Talk:Evolution/Archive 30

Gene flow section
"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)


 * 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)


 * Well put Adam. Why don't you give it a whack. GetAgrippa 23:52, 15 January 2007 (UTC)

Right. This needs a bit more referencing up, but I'm presuming you'll forgive that for now.... It's also a bit rough, as it's late.

Gene flow is the exchange of genetic variation between populations, most commonly of the same species (in which case it is simply an organism from one population migrating to the other population), but also between different species: Where two closely-related species have adapted for different environments, hybrids may form along the border between those environments, [Source: One of Gould's books. Alas, I forget which.] plants commonly hybridize (for instance, most commercially-grown wheat is a hybrid of three different species), [expand this a bit, I think] and Horizontal Gene Transfer in bacteria can share plasmids coding for beneficial traits even among greatly differing species.

Needs more work and length, but I'm dead tired. Tomorrow. But my idea is to use this, then use much of what we have as a section on within a species, then expand out to the hybridisation and HGT sections (probably nicking the HGT section currently up in variation) Adam Cuerden talk 01:11, 16 January 2007 (UTC)

Good suggestions. Hybrids also often are adaptive to extreme environments-alpine butterflies, wild sunflowers, etc. Hybridization in plants often overcomes fertility problems by polyploidy. I think the HGT and hybridization would do well in the Gene flow section. I can help dig up references. GetAgrippa 01:50, 16 January 2007 (UTC)

The Concept of A Theory
May I suggest a minor but critical change? The article does place emphasis on the misunderstanding of theory as "mere theory" in opposition to "scientific theory," but it would be much better to identify and define the word theory more specifically. In scientific terms, which I am familiar with, "theory" is an idea (a concept) that is supported by numerous proven hypotheses. In essence, a theory is, figuratively speaking, a pyramid, in which hundreds, maybe even thousands, of tested hypotheses lead to one general concept - the theory. Therefore, in the scientific community, unless evolution is proven incorrect, modified, etc., evolution is primarily considered a scientific fact. I am not speaking as a proponent of evolution, and I am neutral on this matter; it is my great hope that evolution and religion may one day conciliate. However, it is proper to say that evolution is strongly supported by and grounded in fact, and should not be titled "The Theory of Evolution," a name that unnecessarily fuels fundamentalist religious opposition, and is prone to misunderstanding by the average person. If anyone finds my considerations biased, please let me know before deleting my comments. Thanks. 06:04, 16 January 2007 (UTC)

And one final addition! Some might find my comments already discussed in the "Just A Theory" Discussion Archive. However, that is not the case. The article still lacks a basic definition of theory, something that needs to be addressed. Since it would take too long to discuss the facts of evolution and/or its standing in the scientific/social/religious community, it would be far better if the article mentioned my hypothesis-oriented definition. I sincerely want to add this definition and edit the article, but I want general consensus before moving forward. 06:14, 16 January 2007 (UTC)


 * Unfortunately, there isn't really enough room on this article to give an in-depth discussion of this topic on Evolution; and it is of peripheral relevance in any case, the main article for discussing such a topic being Theory. My recommendation is adding this information to Evolution as theory and fact, where there's more room for clearly explaining the distinctions. We cannot stop using "theory" just because it fuels fundamentalist misunderstandings, however; it is the common term in scientific discourse, and its usage as such outweighs colloquial usage in importance for a scientific article. -Silence 06:22, 16 January 2007 (UTC)

Thanks for your comments, but I believe you misunderstood me. I am not suggesting that we stop using the word "theory." I only wanted for there to be a slight reference to the hypothesis-oriented definition in the article, as there is already a short paragraph devoted to explaining the difference between the scientific and nonscientific versions. The article already includes a "Misunderstandings" section, in which the article explains that theory is not "just a theory," but "in science, a theory is simply an explanation" (Direct quote from article). Since an explanation is already included (a short one that needs at least some mention in the main "Evolution" article, rather than the "Evolution as theory and fact"), I think it is much better to improve upon the "simply an explanation" line and identify theory's roots as an idea supported by a collective body of proven hypotheses. I will, in a few days, commence enacting my suggestions. Look over it, and decide for yourself if it is too long for the article, and merits movement to the side-linked "Evolution as theory and fact" article. LifeScience 08:01, 16 January 2007 (UTC)


 * We did have a section on "just a theory" or "theory vs. fact" in evolution. You can view it at Misunderstandings about evolution, which is where that section is now. The problem is, evolution gets much too long if we put a huge amount of other material besides just the science in it. Anyone who is well-versed enough in science to read evolution already knows what a scientific theory is and does not need to have it spoon fed to them. For those who do not understand what a scientific theory is, there are links to the theory article and links to Evolution as theory and fact. Evolution as theory and fact is being rewritten and will include a lot more material and references soon. If you have more ideas, I would welcome them at Evolution as theory and fact.--Filll 14:32, 16 January 2007 (UTC)

I know what you mean. However, my additions would not be that long. I was suggesting that we change the article's rather meager line that states theory "in science, is simply an explanation." Furthermore, if you look at the article's section "Misunderstandings" (one of the listed subheadings), the article already begins to identify the difference between scientific and colloquial "theory" - something I wanted to expand perhaps one more line beyond the "simply explanation" definition. But I find further discussion of this topic unnecessary, as another user has already changed that line with a more proper, sourced definition. I'll check if the new definition flows with the overall content, and if not, I'll make some minor improvements. LifeScience 16:33, 16 January 2007 (UTC)


 * I gather that this definition of a theory comes from Hawking:
 * "a model of the universe, or a restricted part of it, and a set of rules that relate quantities in the model to observations that we make"
 * It does have some things to recommend it, however it is a bit vague I am afraid. If we are going to get into this level of detail, I would think it is more accurate to say that a theory is used to produce a model, and that model makes predictions which are then compared with observations, or something to that effect. However, I do not think that "explanation" is so bad for an encyclopedia article, especially one in a nonquantitative field like evolutionary biology.--Filll 16:43, 16 January 2007 (UTC)

Gene Flow Work
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)
 * 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)

Article perspective
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)
 * 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)
 * 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)


 * 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)

To some extent, I agree, but let's be careful not to go too far towards one branch of the research, to the exclusion of basic concepts. Adam Cuerden talk 17:05, 17 January 2007 (UTC)
 * 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)

Point. Let's do it. Anything with the Gene flow section rewrite that'll need adapted towards this? Adam Cuerden talk 17:21, 17 January 2007 (UTC)


 * 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)
 * 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)

If I understand correctly, all that is happening is that the model is being refined by understanding where in the model stochasticity arises. This is just reducing misspecification error, as they say in statistics, on the path to variance characterization and reduction.--Filll 14:14, 18 January 2007 (UTC)

I was just pointing out stochastic events (using two reporter fluorescent proteins in bacteria, these experiments have been done in genetically identical populations of bacteria to demonstrate noise) occur but I should add that evolution has generated means to eliminate this noise in many circumstances. Just like many behaviors like bird song are both genetic-nature and learned-nurture, development and gene expression are influenced by environmental factors and generate diverstiy that is not the result of mutation or genetic change. NeoDarwinism propose that random mutations in a population are selected upon and then reproductive isolation generate species. Populations of certain island lizards (limb length) and snails (shell thickness) have been proposed to be speciation by natural selection acting on genetic change, however studies revealed it was phenotypic plasticity and no mutations or genetic alterations had occured from ancestral populations, but it is simple the influence of the environment on gene expression on this population of lizards and snails. There are numerous models for speciation that make different assumptions or address different means of speciation.GetAgrippa 16:58, 18 January 2007 (UTC)

Lead
I've done a few minor tweaks of the lead - nothing at all major. Only thing really of note is breaking the first, somewhat unweildy sentence into two, and rearranging some of its clauses to make it clear that alleles are variant genes, not variant traits. Adam Cuerden talk 16:58, 18 January 2007 (UTC)

"In biology, evolution is the process in which some of a population's inherited traits become more common, at the expense of others, from generation to generation. This is usually measured in terms of the variant genes, known as alleles, that encode the competing traits. "

Perhaps we should mention what the process consists of : 1) Populations of interbreeding organisms demonstrate variability in heritable traits and 2) these traits can become more or less common due to either chance (Genetic drift) or the trait confers an increased ability for these organisms to survive and reproduce within their environment such the trait gains success in a population with successive generations (Natural selection). Then go into gene and also mention gene expression as the phenotype because that what nature really selects upon.

Here is a suggestion: "In biology, evolution is the process in which some of a population's inherited traits become more or less common from generation to generation. The change in traits within a populaion can be the results of chance or more often the success of a trait is conferred from its ability to increase survival and reproduction within a given environment with successive generations." GetAgrippa 14:40, 19 January 2007 (UTC)


 * HAve a look at the whole lead: that's dealt with extensively in paragraph two. The way I read the current structure is:


 * Paragraph 1: Definitions:
 * In biology, evolution is the process in which some of a population's inherited traits become more common, at the expense of others, from generation to generation. Simple definition
 * This is usually measured in terms of the variant genes, known as alleles, that encode the competing traits. Modern synthesis definition
 * As differences in and between populations accumulate over time, speciation, the development of new species from existing ones, can occur. - Procedural definition
 * All known organisms, living or dead, are related by common descent through numerous speciation events starting from a single ancestor. - "Top-down" definition, a.k.a. Macroevolution.


 * Paragraph 2: Processes involved


 * Paragraph 3: History.


 * I'm having problems with this sentence. "All known organisms, living or dead, are related by common descent through numerous speciation events starting from a single ancestor." The part I don't like is the "living or dead". Half the time I laugh becasue it reads almost childishly and the other part of the time I get perplexed as to how it will be interpreted by a reader. Surely time to replace them with "extant or extinct"? Candy 16:23, 19 January 2007 (UTC)
 * Extant is a bit obscure. Is there another term we could use? (past and present?) Adam Cuerden talk 16:41, 19 January 2007 (UTC)


 * sorry Adam, I beg to differ. It's a very common word used in the biological sciences. Besides, we use extinct. I don't think anyone scientist would accept that we use "transparent" and "not see-through" or "non-transparent" in a minerology article surely?  Is opaque is what would be used and it is as obscure as extant is imho Candy 18:41, 20 January 2007 (UTC)


 * The problem I see is that the current definition is just evolution by natural selection because traits are more common emphasizing a competition in traits. Traits also become less common or are maintained. I don't know if traits become more common at the expense of the other trait is appropriate. The new trait may be a modified ancestral trait or a completely new and novel trait so there is not trait competetion just a new solution to increase the ability to survive and reproduce. Species split so the ancestral trait is not neccessarily lost or defective but it is just the new or modified trait and new species that may follow has the advantage in a certain environment. Obviously in the environment of the ancestor the new or modified trait that spurred the change and new species had no advantage-the traits don't neccessarily compete but the environment selects on traits. GetAgrippa 16:57, 19 January 2007 (UTC)
 * Yes, but none of the variants actually deal with this, do they? "Change in frequency over successive generations" says *exactly the same thing*, only in harder to understand ways. And a new, novel trait that provides benefit *does* become more common at the expense of the old ancestral trait, except in situations where a gene is doubled (even in which case you can argue that it beecomes more common or less common relative to a "null" trait.) Adam Cuerden talk 18:48, 20 January 2007 (UTC)

True, but I don't think we should lose the genetic definition to cover it. I'd be inclined instead to add a procedural definition as sentence 3 or so, very simplified, as we'll be discussing it in detail shortly thereafter. Adam Cuerden talk 17:24, 19 January 2007 (UTC)

I agree and that is why the original change in gene allele frequencies was the most accurate. However I think most thought this too complicated and jargony. Evolution occurs and may lead to speciation. Evolution is not defined by speciation but speciation is a by product of evolution-evolution occurs within a species and may lead to speciation or just increase the survival and reproductive success of the current species. GetAgrippa 18:33, 19 January 2007 (UTC)
 * Agreed, but it does say "may lead to speciation." - It's not easy to get all the doubts and niggles into a short lead, but I think, over time, we've been moving towards greater and greater accessibility while maintaining accuracy fairly well. This'll be the next step in that process. Adam Cuerden talk 18:51, 19 January 2007 (UTC)

I think people don't generally see the distinction of Darwin's topic of origin of a species with procedural speciation. Evolution is a genomic change (change in gene allele frequencies) with successive generations and speciation is the process of reproductive isolation of a genome. Evolution the process of traits gaining success by increasing survivability and reproduction with descent, and speciation the processes of reproductive isolation. However that is a fine point for later in the discussion so you are right "may" covers it. Natural selection is the predominate pathway for adaptive evolution so it probably deserves the most attention for the intro also so discuss genetic drift later. I guess I am being too anal-ytical again. Sorry! GetAgrippa 19:54, 19 January 2007 (UTC)


 * So, what's a good one-sentence rocedural definition of Evolution to add to the lead? Having trouble thinking of one short and compact enough. 01:48, 20 January 2007 (UTC)


 * I don't know either but you are on the right track. I think I suck at communication in encyclopedia format. GetAgrippa 00:30, 21 January 2007 (UTC)

Evolution, the Catholic Church and Intelligent Design
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))
 * 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)


 * 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.  &#0149;Jim 62 sch&#0149;  11:46, 19 January 2007 (UTC)


 * If I can bitch and whine just a little longer (apologies &#0149;Jim 62 sch&#0149; ) ...  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)

Experimental evidence?
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)


 * 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)

Yes it is a good paper demonstrating predator driven natural selection. It reminds me of the example of character displacement in Darwin's finches (of course not predator driven). The only weakness is they didn't do genetic analysis to demonstrate true evolution. Phenotypic plasticity would produce the same effect and it could be heritable. Of course now this is considered evolution, but I am curious is it epigenetic or genetic given the rapid nature. GetAgrippa 22:15, 20 January 2007 (UTC)

I tell you some papers that have impressed me are the studies of Reiseberg on hybridization in wild sunflowers. He demonstrates that hybridization can produce adaptive evolution and reiterated the process of evolution. He demonstrated that the adaptive evolution to extreme environments was from hybridization and not mutation. He did so by creating synthetic hybrids from crossing ancestral parent species. The synthetics produced similar phenotypes and proved successful in natural conditions and similar to natural modern hybrid species. GetAgrippa 22:38, 20 January 2007 (UTC)