Talk:Evolution/Archive 30

message: "The evolutionary process of divergence, which ultimately leads to the generation of new species, is thought to occur usually without any gene exchange between the diverging populations. However, until the recent growth of multi-locus datasets, and the development of new population genetic methods, it has been very difficult to assess whether or not closely related species have, or have not, exchanged genes during their divergence. Several recent studies have found significant signals of gene flow during species formation, calling into question the conventional wisdom that gene flow is absent during speciation."Curr Opin Genet Dev. 2006 Dec;16(6):592-6. Epub 2006 Oct 19.   
Recent advances in assessing gene flow between diverging populations and species.Hey J.
Further while I agree gene flow is homogenizing, it can be useful as gene loss is significant in many examples of speciation and HGT and Hybridization can rejuvenate a genome and generate novelty and speciation. The last year has been a boom for HGT and hybridization studies. I guess we need to address this for NPOV. GetAgrippa 20:25, 15 January 2007 (UTC)
replies: text: It's also not written very well anyway, so let's change it. However, do keep the distinction with gene flow within a species and gene flow between species/highly diverged subspecies. In the former, it tends to homogenisation, but in the latter, it may create new species. Adam Cuerden talk 23:40, 15 January 2007 (UTC)
replies: text: Well put Adam. Why don't you give it a whack. GetAgrippa 23:52, 15 January 2007 (UTC)
thread_title: Gene flow section

message: I've set up a new page for this at Evolution/Gene flow - I've done an opening -  alas, without proper documentation, as yet - and sketched out the important categories we should cover. Adam Cuerden talk 13:39, 16 January 2007 (UTC)
replies: text: Now at Talk:Evolution/Gene flow - no subpages in articlespace, guys. Drafts and workspaces should hang off talk:. Opabinia regalis 02:06, 17 January 2007 (UTC)
thread_title:  Gene Flow Work 

message: I hesitate to mention this. The article is written in the perspective of the Modern Synthesis and NeoDarwinism-natural selection acts on mutations. The article is somewhat modernized using different nomeclature for allele or gene than the historical so now it refers to a genomic change. The  article should be modernized to introduce more modern ideas growing in the Modern Synthesis. There is a significant literature of articles and books that challenges the order. Jablonka and Lamb, West-Eberhard, Price, Agrawal, etc. believe that since (even Mayr)natural selection acts on the phenotype that organisms can speciate phenotypically before a genetic change or reproductive isolation-environmental driven isolation and then genetic change. It is recognized that even cloned genetically identical populations of cells will display differences just due to biological noise (stochastic and other)in gene expression even in the same identical environment and history-inherant nature of life. Models indicate a slight change in a protein could change the fitness of those organisms so evolution can be driven environmentally to produce phenotypes before a genetic change occurs. Phenotypic plasticity and epigenetic phenomena can be heritable and promote speciation.
Here is the intro from a MJ West-Eberhard paper: "The evolution of reproductive isolation is a defining characteristic of speciation. Reproductive isolation contributes to the diversification of species by creating genetically independent lineages, the branches of a phylogenetic tree. Each branching point of the tree of life is a speciation event. However, reproductive isolation alone does not create a new branch, because by itself it cannot produce the phenotypic divergence represented by the angular departure of a branch from the ancestral form. In the book celebrated by this colloquium, Systematics and the Origin of Species (1), Ernst Mayr called phenotypic divergence between populations "the other aspect of speciation." Mayr wrote that speciation has two parts: "One part... is the establishment of discontinuities," or reproductive isolation. "The other aspect is the establishment of diversity and divergence, that is the origin of new characters..." (ref. 1, p. 23). The origin of species differences, not reproductive isolation, were the main focus of Darwin's book On the Origin of Species by Means of Natural Selection (2). 
This second aspect of speciation, the origin of new characters, is the subject I address here. In particular, I will pursue Mayr's suggestion that "the workings of this process," the origin of new characters or novel phenotypic traits, "can best be studied if we analyze variation" (ref. 1, p. 23). I will take a close look at the origins of variation, starting with two simple questions. (i) Where does the variation, or the variant that makes a new trait, come from? (ii) What gets this second, divergence part of speciation, the origin of species differences, started?" 
I think the Modern synthesis concentrates so much on genotypes, gene allele frequencies, and reproductive isolation that it misses the point that it is the phenotype which is being selected upon. Maybe this kind of literature belongs in the Current Research in Evolutionary Biology, but it gives perspective. There are also a whole host of models to explain speciation and it would be nice to mention some. The reason being different models support different perspectives. It is just a suggestion. GetAgrippa 16:13, 17 January 2007 (UTC)
replies: text: I agree.  By the way, this is an initiative that I think needs to be carried out on the articles on Gene and Evo-Devo.  I think the key point is "It is recognized that even cloned genetically identical populations of cells will display differences just due to biological noise (stochastic and other)in gene expression even in the same identical environment and history-inherant nature of life. Models indicate a slight change in a protein could change the fitness of those organisms so evolution can be driven environmentally to produce phenotypes before a genetic change occurs. Phenotypic plasticity and epigenetic phenomena can be heritable and promote speciation."  This is why "gene as blueprint" and any overly genetic determinist view of evolution is just wrong, no matter how deeply embedded in the popular imagination. Slrubenstein   |  Talk 16:41, 17 January 2007 (UTC)
replies: text: Question: Is this really a weakness in the "gene as blueprint" analogy? Two houses that use the same blueprints will still be dramatically different from each other in many ways. In addition to simple random differences that will inevitably arise in two houses that use the same blueprints, there may be different constructors, and the environment (foundation, etc.) can have dramatic impacts on how the house is actually built. If I'm in error, could you explain to me more clearly why the "gene as blueprint" analogy is misleading? -Silence 20:56, 17 January 2007 (UTC)
replies: text: I have heard DNA is the blueprint for life, but not the gene is a blueprint. The old classic concept of the gene as a blueprint for a protein is no longer in vogue. It is a heritable unit of information. It is not neccessarily just a blueprint. If so it is encrypted and has to be interpreted into a useful blueprint. Messenger RNA is a blueprint for a protein, but the gene is not just about proteins-regulatory, gene networks, coordinated events, etc. I guess that kind of information could still be considered a blueprint. Natural selection and environment can influence all levels (gene interaction and gene expression) of the development into an organism so part of the blueprint is the environment or at least the environment can change which parts of the blueprint to use. Something to ponder is the experiment where mouse cancer cells were cloned and developed into normal mice (despite drastic mutations, chromosomal abnormalities, and altered gene expression during the development) at birth they just all developed tumors and cancer. Weird, Huh. GetAgrippa 23:56, 17 January 2007 (UTC)

text: I do not think the issue is throwing out the baby with the bathwater - I think we all agree on the importance of genes and natural selection, for example.  I do not think the issue here is moving to far in one direction or another in terms of models of evolution, I think the issue is that no good model of evolution was ever mechanical or deterministic (and the more we learn, the less mechanistic and deterministic we become) but that there has been a tendency in popularizations to make it sound as if evolution is a deterministic mechanical model. Slrubenstein   |  Talk 17:11, 17 January 2007 (UTC)
replies: text: The phrase the "gene as a blueprint" is not a trem I have heard before. I am familiar with the oft used analogy "DNA is a blueprint" from as far back as 1980 or so but it was qualified with the fact that blueprints are modified during the construction process to take into consideration other factors involved with expression within cells. UI don't know why the gene was introduced as "the blueprint" here. It certainly isn't appropriate (and I though we had managed to ditch it a week or so agao. Maybe I was mistaken? Candy 21:04, 17 January 2007 (UTC)

text: Just to clarify, I was using that just as an example of one kind of problem we need to avoid.  I was not trying to rehash a closed discussion, just clarify my point with an example. Slrubenstein   |  Talk 10:46, 18 January 2007 (UTC)
thread_title: Article perspective

message: Right now I am having trouble convincing some editors on intelligent design that the article may be giving undue weight to a non-magesterium Catholic position and also omits that theists reject intelligent design that contradicts evolution. It also omits that theists can reject it for reasons other than moral or ethical grounds, such as scientific grounds. My edit is at the bottom of  but is being rejected by only a few on . If you think what I said has some meaning then pls do weigh in. Thanks to all. (CptKirk 00:43, 19 January 2007 (UTC)
replies: text: I'm certainly not an expert on all things Wiki, but I really think this should be discussed directly on the ID discussion section.  I'm not sure what you're getting at, and I read what KillerChihuaha and Filll have said, and trust me on this, they both are always looking for any POV creep that occurs in edits in any Creationist article.  So they'd support you if they felt you were going in the right direction.  So, I'd go back to that page, make your case logically, and I'm sure that you'll get a say.  I do think there are a few editors who support Creation are using some out of context speeches by the current Pope to make their viewpoint that the RCC supports creation.  However, a careful reading of Ex cathedra statements and the Catechism of the church seem to indicate a rather liberal viewpoint of Evolution.  Orangemarlin 09:03, 19 January 2007 (UTC)
replies: text: Bit off-topic for this page, no?  Bitching and whining should generally be kept to the page to which said bitching and whining refers.  Thank you. •Jim62sch• 11:46, 19 January 2007 (UTC)
replies: text: If I can bitch and whine just a little longer (apologies •Jim62sch•) ...  For the record, accepting evolution has nothing to do with being "liberal".  Or conservative for that matter.  Politics need not interfere with scientific judgement (even if it often does).  Similarly, one can perfectly accept the doctrine(s) of creationism while being a liberal.  The polarisation of science along the political axis is not a ubiquitous feature of the cultural landscape of all countries.  Anyway, enough of my ranting.  ; )  --Plumbago 17:38, 19 January 2007 (UTC)
thread_title:  Evolution, the Catholic Church and Intelligent Design 

message: I recently saw this article(only available to signed-in members of the site) in Science and was wondering if it went in the evolution article, or natural selecion article, or whatever article. If it does, which one? Generalcp702 16:52, 20 January 2007 (UTC)
replies: text: I'm not sure what we can do about this link, since it requires registration.  i doubt you can copy and post it here.  Can you write a quick abstract?  Thanks. Orangemarlin 21:42, 20 January 2007 (UTC)
thread_title:  Experimental evidence?