tag:blogger.com,1999:blog-37148773.post7437557074876643428..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Gerald Fink promotes a new definition of a geneLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-37148773.post-72032297467071636212020-01-01T18:27:52.238-05:002020-01-01T18:27:52.238-05:00Or we could just dismiss you as a quack Or we could just dismiss you as a quack Truthhttps://www.blogger.com/profile/09738149296619817246noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36211161642293625002019-10-04T21:03:36.450-04:002019-10-04T21:03:36.450-04:00Larry seems to be suffering from FDS (Franklin-Dan...Larry seems to be suffering from FDS (Franklin-Dangerfield syndrome). He is not getting any respect!<br /><br />Please, let us respect Larry Moran's 40+ year view that DNA does all kinds of stuff, as it should do. and that junk DNA is prevalent in the genome because it doesn't 'appear' to do stuff, not that Larry Moran knows of at any rate.<br /><br />A note of interest. The following junk DNA string was discovered repeatedly in the Drosophila fly genome: T-A-G-R-E-S-P-E-C-T-A-G.<br /><br />that was fun. that was fun. back to wooooooorrk, people! Stevehttps://www.blogger.com/profile/15246115342112568778noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64087077423146953772019-09-12T16:59:34.318-04:002019-09-12T16:59:34.318-04:00He makes a big deal of the human genome project an...He makes a big deal of the human genome project and the idea that computers could only detect protein-coding genes. Here's a quote from the International Human Genome Consortium paper on the draft sequence published in Nature in February 2001.<br /><br />"Although biologists often speak of a tight coupling between 'genes and their encoded protein products,' it is important to remember that thousands of human genes produce noncoding RNAs (ncRNAs) as their ultimate products. There are several major classes of ncRNA. (1) Transfer RNAs (tRNAs) ... (2) ribosomal RNAs ... (3) small nucleolar RNAs (snoRNAs) ... (4) small nuclear RNAs (snRNAs). <br /><br />Other ncRNAs include both RNAs of known biochemical function (such as telomerse RNA and the 7SL signal recognition particle RNA) and ncRNAs of enigmatic function (such as the Xist RNAs implicated is X dosage compensation, or the small vault RNAs ...). <br /><br />... novel ncRNAs cannot be readily found by computational gene-finding techniques .... We can, however, identify genomic sequences that are homologous to known ncRNA genes using BLASTN or, in some cases, more specialized methods."<br /><br />The Consortium then identifies 497 tRNA genes, dozens of copies of each of the three ribosomal RNA genes, 97 snoRNA genes, 21 snRNA genes, 3 genes for 7SL RNA, 1 gene for RNAse P, 1 gene for telomerse RNA, and several dozed other genes for ncRNAs. They are listed in Table 20 in the paper.<br /><br />One wonders whether Fink or any of his students and colleagues ever read the paper. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21038991028024094822019-09-12T12:40:14.839-04:002019-09-12T12:40:14.839-04:00It's hard to believe that Fink had never heard...It's hard to believe that Fink had never heard of rRNA or tRNA. Did he think they didn't count? If so, why? It's a mystery.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33991344174571223662019-09-12T12:22:16.050-04:002019-09-12T12:22:16.050-04:00I see where you're coming from but I still thi...I see where you're coming from but I still think we need to use the word "gene." It's kind of awkward to be talking about the locus for ribosomal RNA production or the locus for production of triose phosphate isomerase. I think we can distinguish between different loci such as genes and regulatory sequences or genes and centromeres. <br /><br />Also, your definition seems to be restricted to loci that have a discernible effect on phenoptype but traditionally a genetic locus can also refer to neutral alleles such as those used in DNA fingerprinting. A locus can also describe the position of a pseudogene or a fragment of a transposon. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39765974045851750122019-09-12T12:07:45.288-04:002019-09-12T12:07:45.288-04:00We all want to think that our work is very, very i...We all want to think that our work is very, very important and in most cases it is! In Fink's case, his discovery of an important function for some excised introns is novel and exciting. However, the problem I'm addressing is deeper than that. It's similar to the inability of the ENCODE workers to put their results into the proper context.<br /><br />I just don't understand why there are so many prominent scientists who have never thought very deeply about the problem they are investigating. Did Fink really think that the experts in genome studies and molecular evolution actually thought that all noncoding DNA was junk? Did nobody in his lab, or at any of his seminars, ever correct him? Why not? Is this kind of superficial dogma pervasive at places like MIT and the Whitehead? Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19607863259388635592019-09-12T06:09:53.120-04:002019-09-12T06:09:53.120-04:00I prefer to use "locus" rather than &quo...I prefer to use "locus" rather than "gene" when teaching genetics. As Larry describes well, the term "gene" carries alot of historical baggage, including, at minimum, that the "gene" must be transcribed to have an effect on macro or molecular phenotypes. "Locus" bears no such baggage-- I use it to refer simply to a DNA sequence where polymorphisms exist that can have a discernable effect on phenotypes. For example, a mutation/polymorphism that alters a distant, protein-binding enhancer element could have substantial effects on phenotype but surely would not need to be transcribed-- even spuriously-- to exert that effect.SWoodyhttps://www.blogger.com/profile/12836410427909647462noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87186069856809614022019-09-11T22:24:42.554-04:002019-09-11T22:24:42.554-04:00I wonder how much of this is due to the desire to ...I wonder how much of this is due to the desire to have one's own work be very, very important. Find one functional intron, that's nice. But wouldn't it be more exciting to generalize that to all introns? Hype sells.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49458848483331189892019-09-11T22:05:52.529-04:002019-09-11T22:05:52.529-04:00He finds it remarkable that evoltions effects on g...He finds it remarkable that evoltions effects on genes has been so conservative.<br />A mouse and man very alike. <br />A reason for this is likely that genes are based on a blueprint and there has been no evolution affecting genes as thee should be.<br />He was funny and interesting. I understand he invented using yeast to help vaccines and medicine but i think others actually did those things.<br />However the use of yeast seems to be a real accomplishment as I understand it.<br />I didn't know it was questioned what a gene is.<br />i think a gene is a tiny memory byte. Just a tiny reflection of our own working memory.<br />Probably a trivial insight of mine. Robert Byershttps://www.blogger.com/profile/17226386832358052266noreply@blogger.com