tag:blogger.com,1999:blog-37148773.post9211265023882401451..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Debating philosophers: The molecular geneLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-37148773.post-65424866997081673232017-05-08T17:39:03.008-04:002017-05-08T17:39:03.008-04:00If you threw in a random stretch of DNA into a gen...If you threw in a random stretch of DNA into a genome you could probably find an RNA transcript for that random stretch of DNA if you searched hard enough for it. This is why you need to distinguish between just being transcribed and being functional, something that the ENCODE people didn't do.Erichttps://www.blogger.com/profile/09481645265615126897noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62167212448731747082017-05-08T13:09:36.009-04:002017-05-08T13:09:36.009-04:00Generations of undergrads may thank you since they...Generations of undergrads may thank you since they won't have to learn the cis-trans test, but I think that cis-acting elements should definitely be included in your (and Futuyma's) definition of a gene. Mutation in a cis-acting sequence does, after all, lead to a heritable phenotype, which is the most deeply rooted definition. Frankhttps://www.blogger.com/profile/12634273226514511948noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6861259309506875832017-05-05T20:10:57.779-04:002017-05-05T20:10:57.779-04:00RE: Neo-darwinist philosophers vs empiricist (or p...RE: <b>Neo-darwinist philosophers vs empiricist (or physiologist) philosophers!?</b><br /><br />I certainly would concur with your acute observation of the fact that "<b>This is what I mean about philosophers of biology who seem to be out of touch with the discipline they are studying.</b>" -- [or more appropriately who seem to be out of touch with the discipline they are <b>reading and inferring!?</b>]<br /><br />This is because most philosophers have had <b>No</b> “first-hand training” in the “scientific methods and materials” technigues, at all; but merely “reading and inferring” certain theories of their interests: their interests -- being deeply rooted in the prevailing “physicalist, reductionist, and evolutionist perspectives” -- which have had since 1930s-40s been influenced and hijacked by the then newly formularized, synthesized, and dogmatized <b>Neo-Darwinism</b> (please see analyses @ <a href="http://sandwalk.blogspot.com/2013/12/is-modern-synthesis-effectively-dead.html?showComment=1389041508117#c4965021030211790764" rel="nofollow">RE: <b>Neo-Darwinism vs Darwinism: Is Modern Synthesis (MS) effectively dead!?</b></a>).<br /><br />Best, Mong 5/5/17usct19:10; practical public science-philosophy critic (since 2006).Mong H Tan, PhDhttps://www.blogger.com/profile/18303146609950569778noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19101724926277697402017-05-05T10:23:59.027-04:002017-05-05T10:23:59.027-04:00I don't understand your comment. You define a ...I don't understand your comment. You define a gene in terms of an open reading frame. Did you mean to exclude all "genes" for noncoding RNAs? I don't have your book. Did you create a new term for those sequences that specify ribosomal RNA, tRNA etc?<br /><br />Or did you just forget that there are genes that don't encode proteins? Your earlier papers, which I also critiqued, suggest that such genes weren't on your radar. For example, in your 2004 paper the only genes you and Karola discuss are protein-coding genes. <br /><br />But any biochemist or molecular biologist could have told you about tRNA genes—the first gene to be sequenced. I don't understand why you restricted your definition to protein-coding genes. <br /><br />This is what I mean about philosophers of biology who seem to be out of touch with the discipline they are studying. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74337936824147508292017-05-05T08:13:06.431-04:002017-05-05T08:13:06.431-04:00For some reason "Bruces' Philosophers Son...For some reason "Bruces' Philosophers Song (Bruces' Song)" and the "Decomposing Composers" song released on Monty Python's Contractual Obligation Album come to mind.steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54236571830088891092017-05-04T22:01:22.137-04:002017-05-04T22:01:22.137-04:00Stotz and I were following Tom Fogle (a biologist)...Stotz and I were following Tom Fogle (a biologist) who argued that 'gene' is defined by ideas about the prototypical gene (our list of features was meant to be like a prototype) and something is a gene if it has 'enough' of the same features (some cases will be borderline). Psychologists regularly treat concepts this way - prototype and similarity. We don't think this is always how biologists think about genes either, sometimes they take a more top-down, functional approach (does the gene job) as Larry suggests. Paul griffithshttps://www.blogger.com/profile/06372695408357184772noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73828104958623954682017-05-04T19:57:29.569-04:002017-05-04T19:57:29.569-04:00I'm fine with your definition. Just wanted to ...I'm fine with your definition. Just wanted to point out that the question of 'function' and what is meant by it then becomes important to the definition of a gene. I have a lot of respect for philosophers of biology and I follow some of these debates. However, I think that we can still do a lot of biology without perfect definitions of words like gene. As long as everyone having the discussion agrees on the subject being discussed, then we can often sidestep the definitional issues.Anonymoushttps://www.blogger.com/profile/08431171395642583259noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82099120731489756192017-05-04T15:29:23.888-04:002017-05-04T15:29:23.888-04:00Function has to be in there somewhere because othe...Function has to be in there somewhere because otherwise we can't distinguish genes from pseudogenes. <br /><br />We also can't distinguish between real genes and spurious transcripts. It may not be easy to figure out if some RNAs are functional but it has to be part of the definition of a gene. <br /><br />BTW, if you have a better definition then this is the place to tell us about it. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66726434925547915282017-05-04T14:14:06.446-04:002017-05-04T14:14:06.446-04:00Oh and then this will merge with the debate about ...Oh and then this will merge with the debate about ENCODE and how many transcripts are under purifying selection.Anonymoushttps://www.blogger.com/profile/08431171395642583259noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43521393635007836132017-05-04T13:12:13.068-04:002017-05-04T13:12:13.068-04:00I guess the debate then moves to determining the m...I guess the debate then moves to determining the meaning of a 'functional product'. The definition of function in biology has led to even more ink spillage than 'gene'. I don't have a horse in this race, but I thought I'd point this out.Anonymoushttps://www.blogger.com/profile/08431171395642583259noreply@blogger.com