tag:blogger.com,1999:blog-37148773.post7421383249536235164..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: ENCODE, Junk DNA, and Intelligent Design CreationismLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger62125tag:blogger.com,1999:blog-37148773.post-11312062570670058262015-01-18T16:27:39.694-05:002015-01-18T16:27:39.694-05:00So, what will be the result when you throw the wel...So, what will be the result when you throw the well designed computer in the water?<br />Thats why God create live in a way it can survive"under any curcimstances within the edges God ordered. That's what i call well-designed. God gives live a downgrade caused by sin. Junk-DNA fits in my opinion perfect in the case of creation. <br /><br />Why do you think you get older, sick weak and eventually die? Junk DNA i<br />s a misinterpretation. In reality you have to call it ''the results of a downgrade''. Topgooszhttps://www.blogger.com/profile/05460155425551195039noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90312641312488112342015-01-18T11:12:27.557-05:002015-01-18T11:12:27.557-05:00Your programing genius student is correct. If biol...Your programing genius student is correct. If biological organisms were as well-designed as perfect computer code such that changing even one letter would break the code, then evolution would be impossible. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20098480617611173062015-01-18T06:32:48.680-05:002015-01-18T06:32:48.680-05:00Hi, an student of mine who is also a programming g...Hi, an student of mine who is also a programming genius asked me this question after reading details of the Encode project:<br /><br />If all the DNA is functional and it contains cascading step-by-step instructions meaning that each step depends of the results of the preceding one to continue the chain of instructions for assembling the embryos of animals then how the Evolution mechanism of changing one species into another (individual random non-guided mutations to the DNA) would be able to change this chain instructions without ruining it ? He told me that if you change one letter in a computer code it is ruined and does not work since all instructions depend on the precide execution of the preceding ones....Thanks for your help Reuben Alvessonhttps://www.blogger.com/profile/10455863878088668801noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79565449474547210072013-05-02T11:45:17.496-04:002013-05-02T11:45:17.496-04:00Where are you getting these figures from???
The h...Where are you getting these figures from???<br /><br />The hard numbers are the following, which I just pulled out of the latest GENCODE version (v16) and from UCSC's repeatMasker:<br /><br />2.89% exons of protein coding genes (this includes UTRs, which contribute a significant fraction of this percentage)<br />0.20% lncRNAs<br />0.0087% miRNAs<br />~0.003% structural RNAs (rRNA, tRNA, snoRNA, snRNA, etc)<br />0.20% other ncRNAs<br /><br />In total, 3.33% exons<br /><br />In addition to that, there are 0.5% pseudogenes of various types<br /><br />Then we have:<br /><br />3.15% DNA repeats<br />20.28% LINE repeats<br />8.52% LTR repeats<br />12.6% SINE repeats<br /><br />plus a tiny percentage of other types of repeats (defective copies of structural RNAs, etc.)<br /><br />A total of 46.45% annotated repetitive elements<br /><br />In addition to this, there is a single-digit percentage of conserved non-exonic, non-repetitive elements, the exact figure of which varies depending on how you define conserved. Which is mostly regulatory elements, but as a whole it has not been annotated outside of what ENCODE has done, and ENCODE has not really annotated those yet, it has just generated the maps that will provide the foundation for that annotation in the coming years. <br /><br />The earliest GENCODE version I have is v3c, which is from around 2009, in that one there were 2.5% exons of protein coding genes, and the 0.2% of lncRNAs were not annotated. That's a growth of 0.5%, a significant portion of which is of dubious significance <br /><br />So where are you getting the idea that it was 95% functional DNA in 2009, 90% now and soon to become 80%?<br /><br />And do you seriously think those 46% of <b>annotated</b> repetitive elements (people like to talk about how there is a lot of functional DNA left to annotate, but there is likely much more DNA consisting of repeat copies so broken down and degenerated that the repeat annotation programs simply have not picked them up) will somehow magically turn out to be vitally important functional elements??Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74502247137468491952013-04-28T19:19:40.508-04:002013-04-28T19:19:40.508-04:00Hmm... so the official figure now is that 90% of o...Hmm... so the official figure now is that 90% of our DNA is junk. I used to hear that 98% was junk and then in 2009 95% was junk. Now is it is 90% and I have heard the figure 80% being bandied around (for example Dr Merlin Crossley on the Australian ABC's "Ockhams Razor"<br /><br />I suppose that is the beauty of science, facts are only as good as the latest experiment.<br /><br />But if this keeps up then it will take a lot less than 9,000 years to find a function for all DNA.Robinhttps://www.blogger.com/profile/16015911138886238144noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-975481967044449902013-04-07T17:03:50.930-04:002013-04-07T17:03:50.930-04:00Sorry guys but I was not only talking about the in...Sorry guys but I was not only talking about the invention of death but also about the programmed cell death that seems to me to be just a work of art; It is so fine tuned you scientist have no idea about that. I'm sure you can come up with some testable shitheories, but so can I. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23881817356763183392013-04-02T10:14:53.591-04:002013-04-02T10:14:53.591-04:00A bit tangential, but I really love the date of De...A bit tangential, but I really love the date of Dembski's "prediction" on function in junk DNA...nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43402259015353207352013-04-02T00:54:32.740-04:002013-04-02T00:54:32.740-04:00@Negative Entropy
Dominic doesn't know what th...@Negative Entropy<br />Dominic doesn't know what the words spontaneous and by accident means. To him, he seriously thinks there are people who imagine a living cell miraculously assembling itself from scratch, I see this with creationists all the time. I don't know how they got this idiotic idea to begin with, but they all regurgitate it ignorantly repeatedly as if by training. <br />Instead of dealing with the actual science, they're bent on the least charitable caricatures and strawmen they can possibly conjure up. And here I thought that would be in violation of the 9th commandment, silly me. <br /><br /><b>"Life decided to invent death"</b><br />Death is not an invention, it's an inevitability. When you run out of nutrients, you die and decompose. Sooner or later, every organism is going to run into either food scarcity, disease, natural/environmental disaster or a predator. It's that simple. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77844209853336173282013-04-01T12:25:17.929-04:002013-04-01T12:25:17.929-04:00Dominic,
Sure, "spontaneously" must be ...Dominic,<br /><br />Sure, "spontaneously" must be much more far fetched than by magic performed by a being that only exists in people's imagination, and whose complexity, desires, and magic powers don't require any rational explanation for their origins.<br /><br />What makes you think that there was no death before multicellularity? Do you truly believe that the first cell(s) is(are) still floating around?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13707863860044633182013-04-01T11:13:34.862-04:002013-04-01T11:13:34.862-04:00A funny thing about the origin of life is that som...A funny thing about the origin of life is that some believe that life originated spontaneously, by accident etc. Then, it remained simple for millions or billions of years but as soon as it got more complex and became a multicellular organism, life decided to invent death. What a damn luck! Had life not been so inventive, we could live forever! Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85825924730950664942013-04-01T09:52:57.872-04:002013-04-01T09:52:57.872-04:00Joe Felsenstein: “ Thank you for the corrections
...Joe Felsenstein: <i>“ Thank you for the corrections</i><br /><br />It seems that this fellow lutesuite, who has a hidden identity, did not understand you message. He based his derogatory comment on your earliest incorrect statement (see above), so you might want to ask him to apologize.<br /> <br />Also, I don’t think that you take directions from him or Lary on your comments, so I think he should apologize for that, too!<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42455972897192946432013-04-01T08:58:42.789-04:002013-04-01T08:58:42.789-04:00John,
In the original paper (www.ncbi.nlm.nih.go...John,<br /> <br />In the original paper (www.ncbi.nlm.nih.gov/pubmed/2156137) and more recent comments (http://comments.sciencemag.org/content/10.1126/science.337.6099.1159), I proposed an experimental approach that would address a highly significant medical aspect of the hypothesis; jDNA protection against cancer. You might want to evaluate it.<br /><br />It would help to support your assertion that I used “ad hoc parameters” by specifically pointing them out.<br /> <br />Also, it seems that you don’t’ agree that in humans, for example, jDNA protects against inspectional mutagenesis. Does jDNA protects against inspectional mutagenesis, or not? <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14648680801228817102013-04-01T06:22:47.467-04:002013-04-01T06:22:47.467-04:00Please demonstrate instantaneous magical creation ...<i>Please demonstrate instantaneous magical creation of a living organism.</i><br /><br />Dominic will need to acquire a GOD blender, before he hits puree. SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24165350743960920582013-04-01T03:15:08.765-04:002013-04-01T03:15:08.765-04:00I can buy your evolutionary shit, because my twin ...<b>I can buy your evolutionary shit, because my twin brother looks like my neighbor, but the origin of life belongs to THE ONE. Please prove me wrong.</b><br /><br />Theism, attempting to shift the burden of proof since 5000 BCE. <br /><br />Here's how it works dominic. YOu make a claim, you support it. Please demonstrate instantaneous magical creation of a living organism. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71848987939701327012013-04-01T01:06:16.475-04:002013-04-01T01:06:16.475-04:00Also.. what is it with creationism and the origin ...Also.. what is it with creationism and the origin of life always being introduced in discussions on evolution? This topic is about Junk DNA, and there's a creationist babbling about the origin of life? Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14567564244929658872013-04-01T01:04:45.593-04:002013-04-01T01:04:45.593-04:00This is what happens when someone who's essent...This is what happens when someone who's essentially completely clueless starts babbling on the subject. <br /><br />And nobody believes in "prebiotic soup". Creationism: still stuck in the 1800's.<br /><br />Whether RNA came "first", directly from abiotic geochemistry, or it didn't, is immaterial with respect to the fact that we're pretty sure there was an RNA world from which DNA later evolved. What really came before this RNA world is what we don't know, and some have suggested RNA was the very first thing itself, others have suggested it was preceded by metabolism or even simpler kinds of genetic polymers. <br />This is what's wonderful about science, because instead of just giving up and declaring goddidit, scientists are trying to find out how it happened. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-313941551934699472013-04-01T00:23:14.381-04:002013-04-01T00:23:14.381-04:00This is from the idiotic article cited by Dominic....This is from the idiotic article cited by Dominic.<br /><br /><i>They're also within a 58,000-base stretch of so-called "junk" DNA, which contains no known protein-coding genes.</i><br /><br />For the ten millionth time, NO ONE EVER SAID NON-CODING DNA = JUNK. <br /><br />The fact that the author thinks geneticists believed non-coding DNA = Junk indicates he is an IDIOT. Perhaps not an IDiot, but certainly an IDIOT.<br /><br />How many times do I have to copy the list of Nobel Prizes handed out in the last 50 years to scientists who found novel functions in non-coding DNA?<br /><br />Georgi: <i>Enhancers are not junk DNA and never have been</i><br /><br />Thank you Georgi!Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34306968030381975562013-04-01T00:17:43.042-04:002013-04-01T00:17:43.042-04:00you can put all needed components in lab tube-RNA,...<i>you can put all needed components in lab tube-RNA, mitochondria ribosome etc. </i><br /><br />I didn't read that comment before - did he really said "mitochondria"???????? Sigh...Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7064299371180579152013-04-01T00:16:28.158-04:002013-04-01T00:16:28.158-04:00Dominic,
How can you believe in RNA world or meta...Dominic,<br /><br /><i>How can you believe in RNA world or metabolism first, if none of that can be tested in the lab?</i><br /><br />Who said it can't be tested in the lab? Some creationist told you that, and you believed them.<br /><br />However, your idea for how to test it is absurd, and I think deliberately absurd.<br /><br /><i>... you can put all needed components in lab tube-RNA, mitochondria ribosome etc. all that the living cell contains to stay alive, and I guarantee you that a cell will not form out of them.</i><br /><br />Riiight. You got us. Atoms in a blender does not make a living cell.<br /><br />Everybody agrees that multiple steps would be involved, and a free-living protein-based cell comes at the end of all those steps.<br /><br />The point of laboratory tests is not to make a living cell by randomly throwing together whatever, but to investigate particular steps in the transition from abiotic chemistry to the RNA world, and then from RNA world to membrane synthesis. Where metabolism comes in, before or after RNA, is disputed.<br /><br />Your idea that the ingredients in step 1 mixed together in a blender will make the results of step 30 is ridiculous, and it's deliberately ridiculous-- you chose it to misrepresent how science is done.<br /><br />If you want to trash-talk, OK, we'll win at trash-talking. Since you believe in the Bible, you think dirt turned into the people. Put some dirt in a blender and see if it turns into a naked man and woman.<br /><br />One wonders what point is there giving technical answers to creationists? They don't want to learn science, they want to stick science in a blender and hit puree.<br />Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57960118447195329942013-04-01T00:02:57.135-04:002013-04-01T00:02:57.135-04:00This is from Nature:
"Knowles cautions that ...This is from Nature:<br /><br />"Knowles cautions that the study doesn't prove that non-coding DNA has no function. "Those mice were alive, that's what we know about them," she says. "We don't know if they have abnormalities that we don't test for."<br /><br />David Haussler of the University of California, Santa Cruz, who has investigated why genetic regions are conserved, says that Rubin's study gives no hint that the deleted DNA has a function. But he also believes that non-coding regions may have an effect too subtle to be picked up in the tests to far.<br /><br />"Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years," he argues. "Darwinian selection is a tougher test." <br /><br />Link to the article:<br /><br />http://www.nature.com/news/2004/041018/full/news041018-7.html<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24098538845586931102013-03-31T23:49:49.784-04:002013-03-31T23:49:49.784-04:00P.S. Enhancers also tend to be conserved. Not alwa...P.S. Enhancers also tend to be conserved. Not always, there is much higher turnover of enhancer elements than of coding sequences, but nevertheless, one can find a lot of them through comparative genomics alone. And people have been doing that for a decade, ever since whole genome sequences became available.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10989607968716537612013-03-31T23:46:32.648-04:002013-03-31T23:46:32.648-04:001. Enhancers are not junk DNA and never have been
...1. Enhancers are not junk DNA and never have been<br /><br />2. Apparently you have neither followed this blog for long nor are you in general familiar with the mismatch between the hyperbolism of press releases and the reality of the research they report on<br /><br />3. The reason that one paper was exciting is that few people have bothered to knock out enhancers - until very recently, it was quite a difficult technical feat to do just one of them and since there are reasons to think the effects of such a knock will often not be very great, as genes are usually controlled by multiple enhancers, sometimes active in different cells but also often redundant with each other, the incentive to do this has not been great. Pennacchio has been one of the very few to do that. This will change as now we have much more powerful tools for knocking out things - first TALENs, and more recently, and especially relevant if one wants to do this high-throughput, the CRISPR-based protocols for direct genome editing. <br /><br />So you will see a lot more of that type of work in the future. But this will not change the first point I made - enhancers are not junk DNA and have never been considered such, which is why such press releases are deeply misleading. Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18466696164422481052013-03-31T23:35:52.565-04:002013-03-31T23:35:52.565-04:00"How Junk DNA Affects Heart Disease
Research..."How Junk DNA Affects Heart Disease<br /><br />Researchers have figured out how a mysterious DNA region previously tied to heart disease may exert its effect. The discovery could open the door to new prevention and treatment strategies.<br /><br />Heart disease is the leading cause of death in the United States and a major cause of disability. Genome-wide association studies, which scan the genomes of large numbers of people to find genetic variations associated with disease, recently linked gene variations on human chromosome 9p21 with an increased risk for heart disease. The variants only moderately raise the risk of disease, but they’re very common and so may make a significant contribution to heart disease in the population.<br /><br />How these variants affect heart disease has been a mystery. They aren't associated with known risk factors, such as blood lipid levels, hypertension or diabetes. They're also within a 58,000-base stretch of so-called "junk" DNA, which contains no known protein-coding genes. The human genome has about 3 billion human DNA base pairs, with genes making up only a small fraction of that—about 2%. Little is known about the function of the remaining 98% that doesn't code for proteins.<br /><br />Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory led by Dr. Len A. Pennacchio set out to try to understand how this non-coding interval between genes affects heart disease. To do this, they genetically engineered mice to completely lack the interval. The study, partly funded by NIH's National Heart, Lung and Blood Institute (NHLBI) and National Human Genome Research Institute (NHGRI), appeared in the advance online edition of Nature on February 21, 2010.<br /><br />The researchers looked at genes near the deleted interval and found that 2 genes—Cdkn2a and Cdkn2b—were expressed at 10-fold lower levels in heart tissue of altered mice. Cdkn2a and Cdkn2b belong to a family of "cell cycle" genes, which are involved in regulating cell proliferation. When the researchers examined how muscle cells taken from the heart grew in the laboratory, they found that cells lacking the interval multiplied faster than controls and kept proliferating after the control cells had stopped.<br /><br />When the scientists placed 40 of the genetically altered mice and 40 controls on a high-fat, high-cholesterol diet for 20 weeks, blood lipid levels rose to similar levels in both groups of mice. There were also no significant differences in fatty deposits in arteries. However, the diet caused substantially more deaths among the mice lacking the non-coding interval. These results suggest that the interval exerts its effect through a mechanism independent of blood lipid levels and other known risk factors.<br /><br />"We show that this non-coding interval affects the expression of 2 cell cycle inhibitor genes located almost 100,000 base pairs away from the deletion," Pennacchio says. "We believe that something goes awry in variants of this interval, causing vascular cells to divide and multiply more quickly than usual." That may increase the risk for heart disease, the researchers speculate, by narrowing coronary arteries.<br /><br />"Non-coding DNA is a huge area of the genome, waiting to be explored, which could have huge dividends for understanding and treating disease," Pennacchio adds.<br /><br />—by Harrison Wein, Ph.D."<br /><br />http://www.nih.gov/researchmatters/march2010/03012010heart.htmAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87442374702024162332013-03-31T22:41:38.515-04:002013-03-31T22:41:38.515-04:00One does no believe in anything, all you do is ass...One does no believe in anything, all you do is assign a probability estimate on things. RNA world seems likely because there are all sorts what seems to be relicts of the RNA world in modern cells, starting with the ribosome.<br /><br />The problem with the RNA world is that the chemistry doesn't really work - the old cliche goes that the RNA world is the molecular biologist's dream and the chemist's nightmare. <br /><br />Which is why I said the origin of life is an unsolved problem.<br /><br />This is a good book on the subject:<br /><br />http://www.amazon.com/RNA-Worlds-Origins-Diversity-Regulation/dp/0879699469Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16049473598297482392013-03-31T21:56:23.540-04:002013-03-31T21:56:23.540-04:00I don't mind hypothesis but they have to be of...I don't mind hypothesis but they have to be of sound mind. <br />How can you believe in RNA world or metabolism first, if none of that can be tested in the lab? All I know is you can put all needed components in lab tube-RNA, mitochondria ribosome etc. all that the living cell contains to stay alive, and I guarantee you that a cell will not form out of them. No way! So what makes you so certain that this could have occurred on its own in the prebiotic soup by chance? It's totally unrealistic.<br />Anonymousnoreply@blogger.com