tag:blogger.com,1999:blog-37148773.post1207744037356151800..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What do pseudogenes teach us about intelligent design?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger65125tag:blogger.com,1999:blog-37148773.post-23492075607788160382015-11-29T12:21:30.218-05:002015-11-29T12:21:30.218-05:00Sorry, the first paragraph above is a quotation fr...Sorry, the first paragraph above is a quotation from Fair Witness's comment and should have been italicised.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13221742175805998642015-11-29T12:18:50.979-05:002015-11-29T12:18:50.979-05:00It seems to be a ghost gene, but Tomkins makes an ...It seems to be a ghost gene, but Tomkins makes an interesting use of it: he proposes that the synteny argument is "null and void to begin with" because the sequence sits inside an active functional gene. This summary rejection apparently frees him from the obligation to address any details of the question of synteny (never mind the remaining pseudogene fragments). He has played this trick before, so it isn't a new weapon in his arsenal:<br /><br /><i>My analysis confirms that the site is located inside a gene called DDX11L2 on human chromosome 2. Furthermore, the alleged fusion sequence contains a functional genetic feature called a “transcription factor binding site”...</i> -- Sounds familiar, doesn't it?<br /><br /><a href="http://www.icr.org/article/new-research-debunks-human-chromosome" rel="nofollow">New research debunks human chromosome fusion</a>Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44794600308939202452015-11-29T12:03:03.484-05:002015-11-29T12:03:03.484-05:00And it's worth noting that GAMs are supposed t...And it's worth noting that GAMs are supposed to be miRNAs (and the patent has sequences for download, most of which are 22nt in lenght). Long noncloding micro-RNAs seem like a novel idea of Tomkins and a patently silly one at that...<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51578611753193959152015-11-29T11:00:32.337-05:002015-11-29T11:00:32.337-05:00Also, what exactly is the GAM (genomic address man...Also, what exactly is the GAM (genomic address manager) gene Tomkins talks about? I can't find much about it in the literature. The reference he links to (Bentwich 2007) is a patent, not a paper.Anonymoushttps://www.blogger.com/profile/04852803503240037336noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49407728109642166432015-11-29T07:24:12.098-05:002015-11-29T07:24:12.098-05:00It is my understanding that the vitellogenin pseud...It is my understanding that the vitellogenin pseudogene is over 20,000 base pairs in length.<br /><br />That's the chicken gene, not the human pseudogene fragment. The combined length of the 35 exons in chickens is 5,787 bp, or at least so they say here:<br /><br />http://www.ncbi.nlm.nih.gov/pubmed/3477646Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34839402791619397462015-11-28T20:16:38.610-05:002015-11-28T20:16:38.610-05:00PS Compare this nice post by Aceofspades25: LINKPS Compare this nice post by Aceofspades25: <a href="http://tinyurl.com/qgh6an3" rel="nofollow">LINK</a>Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48325579025225715172015-11-28T14:30:24.911-05:002015-11-28T14:30:24.911-05:00If you search Brawand, Wahli & Kaessmann (2008...If you search <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060063#s4" rel="nofollow">Brawand, Wahli & Kaessmann (2008)</a> for "150", you'll get zilch. But their "Supporting Information" incluldes Figure S2: <i>Sequence Alignment of the VIT1 Exon 3 from Human (Homo sapiens), Dog (Canis familiaris), Armadillo (Dasypus novemcinctus), and Chicken (Gallus gallus)</i>. That's where "a mere 150 base fragment of alleged similarity" comes from. As for what made Tomkins think it was the only matching fragment, I haven't the foggiest. Didn't he have a look at Figure 2 in the article and read the accompanying text? The autors say there what Fig. S2 illustrates (boldface added):<br /><br /><i>Exon 3 of VIT1 <b>reveals shared indels between human and dog</b> (Figure S2), which indicates that VIT1 was inactivated before the separation of the human and dog lineages (representing the eutherian superorders Laurasiatheria and Euarchontoglires) ∼90–100 Mya.</i><br /><br />They also say clearly that they<br /><br /><i>identified <b>a few VIT pseudogenic coding sequence remnants (mainly from VIT1 and VIT3)</b> with premature stop codons and frame-shifting insertion/deletions (indels) in regions syntenic to those containing these VIT genes in chicken (Figure 2 and Figure S1)</i>.<br /><br />So either Tomkins honestly believes the fragment of VIT1 Exon 3 shown in Fig. S2 is the <i>only</i> remnant of the whole VIT complex identifiable in humans (which means that he has a serious reading issue) or he is deliberately trying to mislead his readers (or, in plain English, he's lying).Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9878706667104886712015-11-28T11:37:19.045-05:002015-11-28T11:37:19.045-05:00It is my understanding that the vitellogenin pseud...It is my understanding that the vitellogenin pseudogene is over 20,000 base pairs in length. Where does Tomkins get this 150 number? And why doesn't he refer to the VIT1, VIT2, and VIT3 genes by name? And why is this "research" not published in a recognized journal? This smells like a very detailed strawman to me.Fair Witnesshttps://www.blogger.com/profile/02096585841391610098noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11053779511262497632015-11-28T05:35:30.169-05:002015-11-28T05:35:30.169-05:00The first sentence of the abstract already contain...The first sentence of the abstract already contains a lie (or, using a more generous interpretation, proof that the author has a reading problem), and the rest of the paper elaborates on it. Dr Tomkins is the Black Knight of the ID movement.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6986670890522076522015-11-27T22:38:46.174-05:002015-11-27T22:38:46.174-05:00Larry,
What do you make of this:
https://answers...Larry,<br /><br />What do you make of this:<br /><br />https://answersingenesis.org/genetics/dna-similarities/challenging-biologos-claim-vitellogenin-pseudogene-exists-in-human-genome/Anonymoushttps://www.blogger.com/profile/04852803503240037336noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46757749989682016942015-11-25T09:47:36.485-05:002015-11-25T09:47:36.485-05:00Speaking of gems from the old thread:
Laurence A....Speaking of gems from the old thread:<br /><br />Laurence A. MoranTuesday, February 12, 2013 9:13:00 PM<br /><br /><i>Explain to me again where the bases come from? What about the ribose - where does that come from? Did someone "poof" it into existence? As for nucleotides .... not possible.</i><br /><br /><br />Andre GrossWednesday, February 13, 2013 12:17:00 AM<br /><br /><i>Yeah where did it come from?</i><br /><br />Andre's great moment of science: "Yeah, <i>where</i>?"<br /><br />OMG, LOL, etc., etc.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58981307098258982582015-11-25T09:45:00.309-05:002015-11-25T09:45:00.309-05:00Sorry, that should be onion test, not onions test....Sorry, that should be onion test, not onions test.Vincent Torleyhttps://www.blogger.com/profile/18275683804952032659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32055302562843343312015-11-25T09:43:54.617-05:002015-11-25T09:43:54.617-05:00Three quick questions about the onions test, for a...Three quick questions about the onions test, for anyone who'd care to answer them:<br /><br />1. In his book, "The Evolution of the Genome," T. Ryan Gregory argues for the existence of a causal relationship between genome size and cell size, and he goes on to say that cell size influences a number of key physiological parameters, although the manner in which it does so varies considerably between different classes of organisms. He also points out that cell size influences body size and organ (as opposed to organismal) complexity. It's my understanding that onions have very large cells. (I'm not sure why.) If onions require large cells for physiological reasons, then could one argue that the large amount of DNA in their genomes, which enables them to have large size, thereby serves a function? if not, why not?<br /><br />2. In his article on the onion test, T. Ryan Gregory writes that different onion species vary considerably in their genome sizes. Do they also vary in their cell sizes?<br /><br />3. An old article in the Harvard Gazette (see http://news.harvard.edu/gazette/2000/02.10/onion.html ) suggests that some organisms have more DNA because they faithfully copy everything when replicating their chromosomes, whereas organisms (such as fruit flies) which are careless about copying junk DNA when replicating will quickly lose it, and end up with smaller genomes in the process. Has this suggestion been borne out?<br /><br />Thanks very much to anyone who can help me with these questions.Vincent Torleyhttps://www.blogger.com/profile/18275683804952032659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79180673982094951262015-11-25T09:35:39.119-05:002015-11-25T09:35:39.119-05:00That link to Venter on YouTube does not work.
Tha...<i>That link to Venter on YouTube does not work.</i><br /><br />Thanks. Fixed.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27275790777710742102015-11-25T04:07:11.909-05:002015-11-25T04:07:11.909-05:00New development, ID the future:
http://www.kurzwei...New development, ID the future:<br /><a href="http://www.kurzweilai.net/forums/topic/intelligence-design-lab-5-now-on-planet-source-code" rel="nofollow">http://www.kurzweilai.net/forums/topic/intelligence-design-lab-5-now-on-planet-source-code</a> <br /><br />Now carry on, my friends..<br /><br />Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34690730142566111972015-11-24T22:59:23.475-05:002015-11-24T22:59:23.475-05:00"Goodbye Robert."
Larry, please don'..."<i>Goodbye Robert."</i><br /><br />Larry, please don't ban Robert. If you do that, I fear that I will then be the stupidest person here. Well, except for Barry, and Beau, and...William Spearshakehttps://www.blogger.com/profile/09354659259971103985noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60510280225224612902015-11-24T14:33:42.737-05:002015-11-24T14:33:42.737-05:00That link to Venter on Youtube does not work. The...That link to Venter on Youtube does not work. The poster seems to be a serial violator of copyright. Do you have it somewhere else?DGAhttps://www.blogger.com/profile/14520104265481289172noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79631547297356516232015-11-24T09:20:33.449-05:002015-11-24T09:20:33.449-05:00He will be missed. If only in the sense that his ...He will be missed. If only in the sense that his absence will be noticed.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77735937119001565022015-11-24T08:09:39.652-05:002015-11-24T08:09:39.652-05:00Robert Byers last words were ...
The conviction o...Robert Byers last words were ...<br /><br /><i>The conviction of CD for us/primates leads to a too quick convicyion of how to interpretate genetic convergence.</i><br /><br />Goodbye Robert.<br /><br />Take your meds.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6602369914079345152015-11-24T04:39:00.990-05:002015-11-24T04:39:00.990-05:00Robert, what you've just said is one of the mo...Robert, what you've just said is one of the most insanely idiotic things I have read all day. At no point in your rambling, incoherent response were you even close to anything that could be considered a rational thought. Everyone in this thread is now dumber for having read it.<br /><br />What is "the new biology" and how could it possibly bring about hundreds of thousands of identical mutations in identical sequences in unrelated species?<br /><br />> Why not like bodies react in like ways to like needs or like problems<br /><br />Because mutations are stochastic. The vast majority of them happen randomly.<br /><br />> I bet their is lots of genetic things in us/primates but not because of the only option of common descent.<br /><br />Then suggest a reasonable alternative and provide the mechanism for how these common mistakes are highly targeted.Aceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44647333306957180112015-11-23T21:14:41.327-05:002015-11-23T21:14:41.327-05:00The Lorax
This stuff has every impression of being...The Lorax<br />This stuff has every impression of being involved or complicated. Other options for how biology works must be a option.<br />The original state for all like bodies could lead to like results for reasons that matter in those days.<br />I see no reason that like bodies would react the same way. CD is not needed.<br />Marsupials did and do have like bodies and the changes that brought the marsupialism, as i insist they are the same creatures as placentals, would be a factor in the genetics and not allow like genetics.<br />No one actually ever saw genetic evolution. and with its nature being one of complex and mystery its wrong to insist only this or that could be the origin for like genetic details in unrelated beings.<br />The conviction of CD for us/primates leads to a too quick convicyion of how to interpretate genetic convergence.Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6796700658659802172015-11-23T17:34:38.297-05:002015-11-23T17:34:38.297-05:00""Any sufficiently advanced incompetence..."<i>"Any sufficiently advanced incompetence is indistinguishable from malice."</i><br /><br />And its corollary: "<i>Any sufficiently illogical and inarticulate argument is indistinguishable from ID."</i>William Spearshakehttps://www.blogger.com/profile/09354659259971103985noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64245409482878233112015-11-23T16:30:05.080-05:002015-11-23T16:30:05.080-05:00Then explain why 'like bodies' share simil...Then explain why 'like bodies' share similar genetic sequences even though the genetic code is redundant. Why are identical amino acids in a protein sequences specified by codons that demonstrate common descent? Also Australia has some pretty awesome examples of 'like bodies' reacting in very different ways to get to the same point again supporting common descent.The Loraxhttps://www.blogger.com/profile/13361004494346338824noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5118498138588621832015-11-23T15:19:55.714-05:002015-11-23T15:19:55.714-05:00"Wow a person offers his opinion and the Darw... "Wow a person offers his opinion and the Darwin trolls are on high alert."<br /><br />You offered an opinion and other posters pointed out obvious flaws and problems with your scenario. This is not "trolling". If you are too thin skinned to take criticism, steer clear of areas like science and show business.<br /><br />Some questions for you:<br /><br />Why would the original pristine state of genomes contain no junk DNA?<br />Why did the intelligent designer create a system that inexorably degrades over time?<br /><br />Are there examples of other organisms in Earth's history that went extinct because their genomes degraded to the point that they all died?<br /><br />How much time have we got before our genome has degraded to the point that we all die?Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88676172347047121602015-11-23T15:12:47.634-05:002015-11-23T15:12:47.634-05:00Haha, that thread man. Fuckin ell. There was this ...Haha, that thread man. Fuckin ell. There was this gemstone in there though: <br /><br />steve oberski Thursday, February 14, 2013 5:11:00 PM<br />I think it's time to invoke Grey's Law:<br /><br />"Any sufficiently advanced incompetence is indistinguishable from malice."Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.com