tag:blogger.com,1999:blog-37148773.post1353553749412537281..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What is the dominant view of junk DNA?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger49125tag:blogger.com,1999:blog-37148773.post-16849603532597516862019-03-23T13:18:22.134-04:002019-03-23T13:18:22.134-04:00'What we observe in the fossils is no Darwinia...'What we observe in the fossils is no Darwinian style changes whatsoever. The slow and gradual style of development isn't there, anywhere.'<br /><br />In places where the fossil record is good enough this type of gradual change, with one species changing into another through the stratigraphic sequence, can indeed be seen. One example is the early Eocene of the BigHorn Basin in Wyoming (see papers by Phil Gingerich).christine janishttps://www.blogger.com/profile/14520766623263222808noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25349132159218383582019-03-22T14:58:07.903-04:002019-03-22T14:58:07.903-04:00Borger is a funny guy. I read some of his claims ...Borger is a funny guy. I read some of his claims on an internet forum and he had been shown some comparative DNA sequence data and claimed that the changes were so random that they were non-random. He also argued with Lynn Caporale that her own book supported design, not Darwin... IOW - the usual kook. nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15539202935443075562019-03-20T04:00:41.990-04:002019-03-20T04:00:41.990-04:00People should look in plant genomes for the answer...People should look in plant genomes for the answer. In plants, basically everything that is more than 1000 bp away from a gene is not conserved between species. You hardly find any transposable element (TE) that is older than a few million years. Furthermore, number of genes is quite conserved (about 30,000), but genome size (i.e. TE content) varies enormously. Finally, most TE sequences are non-functional (i.e. fragmented by insertions of other TEs or by deletions). These points combined indicate that pretty much everything outside of "gene space" is junk. Gene space can be defined as the 30,000 protein coding genes plus relatively few non-coding genes. Anonymoushttps://www.blogger.com/profile/08450170954813133576noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86457814017028896902019-03-17T18:58:26.960-04:002019-03-17T18:58:26.960-04:00I listened to it last week and was very disappoint...I listened to it last week and was very disappointed. I don't like RadioLab because they don't really conduct interviews. They chop up the words of their interviewees into little soundbites that are demeaning and uninformative.<br /><br />In this case they never came up with the right answer to the question. Redwoods have large genomes because they are full of junk DNA. It's not a problem that needs an answer so the RadioLab crew shouldn't have been shocked or surprised. <br /><br />The average person listening to this podcast will not learn anything important about genomes and evolution. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59465777002253680372019-03-15T12:27:11.549-04:002019-03-15T12:27:11.549-04:00Hi, just to chip in, from my point of view here in...Hi, just to chip in, from my point of view here in England most scientists would probably agree with point 3 with regards to the question. I'm a biology teacher and our syllabuses for 16- 18 year olds are quite lacking in genetics generally, but make perfunctory reference to non-coding DNA with functions. Don't ask me how perfunctory the teaching of evolution is for them and younger cohorts... Then at university here only a small fraction will be exposed to any detail in genetics as courses are so specialised.<br />I wish you could have helped designed the syllabus Laurence, it would be much more interesting and accurate.Similehttps://www.blogger.com/profile/10512192412677575865noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23815105698983063512019-03-14T08:08:29.230-04:002019-03-14T08:08:29.230-04:00Jeanson is not an honest actor and definitely appl...Jeanson is not an honest actor and definitely applies motivated reasoning in his arguments. In his "research" he goes looking specifically for evidence that he can cherry pick to bolster creationist claims while intentionally ignoring scientific data that challenges his creationist claims.<br /><br />You can see a good example of this here where he gets called out for cooking the results in order to come up with a mutation rate that miraculously supports the young earth creationist narrative:<br /><br />https://www.filthymonkeymen.com/2016/05/23/invent-mutation-rate/Aceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87118534497565661872019-03-14T08:01:20.026-04:002019-03-14T08:01:20.026-04:00Hey Larry
Have you had a listen to that recent ep...Hey Larry<br /><br />Have you had a listen to that recent episode of RadioLab where they look at the issue of Junk DNA? They attempt to answer the question: Why do Redwood trees have 8x as much DNA as humans. In exploring the answer to this question, they pick the right person to talk to: T. Ryan Gregory who then talks about the onion test, the numerous other species who have larger genomes than humans and the reasons for these large genomes: duplicated sequences, pseudogenes, transposons, etc.<br /><br />The interesting thing is both the RadioLab presenters and Gregory avoid controversy by carefully avoiding to use the word "junk" when describing these sequences but Gregory was quite explicit in emphasising that these sequences which make up the vast majority of our genome are non-functional.<br /><br />You can listen to the episode here:<br />https://www.wnycstudios.org/story/asking-another-friend<br /><br />The relevant segment starts 41 mins into the episode<br />Aceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26311185258910872602019-03-12T15:29:04.472-04:002019-03-12T15:29:04.472-04:00Accepting a Young Earth, as AIG does, would seem t...Accepting a Young Earth, as AIG does, would seem to disqualify Jeanson from being taken seriously as a scientist. I often wish that geologists and astronomers would do some of the work to refute outfits like AIG, but they seem to leave that to biologists.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91016952079030853032019-03-12T15:26:16.339-04:002019-03-12T15:26:16.339-04:00It may not be just that ID advocates and creationi...It may not be just that ID advocates and creationists assume everyone is reading from some holy book. The Discovery Institute had, as a conscious and deliberate strategy, continually referring to evolutionary biologists as "Darwinists" so that could play the equivalence card. They wanted to be able to argue in court that since evolutionary biology was a religion of reverence for Darwin, that ID should be allowed into the classroom ("teach the controversy" being their slogan at one point).Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32798670737430710972019-03-11T23:18:34.219-04:002019-03-11T23:18:34.219-04:00It's a well known pattern that reveals a lot a...It's a well known pattern that reveals a lot about how they're thinking. <br /><br />Their thinking is based on the authority of a holy book so they approach science the same way, expecting to find the same sort of foundational texts, that can then be studied, picked apart, and attacked. Of course, that is not how science works, but if they understood how it works, they would not be creationists...Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4146928745270947782019-03-11T23:06:56.980-04:002019-03-11T23:06:56.980-04:00So far creationists in this thread have suggested ...So far creationists in this thread have suggested two books - one called "Replacing Darwin" and the other called "Darwin Revisited". Perhaps I could suggest to them my book "Getting Over Darwin: Why Darwin is Not the Be All and End All of Evolutionary Biology and How Obsessively Referring to Him Just Shows Your Ignorance of Modern Evolutionary Theory". (Disclaimer for the dullards: not a real book.)Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28078098200222526132019-03-10T15:54:22.887-04:002019-03-10T15:54:22.887-04:00"Dr. Nathaniel Jeanson holds a PhD in cell an..."Dr. Nathaniel Jeanson holds a PhD in cell and developmental Biology from Harvard University. He serves as a research biologist, author, and speaker with Answers in Genesis and formerly conducted research with the Institute for Creation Research."<br /><br />https://answersingenesis.org/bios/nathaniel-jeanson/<br /><br />There is nothing that Jeanson could say that hasn't been refuted many times over the past few decades. There is no reason to think that Jeanson can overcome his biases and present a legitimate case against evolution. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66652365852705213892019-03-09T21:38:28.012-05:002019-03-09T21:38:28.012-05:00So sorry about that Laurence. I hope the skeptic i...So sorry about that Laurence. I hope the skeptic in you would rise to the occasion and examine the Jeanson book, giving it proper review. If you would like to correct me on any important points, that would be good. I have to say I have greatly benefited from reading Sandwalk. It is great collection of useful data and fair discussion. (I am not trolling, but like to challenge stereotypes, and assumptions which I feel are not worthy of science. I am not suggesting that is the case on these pages).<br />Hopefully you might feel able to reply when you have got over the boredom I caused you. <br />Best wishesSM (Surrey UK)https://www.blogger.com/profile/01414950398626589050noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-178565871324314212019-03-09T15:22:47.343-05:002019-03-09T15:22:47.343-05:00yawn (not arrogant, just bored)yawn (not arrogant, just bored)Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31482223895672187552019-03-09T12:35:28.002-05:002019-03-09T12:35:28.002-05:00Mikkel, Please could you describe precisely why &q...Mikkel, Please could you describe precisely why "too simplistic, and exhibits typical creationist dichotomous thinking" ?<br />Thanks.SM (Surrey UK)https://www.blogger.com/profile/01414950398626589050noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41355587327350290962019-03-09T12:22:40.274-05:002019-03-09T12:22:40.274-05:00Good Evening All. I am with Peter Borger, I think,...Good Evening All. I am with Peter Borger, I think, on this problem. I need to reed his book too. Most of you are scientific evolutionists (some of you believe you are at least!), but what you have are models based on inferences which are unvalidated, or which are only partially validated at best. This whole argument is now being opened up with molecular biology and the associated rapid prototyping of experimental techniques for tracking genetic change from one generation to the next.(I am thinking about the Oxford professor Denis Noble's work in physiology as an evolutionist, and his many associated co-worker. Denis is no slouch and has a library of papers to his credit. Let's see where I think we are:<br /><br />There is compelling evidence that Darwinian change has little to do with some quite remarkable changes which enable an organism to rapidly adapt (or not, and fail) even in the F1 generation (Larmarkian-type change is well validated). It was otherwise believed that all profound changes came about via mutation and n.selection. But you guys also think you still need Darwin to power mass change to make new designs - you think.<br /><br />As stated, the evidence from both genetics and physiology is extraordinarily powerful for non-Darwinian origin of the major groups of life, but a development of life from those distinct and probably immutable groups. What we observe in the fossils is no Darwinian style changes whatsoever. The slow and gradual style of development isn't there, anywhere. If it is anything (and no-one denies change has occurred) then variations on an original theme of course figure, hugely. That is obvious, accompanied by extinction events. We do see stacked fossils in layers, but this demonstrates nothing of Darwin's idea, unless you want to attribute vast ages to each layer, which is not a good model, in many cases. <br /><br />Darwin was aware that this might be a problem, but believed it would be overcome with future discoveries. It hasn't been from the fossil finds, so what did scientists do? They started inferring all sorts of incredible homology stuff from the genes, which assumes, for example, that the ape to man transition occurred (chromosome change) somehow without killing off the species. Believers in this change will not, and cannot show a change control or functional specification diagram for the evolution of the chromosomal changes in man. This is required in engineering rather simpler man-made items, and fully necessary for this idea having the slightest chance of not being shot down by the problematic physiology it would trigger, and the serious (likely lethal) 'disadvantages' to the subsequent generations this could only have produced.<br /><br />If anything the science is even more equivocal, at best. That's not to say that direct evidence for a single 'creation' event exists, but the direction of travel now is strongly away from "Darwin only" and more in terms of bushes of highly active, rapidly adapting genomes that (as some point out) make perfect sense, when we look and notice how every last niche is STUFFED full of adapted life, but which still remains in groups common to the whole biome. There is no evidence anywhere that types of life were developed from other (proto) type-groups. The phyla, classes and many orders are distinct. Peter Borger is, I believe, on the right track. Well done Peter!<br />All of you should review another powerful book: Replacing Darwin, The New Origin of Species (Dr. Nathaniel T. Jeanson)<br />https://www.amazon.de/Replacing-Darwin-New-Origin-Species/dp/1683440757?language=en_GB<br /><br />Anyone who simply yawns arrogantly and refuses to read it, demonstrates their prejudicial bias against other workers who have laboured long to reveal potential new directions and more satisfactory answers towards universally acknowledge problems which, from many positions, look rather like dogma that has had its day and needs some fresh directions from new research.SM (Surrey UK)https://www.blogger.com/profile/01414950398626589050noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16061584862974503032019-03-04T17:10:47.636-05:002019-03-04T17:10:47.636-05:00"The problem is that information is defined i...<i>"The problem is that information is defined in a circular Darwinian way. Everything not conserved is not junk."</i><br /><br />Nobody says that any "not conserved" sequence is junk. First of all conservation comes in degrees, and it is entirely possible that a non conserved locus having previously evolved at a neutral rate has recently come under selection because it has taken on some adaptive function. Conservation is an indication, not absolute proof. It merely makes it possible to do estimations. <br /><br />Your analysis is too simplistic, and exhibits typical creationistic <a href="https://theconversation.com/the-thinking-error-at-the-root-of-science-denial-96099" rel="nofollow">dichotomous thinking</a>.Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23389708355359846412019-03-04T09:22:27.124-05:002019-03-04T09:22:27.124-05:00Cough*onions*cough.Cough*onions*cough.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77345067509862937692019-03-03T21:14:59.737-05:002019-03-03T21:14:59.737-05:00Unknown: "In general, there is no real junk i...Unknown: <i>"In general, there is no real junk in the DNA. The information in the genomes that is evolutionary constrained (essential information) is low, about 25% would be my best estimate, the rest is non-essential or redudant information for variation, adaptation and speciation."</i><br /><br />Okay, so in your worldview three quarters of the genome is needed as a store of variation for adaptation and speciation. A few questions spring to mind: 1) by what mechanism does such voluminous DNA accumulate for that 'purpose', and how would you distinguish that from the accumulation of junk that is predicted to occur in a finite population with a non-zero mutation rate (e.g. Lynch 2007, 2011)? 2) In what way does the abundance of repetitive, broken retrotransposon copies in mammalian genomes reflect this 'design' for adaptation and speciation? Note I am not asking if transposable elements can play a role in evolution, I am asking if the retention of large volumes of non-functioning copies of retrotransposons is consistent with the view that there is no such thing as junk DNA. 3) What methods have you used to arrive at your personal, unreferenced estimate (25%) for the proportion of DNA undergoing purifying selection, given that it is higher than many modern published estimates? 4) Given your thinking, do you predict a positive correlation between speciation rate and genome size?Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4193005654881057282019-03-03T10:48:59.123-05:002019-03-03T10:48:59.123-05:00@Mikkel, many thanks for suffering through that. ...@Mikkel, many thanks for suffering through that. So I don't have to. These folks are really good at stating dramatic conclusions. Less good at saying why they can dismiss decades of work by evolutionary biologists. In this case, hundreds of years of work by geologists too. Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60172202977218282722019-03-03T06:39:42.457-05:002019-03-03T06:39:42.457-05:00I was bored, so I watched it. You're not missi...I was bored, so I watched it. You're not missing out. Weird things said: <br />1) Apparently somebody did some gene knock out experiments on mice, and found that some of these knock outs did not seem to have any measurable effect on mice. That is taken to the conclusion that these genes can not have been selected by natural selection. <br />2) You would not expect DNA repair mechanisms under natural selection. <br />3) Natural selection keeps the status quo, and prevents evolution of organisms in any direction. <br />4) As "everyone in biology" today knows, information has nothing to do with matter, so DNA must have some "outside, immaterial source above matter". This proves biology has an "outside" source "above matter". Something about a guy with "a triple PhD" confirmed it. <br />5) Histone proteins are 100% conserved, they are exactly and completely identical in ALL organisms, ZERO differences between species. There are so many codes in biology, not just the DNA code. Histone codes, sequence codes, codes "almost beyond belief".<br />6) It is now proven that there is no universal common descent, and that has been proven that there was more than one origin. There is polyphyly instead of monophyly (a picture of a tree of life with a network webbing at the root is shown). This is "absolutely proven biological science". We don't come from bacteria, it is "absolutely not so".<br />7) The more you study biology, the more you realize it's a "design concept". Bla bla bla personal revelation, conversion in church, touched by God, babtised. <br />8) The "living spark" in vitalism is actually divine, and comes from the Holy spirit. It says so in the bible, apparently. <br />9) DNA is a four-dimensional computer program code. Whereas a "normal" computer code is only one-dimensional. <br />10) Apparently the immune system works by "genome compression" in some way, otherwise it the genome could not contain all the possible different antibody genes, which it has to be emphasized is a design and it comes from compression, not evolution. Definitely not evolution. It's just clever data compression. This also explains all the speciation after Noah's ark. <br />11) It's just compressed genetic "variability". It has to do with epigenetics, and transposons. Which is just God's way of making variety and beauty. It's "mistaken for evolution", but it's actually "pre-specified variability".<br />12) The final conclusion of his book is that "the genome itself generates the variability, so the role of natural selection is exactly zip".<br />13) Evolutionists and their just-so stories, they don't work. <br />14) In the last 15 years we have found completely new types of genes, RNA genes, which aren't translated into protein. They're ORFan genes, and they were first assumed to just be a fluke. <br /><br />22 minutes in and I'm getting cramps from eye-rolling. I'm out. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67624117066689505372019-03-02T20:29:27.464-05:002019-03-02T20:29:27.464-05:00I suspect I don't have to buy his book even if...I suspect I don't have to buy his book even if I don't watch the video. And that saves watching the video. Bonus!John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5578288892953252692019-03-02T14:56:25.173-05:002019-03-02T14:56:25.173-05:00Here's a link to a video discussion with Peter...Here's a link to a video discussion with Peter Borger who wrote "Darwin Revisited." Borger explains how recent developments in molecular biology can be more easily explained by creation than by evolution. If you watch the video, you won't have to buy his book.<br /><br />https://www.youtube.com/watch?v=SkJg3vi5NqkLarry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51736014591047559012019-03-01T09:50:54.818-05:002019-03-01T09:50:54.818-05:00Sigh.Sigh.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43876186838011433632019-03-01T07:41:16.707-05:002019-03-01T07:41:16.707-05:00Larry, how is you book going? Is it already availa...Larry, how is you book going? Is it already available or are you still working on it?Anonymoushttps://www.blogger.com/profile/06701043819428511370noreply@blogger.com