tag:blogger.com,1999:blog-37148773.post5297897292872952894..comments2024-03-18T09:58:09.828-04:00Comments on <center>Sandwalk</center>: John Mattick vs. Jonathan WellsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger42125tag:blogger.com,1999:blog-37148773.post-9237797580151777412013-08-31T04:40:08.539-04:002013-08-31T04:40:08.539-04:00My error - comments not allowed. Sorry.My error - comments not allowed. Sorry.Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20835584842301408532013-08-31T04:10:24.936-04:002013-08-31T04:10:24.936-04:00http://www.youtube.com/watch?v=ItYAjrVNpM8
Recent...http://www.youtube.com/watch?v=ItYAjrVNpM8<br /><br />Recently added - the lecture is also up on Soundcloud however the youtube location allows comments so this is the place to go for Larry (and others) to let Mattick know how you dispute what he says. The lecture itself was delivered 5 weeks ago.<br /><br />Alternative:<br />https://soundcloud.com/#ansto-1/prof-john-mattick-most<br /><br />As I have said previously I don't endorse these views, I just enjoy the cut and thrust. And the idea that progress could come from it.Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1400998517950306332013-08-28T14:42:53.789-04:002013-08-28T14:42:53.789-04:00@Piotr
I share your perspective. It's too earl...@Piotr<br />I share your perspective. It's too early for complete accord, and theories of how the genome got to where it is now are views to be debated, but all well-informed scientists see that we have junk DNA in some proportion - even Shapiro. I do think it funny, the two sides seeing each other as being not just wrong, but dead wrong. No quarter being given!<br />(Very wrong, however, are the ideologues who crave a genome that is completely functional ... for reasons unconnected to evidence or scientific analysis). Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34129836104069600622013-08-28T08:54:02.995-04:002013-08-28T08:54:02.995-04:00@Rkt
Proclaiming most DNA is squatting, doing very...@Rkt<br /><i>Proclaiming most DNA is squatting, doing very little (or nothing) - and that this is settled science - is fine up to a point. Majority view. It's honestly stated too. It is not a great selling-point if you then seek to do research on it and need to be funded, that's the question I asked.</i><br /><br />I'm not a researcher, but I don't see why a funding committee would have any trouble with a statement that is simply accurate, along the lines of: "While there is considerable evidence that much, and probably most, of the human genome if functionless 'junk', there remains significant portions which may serve a function, even though that function is not yet understood. Our study will evaluate one such sequence, which we hypothesize may have the following function...."<br /><br />That the concept of Junk DNA has stifled research of non-coding DNA is a common creationist claim, which has been comprehensively debunked by T. Ryan Gregory:<br /><br />http://www.genomicron.evolverzone.com/2009/12/the-junk-dna-myth-or-lack-thereof-explained-one-more-time/Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68717603538106701922013-08-28T08:33:15.532-04:002013-08-28T08:33:15.532-04:00"... the vast majority of genomic DNA, includ...<i>"... the vast majority of genomic DNA, including many so-called "non-coding" (nc) segments, participate in biologically specific molecular interactions... "</i><br /><br />No matter how you select "the vast majority of genomic DNA", it will necessarily include mostly non-coding sequences. Nobody denies that a lot of non-coding DNA is functional, but it doesn't add up to anything like a majority.<br /><br /><i>This stuff can't be wished away. How _do_ you convince smart people like Mattick and Shapiro who must have heard all the junk-DNA arguments before?</i><br /><br />Is the purpose of science to convince everyone? There will always be dissenters, and there's nothing wrong with that. It's a healthy thing if mainstream views are constantly challenged. BTW, isn't the burden of the proof on those who claim that most of the genome is functional? If so, it's up to them to come up with something really convincing.Piotr GÄ…siorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1221059422075480022013-08-28T06:41:08.176-04:002013-08-28T06:41:08.176-04:00""The only place you will find 'a gr...""The only place you will find 'a growing number' of creationists is in the cemetery."<br /><br />That's a good one. I'll be sure to quote it sometime, with appropriate credits.Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42438509007335544652013-08-28T05:44:39.235-04:002013-08-28T05:44:39.235-04:00For comparison here's a paper in which James S... For comparison here's a paper in which James Shapiro makes similarly confident assertions (his blog at HuffP has been dormant for almost five months but I guess he will restart it once this appears in print): http://shapiro.bsd.uchicago.edu/Shapiro.2013.How%20Life%20Changes%20Itself%20The%20Read-write%20(RW)%20Genome.Physics%20of%20Life%20Reviews.pdf<br /><br />Has he gone any further in this paper than previously?<br />One JS quote: "As we are learning from the ENCODE project data, the vast majority of genomic DNA, including many so-called "non-coding" (nc) segments, participate in biologically specific molecular interactions [11]. Moreover, the term "gene" is a theoretical construct whose functional properties and physical structure have never been possible to define rigorously. It is telling that genome sequence annotators used to call protein-coding regions (chiefly in prokaryotic DNA) "genes," but now use the more neutral terms CDS, for "coding sequence".<br /> <br />This stuff can't be wished away. How _do_ you convince smart people like Mattick and Shapiro who must have heard all the junk-DNA arguments before?<br /> Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56016240108176137052013-08-27T18:29:29.285-04:002013-08-27T18:29:29.285-04:00@Georgi
You reversed my meaning. Proclaiming most ...@Georgi<br />You reversed my meaning. Proclaiming most DNA is squatting, doing very little (or nothing) - and that this is settled science - is fine up to a point. Majority view. It's honestly stated too. It is not a great selling-point if you then seek to do research on it and need to be funded, that's the question I asked. Birney and co. seem to have had their eyes open to this issue (was he less than honest in his interviews; but at the same time, was he just 'pragmatic'?). Politics.Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28781078293257058532013-08-27T17:11:29.416-04:002013-08-27T17:11:29.416-04:00They've been at it a lot longer than the 1960&...They've been at it a lot longer than the 1960's.<br /><br />http://answersinscience.org/demise.htmlTheOtherJimhttps://www.blogger.com/profile/01727633779107067250noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77349581408483432262013-08-27T15:57:19.265-04:002013-08-27T15:57:19.265-04:001. ENCODE as a whole has not expressed a contrary ...1. ENCODE as a whole has not expressed a contrary view to the one that the most of the genome is junk<br /><br />2. The statement that more work will be supported if the dominant view is that most of the genome is junk is false. Then the funding agencies can just say "Well, if it's junk there is no point studying it". If most of it is functional, then it's a different situation. <br /><br />You seem to be under the impression that ENCODE has not only shown that most of the genome is functional but it has also found out what that function is. Neither is correct.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76220501066807767642013-08-27T15:33:01.836-04:002013-08-27T15:33:01.836-04:00One point I made which needs adding to: when high ...One point I made which needs adding to: when high profile biochemists are convinced a lot of DNA is junk, and keep saying so, is not great for attracting funding to study it! When ENCODE - and scientists like Mattick - express a contrary view, this is both bad and also good at the same time. Yes they show lack of regard for the mainstream view (and the lines of evidence lying behind it) which is bad, and falsely suggest splits exist between scientists - also bad. Yet, by emphasising that more research is vital to bring out more function than is known at present (even if they are overselling the notion to an absurd degree), it will do no harm to the cause of those looking for funding, will it? More work will get supported than if ENCODE had endorsed a view that only 20% was functional, instead of the reverse.<br />Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40763297289813089812013-08-27T14:30:54.825-04:002013-08-27T14:30:54.825-04:00Most obvious difference is Wells' contempt for...Most obvious difference is Wells' contempt for people of the contrary view to his, including the way he repeatedly misrepresents the history - as if he's the smart one who is attempting to end decades of error, waking up foolish biochemists driven by 'ideology' to want to find an abundance of junk DNA. Second, he is deceitful: he leads his readers to believe that he has good guesses as to what all the enigmatic parts of the genome might be doing; Mattick is more content to say it's a real mystery and time will tell. Third, I suppose it could be said that Mattick could reconsider (and certainly will, if the evidence plainly shows he is mistaken - I know, straight away your reply will be that the game is up already - he clearly thinks otherwise). Wells is like a broken record and will never, ever alter what he thinks (or, what he _claims_ to think! I understand very well the view that the guy is dishonest and he is quite capable of saying stuff he knows has previously been refuted, just to keep the audience he holds already and discourage them from listening to other voices).<br />Is that enough? Do either of them have any kind of answer to the onion test - I really don't think so but I have studied this very little - I'm not a working scientist. I would be interested to read something by Mattick that addresses this, if anyone has found some written material (or another podcast, or lecture)? <br />I thought the above podcast was very interesting indeed. I sense the guy is guile-less (I could be wrong). He strongly believes all of it. (Nor do I even sense he saying stuff to improve funding prospects, for cynical motives). He has real hopes for medical advances coming out of better understanding of non-coding DNA. It could be argued that a scientist if his persuasion is likely to stumble onto something neat, at least as likely as another group who thinks their time should be spent on a sub-set of the DNA where genes (in the traditional sense) are found.<br /><br />I must add, finally, I'm more inclined towards your interpretation Larry. Makes better sense. In time, John Mattick is likely to be disappointed.<br />Mattick has less of a 'hypothesis' than Wells does, adopting the approach that much remains to be found out.<br />Wells is not a scientist at all and I am not convinced that he is doing 'science' at all. You will think I am mistaken - but that's my view.<br />(Enigmatic DNA: any chance the term will take off? Blame Birney).<br />Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72596703388368441352013-08-27T13:26:48.069-04:002013-08-27T13:26:48.069-04:00Do you agree that there's very little differen...Do you agree that there's very little difference between the arguments used by John Mattick and those usedby Jonathan Wells?<br /><br />If Mattick's hypothesis is an example of good science then so is Wells' hypothesis. Right?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45112612146027276522013-08-27T11:27:11.338-04:002013-08-27T11:27:11.338-04:00@Larry Moran
It's a touch harsh to compare th...@Larry Moran<br /><br />It's a touch harsh to compare these two (okay, very harsh).<br />Mattick might be three-shades-of-wrong but he has worked for decades in actively doing real science.<br />He also engages in debate - if you really think he avoids the debate, try this podcast (in which IMHO he can't be mistaken for a kook):<br /><br />https://itunes.apple.com/gb/podcast/john-mattick-molecular-biologist/id322054392?i=113263226&mt=2<br /><br />It's from December.<br />The interviewer does what he can with the very limited time available<br />(i.e. not sufficient).<br />Rkthttps://www.blogger.com/profile/14537319324895152785noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76596768304367883462013-08-27T05:09:58.551-04:002013-08-27T05:09:58.551-04:00The big issue from the ENCODE data dump has to do ...The big issue from the ENCODE data dump has to do with the definition of "function". If "being transcribed" is your standard, well that's pretty low.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7188267045393086912013-08-27T01:08:15.999-04:002013-08-27T01:08:15.999-04:00It seems that Dr. Egnor has picked up the old crea...It seems that Dr. Egnor has picked up the old creationist line about "an increasing number of scientists abandoning evolution". As Diogenes has <a href="http://lampofdiogenes.wordpress.com/2013/04/01/97/" rel="nofollow">documented</a>, creationists have been preaching about the imminent death of evolutionary theory since the 1960s. But the reality is, as Diogenes put it: "The only place you will find 'a growing number' of creationists is in the cemetery." And that's as true as it gets.<br />unhttps://www.blogger.com/profile/02527051725365759129noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37612216583555681852013-08-26T20:36:03.916-04:002013-08-26T20:36:03.916-04:00From The Encyclopedia of American Loons - http://a...From The Encyclopedia of American Loons - http://americanloons.blogspot.ca/2010/12/119-michael-egnor.html - Diagnosis: Blissfully ignorant, total moron and dependable fallacy generator. <br /><br />Given the source I think reports of the death of the "materialist Darwinist paradigm" are greatly exaggerated.<br /><br />I will grant your qualifications for detecting second rate minds and third rate ideologies.steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65549935008241865602013-08-26T18:14:56.623-04:002013-08-26T18:14:56.623-04:00Harris:
You're going to find that larger and ...Harris:<br /><br />You're going to find that larger and larger numbers of scientists are making many of the same scientific arguments that Wells makes. The several hundred molecular geneticists involved in the Nature Genetics papers on the myth of junk DNA and Mattick are examples, as well as Denis Noble. <br /><br />(http://whyevolutionistrue.wordpress.com/2013/08/25/famous-physiologist-embarrasses-himself-by-claiming-that-the-modern-theory-of-evolution-is-in-tatters/)<br /><br />Philosophers-- leading philosophers-- are turning on you as well. Nagel has made his disgust with Darwinian/materialist mythology clear in his book, and Jerry Fodor took natural selection apart with impressive and irrefutable skill.<br /><br />Your materialist Darwinist paradigm is headed for the dust bin, along with Marxism and Freudianism, other late 19th century materialist myths. <br /><br />What is most amusing is your reaction. You guys are nothing more than second rate minds pushing a third rate ideology. Materialists/atheists lack even minimal intellectual resources to understand the arguments demolishing their ideology, let along refute them. <br />mregnorhttps://www.blogger.com/profile/11431770851694587832noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75688459824255698782013-08-26T11:24:00.677-04:002013-08-26T11:24:00.677-04:00Wells' "science" is sufficiently sho...Wells' "science" is sufficiently shoddy to dismiss. The reason wells' science is so shoddy is because, in my opinion, of his religion. Instead of simply writing about science, he does the typical creationist hatchet jobs, quotes out of context, purposefully omits parts of quotes that would render his use of them irrelevant, etc. Centrioles are 'designed' because they sort of look like turbines? Really?<br /><br />Mattick's just seems too hyper-focused and dismissive of anything that counters his pet ideas.nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26389440276836939652013-08-26T11:23:17.899-04:002013-08-26T11:23:17.899-04:00Wells' "science" is sufficiently sho...Wells' "science" is sufficiently shoddy to dismiss. The reason wells' science is so shoddy is because, in my opinion, of his religion. Instead of simply writing about science, he does the typical creationist hatchet jobs, quotes out of context, purposefully omits parts of quotes that would render his use of them irrelevant, etc. Centrioles are 'designed' because they sort of look like turbines? Really?<br /><br />Mattick's just seems too hyper-focused and dismissive of anything that counters his pet ideas.nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38341883224954623792013-08-26T08:43:19.268-04:002013-08-26T08:43:19.268-04:00@Georgi Marinov
I've also often wondered what...@Georgi Marinov<br /><br /><i>I've also often wondered what would happen if I sent a grant proposal to NIH where the main argument that I should be given money to do research is what is written in a holy book or a revelation I had.</i><br /><br />Your chances would be a lot better if you sent that one to the John Templeton Foundation.<br /><br />Don't forget to liberally lard it with variations on the them of compatibility between science and religion.<br />steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53796409145018622402013-08-26T06:31:05.013-04:002013-08-26T06:31:05.013-04:00Motivations? Mattick's side job of giving semi...Motivations? Mattick's side job of giving seminars on cruise ships would be in trouble if his "post Darwinism" schtick goes bankrupt. ;-)<br /><br />http://www.insightcruises.com/seminar_f/sa19_seminar.htmlTheOtherJimhttps://www.blogger.com/profile/01727633779107067250noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59822721015457853332013-08-25T21:53:34.501-04:002013-08-25T21:53:34.501-04:00I HAVE engaged the debate many times over the past...I HAVE engaged the debate many times over the past few years. The question was whether there's a difference between the views of Mattick and Wells. I think they are both doing science. What do you think?<br /><br />BTW, where has Mattick published a response to his critics? I must have missed it. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40613626539964173262013-08-25T21:47:59.948-04:002013-08-25T21:47:59.948-04:00Would it be okay to promote Mattick's views in...<i>Would it be okay to promote Mattick's views in a science course but not those of Jonathan Wells? </i><br /><br />Sure. For Mattick, the hypothesis that such-and-such an RNA possesses a function as a non-coding RNA follows from the fact that many such RNAs do possess such functions. It's a reasonable hypothesis, and one that has borne much fruit as far as the identification of new and interesting non-coding RNAs.<br /><br />For Wells, functionality of so-called junk DNA is required by his religion, and has nothing to do with what he knows (which is pathetically little) about gene expression. Not much point in bringing this to a science class.<br /><br />I've a question for Larry and commenters here - in your opinion, do RNA polymerases IV and V have functions?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15776023068463240792013-08-25T21:07:01.180-04:002013-08-25T21:07:01.180-04:00"Why not just engage the debate, without the ..."Why not just engage the debate, without the insults and anti-Christian hate?"<br /><br />I think that's exactly what Larry was advocating, which you might realize if you considered his argument without anti-atheist blinders on.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.com