tag:blogger.com,1999:blog-37148773.post6213648283787033300..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The fuzzy thinking of John Parrington: pervasive transcription Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger26125tag:blogger.com,1999:blog-37148773.post-74108452135135741282015-07-22T08:23:41.588-04:002015-07-22T08:23:41.588-04:00Telomeres are not junk.
See: What's in Your ...Telomeres are not junk. <br /><br />See: <a href="http://sandwalk.blogspot.ca/2011/05/whats-in-your-genome.html" rel="nofollow">What's in Your Genome?</a>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-92096319534490010352015-07-22T05:41:38.986-04:002015-07-22T05:41:38.986-04:00I'm confused....
Is Skeptical Mind's stat...I'm confused....<br /><br />Is Skeptical Mind's statement about junk DNA and telomeres true at least regarding aging? I think it is....<br /><br />Knockouts showed that the telomere length shortens much faster drastically affecting the lifespan of mice.....<br /><br />I personally don't believe junk DNA used to be responsible for immortality.... as the Bible talks about the "tree of life" being a source of everlasting life whatever that tree represented.... but who knows....Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41526934507835646092015-07-22T00:03:27.180-04:002015-07-22T00:03:27.180-04:00We have gone over this many times in the past. Why...We have gone over this many times in the past. Why do we have to do it again?<br /><br />The worst part about the fact that creationists are trying to use ENCODE to disprove junk DNA is not that ENCODE data does not do that, it is that the arguments for most of the genome being junk do not even require evolution to be true. Originally, the idea appeared because a back-of-the-envelope calculation shows that for such a genome size and such a mutation rate, if all of it is functional, we would basically not exist. That argument is just as valid under a model in which we were specially created 6000 years ago and have absolutely no phylogenetic relationship to other organisms as it is under the evolutionary model of modern science. Sure, it makes a lot more sense in the light of evolution, but so does all of biology. Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15688715802695213182015-07-21T23:47:23.035-04:002015-07-21T23:47:23.035-04:00Thank you for replying, Dr. Moran.
I didn't s...Thank you for replying, Dr. Moran.<br /><br />I didn't say junk DNA had function. I already said in another thread I agree with you there could be junk DNA and that ID theory didn't predict junk DNA is functional. I was pointing out it certainly is premature to say it doesn't. <br /><br />Evolutionary theory is to ambiguous to be used as a guide for the physiology and function of DNA. The fact that this is a disagreement between ENCODE evolutionists and Graurists is evidence of the ambiguity.<br /><br />Thanks for your response.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59460610693317853902015-07-21T14:28:34.154-04:002015-07-21T14:28:34.154-04:00Beau asks: Do you have a problem with believers in...Beau asks: <i>Do you have a problem with believers in general or just those who fight science?</i><br /><br />I don't think it matters, but I have a problem with believers who fight science, or who want to use taxpayer money to violate church/state separation, or those who say they've got evidence of God's existence and the evidence is a joke, or who take a cavalier/whitewash attitude toward genocides in the Bible, Confederate slavery in the US, etc. <br /><br />In short, politicized applied conservative religion I have a problem with. <br /><br />Beyond that, all of us have religious family members and we have to get along.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51314840494136118142015-07-21T13:33:25.061-04:002015-07-21T13:33:25.061-04:00Dr. Moran, I should have waited longer to respond ...Dr. Moran, I should have waited longer to respond to Liarsfordarwin. You said what I tried to say, but better. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21215876579815263372015-07-21T13:04:25.190-04:002015-07-21T13:04:25.190-04:00To me, this is a question about where the burden o...To me, this is a question about where the burden of proof lies. One can't prove that an RNA transcript is useless. As Liarsfordarwin demonstrates, one can always imagine some more subtle function that a transcript might perform. However, one can prove (as well as anything in science is proved - let's not quibble) that an RNA transcript does perform a function. I think that the burden of proof lies on those who think all transcripts have useful functions.<br /><br />I do think that there is good evidence that "all RNA transcripts have useful functions" should not be the default position. When very sensitive tests are run, RNA transcripts are found for most of the DNA -- but most occur at a frequency of less than one transcript per cell. It's hard to see how those RNAs could do anything useful. <br /><br />Some of the reasons to think some transcripts are non-functional are the same reasons we think some DNA is junk. Surely the default assumption about RNA transcripts formed from the viruses that make up 8% of our DNA should be that the transcripts are useless to us (unless proved otherwise, as at least one has been). If mice seem to do well with 3% of their DNA removed, surely the burden of proof lies with those who want to argue that any RNA transcripts made from that 3% of DNA are functional. <br /><br />We have a great deal to learn about the function and lack of function of RNA transcripts. Starting from the assumption that they're all functional (often in really subtle ways) would be as foolish as working from the assumption that none of them are. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42289875910684979232015-07-21T12:55:50.040-04:002015-07-21T12:55:50.040-04:00How do biochemists actually know RNA transcripts a...<i>How do biochemists actually know RNA transcripts are non-functional? How many GWAS, RNA-Seq, ChIRP-seq, Chip-Seq, etc. experiments on the quadrillion transcriptomes would be adequate to establish non-function?</i><br /><br />Throwing fancy terms around without really understanding what they mean usually leads to self-embarrassment, not to successfully making your point. Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44301406842178663982015-07-21T12:51:50.544-04:002015-07-21T12:51:50.544-04:00"liarsfordarwin" lives up to his name in..."liarsfordarwin" lives up to his name in a comment where he asks,<br /><br /><i>How do biochemists actually know RNA transcripts are non-functional?</i><br /><br />We don't. But since spurious, nonfunctional, transcripts are expected by everyone who understands biochemistry, the onus is on the true believers to prove that transcripts are functional. <br /><br /><i>How many GWAS, RNA-Seq, ChIRP-seq, Chip-Seq, etc. experiments on the quadrillion transcriptomes would be adequate to establish non-function?</i><br /><br />None. Those techniques identify transcripts that are potentially functional but most likely are not. It's up to real biochemists to do the dirty work and figure out which ones really have a significant biological function. Most genomics labs would rather just skip the dirty work and claim that they've revolutionized biology by applying those techniques to entire genomes. <br /><br />They don't even realize how silly they look when they make unwarranted conclusions based on whole genome analyses. <br /><br /><i>Many functions, such as those involved in recovery from injury, are not detected unless the back up nature of this redundancy is called upon. </i><br /><br />See what I mean?<br /><br /><i> It's just prejudice against the idea of deep integrated functionality in biological systems. And prejudice is not experiment and observation.</i><br /><br />The belief in "deep integrated functionality" is not only a prejudice, it's a really stupid prejudice because it flies in the face of all we know about biochemistry and evolution. <br /><br />It's people like you who are claiming a vast amount of function based entirely on the unsubstantiated belief that if it's detectable, it must have a function. That's not experiment and observation; it's a conclusion. It's not science. <br />Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9289674265222070012015-07-21T11:26:53.384-04:002015-07-21T11:26:53.384-04:00Speaking of only 30,000 genes, they are part of ge...Speaking of only 30,000 genes, they are part of generating possibly billions or trillions or more protein isoforms and glycoforms produced from a quadrillion transcriptomes. Plenty of room for RNAs to do work in coordinating all these buzzillion isoforms. We haven't even scratched the surface with RNA-seq experiments, but papers are coming out on the role of RNAs in isoform creation and cellular differentiation. The field of RNA interactomes has just barely gotten off the ground. What may look like noise to Graur looks like interactome machinery to ChIRP-SEQuencers.<br /><br />How do biochemists actually know RNA transcripts are non-functional? How many GWAS, RNA-Seq, ChIRP-seq, Chip-Seq, etc. experiments on the quadrillion transcriptomes would be adequate to establish non-function? Many functions, such as those involved in recovery from injury, are not detected unless the back up nature of this redundancy is called upon. <br /><br />How do you distinguish spare tires from junk without all these requisite experiments? Even recently we found quadruplex DNA may have functional role. Example: miles and miles of repeated TTAGGG the are often incorporated in nuclear only telomeric repeat-containing RNA (TERRA), and these repeats have biophysical function in preventing error.<br /><br />Steve Matheson kept saying many RNAs don't even leave the nuclear complex. Did it occur to him then that maybe these RNAs are used to do something that's done in the nuclear complex alone, like creating and regulating part of the manufacture of ribosomes? It's to early to tell what these RNAs do. Simply saying they have no function because people like Matheson and Graur don't perceive the function is not a basis for declaring there is no function. It's just prejudice against the idea of deep integrated functionality in biological systems. And prejudice is not experiment and observation.<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54940116333419523862015-07-21T08:42:21.161-04:002015-07-21T08:42:21.161-04:00Hey Beau - Yes.Hey Beau - Yes.steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49533942721130107212015-07-20T22:56:17.844-04:002015-07-20T22:56:17.844-04:00Diogenes may I ask you a question? Do you have a p...Diogenes may I ask you a question? Do you have a problem with believers in general or just those who fight science? I'm starting to understand your frustration a bit more and I'm a believer. It seems many religious people have created a battle that isn't really necessary or likely winnable. Beau Stoddardhttps://www.blogger.com/profile/03617924374387662273noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83281841410978728062015-07-20T21:13:26.275-04:002015-07-20T21:13:26.275-04:00How would you know this, without assuming religiou...How would you know this, without assuming religious beliefs?<br /><br /> As I've argued over and over, ID can only make testable predictions if it admits its religious beliefs about the purposes of God.<br /><br />Consider another ID "theory": junk DNA, at an unspecified time in the past, used to make our lives *shorter*. That was the Designer's purpose. Then mutations disabled this function, so we live longer now.<br /><br />How is this ID theory worse than your ID theory? How do they differ? Different assumptions about God's purposes.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5579540384343947462015-07-20T17:43:32.888-04:002015-07-20T17:43:32.888-04:00No, I've been through it with a fine-tooth com...No, I've been through it with a fine-tooth comb and it's absolutely watertight. We will remember this day. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57951429386050042122015-07-20T17:05:17.680-04:002015-07-20T17:05:17.680-04:00What the hell is this complete void-skull even try...<i>What the hell is this complete void-skull even trying to say?</i><br /><br />He's trying to claim that junk DNA, before it was inactivated by mutations beginning after the Fall, made people immortal or at least very long-lived, e.g. Methuselah. And thus we conclude Jesus.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85526976538603445832015-07-20T16:56:26.654-04:002015-07-20T16:56:26.654-04:00"The so called jDNA controls telomere length ...<i>"The so called jDNA controls telomere length that serves as a molecular clock that helps controlling aging. Here is one clue as to how jDNA could have been responsible for influencing immortality."</i><br /><br />What the hell is this complete void-skull even trying to say? Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40040526165706150112015-07-20T14:21:17.017-04:002015-07-20T14:21:17.017-04:00Here is one clue as to how jDNA could have been re...<i>Here is one clue as to how jDNA could have been responsible for influencing immortality.</i><br /><br />Right, so since "junk DNA" is actually good for something, that's why we're immortal...oh, wait.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27223342226522477992015-07-20T12:45:48.132-04:002015-07-20T12:45:48.132-04:00You never get tired of displaying your ignorant st...You never get tired of displaying your ignorant stupidity in unambiguous terms.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14287763316712041842015-07-20T11:13:54.286-04:002015-07-20T11:13:54.286-04:00The Wikipedia entry is very poorly written, unfort...The Wikipedia entry is very poorly written, unfortunately. And there is no English translation of the movie I am aware of (the movie itself is on YouTube in its entirety). But the parallels are striking - the way facts and interpretations get embellished as they travel through the chain of transmission, the institutional and sociological factors that drive it, everything....Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17309055915045928782015-07-20T11:02:15.186-04:002015-07-20T11:02:15.186-04:00The so called jDNA controls telomere length that s...The so called jDNA controls telomere length that serves as a molecular clock that helps controlling aging. Here is one clue as to how jDNA could have been responsible for influencing immortality. Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42447697717725502632015-07-20T10:36:12.098-04:002015-07-20T10:36:12.098-04:00Thanks Georgi, that was an interesting read. My b...Thanks Georgi, that was an interesting read. My brother's partner is Bulgarian, will have to ask him if he's familiar with it.<br /><br />It appears that a lot of <b>junk DNA</b> writing is indeed <b>junk</b> DNA writing.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71780779776281905702015-07-20T07:49:15.095-04:002015-07-20T07:49:15.095-04:00This passage illustrates my difficulty in coming t...<i>This passage illustrates my difficulty in coming to grips with Parrington's logic in The Deeper genome.</i><br /><br />Tedious is right. This is a good example of the author being "not even wrong". Functional RNAs do not violate the Central Dogma, nor even the common misinterpretation of the Central Dogma (the Sequence Hypothesis).SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59632181852737496662015-07-19T23:53:19.534-04:002015-07-19T23:53:19.534-04:00What do you expect from a blog post headed by a pi...What do you expect from a blog post headed by a picture which displays left-handed DNA in a human head? Seemingly, the likely original further down the page contains a right-handed molecule and they just carelessly mirrored it.SPARChttps://www.blogger.com/profile/09563722742249547887noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71315012234704383032015-07-19T22:40:31.824-04:002015-07-19T22:40:31.824-04:00Wow that's bad. You'll love this piece, fr...Wow that's bad. You'll love this piece, from the same guy. Note that he suggests that RNA is transmitted from the brain to sperm, but the study he links doesn't say that at all. Maybe he's just generally sloppy.<br /><br />http://blog.oup.com/2015/05/the-genetics-of-consciousness/<br /><br />I would have thought Oxford University Press would do better...NickMhttps://www.blogger.com/profile/04765417807335152285noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62755284363425022572015-07-19T21:53:25.470-04:002015-07-19T21:53:25.470-04:00The study [ENCODE] also found that 80 per cent of ...<i>The study [ENCODE] also found that 80 per cent of the genome was generating RNA transcripts having importance, many were found only in specific cellular compartments, indicating that they have fixed addresses where they operate. Surely there could hardly be a greater divergence from Crick's central dogma than this demonstration that RNAs were produced in far greater numbers across the genome than could be expected if they were <b>simply intermediates between DNA and protein</b>.</i><br /><br />Wait, wha, wait-- hold the phone!! You mean to tell me that RNA transcripts are *NOT* just intermediates between DNA and protein?<br /><br />Jesus Christ in a cheerleader uniform! This completely changes the science of 1954!<br /><br /><a href="https://youtu.be/wxlhyX-4qKI" rel="nofollow"><br />https://youtu.be/wxlhyX-4qKI</a><br /><br />Call Doctor Who! Or make me a Tardis. We must alert the media of 1954!Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.com