tag:blogger.com,1999:blog-37148773.post3699157244457316789..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What did the ENCODE Consortium say in 2012?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger28125tag:blogger.com,1999:blog-37148773.post-64750890278460367262014-05-30T21:37:19.287-04:002014-05-30T21:37:19.287-04:00When thinking about the evolution of genome size a...When thinking about the evolution of genome size and C-value enigma, it is critical to realize that genomic DNA can play informational (iDNA) roles or functions, which are based on sequence specificity, or it can have non-informational (niDNA) functions, which are independent of the nucleotide sequence. <br /><br />We have known for half of century or so (and for good reasons, such as sequence variation and mutational load) that in organisms with high C-value, such as humans, only a low percentage of the genomic DNA can be iDNA. We have also known for a very long time that most of the genomic DNA in species with high C-value consists of retroviral and transposable elements sequences or their products or remnants, and that *some* (a few percentages at the most) of these sequences have been co-opted as iDNA or niDNA.<br /> <br />Based on these facts and rationale, the primary question addressed by the scholars in the field was whether the bulk of the genome (90% or more in the human genome), which consists primarily of viral and transposable elements, was simply parasitic or ‘junk DNA’ (jDNA) or it was functional niDNA.<br /><br />As described by Doolitlle in his PNAS paper (<a href="http://www.ncbi.nlm.nih.gov/pubmed/23479647" rel="nofollow"> http://www.ncbi.nlm.nih.gov/pubmed/23479647</a>), the two prevalent hypotheses advanced by the scholars in this field regarding potential non-informational functions for the so called jDNA were the ‘nucleo-skeletal’ (Cavalier-Smith) and ‘nucleotypic’ (Gregory) hypotheses:<br /> <br /><i>The “selfish DNA” scenarios of 1980 (20–22), in which C-value represents only the outcome of conflicts between upward pressure from reproductively competing TEs and downward-directed energetic restraints, have thus, in subsequent decades, yielded to more nuanced understandings. Cavalier-Smith (13, 20) called DNA’s structural and cell biological roles “nucleoskeletal,” considering C-value to be optimized by organism-level natural selection (13, 20). Gregory, now the principal C-value theorist, embraces a more “pluralistic, hierarchical approach” to what he calls <b>“nucleotypic” function</b> (11, 12, 17).</i><br /><br />In the material I suggest you might want to read, I proposed that the ‘nucleo-skeletal and ‘nucleotypic’ hypotheses cannot explain the C-value enigma (i.e. do not pass the ‘onion test’), and I discussed an old hypothesis that explains the evolution of genome size and the C-value enigma:<br /><br /><a href="http://www.ncbi.nlm.nih.gov/pubmed/23479647#cm23479647_1429" rel="nofollow"> http://www.ncbi.nlm.nih.gov/pubmed/23479647#cm23479647_1429</a><br /><a href="http://biorxiv.org/content/early/2013/11/18/000588" rel="nofollow"> http://biorxiv.org/content/early/2013/11/18/000588</a><br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60416587135733889032014-05-30T19:26:54.791-04:002014-05-30T19:26:54.791-04:00@ Claudiu (con’t)
I am now scratching my head at ...@ Claudiu (con’t)<br /><br />I am now scratching my head at the continuing exchange and your rebuttal. We are no longer talking about whether selfish DNA is functional, but rather whether the repetitive sequences of ancestral retroviral symbiotic bulk DNA has been co-opted for global gene regulation and cell differential <b>and</b> whether this new state of affairs merits the designation of “functional DNA”.<br /><br />I am still attempting to wrap my head around exactly what is meant by “bulk” DNA and how to assess positive selection.<br /><br /><i>“…repeated DNAs display very high frequencies of sequence changes during evolution that become homogenized across genomes. These observations suggest the presence of mechanisms that balance interactions and exchange of information between heterochromatic sequences with the need to avoid negative consequences to genome stability.” <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814359/" rel="nofollow">link</a> </i><br /><br />Now that I find interesting… If I understand all this correctly, positive selection for conservation of sequence “type” is not equivalent to conservation of the original sequence; but that said, positive selection is still very real and very real for real important reasons. <br /><br />If so, I have addressed Allan's rebuttal.<br /><br />If so, then I also understand where Claudiu is coming from together with Claudiu's criticism of Doolittle’s PNAS rebuttal.<br /><br />Larry came up with a great list:<br /><br /><i>1. The skeletal DNA hypothesis (more DNA = larger nucleus and more nuclear pores) (Cavalier-Smith)<br />2. Spacers and loops (Zuckerkandl)<br />3. Mutation protection (various authors)<br />4. Teleological hypotheses (excess DNA is necessary for the evolution of new genes and new regulatory functions)</i><br /><br />I wonder out loud if this list is incomplete. So I will repeat myself:<br /><br />Let’s talk about heterochromatin “function” along epigenetic lines. I paraphrased a review above along these lines:<br /><br /><i>Heterochromatin is employed as a platform for the recruitment of effectors across extended domains along chromosomes including but not restricted to silencing and anti-silencing factors. It gets better: Heterochromatin (both facultative and constitutive) also regulates cell-type specific spreading of protein complexes along chromosomes that ultimately controls transcription, chromosome segregation and long-range chromatin interactions.<br /><br />Sounds pretty <b> “FUNCTIONAL” </b>to me. <br /><br />Now of course – The exact sequences of “functional” murine heterochromatin would not be identical to the human equivalent making assay and identification difficult. <br /><br />That said – I am betting that strong positive selection exists for the maintenance of karyotype commonalities between primates (for example).<br /><br />So I wonder out loud: is it possible that ENCODE was right for all the wrong reasons?</i><br /><br />It would appear that ancient retrovirus sequences are the <i>sine qua non</i> of cell differentiation and global gene regulation (at least in primates) and do constitute <b>functionality</b> along lines originally espoused by ENCODE. I humbly suggest that 18–12 million years is a very long time to maintain karyotype commonalities in apes.<br /><br />Of course there still remains the entirely separate question of whether ENCODE had the data in hand to justify such lines of hypothesis... a completely separate question, altogether. <br /><br />Just the same, being guilty of hubris is not tantamount to being guilty of falsehood. <br /><br />Furthermore, even if some organisms and perhaps even some lineages (Ecydysozoa perhaps) do not manifest such “functionality”; that does not translate <i> a priori </i>to the conclusion that the importance of such functionality never exists.<br /><br />OK – somebody please help me out… what am I missing?<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6197724678291482512014-05-30T19:13:40.682-04:002014-05-30T19:13:40.682-04:00Claudiu OK – this is where I get confused…
In a p...Claudiu OK – <a href="http://sandwalk.blogspot.ca/2014/05/how-does-nature-deal-with-encode.html?showComment=1401462856431" rel="nofollow">this is where I get confused…</a><br /><br />In a previous post on that thread, I asked the following:<br /><br /><i> <br />I always understood that retroviruses co-opted host regulatory machinery and vice versa constituting the acme in molecular host-parasite coevolution.<br /><br />http://www.nature.com/nature/journal/v487/n7405/full/nature11244.html<br />http://www.sciencedaily.com/releases/2007/11/071114121359.htm<br /><br />Meanwhile, the different distributions of Alu and LINE1 in the genome would suggest that selection pressure may be involved. Do Alus direct methylation? Are Alus and Line1 DNA symbionts?</i><br /><br />Claudiu, you agreed – and elaborated even further above. Let's see if I managed to capture your drift...<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54846495020626548292014-05-17T05:28:36.135-04:002014-05-17T05:28:36.135-04:00Byers said:
"Unless these nobel folks study ...Byers said:<br /><br />"Unless these nobel folks study evolution as their job WHO CARES what they think about evolution UNLESS they prove its a private study done well?"<br /><br />Robert, so that I'm fully aware of what you mean by a "private study", will you explain what you mean by that? Will you also tell me the names of some creationists (at least 5) who are privately studying origins and evolution without using any of the scientific methods, tools, studies, observations, data, inferences, hypotheses, theories that you and other creationists claim are wrong, useless, and non-scientific? <br /><br />Tell me who is doing "private study" using only creationist (and especially only YEC) methods, tools, etc., etc., etc., and exactly how they go about it. <br /><br />What about non-christian creationists, including non-christian YECs? Are they doing "private study" too, using the same methods, tools, etc., etc., etc., as christian creationists, and are they correct in their conclusions? <br /><br />Why should anyone with a clue care what you and other creationists think about evolution or anything else since you conveniently deny the parts of science and reality that oppose your non-scientific, religious beliefs that are based on impossible fairy tales? YOU, in fact, even claim that science doesn't exist, yet you take advantage of many things that science makes possible and available. Tell me, Robert, why didn't the biblical character jesus have an Ipad? Since jesus is god and god is all knowing and all powerful, was he too stingy to give himself an Ipad? And what about the internet? Wouldn't jesus/god/holy ghost have had a much easier and more effective opportunity of reaching and ministering to the people of the world if he had created computers and the internet for everyone from the 'beginning'? What's with the stone tablets when 'God' could easily have put the ten commandments on a blog? <br /><br />Do you believe that a serpent talked, as claimed in the bible? Do you believe that a man lived inside a fish for days and survived, as claimed in the bible? Do you believe that babies should be dashed against rocks, that people should suffer and even burn in Hell for eternity for the alleged sins of the biblical characters Adam and Eve, that people should be stoned to death for disobeying the alleged commands of an imaginary, so-called god, and that that so-called god is perfect, loving, and merciful? <br /><br />Do you believe that your so-called god is all powerful? If so, why hasn't your so-called god ever caused/enabled a person to regrow a severed limb? A lowly crab can regrow a severed limb, some lizards can regrow a severed tail. If humans are so 'special' and superior, why can't humans regrow severed limbs? Shouldn't humans be able to do anything and everything that any other life form can do plus much, much more? You often claim that humans got the best body from your so-called god, but our bodies are grossly inferior to the bodies of many animals and plants. How do you explain that if humans are special and superior? Surely many people are staunch christians and have prayed over and over again for a new arm or leg for themselves or others but for some reason your loving, merciful, perfect, all powerful, so-called god never answers those prayers in a positive way. And there are all of the people and animals that suffer with diseases, disfigurements, disabilities, injuries, horrible pain, etc. that your loving, so-called god should be able to fix in an instant. Doesn't anyone or anything deserve 'God's' love and mercy? What have animals and plants done to deserve being punished for Adam and Eve's alleged 'sin' against 'God'? <br /><br />And one last question, for now: WHY do you believe in, worship and promote an imaginary, genocidal, ecocidal, tyrannical, petty, destructive, hateful, narcissistic, sadistic MONSTER? <br />The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8654206022898114592014-05-17T01:03:37.209-04:002014-05-17T01:03:37.209-04:00All of them. Those who apply themselves to YEC siu...All of them. Those who apply themselves to YEC siubjects and some iD folks are the advanced thinkers on these subjects.<br />Thats why there is a revolution going on.<br />The opposition is just responding to it but by its response raises the stakes.<br />This is either a movement that will overthrow in a big way many conclusions in these subjects oR a movement that will uniquely crumble and be a proverb and a story for decades to come.<br />Right or wrong its YEC and ID who are the great revolutionaries in our times.<br />We are the thinkers about big things here. Right or wrong.Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2012469603370791962014-05-17T00:55:19.408-04:002014-05-17T00:55:19.408-04:00Robert says: YEC are the real thinkers and movers ...Robert says: <i>YEC are the real thinkers and movers in ideas in our times on these subjects.</i><br />...<br />Please name some, with reference to their real thougths, writings and 'moves', excluding your own tripe.Rolf Aalberghttps://www.blogger.com/profile/12878337054438652463noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86354857456132003292014-05-16T10:13:31.906-04:002014-05-16T10:13:31.906-04:00Where'd Greenie go? She was telling us we are ...Where'd Greenie go? She was telling us we are not allowed to prove Ewan Birney, FRS's 2012 claims wrong with actual facts, because he's a FRS and we Americans & Canadians are not eligible. Somebody copies in a quote from 2007 in which Ewan Birney, FRS, bet a case of champagne that OUR position was right & his 2012 claims would be false. Remember Greenie, you're not allowed to disagree with a FRS and Ewan Birney, FRS, said we're right.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1595534319429012672014-05-16T05:11:27.920-04:002014-05-16T05:11:27.920-04:00Unless [people] study evolution as their job WHO C...<i>Unless [people] study evolution as their job WHO CARES what they think about evolution UNLESS they prove its a private study done well?</i><br /><br />Tee hee. So 'ID leaders and creationists' are an example of 'private study done well'? Sproing! Another irony meter bites the dust. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74260331207965747622014-05-16T02:07:21.068-04:002014-05-16T02:07:21.068-04:00Depends on the ladders direction!!
Unless these no...Depends on the ladders direction!!<br />Unless these nobel folks study evolution as their job WHO CARES what they think about evolution UNLESS they prove its a private study done well?<br />In fact mu impression of nobel winners is they are obscure because what they get prizes for doesn't really advance things. They just need winners every year.<br />Only a few do actual important accomplishments for the ages.<br />I wish them well in their work but mostly they are not remembered.<br />Unlike creationists who are taking on and winning a revolution in conclusions on origins.<br />The ID leaders and YEC are the real thinkers and movers in ideas in our times on these subjects.<br />Not cell watchers or chemists or string theory dreamers.<br />They are not famous for a reason. Their stuff is just the next step in a simple knowledge progression.<br />Creationism is a leap and a stomp on science conclusions.<br />More thoughtful and more resisted because its a paradigm change threat.<br />Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13619079117341756932014-05-15T23:14:49.929-04:002014-05-15T23:14:49.929-04:00Pioyr - Fred Hoyle's knighthood was just a coi...Pioyr - Fred Hoyle's knighthood was just a coincidence. British scientists who chaired a Research Council committee or later became Director General of one of the Research Councils which resulted from the breakup of the SRC, automatically received a knighthood for their services (or for women being made a Dame like the research supervisor of my master's research project).<br /><br />However it did raise some controversy at the time. Some were in favour recognizing it as a poor substitute for the Nobel prize he should have won for his work on stellar nucleosynthesis. Others objected because he had turned into a nut. While others because he had resigned from his postion at the SRC and was not entitled to the automatic knighthood. Thsi was in in argument about the sighting of a new telescope. Now astronomers recognize he was right on this but it was controversial at the time,<br /><br />However it was essential a formal bureaucratic decision and not designed as far a one can tell a reward for his emerging raving looney scientific opinions. chemicalscumhttps://www.blogger.com/profile/00456611765432242326noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25457363541117792822014-05-15T17:58:29.005-04:002014-05-15T17:58:29.005-04:00Are you being sarcastic??Are you being sarcastic??Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60017693974237708892014-05-15T12:52:02.917-04:002014-05-15T12:52:02.917-04:00I'm puzzled by the parenthetic comment on fugu...I'm puzzled by the parenthetic comment on fugu: "(note vertebrate, not mammal, but still, vertebrate are *very* complex)". It sounds like something inspired by the Dog's Ass Plot.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60449065785084253892014-05-15T12:50:33.162-04:002014-05-15T12:50:33.162-04:00OMG!OMG!Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17592102238934579582014-05-15T10:46:06.372-04:002014-05-15T10:46:06.372-04:00As I pointed out in another Sandwalk thread based ...As I pointed out <a href="http://sandwalk.blogspot.de/2014/05/the-case-for-junk-dna-onion-test.html?showComment=1400159862904#c880567004252841379" rel="nofollow">in another Sandwalk thread</a> based on his <a href="http://www.genomicron.evolverzone.com/2012/09/birney-thinks-onion-test-silly/" rel="nofollow">2012 Tweet on the onion test</a> which said "<i>@leonidkruglyak (re:onions etc); polyploidy and letting your repeats go crazy</i>" I think it is quite unlikely that Birney wasn't convinced of the 80% figure back then. Or should this be one of the <a href="http://genomeinformatician.blogspot.de/2014/01/new-media-for-science-3-years-in.html" rel="nofollow"> Humour doesn't work on Twitter</a> cases?SPARChttps://www.blogger.com/profile/09563722742249547887noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29783687896650150942014-05-15T09:52:58.936-04:002014-05-15T09:52:58.936-04:00Right now I'm reading a review article about t...Right now I'm reading a review article about transcription in Cell. Two of the authors are Michael Levine and Robert Tjian. They discuss the ENCODE results favorably and say, refering to TFs specifically ( I think): "This amounts to a remarkable fraction of our genome-25% and probably more- devoted to regulatory information..."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2285349056145094162014-05-15T09:40:03.251-04:002014-05-15T09:40:03.251-04:00Why don't they just put all to rest and define...Why don't they just put all to rest and define function to the genome as any sequence that is replicated (and / or is subject to telomerase activity) and in one fell swoop, they will be able to claim that 100% of the genome is functional.Enrique Amayahttps://www.blogger.com/profile/01230765303829721370noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17103957696986035922014-05-15T08:37:01.290-04:002014-05-15T08:37:01.290-04:00Robert, at the left of this blog you'll find m...Robert, at the left of this blog you'll find many links that should be of great interest to you because of your keen interest in evolution - albeit from a YEC viewpoint, i.e. the viewpoint that evolution = atheism = nonsense. <br /><br />Anyway, you'll find a list of Nobel laureates below the label <strong>Themes</strong> (http://sandwalk.blogspot.com/2007/11/theme-nobel-laureates.html) and I think it is safe to think that very close to 99.999 % are 'evolutionists' That's just Nobel prize winners, how many more do you think there are? <br /><br />What does that list tell us?<br /><br />That there is not any shortage of evolutionists in science at a level no creationist ever could aspire to.<br /><br />Where do you put yourself on the ladder of knowledge, understanding and intellectual achievment? <br /><br /><br />Rolf Aalberghttps://www.blogger.com/profile/12878337054438652463noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12814020368227845732014-05-15T03:39:37.627-04:002014-05-15T03:39:37.627-04:00Robert, have you ever seen a science paper or scie...Robert, have you ever seen a science paper or science book? Did you notice the references? Your problem is the lack of creationism worth the paper it is printed on. Do you know any?Rolf Aalberghttps://www.blogger.com/profile/12878337054438652463noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46465018889346285862014-05-15T00:16:48.558-04:002014-05-15T00:16:48.558-04:00I just wonder why Ewan Birney defended the 80% cla...I just wonder why Ewan Birney defended the 80% claims in 2012 when he bet in 2007 that the number is much lower.<br /><br />BTW, publishing some halfhearted non-retraction to obscure their 2012 mistakes doesn't really help and makes Nature look hypocrite especially, when they publish a new <a href="http://www.nature.com/nrg/journal/vaop/ncurrent/abs/nrg3722.html" rel="nofollow">Mattick paper</a> that is putting forward the very same 80% number although worded more carefully (actually, Mattick omitts the term junk in the paper). He says<br /><br />"<i>ENCODE reports that ~80% of the genome is transcribing ncRNAs</i>" <br /><br />and <br /><br />"<i>The initial findings were confirmed in 2005 (REFS 156–159) and extended by the Encyclopedia of DNA Elements (ENCODE) project, all of which showed that the vast majority (at least 80%) of the human and mouse genomes are differentially transcribed in one context or another; other studies also reported similar findings in all organisms examined. Indeed, it seems that most intergenic and, by definition, intronic sequences are differentially transcribed, and that the extent of the transcriptome therefore expands with developmental complexity</i>"<br /><br />He just omitted the dog's ass plot this time.SPARChttps://www.blogger.com/profile/09563722742249547887noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42200592932171102782014-05-14T23:27:04.136-04:002014-05-14T23:27:04.136-04:00Byers, the IDcreationists lied when they said ENCO...Byers, the IDcreationists lied when they said ENCODE had assayed & identified functions in most of the genome. Since they lied about this, IDcreationists cannot have any credibility <br /><br />To repair your freako logic: <br /><i><br />if the creationists are so wrong in things they are paid and degree-ed not to be wrong about THEN scientists should say to the public that the evidence for creation is NOT well researched by the creationists that communicate with the public.</i><br />Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74177985897707009142014-05-14T23:04:13.700-04:002014-05-14T23:04:13.700-04:00From the origins struggle view.
if the media is so...From the origins struggle view.<br />if the media is so wrong in things they are paid and degree-ed not to be wrong about THEN creationists can say to the public that the evidence for evolution is NOT well researched by the media that communicates with the public.<br />Leaving evolutionism in the hands of very small numbers of people now and in the past.<br />Thats why its lingered and thats why its never been criticized in a schiolarrly way by science reporters.<br />Just making a common creationist complaint here.Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74355369182622236872014-05-14T17:03:29.258-04:002014-05-14T17:03:29.258-04:00From Larry's blog post on Mattick (see the lin...From Larry's blog post on Mattick (see the link above). Quotation:<br /><br /><i>Others are less convinced. Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, has bet Mattick that of the processed RNAs yet to be assigned a function - representing 14 per cent of the entire genome - less than 20 per cent will turn out to be useful. "I'll get a case of vintage champagne if I win," Birney says</i> [in 2007]<br /><br />Does anyone know if he got that case? The champagne could have been doped with something. You never know what lengths those rogue scientists will go to.<br /><br />Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23658001422337303322014-05-14T16:43:42.481-04:002014-05-14T16:43:42.481-04:00Is it a tendency perhaps? When Fred Hoyle left Cam...Is it a tendency perhaps? When Fred Hoyle left Cambridge and started turning maverick, he got knighted the very next year.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38656959258003948872014-05-14T16:42:23.302-04:002014-05-14T16:42:23.302-04:00One thing I try to teach any scientists who read m...One thing I try to teach any scientists who read my comments, is that arguing with dishonest people is not like a normal scientific argument. Dishonest people employ tricks not normally involved in real scientific controversies. These include:<br /><br />1. Equivocation: switching between definitions between major and minor premise. e.g. "80% of the genome has a biological function, by 'function' we means a molecule interacts with it, therefore there is no Junk DNA"<br /><br />2. Evasion, changing the subject when you're caught in a contradiction or falsification. Gish Gallop.<br /><br />3. Insinuating the "facts" support your thesis, when the actual facts are the opposite, but you don't want to say something clear and explicit, because that would be falsifiable and you could be proven to be lying. But you insinuate the fake "facts" you need to support your thesis without stating them directly.<br /><br />So you have to deconstruct dishonest opponents. In this case, let's deconstruct the language used by Kellis et al. 2014:<br /><br /><i>"The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far <b>more important than any interim estimate</b> of the fraction of the human genome that is functional."</i><br /><br />Here they use insinuation rather than explicitly making a claim that they need to be true, because if they said it explicitly we could prove they're lying.<br /><br />Their previous claims were: <br /><br />1. 80% of the genome has biological function (so says the peer-reviewed publication), <br /><br />2. this definition of function is the proper definition to disprove Junk DNA (so says the press release), <br /><br />3. This disproof of Junk DNA was hugely important and <br /><br />4. <b>It was the whole purpose of ENCODE, they said in 2012</b>.<br /><br />But Kellis et al. 2014, with their "unimportant interim estimate" garbage, insinuate that they never, ever made the above three claims. Instead they insinuate that they <i>really</i> said:<br /><br />1. 80% of the genome has biochemical activity, they never said it was function,<br /><br />2. they never said this disproves Junk DNA,<br /><br />3. A disproof of Junk DNA is not important, what matters is a big list of TF binding sites,<br /><br />4. <b>Disproving Junk DNA was never the whole purpose of ENCODE, they say in 2014</b>.<br /><br />"Far more important than any interim estimate"! my ass.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67513176586319263912014-05-14T16:29:05.658-04:002014-05-14T16:29:05.658-04:00Yeah, that's worse. At least Birney is capable...Yeah, that's worse. At least Birney is capable of shame. He's like a little boy standing next to a broken cookie jar, making excuses. He knows he did wrong.<br /><br />But Mattick! <br /><br />Look Larry, you have to write a book and kick ass. Take a sabbatical or something and write the book. Run it past Georgi and Joe first.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.com