Talk:Evolution/Archive 24

message: Some rough draft versions of infobox type tables on this subject are available for your inspection at Talk:Evolution/FactvsTheory.--Filll 16:09, 14 December 2006 (UTC)
thread_title: Potential infoboxes for fact vs. theory

message: I have talked about it but hadn't noticed that it is not mentioned in the article. Hybridization is significant in speciation in plants and birds to some degree (one in ten of known bird species and estimated to be much higher). There are also examples of mammals too. I think a plant person could give a sound argument to mention hybrization in plants especially. Perhaps a small section after HGT or mention it in the  mutations section.  GetAgrippa 00:54, 12 December 2006 (UTC)
replies: text: Oops! Hybridization is mentioned in HGT, but should be in Gene flow section.GetAgrippa 06:31, 12 December 2006 (UTC)
thread_title: Section on hybridization

message: Shouldn't HGT be included in Gene flow section? It would fit with Gene flow article that includes HGT. I guess hybridization should be included in Gene flow article also. GetAgrippa 06:24, 12 December 2006 (UTC)
thread_title: Propose fusing Horizontal gene transfer with Gene flow

message: Evolution by Natural Selection, an introduction to the logic of evolution by natural selection Maybe it will be back up later?--Filll 18:22, 12 December 2006 (UTC)
thread_title: Dead link

message: There is a common misunderstanding (which I think many biologists shared in earlier times), on the effect that evolution in itself should further stronger, more agile, more intelligent, or in similar respects 'better' individuals.  Nowadays (thanks to Richard Dawkins and others) I believe most agree that (long term) gene reproductive success is the only selective factor on an individual level.  Thus, sometimes selection will favour stronger individuals, but other times weaker ones; sometimes individual survival will be be favoured, but other times (as in the 'suicide' of mating drones) an abrupt early death is favoured, or (as with the sessile tunicates) less intelligence.
There have been some unpracticed editors adding things implying favouring the strongest.  This is probably due to such misunderstandings. I am slightly worried when an insightful 'editor pro' like User:GetAgrippa adds and survival on a number of places, where primarily only reproductive success is of interest (and better ability to survive only has a secondary interest, to the extent this furthers reproductive success).  I think this risks to increase the layman misunderstanding; and therefore, I'd like GetAgrippa to reconsider and preferrably remove these additions.--JoergenB 14:10, 13 December 2006 (UTC)
replies: text: All right; I'll compare with natural selection, too.--JoergenB 15:45, 13 December 2006 (UTC)
replies: text: I think you do make a good point that natural selection does not create perfect, purposeful, or more complex structures. This statement is true but there is no denying that organisms and ecosystems have become more complex. Science. 2006. 314:5803. pp 1289-91.Abundance Distrubtions Imply Elevated Complexity of Post-Paleozoic Marine Ecosystems.GetAgrippa 16:56, 13 December 2006 (UTC)
thread_title:  Avoid putting 'survival' on equal footing with 'reproduction' 

message: Consider something like the following:
-----------------------------------------------------------------------
In biology, evolution refers to the processes that cause a change in the features of organisms from one generation to another. The most important of these evolutionary processes is natural selection. Natural selection is a mechanism for choosing those characteristics which best enable an organism to survive and reproduce. When the organism reproduces, some of these useful traits are passed along to its descendents.
*First paragraph is compact. Just a few sentences. Fairly short. No big words that are undefined. Does not overuse "trait", but defines it by subtle means. Does not give a laundry list of traits.
These traits include pre-existing inherited traits, new traits produced by mutation, and those brought in by the migration of organisms from one population to another.This is known as lateral transfer of genes, or "gene flow". Gene flow is relevant when looking at populations, as opposed to the species as a whole. The information about these traits is carried in a unit of biological information called a gene. Genes are passed from the parents to the offspring. The study of how this happens is called genetics.  
*Now your laundry list of traits. And introduce the concept of genes. 
There are other processes in evolution besides natural selection. Given enough time, the passive processes of evolution can result in varied adaptations to changing environmental conditions and, eventually, the development of new species from existing ones--a process known as speciation. With its enormous explanatory and predictive power, evolution has become the central organizing principle of modern biology,National Association of Biology Teachers Statement on Teaching EvolutionIAP Statement on the Teaching of Evolution Joint statement issued by the national science academies of 67 countries, including the United Kingdom's Royal Society (PDF file)From the American Association for the Advancement of Science, the world's largest general scientific society: 2006 Statement on the Teaching of Evolution (PDF file), AAAS Denounces Anti-Evolution Laws relating directly to topics such as the origin of antibiotic resistance in bacteria, eusociality in insects, and the biodiversity of Earth's ecosystem.
However, evolution's putative conflicts with religious teachings have resulted in social and religious controversies since its publication.This article by G.R. Morgan documents one aspect of the debate from reaction against the milder theories of Darwin's predecessors to the present day.
The interested reader is directed to other companion articles where these controversies are explored more fully. 
*finish with your previous paragraphs, removing founder effect etc to footnote.
===Notes===
--------------------------------------------------------------------
Take a look at it and consider it. I think the first paragraph should be very accessible. Later paragraphs in the lead should have short sentences. There should be minimal parenthetical remarks. Readers should not have to look everything up in links.--Filll 14:34, 13 December 2006 (UTC)
replies: text:  I found this to be very concise.  It is a challenge to capture the spirit and details of such a complex topic in a few lines. This is the best I've seen to date. I hope others will support implementing this change. In addition, I would assume silience (which may be the response to your suggestion) as acceptance. If that be the case, then proceed with the change. --Random Replicator 14:40, 13 December 2006 (UTC)
replies: text: In biology, evolution refers to the processes that cause some traits to become more common over time. The term "processes" bothers me. Perhaps we should say:evolution refers to the fact that some traits become more common over time. I don't know perhaps a clever way to feed the trolls. A creationist can just add God in processes and be happy! Evolution is change with descent, so a strong statement of fact would be a good start. The "processes" often are theory that scientist debate. A simplestic example. Darwin's finches display modification with descent (evolution a fact). Natural selection can be demonstrated in Darwin's finches (a fact). A thirty year study of Darwin's finches demonstrated evolution was unpredictable. One could (I wouldn't) argue the significance of natural selection in this evolution. Well it makes the point.GetAgrippa 14:50, 13 December 2006 (UTC)

text: This theory is so perfectly general that it does not cover a single known special case.--Filll 15:01, 13 December 2006 (UTC)

text: If you have ever looked at something in the outer reaches of Category theory or differential topology, you will see what I mean. The reader is confronted with a snowstorm of terms which are very complicated, or have adopted new meanings that are not in any dictionary, or made-up words and a profusion of symbols from German Gothic, Greek, Glagolithic, Sanskirt and Hebrew scripts in strange fonts, with superscripts, subscripts, diacritical marks, sometimes written backwards or upsides down. There is very little recognizable that has any relation to arithmetic or algebra. The only numbers present will be page numbers. There are of course no applications mentioned, and none are apparent. Applications are beneath anyone who is working in such an erudite and involved area. Even number theory is looked down on as being too applied and "dirty".--Filll 15:15, 13 December 2006 (UTC)
thread_title: Introduction section again

message: --------------------------------------------------------------------
Take a look at it and consider it. I think the first paragraph should be very accessible. Later paragraphs in the lead should have short sentences. There should be minimal parenthetical remarks. Readers should not have to look everything up in links.--Filll 14:34, 13 December 2006 (UTC)
replies: text:  I found this to be very concise.  It is a challenge to capture the spirit and details of such a complex topic in a few lines. This is the best I've seen to date. I hope others will support implementing this change. In addition, I would assume silience (which may be the response to your suggestion) as acceptance. If that be the case, then proceed with the change. --Random Replicator 14:40, 13 December 2006 (UTC)
replies: text: In biology, evolution refers to the processes that cause some traits to become more common over time. The term "processes" bothers me. Perhaps we should say:evolution refers to the fact that some traits become more common over time. I don't know perhaps a clever way to feed the trolls. A creationist can just add God in processes and be happy! Evolution is change with descent, so a strong statement of fact would be a good start. The "processes" often are theory that scientist debate. A simplestic example. Darwin's finches display modification with descent (evolution a fact). Natural selection can be demonstrated in Darwin's finches (a fact). A thirty year study of Darwin's finches demonstrated evolution was unpredictable. One could (I wouldn't) argue the significance of natural selection in this evolution. Well it makes the point.GetAgrippa 14:50, 13 December 2006 (UTC)

text: This theory is so perfectly general that it does not cover a single known special case.--Filll 15:01, 13 December 2006 (UTC)

text: If you have ever looked at something in the outer reaches of Category theory or differential topology, you will see what I mean. The reader is confronted with a snowstorm of terms which are very complicated, or have adopted new meanings that are not in any dictionary, or made-up words and a profusion of symbols from German Gothic, Greek, Glagolithic, Sanskirt and Hebrew scripts in strange fonts, with superscripts, subscripts, diacritical marks, sometimes written backwards or upsides down. There is very little recognizable that has any relation to arithmetic or algebra. The only numbers present will be page numbers. There are of course no applications mentioned, and none are apparent. Applications are beneath anyone who is working in such an erudite and involved area. Even number theory is looked down on as being too applied and "dirty".--Filll 15:15, 13 December 2006 (UTC)
thread_title: Notes

message: I fused it all,but left all intact. It was confusing to talk about pop. structure and founder effect twice in both sections. It defines gene flow and genetic drift, and it adds the effects of population structure on natural selection and genetic drift and gives the special case founder effect. It also puts HGT with gene flow and founder effect with genetic drift. It seems reasonable. GetAgrippa 17:54, 13 December 2006 (UTC)
replies: text: Done. Adam Cuerden talk 00:51, 14 December 2006 (UTC)
thread_title: Fused Gene Flow and population structure with Genetic Drift

message: I admit that the reference that was just removed from the article was not directly related to biology, the editor had a good point. It is possible that more complex systems will be more able to survive. Should this be mentioned?--Filll 19:48, 14 December 2006 (UTC)
replies: text: I think that particular editor's statement about not "promoting" your own research was a matter of personal opinion.  See the comment on my talk page about referencing your own published work - according to the admin that I queried, that's a valid reference and totally ok.  It might have been helpful if there had been a better contextual tie-in to the topic, though--maybe you could have avoided the reversion . . . or maybe not.  But I don't think you violated any policies.--Margareta 04:57, 15 December 2006 (UTC)

text: Thank Margareta for the message. It is helpful to me.  The research was from some argues and thoughts several years ago.  I once heard that some people say that competition itself will make lots of things go complex.  Yes, it is true.  But competition will also destroy lots of things and turns them into random dirts.  Competition is just a rule. It does not necessarily favor more complex competitors.  There is a huge gap in the argument to be filled in.  So I have tried, based on some scientific theory (in particular computational complexity theory), to prove that more complex network systems (with certain constrains like negligibility requirements) do have probabilistic security advantages over their less complex counterparts (by the term "counterparts" I mean those entities with same structure but less scale in network size).  All listed publications were reviewed by 2 to 4 peer experts in the same research area of me.   Is this network-centric conclusion applicable to biology (if we treat a biological body as a network of living cells)? So far I am not qualified as a biologist to make any conclusion, but I believe it is applicable, and I am trying.   As an early notice to people who are interested in this topic, currently I am working on a cyanide poisoning analysis based on the same theory.    --Jiejunkong 19:51, 15 December 2006 (UTC)
thread_title: Entropy and life

message: Thanks to some of your input, I have rewritten the lead section again. Consider the following:
-----------------------------------------------------------------------
In biology, evolution refers to the changes in organisms from generation to generation. Some organism traits become more common over time. The most important of evolutionary process is natural selection. Natural selection is a mechanism for choosing those characteristics which best enable an organism to survive and reproduce. When the organism reproduces, some of these useful traits are passed along to its descendents.
*First paragraph shortened, removing some problem statements, wording, phrases. Still introduces the semi-technical word "trait" gently. Question: should "survive" be removed? It is more about reproduction and less about survival I think. Some rewording of the first sentence as suggested. An extra sentence is included as suggested. Possibly too many sentences? Question:How do we ensure we get it clear that natural selection applies to individuals and evolution to populations? Is this not clear from the paragraph above?
These traits include pre-existing inherited traits, new traits produced by mutation, and those brought in by the migration of organisms from one population to another.This is known as lateral transfer of genes, or "gene flow". Gene flow is relevant when looking at populations, as opposed to the species as a whole. The information about these traits is carried in a unit of biological information called a gene. Genes are passed from the parents to the offspring. The study of how this happens is called genetics.  
*Now your laundry list of traits. And introduce the concept of genes. 
There are other processes in evolution besides natural selection. Given enough time, evolution can result in a variety of adaptations to changing environmental conditions. Eventually, these changes can lead to the development of new species from existing ones, a process known as speciation. With its enormous explanatory and predictive power, evolution has become the central organizing principle of modern biology,National Association of Biology Teachers Statement on Teaching EvolutionIAP Statement on the Teaching of Evolution Joint statement issued by the national science academies of 67 countries, including the United Kingdom's Royal Society (PDF file)From the American Association for the Advancement of Science, the world's largest general scientific society: 2006 Statement on the Teaching of Evolution (PDF file), AAAS Denounces Anti-Evolution Laws relating directly to topics such as the origin of antibiotic resistance in bacteria, eusociality in insects, and the biodiversity of Earth's ecosystem.
*Word "passive" is removed.
However, evolution's conflicts with religious teachings have resulted in social and religious controversies.This article by G.R. Morgan documents one aspect of the debate from reaction against the milder theories of Darwin's predecessors to the present day.
The interested reader is directed to other companion articles where these controversies are explored more fully. 
*Break up some compound sentences for clarity. Removing putative. Still have a link to controversy page(s).  
Since the only purpose of that paragraph is to provide the link, it doesn't seem appropriate for the lead. Better to link it further down in the article.
===Notes===
--------------------------------------------------------------------
Take a look at it and consider it. I think the first paragraph should be very accessible. Later paragraphs in the lead should have short sentences. There should be minimal parenthetical remarks. Readers should not have to look everything up in links.--Filll 18:18, 14 December 2006 (UTC)
replies: text: It must be said that WP:LEAD does recommend a three to four paragraph lead for an article of this length, and they're pretty short paragraphs. Adam Cuerden talk 01:25, 15 December 2006 (UTC)
replies: text: Ok you've convinced me.--Margareta 04:59, 15 December 2006 (UTC)

text: I think that this basically says the obvious: that the rest of the article also needs some rewriting and reorganizing. I think that if you believed that the previous lead gave a clear description of evolution for the layperson, you are sadly mistaken. I could probably  find quite a few editors who would agree with me as well on this point. It is fine to get technical and fancy, but do it in the body. The lead should tell you what the article is about. Most people will read no farther. It should not include every bit of detail and minutae possible. If another section needs to be written so the reader understands the basics, then write one and include it. If the history section clogs it up too much, spin it off into a separate article. What you had before did not explain things for you. It was an awful mess, to be frank.--Filll 02:01, 15 December 2006 (UTC)
replies: text: Maybe I am blind, but where do I write "it is observed"?--Filll 02:04, 15 December 2006 (UTC)
replies: text: OK I was blind. I saw it. I agree that could be simplified. Good. In fact, I will change it now here.--Filll 02:05, 15 December 2006 (UTC)
replies: text: Oh, no.  I meant the current version, which seems a nice balance. My original version was probably still trying too hard. It's just that, well, your version seems to lack "flow". For instance, this section:
The information about these traits is carried in a unit of biological information called a gene. Genes are passed from the parents to the offspring. The study of how this happens is called genetics.
*First sentence repeats the word "information" twice. 
*"The study of how this happens is called genetics"  is excessively wordy and does not provide any particularly relevant information. Is this really one of the top 50 most important facts and concepts related to evolution? Because that's about the maximum number of facts we can get into the lead. 
*Between the first and second sentence, we have "gene. Genes" 
*Second sentence gives an accurate fact, but give no context for why this is important, nor does anything around it. 
*Each sentence provides no more than one fact, and uses more words than necessary to get to the point. Writing, in my opinion, should attempt to say something in as few words as can explain it clearly (which is possibly why I end up with so many clauses, but I think there's room between your style and mine that might be more appropriate.
Agreed though that we ought to continue by simplifying and reworking the rest of the article. Adam Cuerden talk 04:27, 15 December 2006 (UTC)
thread_title: Lead section rewritten again

message: --------------------------------------------------------------------
Take a look at it and consider it. I think the first paragraph should be very accessible. Later paragraphs in the lead should have short sentences. There should be minimal parenthetical remarks. Readers should not have to look everything up in links.--Filll 18:18, 14 December 2006 (UTC)
replies: text: It must be said that WP:LEAD does recommend a three to four paragraph lead for an article of this length, and they're pretty short paragraphs. Adam Cuerden talk 01:25, 15 December 2006 (UTC)
replies: text: Ok you've convinced me.--Margareta 04:59, 15 December 2006 (UTC)

text: I think that this basically says the obvious: that the rest of the article also needs some rewriting and reorganizing. I think that if you believed that the previous lead gave a clear description of evolution for the layperson, you are sadly mistaken. I could probably  find quite a few editors who would agree with me as well on this point. It is fine to get technical and fancy, but do it in the body. The lead should tell you what the article is about. Most people will read no farther. It should not include every bit of detail and minutae possible. If another section needs to be written so the reader understands the basics, then write one and include it. If the history section clogs it up too much, spin it off into a separate article. What you had before did not explain things for you. It was an awful mess, to be frank.--Filll 02:01, 15 December 2006 (UTC)
replies: text: Maybe I am blind, but where do I write "it is observed"?--Filll 02:04, 15 December 2006 (UTC)
replies: text: OK I was blind. I saw it. I agree that could be simplified. Good. In fact, I will change it now here.--Filll 02:05, 15 December 2006 (UTC)
replies: text: Oh, no.  I meant the current version, which seems a nice balance. My original version was probably still trying too hard. It's just that, well, your version seems to lack "flow". For instance, this section:
The information about these traits is carried in a unit of biological information called a gene. Genes are passed from the parents to the offspring. The study of how this happens is called genetics.
*First sentence repeats the word "information" twice. 
*"The study of how this happens is called genetics"  is excessively wordy and does not provide any particularly relevant information. Is this really one of the top 50 most important facts and concepts related to evolution? Because that's about the maximum number of facts we can get into the lead. 
*Between the first and second sentence, we have "gene. Genes" 
*Second sentence gives an accurate fact, but give no context for why this is important, nor does anything around it. 
*Each sentence provides no more than one fact, and uses more words than necessary to get to the point. Writing, in my opinion, should attempt to say something in as few words as can explain it clearly (which is possibly why I end up with so many clauses, but I think there's room between your style and mine that might be more appropriate.
Agreed though that we ought to continue by simplifying and reworking the rest of the article. Adam Cuerden talk 04:27, 15 December 2006 (UTC)
thread_title: Notes

message: It might be worth mentioning that some eukaryotic cells are as small or smaller than bacteria. That some bacteria have nuclear like structures. That the complexity (size of genome and number of genes)of the genome does not correlate with complexity. 
I agree that evolution doesn't neccessarily produce more complex structures or ecosystems, but it obviously has.
Science 24 November 2006:Vol. 314. no. 5803, pp. 1289 - 1292.Abundance Distributions Imply Elevated Complexity of Post-Paleozoic Marine Ecosystems Peter J. Wagner,1* Matthew A. Kosnik,2 Scott Lidgard1.GetAgrippa 23:45, 14 December 2006 (UTC)
thread_title: Evolution, compexity, devolution

message: I deleted two paragraphs in this section.
There are very controversial contents in the two paragraphs (if not scientific errors).
First, it is well-known in information theory, in Maxwell's demon paradox, the demon reduces the thermodynamic entropy of a system using information about the states of individual molecules; however, the demon himself increases his own entropy in the process, and so the total entropy does not decrease, thus resolves the paradox.  There are formulas in information theory textbooks to convert information entropy into thermodynamic entropy, and vice versa.  In a nutshell, the 2nd law does apply to information entropy.  The author of the deleted paragraph obviously did not know this scientific conclusion and misclaimed that thermodynamic entropy and information entropy are not interchangable.
Second, as the remaining paragraph explains, complexity-increasing biological systems may not violate the 2nd law of thermodynamics.  This is okay and this is where it should stop.  Clearly, the 2nd law of thermodynamics does not justify this complexity-increasing phenomenon either.  It's improper to list some irrelevant complexity-increasing things in the world to justify the correlation between the 2nd law of thermodynamics and the evolution theory.  The authors of the paragraph failed to explain the reasons why these texts should appear here.
--Jiejunkong 01:21, 15 December 2006 (UTC)
thread_title:  Entropy and life 

message: As things currently are, once you leave the lead, the next time you'll get any coherent description of Evolution itself is in the complex section on the Modern Synthesis, AFTER a long section on evidences. Surely we can organise things better than that! Also, it might be worth spinning out much of history of evolutionary thought. It seems a bit secondary for the main article. Adam Cuerden talk 01:44, 15 December 2006 (UTC)
thread_title: Restructuring

message: The layout of the summary section of the article looks, well, wrong.  The sidebar seems to be in the wrong place.  Any ideas of what's wrong? i kan reed 07:08, 15 December 2006 (UTC)
replies: text: I screwed up in editing. It should be ok now.--Filll 08:29, 15 December 2006 (UTC)
thread_title:  Layout seems to be broken 

message: I replaced the old one with a shorter new one with a couple of infoboxes, and a link to a much longer discussion with more references and detail. Hopefully this is shorter and clearer.--Filll 08:32, 15 December 2006 (UTC)
replies: text: While I appreciate the effort, I think you vastly oversimplified and this will cause confusion for many readers. Slrubenstein   |  Talk 12:46, 15 December 2006 (UTC)

text: You may mean "words" but I think you are wrong, and I mean "concepts".  "fact" is an English word that signifies an idea (thus, concept).  "Fact" is not a Spanish or Russian word, but the "concept" that English-speaking scientists mean when they use the signifier "fact" exists in those other languages, in the form of other words.  What we are talking about here is concepts, not the words that, in a specific language, refers to those concepts. Slrubenstein   |  Talk 13:15, 15 December 2006 (UTC)
replies: text: As I think about the discussion here, it seems to me that either you are not a native English speaker, and then this problem you are having is understandable. However, you might have to bow to those who are native English speakers in these matters, I am afraid. Another potential option, which I would rather not be true (but might be true, I fear) is that you are attempting to be overly pedantic. Certainly the text that you produced either shows a poor knowledge of English, or a voracious pendantry that manages to trip over itself and create nonsensical text. Sorry.--Filll 19:43, 15 December 2006 (UTC)
replies: text: Reading it over again, I have replaced the word "you" in my text with the word "one". If anyone is a nonnative English speaker, they might mistake my use of the word "you", and imagine that I am referring to the reader. I am not, in fact referring to Slrubenstein with the pronoun "you" above (at least not always). It is common in English (but confusing) to use "you" when in fact "one" or "someone" or "a person" etc might be more accurate and less likely to be misinterpreted. Sorry.--Filll 19:50, 15 December 2006 (UTC)

text: Fill is making two big mistakes.  First, he is assuming that editors own articles.  i do not claim to own the article.  I never added the Gould quote, I never made an argument about the Gould quote.  It is true I never deleted it but that is because I do not own this article; Wikipedia is a collaborative project.  Second, Fill is guilty of violating Wikipedia:No original research and perhaps Wikipedia:Neutral point of view.  He is deleting a verifiable cource because he does not agree with it.  Fill, we are not allowed to put our own views into articles.  It does not matter what you or I think of Gould.  Gould is a verifiable source, and was a respected scientist.  if you think there are other views than gould's which ought to be represented in the article, by all means add them - as long as you are drawing on verifiable sources, not just your own views. Slrubenstein   |  Talk 13:51, 15 December 2006 (UTC)
replies: text: I go away for a day, and there appears to be an edit war.  I disagree with you wholeheartedly Sirubenstein.  I hate to stand on a soapbox, but lets be honest.  A lot of people who will read this article have their mind made up about evolution.  They've listened to the uneducated Christian right in the US, and believe that we rose up in the Garden of Eden a few thousand years ago.  One of the persistently idiotic arguments of these christian mythologists is that Evolution is ONLY a theory.  Most of us who are brainwashed by Christian myth and dogma, understand what that means.  The religious nuts will believe whatever they want.  But the group of people who actually have an open mind and are still resistant to that mythology espoused by the Christian right may read this section, and think, "ok, that makes sense."  But when I read the Fact vs. Theory page, it really sounds like doublespeak.  Like I wrote before, it really sounds like a politician wrote it.  What Fill has done (with minor help from a few of us) really makes it easy to read AND does not change the essential character of the section.  I have no clue why you are so dogmatic about change.  And finally for all the good Gould has done, he comes across as a Ivory Tower intellectual.  His quote is really bad, but everyone seems to like it.  I understand what he's saying, but then again, I have multiple degrees in the sciences.  OrangeMarlin 18:49, 15 December 2006 (UTC)
thread_title: New fact and theory section

message: Please go to Talk:Evolution/LeadComparison for a comparison of the different leads. What direction do people want to go? Short and technical? Short and accessible? Long and accessible? Long and technical?--Filll 17:23, 15 December 2006 (UTC)
replies: text: Medium (no more than 4-5 reasonable paragraphs) and accessible.--Margareta 18:08, 15 December 2006 (UTC)
replies: text: I think it needs to have both short and accessible basic, and then advanced long and technical,or two linking articles. I do agree that the first paragraph in particular needs to be accessible to a broad audience with simple ideas-evolution is change or modification with descent. It is reasonable to mention shifts in frequency of gene alleles as it is the modern working definition. So some sort of compromise should be a viable alternative.GetAgrippa 18:26, 15 December 2006 (UTC)

text: I might note that many people here seem to want to pretend that this article has to be really sophisticated and cannot even drop down to undergraduate level in many places. Well if we want to do that, then let's be FULLY professional here and do what the big boys do. An abstract and an introduction, BOTH. This is not like explaining the different kinds of transportation that is available in Finland, or the types of food that people eat in Hokkaido. This is science. It is a bit more complicated and demanding (although this subject is not as demanding as people seem to want to pretend). So we should take that into account. --Filll 19:07, 15 December 2006 (UTC)
replies: text: I think the subject is sophisticated in its greatest scope (articles and books by the thousands 
over decades), but this is an encyclopedia. I do think the real advantage of Wikipedia is that it can be  a role model for encyclopedias with more current information and provide more specifc information than standard encyclopedias.Of course the info is useless if no one can understand it, so it needs to provide the info in a user friendly manner. It doesn't need to read like a science journal. I do like the idea of an abstract like prelude to the article. Then go ahead with Intro, Body, Discussion-Social, Fact vs Theory, etc. It will keep most of the previous work intact (with improvement where needed) and provide accessible info for quick review. I don't like all the time spent on misconceptions. It makes the article seem defensive and preoccupied witht creationism, even though it is only of secondary interest and not pertinent to the science of evolution. However, given the climate of this Wiki it has to be entertained. I find it incredibly annoying, distracting, and unproductive. In a perfect world I would just reference the articles on the social issues,etc. That is one of the major reasons the article is needlessly long is having to address these side issues.  Nothing to do about it really. I think there are so many elegant examples and beautiful images that would enhance the article. It is a shame really. A picture is worth a thousand words. GetAgrippa 21:32, 15 December 2006 (UTC)

text: Quite frankly, I think we're better tweaking the body before tweaking the lead again. Let's get it friendly and not too technical, *then* simplify the lead. That said, I far prefer C1. Adam Cuerden talk 01:10, 16 December 2006 (UTC)
thread_title:  Invitation to compare proposed leads to article 

message: I've rearranged the article into what seems a far saner presentation order, but haven't changed the text. Just put the more relevant sections first.Adam Cuerden talk 01:36, 16 December 2006 (UTC)
replies: text: Very smart. I like it. It makes a lot of sense to me.--Filll 02:12, 16 December 2006 (UTC)

text: I'm not convinced abstracts are advisaable, except in the trivial sense that the opening paragraph should contain only the most important facts about evolution. Most of the abstracts I'v e seen for this seem to be lumping everything into a few disjoited sentences, then someone else comes in and adds more jargon, and in the end it's only an abstract in the sense that you have to read the whole article to  understand it. Perhaps I'm unduly pessimistic, but I'd rather think of it as an opening paragraph that puts forth the most important concepts with minimum jargon. Adam Cuerden talk 03:02, 16 December 2006 (UTC)
thread_title: Rearrangement of sections

message: Regarding found on the Social and religious controversies section:
""Because animals that are inferior creatures do demonstrably exist, those criticising evolution sometimes incorrectly take this as supporting their claim that evolution is false.[63]""
Am I reading this the wrong way?
The way it is now suggest that there are "inferior" creatures just below human species, just the point it is trying to correct.
Evolution is the proof that there are no "inferior" or less evolved creatures.
201.233.30.222 05:04, 16 December 2006 (UTC)
replies: text: Just because a species is superior over another doesn't mean that the inferior species magically becomes extinct.  Also, sometimes due to unexpected environment changes the superior species can become extinct while the inferior species prospers.  Dionyseus 05:17, 16 December 2006 (UTC)
replies: text: 201 has a point here that the 'inferior creatures' sentence is badly phrased; it seems to concede the claim in the previous sentence that humans are 'superior'. Those words only really make sense in the context of a particular niche, which is not specified in this particular sentence. Opabinia regalis 05:31, 16 December 2006 (UTC)

text: I think the point is that the critics/creationists etc use these terms, and that is pretty easy to document.--Filll 13:55, 16 December 2006 (UTC)

text: I think that the section is not clear, but not because we do not describe why evolutionary biologists do not use the terms "inferior" and "superior". That might be useful, but I would only make it a footnote since it is another parenthetical remark. And the article is rife with parenthetical remarks that break up the flow and make it impossible to read.--Filll 14:55, 16 December 2006 (UTC)
thread_title:  Inferior creatures? 

message: As you're probably all aware, I rearranged the sections recently. However, though this was probably for the best, it has left a few problems, most notably in the headings not always being the right level, which is relatively trivial to fix, but it has left a few slight awkwardnesses in that a few sections could use a bit better introductory paragraphs. Most notably "Mechanisms of Evolution". I'm also not entirely sure about the order in this part:
* 1 Sources of evolution
** 1.1 Variation
*** 1.1.1 Mutation
* 2 Mechanisms of Evolution
** 2.1 Selection and adaptation
** 2.2 Recombination
** 2.3 Gene flow, genetic drift, and population structure (There's no particular reason why this should be one secion.
The headers "Sources of evolution" and "Mechanisms of Evolution" qare probably awkward. If someone can come up with something better, please, oh, aye, please change them. Adam Cuerden talk 22:01, 16 December 2006 (UTC)
replies: text: I made it one section because pop structure and founder effect was redundant to each section. We could have three separate section:Genetic drift, gene flow, and then population structure. GetAgrippa 15:10, 22 December 2006 (UTC)
thread_title: The Rest of the Article

message: With some trepidation, (cos this is a featured article) I have, in addition to straigtening out the slight glitch in the levels, introduced Cooperation as the 3rd principle of evolution after variation and selection, following Nowak's proposal in his stunning review paper in Science.  Nowak is the pre-eminent evoltionary dynamicist, totally mainstream, and what he suggests is so obviously correct (after all organisms only exist because "selfish" genes in fact cooperate - without cooperation we'd still be in an RNA Microworld) that I think it is well worth inserting. Do read his review paper in Science before reverting this! NBeale 00:18, 17 December 2006 (UTC)
replies: text: I'd be inclined to change it into a less anthromorphosising section title, if possible. Adam Cuerden talk 00:39, 17 December 2006 (UTC)
replies: text: Nowak has a number of Science papers (which one?-give full reference). Cooperation is talked about (not explicitly) in kin selection. Perhaps some mention should be made of cooperation in contrast with the selfish gene. GetAgrippa 12:36, 17 December 2006 (UTC)

text: I'm pretty sure there's more papers on this subject - indeed, Dawkins briefly references it in Selfish Gene (where he talks about genes meeting their same neighbours in organism after organism. It's also highly similar to important developmental biology concepts, where multiple layers of gene-controlled orginisation tend to interact, affecting both the lower and higher levels. That said, as it stands, it lacks depth. Can we flesh this out into a viable, less trivial statement, that references more papers? Adam Cuerden talk 17:54, 17 December 2006 (UTC)
replies: text: Yes there is lots more, although and is a rapidly developing field.  Nowak is considered the leading player in this, and a Review Paper in Science is a bit more than "only...one paper".  I've straightened out the wording a bit - agree it might be good to expand further but don't want to make the section over-long unless there is a consensus to do so. NBeale 07:24, 20 December 2006 (UTC)
replies: text: Don't need to mention Nowak's name just his work-sounds like advertisement (he is just one of many investigators). The article would be inundated with names otherwise. Content. The recent Science article on the evolution of complex ocean organisms and ecosystems the last 540 million years supports the notion of cooperation-ecological cooperation. Co-evolution of hummingbirds and certain plants also of interest. Oops I see a quotation. It needs to be paraphrased. GetAgrippa 13:50, 20 December 2006 (UTC)
thread_title:  Cooperation as 3rd Principle 

message: Also with some trep. I have (minor) added Anglicanism as a faith tradition with no probs with E. and (more substantially) straghtened out a couple of confusions in the controversy section. It's not just that humans are related to primates, all animals (indeed all life) is related.  And its not that E. shows that "humans are animals, and related", by that "humans, as animals, are related".  Everyone has always known that humans are, biologically, animals just as we are, chemically, bundles of chemicals undergoing complex reactions or physically, objects with mass about 50kg and specific gravity of about 1. The traditional religious claim is that we are "formed out of the dust of the earth" - E. gives a scientific account of how this was done.  But any claim that we are "nothing but" animals/chemicals/objects is unwarranted scientifically - there is no science of "nothing but". NBeale 08:24, 17 December 2006 (UTC)
replies: text: Your changes seem fine to me. However, I know next to nothing about the Anglican church so I request you ref it - maybe something from the archbishop of Cantebury? (The Catholic bit is of course easy to prove - Pope John Paul II issued an encyclical in support of evolution in the 90s). Mikker (...) 09:32, 17 December 2006 (UTC)
replies: text: Do you realise that you have just asked for something from the Primate of All England on Evolution ? This is such an old issue dating back to Darwin (e.g. Canon H.B. Tristram of Durham ) but the most recent statement could be,  I think, in which it is reported, Asked specifically whether creationism should be taught in schools, the archbishop responded, "I don't think it should, actually." But he added that opposing creationism in the curriculum was "different from discussing, teaching about what creation means."  Ttiotsw 21:58, 17 December 2006 (UTC)

text: Hi NBeale. I have a few issues with these statements of yours on this discussion page. The first is "Everyone has always known that humans are, biologically, animals just as we are, chemically, bundles of chemicals undergoing complex reactions or physically, objects with mass about 50kg and specific gravity of about 1". It is untrue that everyone has always known. I won't go into the history of scientific or religious thought but this statement is outrageous in every respect. It also makes no sense ... we are humans so what do you mean by, "humans are, biologically, animals just as we are..."? I appreciate you may be trying to straighten out a controvercy but you are also making one as well. Candy 10:17, 17 December 2006 (UTC)
thread_title:  Straightening out Controverises 

message: In this "fact and theory" section, as in the other sections of this article, I think one has to step back and decide what are the goals:
*Should this section be simple to understand, or pedantic and asbtuse?
*Should this section exhibit how learned the authors are, or how willing they are to communicate to the average reader?
*Should this section repeat the same failed arguments as before
*Should this section remained unchanged no matter what as a matter of tradition?
*Should the words of Gould be enshrined like the words of a god, unassailable and unquestionable?
*Should evolution scientists divorce themselves from the rest of science and the standards and language of the rest of science? 
*Should this section grow longer and longer to include all the text that has been created on this issue over the last several years?
*Who is this section for?
**academics in evolutionary biology?
**other academics?
**the average reader who wants to learn the various issues in the controversy?
**to give succinct clear arguments for people to use to defend themselves against creationists?
**to persuade people who are more or less undecided on the issue?
**to change the minds of creationists?
**to stop the arguments over this "fact and theory" issue which are basically a matter of confusion and misunderstandings?
I personally would argue that this section should be short, clear and simple to understand, meant to communicate to the average reader. I think tradition is not helpful on this issue. I think Gould was a smart guy, but let's face it, he was not some sort of genius whose every utterance was worthy of being worshipped from now until the end of time. This section should be useful to those trying to defend themselves against creationist attacks, and to educate those who want to learn about the issues. One will never convince "true believers" and the irrational and deranged and deluded, but one might sway the undecided if one is clear and avoid double talk. Just screaming "EVOLUTION IS A THEORY AND A FACT", with no explanation, over and over is worse than useless. It is handing victory to the creationists. Is this the true goal of this section?--Filll 18:05, 17 December 2006 (UTC)
replies: text: Here is an abstract from a 82' Science article from Gould that I think is a good example:
"The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level "individuals" as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, has strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level." That is Gould's style of writing. I don't think it is what Gould is saying as how he says it is the problem for some people. There is some merit that some people may not understand Gould because of his floral style. I am a big Gould fan so I don't want what he says to be lost in translation.GetAgrippa 21:49, 17 December 2006 (UTC)
replies: text: I would agree. I like Gould. I have read a lot of Gould material. I think he was a brilliant guy. But you are not going to win any arguments with that style and you will not defend yourself and your theory with that sort of argument. You will be cut to ribbons.--Filll 23:06, 17 December 2006 (UTC)
replies: text: In fact, I would say compare Feynman or Hawking with Gould. What Feynman and Hawking write about is far more controversial and shocking from just about any perspective. And yet, Feynman and Hawking write clearly about infinitely more complicated and controversial material. Stuff that is beyond human senses. And yet they get the point across. No need to put on airs and prance around.--Filll 00:04, 18 December 2006 (UTC)
thread_title: Have to decide on goals

message: I think this section could stand a lot more expanding out - it hints at several major biological concepts, but, ideally, we should be pulling them into the limelight. As my father arrives tomorrow, I can't guarantee I'll be able to do much, but some concepts we might include:
*Orginisational levels in developmental biology tend to interact with each other to modify the action of the genes in the levels above and below them. While to some extent competition between different orginisational levels, the manipulation of the levels allows many body plans to be created through the interaction of them, which is similar to cooperation
*Dawkins' The Selfish Gene itself mentions how genes tend to keep meeting the same groups of other genes, and thus can evolve to work with them well. Hence, Dawkins himself allows co-operation as a higher-order orginisation.
*The formation of complexity, with all its co-opting of other genes (and copies of genes) and such is a clear example of the formation of cooperative systems of genes. 
*Kin Selection is an important top-level version of this.
*T. H. Huxley's Evolution and Ethics Prologomena (fairly easy to find online) points out that ethics are necessary for society, and society provides protection from the struggle for survival, thus ethics can be evolved. 
Adam Cuerden talk 18:08, 17 December 2006 (UTC)
thread_title:  Cooperation in Evolution 

message: My father arrives in an hour for a long visit. Can someone do something about the awful Universal common descent and Common descent articles? They've been split, but not well. Adam Cuerden talk 11:05, 18 
December 2006 (UTC)
:Have a good visit with your Dad, and Merry Christmas! I had to bring home my aged mother and aunt for various health issues-broken arm, heart failure,etc. My father passed away ten years ago. I miss him. He was a Ph.D. then M.D.-family practice twenty years back to Med school to become a cardiologist for another fifteen years. His father was a Rhodes scholar and neurosurgeon then psychiatrist. I only wish I had half the brains and success as they, but they planted that seed to always grow. I was a professional student till I married and my wife said no more degrees. Anyways I digress, Enjoy your Dad and the holidays!!GetAgrippa 12:48, 18 December 2006 (UTC)
thread_title:  UCD 

message: Some critics of evolution claim that it is merely a theory. This criticism makes two claims: that evolution is a theory and therefore not a fact, and that theories are less established than facts (and less well supported than other beliefs). In other words, laypeople often use the word "theory" to signify "conjecture", "speculation", or "opinion". In science however, a theory is a model of the world (or some portion of it) that makes predictions that can be tested through controlled experiments. Evolution is a theory as it explains and interprets observations, and is used to make successful predictions.
:This paragraph is overly long and confusing. Some particular comments:
:*controlled experiments are not possible or necessary or part of many sciences, such as the observational sciences (astronomy for example). Can you do a controlled experiment with an earthquake? With a supernova? Nope? Well there are still scientific theories about them, nevertheless.
:*Some critics is as bit vague. I would just call a spade a spade; creationists. With references too.
:*It is using some hand waving about beliefs. Are facts beliefs? Are theories? The word belief is a bit of a loaded word when dealing with religion etc.
:*Not sure I like the word signify.
A second linguistic confusion has arisen around the word "fact". Fact is often used by scientists to refer to empirical data, objective verifiable observations. But fact is also used in a wider sense to include any hypothesis for which there is overwhelming evidence. In this usage "the sun is at the center of the solar system" and "objects fall due to gravity" are considered to be facts.
:*Again continuing to try to be overly wordy and erudite. You can be as abstruse as you like in the technical sections, as long as you are correct. But in these sections, you slit your own throat with being wordy.
:*Empirical data is experimental data. Again you have left out huge areas of science that rely on observations like oceanography and most of meteorology and astronomy etc.
:*As I discussed extensively on the controversy page, those two examples are not very useful in this context. For one thing, the sun is not at the center of the solar system. And the statement that objects fall due to gravity is essentially a meaningless content free statement. It is more akin to a definition. We call gravity that force that appears to pull objects towards the center of the earth.
:*Theory and hypotheses are confused in this paragraph as well
Evolution, the observation that populations of one species of organism do, over time, change and form new species, has been extensively supported by empirical evidence and has explanatory and predictive power: it is therefore correctly described as both fact and theory.
:*After wasting a huge amount of space in previous paragraphs explaining very little, then the statement that "evolution is a  theory and a fact" statement which is completely confusing and contradictory and irritating to most creationists is shoved in under the door. This is a long ugly compound sentence. And I am not sure that speciation has been directly observed, although I might be wrong. It certainly should have a reference if it has been directly observed.
The fact of evolution is itself explained using theories that provide deeper understanding: the causes of evolution are the mechanisms of natural selection, genetic drift etc. "The theory of evolution" is generally used to refer to the idea of evolutionary change ("descent with modification") together with the mechanisms that cause it.
:*Now even though the reader has very little idea about what the distinction between fact and theory is, he gets a sentence that uses them both in a confusing way, after having been told that they are the same thing sort of in the case of evolution in the preceding paragraph. Not good. Confusing at best. 
:*Now the phrase "the idea of" is shoved in to make things even worse and confusing and inaccurate. I do not believe that evolutionary change refers only to "descent with modification", but I might be wrong. Given the incredible amount of complication that has entered into evolution, I am not sure this is true. However, there is no need to restate this. That is what the rest of the paper is for. No reason to belabor constantly what evolution is and redefine and reredefine it again and again.  
:*This paragraph is wrong and confused and will just confuse the reader more. And will not convince anyone who is not already convinced.
So given this, I have to say I do not think this contribution really helps the situation. But I am starting to understand what the problem is, having discussed it on the Controversy article talk page  here and on this page.--Filll 01:09, 19 December 2006 (UTC)
replies: text: Though I welcome the critique, you lose credibility by failing to show anything positive especially having one said "some of the arguments resonate". If an editor is sincerely intending to improve an article you must do better than this. By resorting to hysterical rants and personal abuse we no where. I suggest you cool down for a bit before contributing to Wikipedia any more until you are able to contribute in a balanced and supportive way. — Axel147 16:55, 19 December 2006 (UTC)
replies: text: I would respectfully disagree. I told you explicitly previously what part of your suggestion I found appealing. Perhaps you missed it? I would be glad to find it for you again if you cannot find it. I would dispute your characterizations. I am calm. If it is determined through consensus that your version is the most appropriate and clear, then I will gladly accede. I am giving my feedback, which I believe I am allowed to do. You and others are free to ignore it of course, if you think it is in error or I have misunderstood. I would suggest that the most constructive thing would be to pay attention to my comments and those of orangemarlin and others.--Filll 17:09, 19 December 2006 (UTC)

text: I think that Axel147 is quite correct when he asserts that trying to understand the statement "evolution is a theory" in two or more different ways is overly complicated for the purposes of the section here. It might be quite appropriate for a more scholarly discussion of this entire area, however. I think that what the difficulties are pointing out here is the need for more careful scholarship to address the issues that have been copiously revealed. And that is the benefit of these discussions, however rancorous; there is clearly some underlying problems that are being exposed. --Filll 16:45, 19 December 2006 (UTC)
replies: text: I think we need to distinguish certain facts:evolution, natural selection, genetic drift (and gene flow), speciation, and microevolution are fact and can be demonstrated. Then the theory that these facts and mechaninisms are responsible for all the diversity that exists and has existed on this planet-macroevolution. There are huge amounts of information supporting the link, but that is the weakest link in the chain. The fact of random global extinctions and then boom of diversity has molded life to a great degree so add a little chaos to the formula. This was true of the Darwin's finch thirty year study-evolution was unpredictable. GetAgrippa 20:21, 19 December 2006 (UTC)

text: I am sure we have observations that support speciation. I am sure we have thousands or tens of thousands or hundreds of thousands of those. However, what I am curious about is how direct our observation of speciation is. For example, have we ever had a case where we had a species of fruit fly or something else in the laboratory that after enough generations, resulted in two or more species that could not interbreed? Have we ever had bacteria in the laboratory that we watched over many generations that resulted in two or more divergent species? I know the nylon eating bacteria might be viewed as a new species observed in the field. This is almost a direct observation of course, and might suit my purposes. I presume that the nylon eating bacteria would be judged a separate species from regular bacteria, although they are not a species that has sex so it might not be the example I want to use. The reason that I am asking is that one of the objections raised constantly by creationists is that "yes, we creationists will concede that evolution happens but only results in small changes, never in speciation." I would love to have a reasonably good example to shoot them down with.--Filll 01:07, 20 December 2006 (UTC)
replies: text: The stickleback fish has become a supermodel of evolution studies. Here is a good review by Elizabeth Pennisi:Science 18 June 2004:Vol. 304. no. 5678, p. 1736 Changing a Fish's Bony Armor in the Wink of a Gene. More recent articles determine that shifts in ectodysplasin alleles correlate with speciation within decades time frame. There is also a good Science paper on genomic change and speciation in Siberian warblers as I recollect, and a large number of plant examples. The review article has some dramatic images demonstrating the changes in spines and lateral plates with speciation in marine and freshwater fish populations. I always thought the images of lateral plate loss was  dramatic evidence of evolution.
Here is a recent plant paper from Science:Science 29 August 2003: Vol. 301. no. 5637, pp. 1211 - 1216 Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization Loren H. Rieseberg,1* Olivier Raymond,2 David M. Rosenthal,3 Zhao Lai,1 Kevin Livingstone,1 Takuya Nakazato,1 Jennifer L. Durphy,1 Andrea E. Schwarzbach,4 Lisa A. Donovan,3 Christian Lexer1. 
Here is a Science bird paper that is interesting:Science 21 January 2005:Vol. 307. no. 5708, pp. 414 - 416
Speciation by Distance in a Ring Species Darren E. Irwin,1* Staffan Bensch,2 Jessica H. Irwin,1 Trevor D. Price3. There are others but I get Science and it is easy to search for general papers on evolution. 
Here is another Science review paper by Pennisi. She must have more Science papers than anyone. Science 10 March 2006:Vol. 311. no. 5766, pp. 1372 - 137.Speciation Standing in Place.Elizabeth Pennisi.
Here is heritable phenotypic plasticity and evolution in birds Science 14 October 2005:Vol. 310. no. 5746, pp. 304 - 306. Selection on Heritable Phenotypic Plasticity in a Wild Bird Population 
Daniel H. Nussey,1,2* Erik Postma,1 Phillip Gienapp,1 Marcel E. Visser1 GetAgrippa 02:49, 20 December 2006 (UTC)
thread_title:  A preliminary inspection of the present fact and theory section