Talk:Evolution/Archive 32

message: Evolution is a very complicated and, by many, poorly understood subject.  I can think of few articles more deserving of length than Evolution.  Longer articles are accepted for FA, and Evolution should not have to be pared down to be accepted. --Savant13 17:29, 23 February 2007 (UTC)
thread_title:  Reducing the article to 40 kB is bad 

message: As I mentioned above, I believe this is the first section we should focus our efforts on improving. Here is the current lead of the Evolution#Basic processes section:
Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing genes. Paleontologist Stephen Jay Gould once summarized this as "variation proposes and selection disposes". There is a certain amount of variation in apparent traits, or phenotypes, in populations. This phenotypic variation is primarily the result of genotypes, the specific genetic makeup encoded on DNA molecules. There may be one or more functional variants of a gene or locus, and these variants are called alleles. Most sites in the genome (i.e., complete DNA sequence) of a species are identical in all individuals in the population; sites with more than one allele are called polymorphic, or segregating, sites. Interactions between a genotype and the environment may also affect the phenotype through phenotypic plasticity.
We must keep in mind that this will be the first section readers are exposed to after reading the lead section. This is therefore by far one of the most important sections of the page, and needs to be one of the clearest and most informative areas.
The first three sentences are adequate (though I see the Gould quote as optional, since it isn't particularly enlightening to any uninformed readers), but lack a clear explanation of what "variation" is in the first place, in the context of evolutionary biology. Evolution#Variation does nothing to remedy this ambiguity. (I could also see a strong case being made for merging the contents of the "Variation" section with the first "Processes" para, since much of it is relevant to evolution in general, not variation. At the very least this section should be thoroughly rewritten.)
The fourth, fifth, and sixth sentences are not quite adequate, because they lack any explanation of what a "gene" is in the first place. As this is not explained anywhere in the lead section, it looks like somewhere near the top of "processes" is the place to do this, and it's very important that it be done. The fourth sentence is particularly opaque: what is a locus? What is a "site"? "Allele" could also be explained a bit more clearly, and it would be helpful to have a little information on the chemical basis of DNA, genes, etc. Lastly, the end of this paragraph will be complete gibberish to most of our reader base, and I question whether the info on polymorphism and phenotypic plasticity is even relevant here.
One of the central problems with this paragraph is that the topics don't coherently flow together. They seem to be a patchwork of unrelated factoids. The first two sentences discuss variation and its basic processes, but whereas one would expect this to be followed by a brief explanation of these processes (perhaps we could even move the one from the lead section to here, so as to make the lead section more concise and less jargon-heavy), what actually follows is a two sentences spent defining variation of genotypes and phenotypes, which one would almost expect to have been placed before the sentence on variational processes. Then, to make things even more confusing, just as readers are starting to get a grip on the new terms "phenotype" and "genotype", they're barraged with an opaque, technical tangent on alleles and genomes that fails to provide an understandable link to the overall topic, even though it shouldn't be difficult to do so (i.e., directly explain their relevance to variation and its processes). Rather than seeming like a discussion of various aspects of one cohesive topic, the paragraph comes across as a poorly-structured patchwork that will surely confuse or scare away casual readers. What is needed here is a reorganization, expansion, and clarification of this section to improve clarity and informational value for the reader.
Do any people here feel up to the task of rewriting this section? Unlike trivial debates over "see also" and "40kb", this portion of the article is an essential "heart" of the overall topic, and is something that genuinely needs a lot of serious work if this article's ever going to have a shot at FA again. -Silence 04:57, 8 February 2007 (UTC)
replies: text: Should we add in first paragraph's sentence a mention of gene flow:Genetic drift acts to randomly increase the occurrence of a trait, gene flow acts to homogenize a trait, and natural selection acts to propagate a favorable beneficial trait. I added a mention of gene flow, and I have noted many people take exception to "filter" so I offer "propagate" (reproductive success). Genetic drift doesn't randomize but randomly increases a trait as a stastical effect. I would also suggest: Interactions between a genotype and the environment may also affect the phenotype, and this is reflected in developmental and phenotypic plasticity. Maybe a better example of polymorphism would be in coloration of hair or bird plummage, or variations in butterfly or moths. This is much improved over the original version. My suggestion for the first paragraph doesn't fit in the structure as I look at, but I think Silence can fix it. Genetic drift acts randomly increasing the occurrence of a variation, gene flow acts to homogenize a variation, and natural selection acts to propagate a favorable variation as a beneficial trait. ??? Still awkward but I like Silence's idea for this sentence as it fits reality in that all the processes occur simultaneously. Population structure and other factors can influence what dominates but all can be at play. Sheez, It is a lot easier to criticize than offer solutions. I tend to become long winded as I think how to address it. I like it pithier. GetAgrippa 18:16, 8 February 2007 (UTC)
replies: text: I've tried to implement some of these ideas; feel free to fix anything you can word better (I'm especially unsure that I'm explaining polymorphism clearly). Could you clarify for me what you mean by "gene flow acts to homogenize a trait/variation"? We should try to word this more simply in the article. -Silence 05:10, 9 February 2007 (UTC)
replies: text: Well the more I think about it many editors would say just develop gene flow later in article. Gene flow tends to spread a gene around so it is homogeneous in a population. Often populations are isolated and migration can bring in new genes, or HGT, or hybridization within similar species. Because speciaton is usually the divergence and isolation of gene pools within a population to generate a new species, gene flow is usually considered to be counterproductive to speciation. I also think your example of polymorphism is fine. I think it is excellent sorry for the knee jerk. So lets leave like it is and move on to History? GetAgrippa 12:59, 9 February 2007 (UTC)
thread_title: Basic processes

message: User:GetAgrippa is proposing we reduce the external links to *these nine*:
#Understanding Evolution from University of California, Berkeley
#Everything you wanted to know about evolution (provided by New Scientist)
#Howstuffworks.com — How Evolution Works
#Synthetic Theory Of Evolution: An Introduction to Modern Evolutionary Concepts  (anthro.palomar.edu)
#Evolution News from Genome News Network (GNN)   (genomenewsnetwork.org)
#Understanding Evolution: History, Theory, Evidence, and Implications (rationalrevolution.net)
#Talk.Origins Archive — see also talk.origins
#National Academies Evolution Resources
#Charles Darwin's writings online
I see that he's proposing to drop the simulators as well. (None of these changes has been made yet). Reducing the number of external links is taken very seriously in FA reviews. (Some of the links being dropped may find a home in one or more subarticles). 
Please respond if you care about this set of external links, in either direction.  We need a Talk page consensus if at all possible. If you don't care at all, it would still be helpful  to get your comment. EdJohnston 15:52, 8 February 2007 (UTC)
thread_title:  Need your approval for reducing the external links to nine 

message: The theory of evolution by natural selection was first put forth in detail in Charles Darwin's 1859 book On the Origin of Species. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis.[5] With its enormous explanatory and predictive power, this theory has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.
This potted history seems a little awkwardly placed, and I think we'd be better off spending a little more time on, say, speciation, or universal common descent in the lead, instead of just a sentence in the opening paragraph.  Adam Cuerden talk 15:00, 9 February 2007 (UTC)
replies: text:  No, despite my remarks above, I like this bit, so please dont cut it. It satisfies the WP:LEAD bit about context and making the reader want to read on. Poujeaux 15:26, 9 February 2007 (UTC)

text: I don't see the need. Why not try to explain these things in the article text, rather than trying to cram everything into the lead section? -Silence 16:01, 10 February 2007 (UTC)

text: Well, I've always thought this lead was pretty good.  Are we looking for perfection (which reminds me of the old engineering adage, "the greatest enemy of good enough is perfection")?  This lead meets some minimum standards:  it's readable (and therefore accessible), it summarizes evolution in a few words, and is NPOV.  Let's not tweak it too much, or we might have all kinds of issues, not the least of which are complaints from the anti-evolution groups.  Orangemarlin 18:44, 10 February 2007 (UTC)
thread_title:  Should we lose the third paragraph of the lead? 

message: The bacterium Wolbachia has a deep impact on the evoltion of among athropods.  http://unisci.com/stories/20011/0208011.htm Where would it fit in in the article? 193.217.193.118 15:55, 9 February 2007 (UTC)
replies: text: Hmm. Arms races? Though I don't think we actually have a section on that... we really should. Adam Cuerden talk 17:45, 9 February 2007 (UTC)
replies: text: For that matter, Evolutionary arms race needs a lot of work too. Adam Cuerden talk 17:57, 9 February 2007 (UTC)
replies: text: Why not add it under a new section for "Competition", right above or below Evolution#Cooperation? We seem to over-emphasize cooperation in our current article, in order to help correct that old "survival of the fittest" misconception; but competition is highly important in evolution too. -Silence 03:57, 10 February 2007 (UTC)
thread_title: Wolbachia

message: I really appreciate the effort of cooperation to improve this article. I would be the first to admit that I can be contrary. It reminds me of the contrary indians in the movie Little Big Man with Dustin Hoffman. Anyways lets keep it going while we have the momentum. GetAgrippa 18:36, 9 February 2007 (UTC)
thread_title: Thanks to Editors

message: 1)  “Species problem”-I am unable to find the particular definition used in this article for the word “Species”.   It should be included so as to differentiate the word microevolution from macroevolution.
2)  Original research (OR) - I am also unable to find the particular reference for the following statements:
 “Evolution is also frequently misinterpreted as stating that humans evolved from monkeys”
::::Well, I think you are correct to ask for a citation but that will be an interesting one to get. However, I don't think it is OR. I mean this is simply overwhelming. For instance, a simple googling gives me this site which is so sad it's true 8((((  Candy 21:28, 12 February 2007 (UTC)
replies: text: Hi Candy,Thanks, you are correct; I think it is a NPOV omission.I wasn't able to find anything about monkeys at  (I did however find allot of expletives and emotional outbursts.) HFAS 00:06, 13 February 2007 (UTC)
thread_title:   “Species problem” and Original research (OR) 

message: If anyone cares, have a look at Wikipedia:Articles_for_deletion/Baraminology. Adam Cuerden talk 21:45, 12 February 2007 (UTC)
thread_title: Baraminology

message: The first sentence:
:In biology, evolution is the change from generation to generation in how common various inherited characteristics are within a population, usually measured in terms of the genes encoding them.
suffers from some awkward English.--Filll 00:04, 13 February 2007 (UTC)
replies: text: Could you be a little more specific? -Silence 00:19, 13 February 2007 (UTC)
replies: text:  Yes, Filll, this is still unclear, or at least causes the reader to stumble in the very first sentence, which is a shame. The difficulty is with 'in how common various inherited characteristics are'. One solution is to drop the 'how common' part as you suggest, In biology, evolution is the change from generation to generation in various inherited characteristics within a population, usually measured in terms of the genes encoding them. This is much more readable but I expect some will object to the oversimplification -  it is really not the characteristics that are changing. Or we could go back to the version with "frequency"! Sorry, I see silence has done something like this. The lead is now excellent I think! Poujeaux 13:45, 13 February 2007 (UTC)
replies: text:  Actually, it is the characteristics that are changing, at least in a sense. "Change in frequency of a characteristic" is a type of "change in a characteristic", from the perspective of change in organisms. If there is concern with such wording, it seems trivial to me. I simplified the wording in the first sentence; if anyone has any further suggestions, feel free to make more changes or comments. -Silence 15:01, 13 February 2007 (UTC)
thread_title:  Awkward English 

message: I am unclear exactly where in Wikipedia this should be dealt with, but I know the people who make such choices read this talk page. This New York Times article called Believing Scripture but Playing by Science’s Rules is worth reading for the issues and examples it raises (but not as a refutation of any part of science). One issue it raises is, Are you a scientist if you merely memorize the right things? Or is it more than that? Suppose you believe a 6,000 year old Earth yet write a science paper based on standard chronologies. Does your belief count agianst you?   4.250.177.25 00:58, 13 February 2007 (UTC)
replies: text: The appropiate page is Creation-evolution controversy. --Michael Johnson 01:38, 13 February 2007 (UTC)
thread_title: FYI

message: I am surprised that the article uses the terms "micro evolution" and "macro evolution." I thought those were invented by people who seek to discredit the theory.  Are there any accredited biologists who use the terms? A reference would be welcome. Jive Dadson 05:56, 15 February 2007 (UTC)
replies: text: Yes they are used by biologists, but not always in a consistent fashion or meaning the same thing. One well respected example textbook that uses the terms is Carroll's Patterns and Processes of Vertebrate Evolution. JoshuaZ 06:04, 15 February 2007 (UTC)
thread_title:  "Macro" and "micro" 

message: This Talk page is now up to 223 Kb, which is huge. How about I archive items 1 through 19 ('Phenotypic plasticity' through 'FA removed'). See Table of Contents for the numbering. That will leave items 20 through 35 in place, some of them very long, but many are still quite active topics. If you have concerns about this move, please respond. EdJohnston 19:16, 15 February 2007 (UTC)
thread_title:  Archiving proposal 

message: I would like to edit one sentence for clarity: "Given enough time, this passive process result in varied adaptations to changing environmental conditions." would, I think, read better as "Over time, this process results in varied adaptations to changing environmental conditions."
66.192.94.185 21:09, 15 February 2007 (UTC)
replies: text: I also have a suggestion. I agree that "Minor random changes" does produce speciation, but this ignores aneuploidy and ploidy where gene and chromosome dosage appears to play a role. Given the emphasis on polymorphisms later it seems reasonable to mention duplication events. While the genetic change at even given locus is random the loci are not random. Every genome sequenced to date indicates that evolution occurs in hot spots and some of the genome is immune to any changes. Ernst Mayr never believed that Kimura was correct with Neutral molecular evolution and in his last book before his death never even breached the subject (but that is POV). Also environmental induced mutagenesis is well recognized, so no changes without environmental stress or change. I'd just say "Random changes" because not all changes are minor. Of course there are examples of minor changes with speciation, but for NPOV I don't think you can say that with impunity. GetAgrippa 14:54, 16 February 2007 (UTC)
replies: text: Hmm. I've never liked either of those sentences anyway. Go for it.  Adam Cuerden talk 00:38, 17 February 2007 (UTC)
replies: text: Gave it a go. Minor tweaks. Does it read better?? I thought the anonymous suggestion was good so I added it too. Anyways the article is really tight and the intro is a good synopsis for a quick read. I think adding on to the history section was a good suggestion by Silence. The whole article is much more manageable. GetAgrippa 03:20, 17 February 2007 (UTC)
replies: text: "Minor changes" is limiting. "Alterations" in gene would include epigenetic change which is not a direct change in the gene but methylation or RNA directed gene silencing. GetAgrippa 04:00, 17 February 2007 (UTC)

text: Thanks for adding my anon suggestion (I have a username now :-). Now it looks much better, but I noticed a typo in the second sentence: "Minor random changes in the genes that encode these traits, produces new traits..." The subject is plural ('changes') but the verb ('produces') isn't. I would fix that myself but I can't find the edit button.SheffieldSteel 03:52, 17 February 2007 (UTC)
thread_title:  Small change to intro paragraph