoretical and factual arguments of what any part of a fractal genome is doing. Since it does not seem overly meaningful, you would not count the numbers of pixels with various colors in a Mandelbrot-set to arrive at Z=Z^2+C, would you?Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71759897125079840672011-10-06T05:37:28.358-04:002011-10-06T05:37:28.358-04:00Pellionisz
Missed this, but worth a belated comme...Pellionisz<br /><br />Missed this, but worth a belated comment:<br /><br /><i>As for Alus, read e.g. this fresh reference by V. Lunyak et al. Victoria (a Founding Member of the HoloGenomics Society) will be glad to mail a full .pdf upon request.</i><br /><br /><b>“Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal.”</b><br /><br />"Upregulation of Alu retrotransposon transcription upon ex vivo aging causes nuclear cytotoxicity associated with the formation of persistent DNA damage foci and loss of efficient DNA repair in pericentric chromatin.<br />[...]<br />“Our results demonstrate that the cytotoxicity of induced Alu repeats is functionally relevant for the human adult stem cell aging. Stable suppression of Alu transcription can reverse the senescent phenotype,”<br /><br />You are arguing that the function of Alu is to cause DNA damage? That is an eccentric reading of the term ‘function’ IMO. I should also note that the pericentromeric region referred to is a narrow part of the chromosome; Alus appear all over the place. I would suggest that the existence of an effect (a “function”, in a very broad reading of that word) does not explain more than a fraction of the 1.1 million Alus we possess. My point is not that no Alus do anything, but that most Alus do nothing. Like Creationists, you have trouble with the distinctions between approximate quantities such as “some”, “many” or “all”.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74785210648836309312011-09-30T03:42:15.161-04:002011-09-30T03:42:15.161-04:00Pellionisz said...
.. started to actually read ...Pellionisz said... <br /><i> .. started to actually read The Principle of Recursive Genome Function. </i><br />That article is irrelevant to the subject under discussion.<br /><br /><i> drop twisting the words ("reverse transcription") that Crick never said </i><br />Crick said the content: no reverse translation. He did not use the actual word, but to focus on that is nitpicking. AND: the Central Dogma is about reverse <b>translation</b>, NOT about reverse <b>transcription</b>. Pellionisz should pay attention. <br /><br />Pellionisz should do better to read, to READ and UNDERSTAND, what CabbagesofDoom writes. There is the real science of the subject. That is the reality of biology. Pellionisz has as yet to show he understands the reality of biology.<br /><br /><i>After over half-of-a-thousand blog entries, no-names and those yet to write their first Ph.D. thesis have .. </i><br />That is gratuitous offensiveness by Pellionisz. In a debate by blog comment it does not matter two hoots who anyone is or what academic grade one has. It is the quality of the argument and the knowledge shown that counts. Up to now, the quality of the argument or the knowledge shown is not with Pellionisz. Pellionisz seems not to have grasped the major findings of molecular biology. –DG and Cabbages-of-Doom do much better.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10462728919014548312011-09-30T03:24:24.059-04:002011-09-30T03:24:24.059-04:00@Pellionisz: Well, I am flattered that you treat m...@Pellionisz: Well, I am flattered that you treat my comments here with the same rigour, care and attention to detail as the scientific literature of the past 60 years. (Selective reading/quoting and failure to address many elephants in the room.)<br /><br />Bad news, though: reality is not determined by debate. You can play your funny word/quote games and redefine terms all you like but unless you can demonstrate some link to actual reality, no one will care. <br /><br />In fact, your treatment of The Central Dogma now makes me wonder whether your "recursive genome function" is actually something very old and simple but just called something else. Until you define it clearly, I guess we'll never know. (It certainly isn't fractal without some tremendous unusual definitions.)<br /><br />I'm off to use recursion (where appropriate) in my <i>programming</i>, but not (where inappropriate) in my genome function.I doubt that we will have much scientific communication, though, as you do not communicate science. References and links should be used to <i>support</i> your ideas and statements, not <i>replace</i> them.Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-951168550790534042011-09-29T19:26:56.516-04:002011-09-29T19:26:56.516-04:00I have a PhD in Genetics ... I program and make u...<i>I have a PhD in Genetics ... I program and make use of recursion. ... <b>I don't really care what "The Central Dogma" is.</b></i><br /><br />Great - the debate on dead-as-a-door-nail-"Central-Dogma" is finally over. Goodbye Central Nonsense!<br /><br />I look forward to looking up your papers utilizing recursion (presumably in relation to genome function). References and/or links (as I have provided) would help our scientific communication in regular means.Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61081954079167462822011-09-29T16:36:52.214-04:002011-09-29T16:36:52.214-04:00@Pellionisz: Sorry to disappoint you but I have a ...@Pellionisz: Sorry to disappoint you but I have a PhD in Genetics and a couple of dozen (rigorously) peer-reviewed publications under my belt. I have reviewed numerous papers and worked upstairs of the Shannon Institute - I use entropy and information theory in my own work and while, admittedly, not a mathematician, I understand what it is. I program and make use of recursion. None of this makes your paper or enigmatic references to fractals and recursion make any more sense.<br /><br />My PhD supervisor always told me that if someone with the appropriate background doesn't understand your paper then you, as author, have to take the lion's share of the blame. Papers are about communicating effectively. If no one understands what your point is, this suggests that you need to explain it clearer. The way to explain it clearer is not by repeating/quoting the same sentences that people took issue with in the first place.<br /><br />To be honest, I don't really care what "The Central Dogma" is. I care about the reality of biology. Does reverse translation happen? No. Do proteins regulate gene expression and chromosome structure? Yes. Does signalling "information" pass from protein to protein and protein to nucleotide? Yes. Does this take the form of sequence information? No. Is all non-coding DNA "junk"? No. Is all "junk" DNA functionless? No. Is a large fraction of the average eukaryotic genome still functionless "junk", as far as we can tell? Yes. Is any of this particularly new or controversial? No. Does any of it lead to the conclusion that the genome is fractal or recursive? Explain what this means, with biological examples if possible, and perhaps we can decide. <br /><br />My instinct based on everything I know about gene regulation, cell signalling and recursion, is "no". (Unless by recursion you mean self-replication, which is recursive in some sense.) The onus is on you to convince us otherwise. It is not our responsibility to try and make your game-changing theory make sense. Currently, your theory opens up no new perspectives because no one cares because it makes no sense. It's just words. If you really thought there was something in it, you would spend much more time trying to explain its evidence and ramifications and much less time insulting the academic credentials of those who disagree with you and/or don't understand your proposal.Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73415691345333062632011-09-29T15:34:21.931-04:002011-09-29T15:34:21.931-04:00Pellionisz: There are direct quotes in your own pa...Pellionisz: There are direct quotes in your own paper where "sequence to sequence information" is specified. Not "Information" in the sense of Shannon and other Information Theoreticians. So why do you keep twisting it around in order to try and show that Protein-DNA interactions violate that very specific definition for information transfer. <br /><br />BTW, good job denigrating people at different parts of their academic career tracks as if they have nothing worthwhile to add to the discussion. Man am I glad none of the senior professors who I feel privileged counting as mentors to me ever talked that way.<br /><br />Instead they hold up the work of their trainees (or the trainees of others whom they work with) as examples ans foster our intellectual development. And many of them are scientists who have "cut against the grain of conventional scientific wisdom" without falling into kook territory.-DGhttps://www.blogger.com/profile/16018033631187602248noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28099612488567209782011-09-29T15:06:18.918-04:002011-09-29T15:06:18.918-04:00After over half-of-a-thousand blog entries, no-nam...<b>After</b> over half-of-a-thousand blog entries, no-names and those yet to write their first Ph.D. thesis have started to actually <b>read</b> <a href="http://ww.junkdna.com/pellionisz_principle_of_recursive_genome_function.pdf" rel="nofollow">The Principle of Recursive Genome Function</a>. (How could they quote the paper if they have not read it till now - let alone never wrote a paper of their own?)<br /><br />By admission it is clear that the algorithm of fractal iterative recursion is yet to be understood (but the current emerging generation will soon claim that "everybody - especially them - always thought that the genome was fractal").<br /><br />For now, some decency will suffice "not to bite my finger, but look where I am pointing", drop twisting the words ("reverse transcription") that Crick never said (yes, he could have thought about a myriads of things but they don't matter if he elected to put out dogma instead of definition). <br /><br />For the select few who wonder "how to put it all together" go back to study Schrodinger and Shannon to learn what "information" was for them, how Crick could never master math (though he was a physicist...) - and work Genome Informatics as it is meaningful for us, half a Century later.<br /><br />"Papering over" the paradigm-shifts Crick and Collins (originators of Central Dogma and ENCODE) themselves declared, will not work. Read again <b>their</b> statements (that I quote in my Principle paper for The Central Dogma and ENCODE, respectively):<br /><br /><b><i>If it were shown that information could flow from proteins to nucleic acids, he said, then such a finding would “shake the whole intellectual basis of molecular biology” (17, p. 563). (Quote from Darden 63, emphasis added AJP)</i><br /><br /><i>Upon publication of the results of project ENCODE, a four year research effort led by the US Government, its architect issued a mandate: “the scientific community will need to rethink some long-held views”</i></b>.<br /><br />They issued the mandate - I am just following up on their unfulfilled rhetoric. The better part of your generation will shore up - "Junk DNA" and "Central Dogma" relics will soon fetch a yawn (5, not 500+ entries) in view of the perspectives opened up by fractal recursive algorithms of genome function.Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39615352305479535372011-09-29T09:42:41.033-04:002011-09-29T09:42:41.033-04:00I too spent time reading the posted paper, and add...I too spent time reading the posted paper, and add me to cabbageofdoom and heleen's comments.<br /><br />The paper provided lots of historical references, but failed to interpret them properly much of the time. Including paragraphs that were directly quoted. It was abundantly clear, that the information flow referred to, time and again, was sequence-to-sequence information. Not "information" in a more general mathematical usage.<br /><br />It's all never terribly clear at any point, unless I missed some sort of succinct explanation at the end of the paper, what exactly this fractal, recursive genomics theory actually IS, why it is different, and what it offers. There appears to be a hell of a lot of excess verbiage and dense mathematical discussion that never seems to really describe much of anything, at least not in a clear and concise manner.<br /><br />Colour me shocked as well that the paper is published in a journal for which most of the article is incredibly off topic (except that an analogy of neural growth is shoehorned in) and that the paper went from being received to accepted in about a week.<br /><br />Obviously thorough and appropriate peer-review was lacking...<br /><br />As for Post-ENCODE genomics, bunch of bullshit. There is a hell of a lot of evidence, discussed on this blog and elsewhere, that much of ENCODE's findings were a)overhyped and b)artefactual. Direct RNA-Seq based experiments are much better suited to asking the sorts of questions ENCODE wanted to ask, and don't show the same pattern of global transcription and activity of the human genome.-DGhttps://www.blogger.com/profile/16018033631187602248noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56179874180186343272011-09-29T07:10:54.081-04:002011-09-29T07:10:54.081-04:00@Pellionisz: Sorry. Just spotted a major typo in m...@Pellionisz: Sorry. Just spotted a major typo in my last comment...<br /><br />> No one would argue that "information", when not restricted to sequence information, flows from nucleotide to protein AND protein to nucleotide.<br /><br />This should, of course, be that no one would argue that this bi-directional flow of (non-sequence) information does NOT happen! (I think this was clear from the context but sorry for any confusion.)Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60904774483442220862011-09-29T05:03:27.821-04:002011-09-29T05:03:27.821-04:00It is extremely surprising that Pellionisz (despit...It is extremely surprising that Pellionisz (despite multiple degreed) is not able to distinguish molecular and chemical fact from spun out fiction.<br /><br />None of the comments Pellionisz made have anything to do with the central point first explicitly made by Crick: reverse translation has never been observed.<br /><br />It has already been explained to Pellionisz that his insistence Crick did not use the term 'reverse translation' is nothing but nitpicking, denying the obvious content of Crick's remarks. Crick referred to molecular processes, not to information in any mathematical sense. This is clear to about everyone but Pellionisz.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79977178388475728012011-09-28T17:25:42.108-04:002011-09-28T17:25:42.108-04:00@Pellionisz: I've just read your article. I mu...@Pellionisz: I've just read your article. I must confess that I don't really get your point. It seems to be largely attacking very old ideas, whether they are the correct definition of "the central dogma" or "junk DNA" or not. Irrespective of definitions, no one would argue that proteins do not influence gene expression (and replication) nor that *all* non-coding DNA is "junk".<br /><br />No one would argue that "information", when not restricted to sequence information, flows from nucleotide to protein AND protein to nucleotide. Transcription factors and the histone regulation are not new concepts nor controversial ones. More importantly, they pre-date the ENCODE project.<br /><br />In your article you keep referring to "pre-ENCODE" versus post-ENCODE (or even "PostGenetics"?!) - can you please explain what discovery of the ENCODE project is so game-changing and how this relates to Recursive Genomics? Is it simply that much more non-coding DNA appears to be expressed than we thought? (Assuming it is not an artefact.) <br /><br />Ironically, the biggest revolution of recent times, exemplified by ENCODE, is nothing to do with "Central Dogma" violations of protein -> nucleotide. It is the recognition that RNA does a lot more gene regulation functions (miRNA etc.) that were previously assumed to be performed <i>by proteins</i>. This might increase the nucleotide -> nucleotide information transfer - and definitely decreases the amount of functionless junk by a small amount - by I don't get how it leads to conclusions of a "fractal genome".<br /><br />It is also worth remembering that there is always DNA, RNA *and* protein (and lipids and other metabolites) in any cell, so any linear flow of information is meaningless, unless restricted to the specific flow of <i>sequence</i> information (replication, transcription and translation).Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15771226484508870892011-09-28T14:03:04.047-04:002011-09-28T14:03:04.047-04:00It is extremely surprising that Pellionisz (despit...<i>It is extremely surprising that Pellionisz (despite multiple degreed) is not able to distinguish molecular and chemical fact from spun out fiction.<br /><br />None of the comments Pellionisz made have anything to do with the central point first explicitly made by Crick: reverse translation has never been observed.</i><br /><br />For a "no name" ignorance is not surprising at all that Crick entitled his (admittedly unsupported) fiction "Central Dogma of <b> Molecular Biology</b>" - and he never wrote explicitly about <i><b>"reverse translation"</b></i>. Crick referred to "sequence information". The irony is, that Crick was a physicist, thus familiar with Shannon's Information Theory - but suspected that there may be more to "sequence information" beyond the 2-bit string of A,C,T,G bases. (Crick's knowledge on methylation and chromatin modification, impacting "access to sequence information" was understandably immature.) <br /><br />In his 1970 “correction” his Fig. 1. “arrows show all the possible simple transfers…” but just above his “reduced” Fig. 2. he says “Now if all possible transfers commonly occurred it would have been almost impossible to construct useful theories. Nevertheless, such theories were part of our everyday discussions. This was because it was tacitly assumed that certain transfers could not occur. It occurred to me that it would be wise to state these preconceptions explicitly.”<br /><br />What appeared to Crick half a Century ago as a “good idea” (to stiffle by pontification possible theories) is now plainly untenable. A leader said lately “our concepts of genome regulation are frighteningly unsophisticated”. It is imperative that unsupported preconceptions are superseded after half a Century delay by <a href="http://ww.junkdna.com/pellionisz_principle_of_recursive_genome_function.pdf" rel="nofollow"><b>The Principle of Recursive Genome Function</b></a>.Pellionisznoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20732929164302048932011-09-28T04:38:14.602-04:002011-09-28T04:38:14.602-04:00It is extremely surprising that Pellionisz (despit...It is extremely surprising that Pellionisz (despite multiple degreed) is not able to distinguish molecular and chemical fact from spun out fiction.<br /><br />None of the comments Pellionisz made have anything to do with the central point first explicitly made by Crick: reverse translation has never been observed.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.com