Talk:Evolution/Archive 36

What's it all for, anyway?
Let me just say first off, Silence rocks.

I am in the middle of massive projects in real life right now, so haven't had a lot of time to commit to this or other articles lately (and won't for awhile), but there has been something buzzing around in my mind for awhile that I really want to bring up. It came to mind during one of the numerous discussions over the lead. It seems that we here have been ignoring--or are simply unable to follow--the cardinal rule of good writing: know your audience. There is a lot of back-and-forth on length, how much detail to include in the lead and the article, how much "jargon" to use, how much background to expect etc., with different editors clearly holding different opinions on the matter. But we haven't really asked what it is that we think readers want from this article.

TxMCJ drew attention to the fact that this page is the first one that comes up on a Google search of "evolution." So who's Googling "evolution?" What information are they looking for? I think little bit of dicussion of this question could go a long way to helping focus the article, and in particular improve the lead (which, as you all know, is what most people will read).

Chances are we can come up with a few categories of people who will be browsing to this article. Of course we can't know for sure, but I think for the most part this is a fairly perceptive bunch of editors, so we can make a good start. Once we have those categories, I think it would help to make sure that the lead, at least, provides something for each of them, directing them, if necessary, to the article or section that will answer their questions. It might also help with the occasional discussions that come up over moving, renaming, splitting, etc. the main article.

So I'll start with some ideas:


 * People Googling "evolution," or searching for it on Wikipedia, may include:


 * People like TxMCJ, who are well-versed in the subject but want to see what else is being said about it. Probably these people should not be considered part of this articles true "audience."
 * People who know little about the subject, or who may have gotten some misleading information in the past, or who have heard one side or another of the ID-evolution "debate" and are trying to find more information to make up their own minds (I originally came to this article looking for a good place to point these sorts of people to, as I found I could locate remarkably little about evolution that was written in an engaging, lay-oriented style).
 * High school or even university students looking for something to use in an assignment.
 * People who know a little about biology, or maybe just saw a documentary or zoo/aquarium exhibit that piquesd there interest, and want to learn more.
 * Creationists wanting to see if there is "bias" in the articles and "correct" it if they find it. (Again, probably not our target audience--unless they are what I would call "soft" creationists, i.e. folks like those in #2 who may be fence-sitting or leaning towards ID because they heard some convincing, but incorrect, arguments, in which case providing them with corret information could help bring them around).

Additionally, considering that most people will read only the lead, and that they will probably remember at most 2 or 3 main concepts from it, what is the "take-away" message that we want them to have after they read it? If they remember one thing a month from now, what should it be? Agree on that, and you'll be halfway to the perfect article IMHO.

Finally, I'm sure most of you have seen the National Geographic article from a few years ago, "Was Darwin Wrong?" This is one of the best lay introductions to evolution I have seen, and perhaps some of it could be used as a model for this article. If you haven't seen it, do check it out.

Ok, I'm outta here for awhile. I'll be back in a few weeks to help copy-edit and cite check. A big thanks to every single one of you for all the work you're doing here.--Margareta 15:48, 13 April 2007 (UTC)


 * Hi -- I would like to point out that my interest in this article has nothing to do with "wanting to see what else is being said about it", and everything to do with the fact that I'm a science educator and would like to see all of the people in the categories below * above have immediate access to a quality, accurate, and complete article. I have stated this point on a number of occasions. Thanks TxMCJ 16:25, 13 April 2007 (UTC)
 * Man TxMCJ you don't get a break. Even if you were an elitist egomaniac that doesn't deny your valid concerns and contribution to the article (as you pointed out there was some basic information either partially described or not at all). As I have said before this is often a poor medium to communicate and often debates are semantic, often editors can jump the gun in conclusions without fully researching the debate and proponents, and some people are just abrasive (but who cares if they do good work!). The process can be like a ward of bipolar obsessive compulsives arguing over the meaning of life.GetAgrippa 17:06, 13 April 2007 (UTC)
 * I don't think Margareta's post was in any way intended to be critical of MCJ. Gnixon 17:12, 13 April 2007 (UTC)
 * No, it really wasn't. Had I thought that there was any way to construe what I said as critical of anyone, I would have left any and all user names out of my comment--as I wish I had done, because regrettably it seems the point I was trying to make was totally obfuscated by this little sidetrack.  And for the record, I have never said, nor do I believe, that anyone's concerns are invalid.--Margareta 21:38, 14 April 2007 (UTC)
 * Jeez I made my own point about a poor medium to communicate. I just described myself, and bipolar obsessive compulsive probably fits also. Sorry! My misunderstanding!GetAgrippa 17:15, 13 April 2007 (UTC)
 * The meaning of life is obviously cheese. Graft | talk 17:38, 13 April 2007 (UTC)
 * 42 Gnixon 17:39, 13 April 2007 (UTC)
 * (*Re-threading this to keep individual comments together, and small edit to TxMCJ's comment so the re-threading makes sense...) Sorry, of course that's what I was trying to say, but of course you can state your intentions better than I.  What I meant was, seeing "what else is being said about it" is the first step in  finding out if "what else is being said" amounts to "immediate access to a quality, accurate, and complete article."  After all, if you'd found that when you came here, we wouldn't be having this discussion, right?  And a "quality, accurate, and complete article" might amount to different things for different groups.--Margareta 16:40, 13 April 2007 (UTC)


 * Excellent points. I would add as major components of the readership
 * Undergraduate biologists learning the field, wishing to "read ahead" or read deeper, and wanting to help out by editing the stuff they already know about.
 * Grad student biologists, a more advanced version of the above breed, possibly with more time and inclination to contribute.
 * I would also suggest that creationists, particularly "soft creationists" (as defined by Margareta) are a larger part of the readership than most editors here appreciate. I think we could better address the interests of those readers without turning this article into creation-evolution controversy.  Gnixon 15:59, 13 April 2007 (UTC)

Sections
In hopes of provoking a better organization of the article, here are some thoughts on the major sections:


 * Basic processes Probably too detailed and certainly misplaced.  Why are we leaping into genetics immediately after the lead?  Section doesn't follow its intro, which refers to drift and selection, in the next section.  Why are there separate "Variation" and "Mutation" subsections?
 * Mechanisms of evolution Starts out well with a reasonable discussion of natural selection and adaptation.  Again, too much -level enetics in the rest of the section.  Having more than "natural selection" and "genetic drisubheadings is inconsistent with the intro.  "Speciation" is not a mechanism.
 * Evidence of evolution I have no idea why this section exists in its current form.  Are we trying to prove evolution?  Is the existence of evolution debated among scientists?
 * History of life Thi robably contains the information that most general readers are most interested in.  It's sad that it has to be a separate section so that readers don't have to slog thrtextbook-like other s to find this info.  Obviously not well organized.
 * Study of evolution Subsections "History of evolutht" and "Academic disciplines" ar related.  Not sure history needs its own section.  Isn't current research more notable than "academic disciplines?"

Gnixon 18:57, 13 April 2007 (UTC)

Proposal
Related to my thoughts above, I would propose that the following makes a better outline:


 * Observations. The data on which the theory of evolution rests and notable consequences of evolution.  Discuss the fossil record in detail, including common descent, speciation, etc.  Discuss how organisms appear to fit into categories and have commonalities.  And so on.  I might start the section with a brief historical outline of pre-Darwin observations, Darwin's studies of finches, etc., Mendel's studies leading to genetics, then mention that they lead to evolution by natural selection via transmitting genetic information, then discuss all the various interesting aspects of evolution we've seen since then---without detailing the theory.  Distinguish immediately between observations and the theory explaining them.  Some material is available in "Evidence," but it needs to be refocused and greatly expanded.
 * Theory. Here, give a full-blown exposition of the theory of evolution.  Not the idea that evolution happens, but the explanation of how and why.  Maybe start with a brief outline of the synthesis of Darwin and Mendel.  Give MCJ's very nice argument that natural selection is a logical consequence of certain simple facts.  Say the same thing about genetic drift.  Detail the processes of variation and heredity.  Discuss all the notable aspects of genetics.  Discuss explanatory power along with examples of predictions and verifications.  First two sections of current article should go here.
 * Research. Discuss here the wide array of ongoing research in EB, mol bio, etc.  Sadly, there's not much material currently in the article, except for a bit from "Academic disciplines."
 * Social impact. Keep this section very brief, even though it's very important to our readers.  Again, I would start historically.  Discuss reception of Darwin's theory and its acceptance by science.  Discuss when and how controversial social ideas flowed from it.  Briefly discuss the conflict with religious origins beliefs, and the history of opposition to evolution's ideas, particularly regarding public education in the U.S.  Mention current status, keeping in mind regional distinctions.

I think the above outline would improve the article significantly, but I don't have the perspective to carry out such a reorganization. We need an expert on the subject matter (late-stage bio grad student or a postdoc, perhaps?) who is capable of writing well and willing to write each section at its appropriate level. If and when the article takes on some sort of reasonable overall structure, I'll be much more capable of improving it directly, and I'll be glad to do so. Best, Gnixon 18:57, 13 April 2007 (UTC)

By the way, I'd point out that starting to enact that proposal wouldn't be a gargantuan task---one could rearrange text and compose a few transition sentences in probably under an hour. After the completion of that crucial first step, others could fill things in and improve consistency in the evolutionary style that Wikipedia is so good for. That style only works when there's already a reasonable overall structure. Gnixon 20:33, 13 April 2007 (UTC)

Discussion of proposal
I cannot support either of these proposals: Genetics is important to evolution, indeed, much of evolution is applied genetics. Removing as much from the basic processes and mechanisms sections as you suggest and cutting(monkey man darwin)ld leave the article much less useful. Also, the history section i(monkey man darwin)ably the least relevant, and there have(monkey man darwin) proposals to cut it. This places it at the top and expands it, while specifically refusing to allow it to begin to communicate information about evolution proper. No. Simply no. Adam Cuerden talk 22:14, 13 April 2007 (UTC)


 * Strongly agreed. This article needs to focus on processes and mechanisms. TxMCJ 01:29, 14 April 2007 (UTC)

Wait a minute. I must not have been clear. I made one proposal, which was to reorganize the article. (I objected separately to how we slam readers with genetics from the very beginning.) I'm just suggesting t(monkey man darwin)involved details should come a little later in the article. I'm not proposing a history section at the top---in fact, I'm arguing that we should cut any separate section on history. I only mentioned that briefly intr(monkey man darwin)ch subtopic in a historical style can be useful for situati(monkey man darwin) Does that resolve your objections? Also, after reviewing the table of contents, do you think the article is properly organized now? Thanks for responding. Gnixon 22:23, 13 April 2007 (UTC)
 * I'm not sure i follow either proposal, then. Could you re-explain in more detail what you want done? As for how it is now... well... a lot of nonsense down at the bottom; I did the last major reorginisation, but couldn't garner support for removing much, so I just put the less useful sections last. A couple of them la(monkey man darwin)get removed, I believe; we used to have a huge section on misunderstandings of evolution. I don't think we really need the "study (monkey man darwin)lution" section, and there might be a case for swapping "evidence of evolution" and "history of life".
 * I must admit to utter confusion as to what your "Observations" section would contain. Adam Cuerden talk 22:42, 13 April 2007 (UTC)


 * Concurred TxMCJ 01:29, 14 April 2007 (UTC)


 * Well, the proposal is simply to have an article based on the second outline rather than the first. I think we could get there largely by rearranging what's already in this article.  For "Observations" I'm imagining all the facts that support and illustrate the theory---a major component would be the fossil record.  I realize the distinction between data/observation and theory is clearer in, say, physics (e.g., big(monkey man darwin)ogy based on Hubble redshift rela(monkey man darwin)presence of cosmic microwave background, etc.), but it's relevant here, too, and could provide structure.  It would also help with theory/fact iss(monkey man darwin)ause things like common descent, speciation, etc., can be discussed as "observations" directly inferred from fossils, genetics, and so forth.  They would be obviously distinct from i(monkey man darwin)ne generation to the next.  Gnixon 01:12, 14 April 2007 (UTC)


 * I've tried rephrasing parts of the "proposal" to be more clear. I'll also rephrase my comments under "Sections" so they won't be co(monkey man darwin)th the proposed outline.  Gnixon 01:30, 14 April 2007 (UTC)

MCJ, I lost track of your comments within those threads. Can you please clarify what you were agreeing with and concurring o(monkey man darwin)ser:Gnixon|Gnixon]] 01:40, 14 April 2007 (UTC)

''Discussion above this point seems to be focused on my comments about the current organization, not the "proposal" for (monkey man darwin)line. I've cut any suggestions fr(monkey man darwin)s under "Sections" in order to avoid further confusion.'' Gnixon 01:49, 14 April 2007 (UTC))

Another suggested structure
Another way to write this article would be to organize it into the basic themes that all Evolutionary textbooks (e.g. Futuyma's two texts) and most university courses in Evoluion are taught. I know this article isn't a textbook nor a college course, but there exists a time-tested logic and effectiveness of the way Evolutionary concepts are organized for people new to the concepts, and I think we'd be doing well to use those models. Understanding basic genetics is genererally a prerequisite for Evolution, so although genetics are essential to Evolution there may be a way to crosslink this article to genetics articles, and trim a lot of RAW genetics info out of here.

Based on courses I have taken, TA'ed, and taught myself (all in all, involving maybe 10 different professors at 3 universities), I recommend something like this. Note that other than the lead, I am being very specific here as to the *actual* topics and themes.

1. The lead

2. Observable aspects of the natural world that imply shared ancestry and descent with modification (fossils is only one of about ten or so things, a few others of which I've listed above. Don't emphasize fossils -- that is only one record, and it is one of the weakest records because it is piecemeal and incomplete.  There are plenty of things we can observe *TODAY AND NOW* that imply shared ancestry and descent.  Focus on those.)

3. The step by step, self evident mechanism of natural selection (this section would also describe variation, and fitness)

4. Population genetics/dynamics: would include gene flow, migration, and drift

5. Special cases of selection: would include sexual selection, kin selection, and adaptation

6. Speciation (mechanisms) and extinction

7. Molecular evolution: would include more detailed information on mutation and chromosomal/genome evolution (e.g. gene and genome duplications, a *huge* component of eukaryote evolution), HGT, and the like

8. A rundown on phylogenetics ("tree-thinking"), and how this field are used and applied to all fields of comparative biology (this is the "evolution is the central organizing principle" section)

9. Biogeography... integrated history of landmasses and taxonomic groups

10. Coevolution (why are angiosperms and insects so diverse? What's an evolutionary arms race?  Parasites/herbivores/hosts/mutualisms/pollinators, etc.)  A short coevolution section is sorely missing from the article.

11. Evo-Devo (evo devo is a very prominent theme now for eukaryote evolution) I can help write this section. A HOX genes blurb would be great, even though some people think it's too specific or jargony, it is a wonderful and fascinating story in Evolution, and really gets to core themes like origin of novelty, evolvability, homology, etc.)

12. Early origins of life on Earth (including early chemical evolution of earth and the RNA world... endosymbiosis, etc.)

13. "The big epic story"... a synopsis/rundown of the diversification of major lineages of life (3 domains, then basic Eukaryote diversification, major adaptive radiations and extinction events, etc.)

14. Common misconceptions (yes I think the article would be well served by this... this is where you define the words theory and fact, and talk about adaptations and exaptations, and ideas of generalism vs. punc. eq., and ideas of contingency vs. optimizing "improvement", etc.

15. History of Evolutionary thought... talk about Malthus, Darwin/Wallace, Lamarck, and the Modern Synthesis. BTW, does this article currently mention Lamarck? That is a gigantic topic and a very important one that MUST be included (the fact that acquired traits are not inherited)

16. Social controversies (keep this BRIEF, SHORT AND SWEET, and link out of this page). Focus on legal cases involving schools.

17. Links and references

This may seem like a lot, but I really can't justify leaving any of the above topics out of this article. The article is incomplete if any of the above are omitted... and there may be a couple of things I'm forgetting. TxMCJ 01:57, 14 April 2007 (UTC)

Discussion of structure

 * Should we have 17 separate sections in this article? Gnixon 02:01, 14 April 2007 (UTC)


 * Why not? Is that some kind of sarcastic comment?  Meaning: are you really asking if seventeen is the magic number?  I don't care if it's seventeen or seven or seventeen thousand, you've got to be complete.  The number is arbitrary and irrelevant.  Your comment reflects the type of wholly trivial concern that in the past has prompted me to say: stop micromanaging the irrelevant, and focus on content.TxMCJ 02:05, 14 April 2007 (UTC)


 * I was not being sarcastic. Let's not get involved in another silly fight for no good reason.  17 main sections is far too many for an encyclopedia article.  Your outline in it's current form would only be appropriate for a textbook.  I think the outline I offered above is much more appropriate for an encyclopedia, but yours might be acceptable if you grouped sections within a hierarchy.  Gnixon 02:11, 14 April 2007 (UTC)


 * Please provide the impeccable math by which you calculated 17 as too high of a number of sections. I'm sorry that this article won't fit onto a matchbook cover, but we're not talking about a synopsis of an I Love Lucy episode.  We are talking about the history of life on Earth, and how it came to be, and the mechanisms involved, and damn it, it's just not short and simple.  If any article in Wikipedia justifies completeness, it's this one.  If you can think of a way to classify all the above topics into a fewer number of sections (though the actual article length wouldn't be shortened by that), and if those section headings are well-descriptive and not too overgeneralized, then please be my guest.  But you're going to have a very hard time justifying omission of any of those topics, with the possible exception of the last 2, history and controversy sections. I would support removal of those if length is a concern. TxMCJ 02:15, 14 April 2007 (UTC)


 * See my proposal above. Subsections would obviously be appropriate.  I wish your tone was less combative.  Gnixon 02:20, 14 April 2007 (UTC)


 * And I wish, for the sake of progress, you'd focus on content rather than "how many sections will there be". My outline above was simply dividing topics up conceptually, not a demand for precisely seventeen sections, and this is a topic that I cannot believe you are even remotely concerned about.  The length of the article in terms of word-count is a totally different issue from how many subdivisions there are. TxMCJ 02:33, 14 April 2007 (UTC)

Also, I don't think starting from the traditions of textbooks and college courses is likely to yield a good format for this article. College courses and textbooks have goals and responsibilities that are entirely different from encyclopedia articles. For example, a good encyclopedia article on quantum mechanics would look nothing at all like a textbook on the subject. The goal of a textbook is to help students practice and understand the hard parts of the theory. The goal of an encyclopedia article is to inform a general readership about the big picture. Gnixon 02:20, 14 April 2007 (UTC)


 * Trust me: nobody is trying to write a textbook here. This article can include all of the above topics without being overly long, technical or verbose. Don't believe me? I could produce the thing myself, and I guarantee it would be about 1/100th the length of a textbook.  The only "big picture" in Evolution is a complete picture.   Please reread what I posted above in my preface to the outline: I am well aware this isn't a textbook nor a college course, but the logical structure and flow of textbooks and college courses are TIME-TRIED and TIME-PROVEN MODELS for how to organize this information.  We can learn from those models and it would be moronic to instead follow some kind of vague "how are encyclopedia articles written?" model that nobody here has any real professional experience in (although if you'd like, why don't we just have a look at the Britannica article for comparison, if "encyclopedia article format" is our goal?  I would support that little experiment.)  Furthermore: I cannot fathom, for the life of me, what possible objection you might have to the actual content I've suggested.  ONCE AGAIN: PLEASE FOCUS ON CONTENT.  Just take a moment to compare your proposal with mine.  Yours is strictly organizational, and nothing more than that. You suggest almost no content.  Mine is organizational AND it provides the required content.  Want to cut down on what I've suggested?  Fine --tell me what content you would omit.  I've already suggested omitting the history and social controversy sections. TxMCJ 02:33, 14 April 2007 (UTC)


 * Obviously your outline is focused on content over organization, whereas mine focuses on organization over content. I happen to think the organization is more important at this point.  Please read what I posted immediately above your last comment:  I don't think starting from the traditions of textbooks and college courses is likely to yield a good format for this article.  Gnixon 02:40, 14 April 2007 (UTC)


 * I am not talking about *traditions* of textbooks and courses. I am talking precisely about the thing you claim to be so concered with: organization.  And furthermore, this is what really boggles my mind, and what I mean when I say that your "facilitation" is an obstacle to progress with the article.  Why are you spending so much energy arguing how many sections there will be, and waxing philosophic about your perceived differences between encyclopedia articles and other forms of information delivery... and so LITTLE energy on considering what content to include and how to organize it?  Here is some good faith for you, and a peace pipe you may choose to smoke, or not.  If you're *really* interested in facilitating things and *really* interested in organization, and you've already admitted a number of times that you do not really have the background to provide core content, then I have a kind suggestion, and request for you.  Go through my outline above, develop and present sound arguments here for anything I listed that you think should be omitted (or anything you feel I forgot), and once you've done that, group all of the resulting *specific* topics of content into a set of organization categories that you think fit within your idealized model of what an encyclopedia article should look like.  In all good faith and honesty: that would be truly helpful at this point, and I will thank you in advance.  Produce that document, and we're ready to go, and you will have been the facilitator.TxMCJ 02:47, 14 April 2007 (UTC)


 * Three points:
 * A 17-item laundry list of topics to cover does not constitute organization


 * Gnixon: my list above is *absolutely* organized into a logical and clear order, where each point builds on the previous one, and I have absolutely organized specific topics under each of those headings. It is organization AND content.  Like I said, I don't care if the article has 17 headings or 7, but that is the list of information that belongs in ANY article about evolution.  Still want to argue this futile point and continue wasting time?  A few sections above you tried to argue that "organization at this point is more important than content".  REALLY?  Well here's a painfully obvious question: what exactly is it that you are "organizing", if it's not topics or information?  Organization of an article without a "laundry list" (as you call it) of what goes into the article, is an inane exercise in utmost futility, and it is what I refer to as micromanagement. Please: if topics and information are not what you're organizing, then what *are* you organizing?  And don't answer "the article", as that is not a meaningful response.  The only thing there is to organize here, is information INTO an article. TxMCJ 06:28, 14 April 2007 (UTC)


 * I'd just be repeating myself if I tried to respond. An ordered laundry list of topics still does not constitute organization.  Gnixon 14:25, 14 April 2007 (UTC)


 * And I'd be repeating myself to counter, again: I don't care how many subheadings there are, my outline above does *organize* the topics into a hierarchical conceptual structure. #2, Observations/Evidence: I list further up what belongs in this section.  #4 Population dynamics:  I list what belongs in that section.  #5 Special cases: I list what belongs in that section.  #7 Molecular evolution: I list what belongs in that section.  Continue reading my outline.  It is not a laundry list, it is a conceptual breakdown of topics.  I will also add, that perhaps the most important organizational aspect you can introduce is what *order* to present the information in, and I have also provided a logical suggestion for that. TxMCJ 16:03, 14 April 2007 (UTC)


 * I think your constant, lengthy complaining about all things under the sun, and your frequent attempts to pick fights are more disruptive here than anything I've done. Please just be nicer.


 * I have complained about only one thing: debate about pointless things standing in the way of progress. I will be a lot nicer (i.e., less impatient with this process) if you would stop immediately objecting to every contribution of content I provide, and countering it with some banal complaint about encyclopedia philosophy or organizational structure or not wanting to follow educational models or textbook models.  Those objections are not meaningful.  You are not contributing substance.  You are impeding the process.  You have objected to my information-packed outline for totally absurd reasons, none of which have anything to do with the information itself.  You are not commenting on the information or suggesting what to include or not to include.  You are wrapped up in meaningless jibberjabber about vague organization of mysterious unidentified content that you have not laid out.  What I've done above is laid it out.  If you want me to be less impatient (or more "nice"), then quit trying to *own the article* as others before me have accused you of, and as is abundantly clear now.  My snappy tone is not arrogance or nastiness -- it only comes from impatience with your refusal to consider and focus on the pertinent information and content, while instead building eternal obstacles of vague objections and wikibabble.  Please, stop. TxMCJ 06:28, 14 April 2007 (UTC)


 * I can think of one other editor who said I was trying to own an article, and some other editor said he was just being a troll. But you knew that.  Your snappy tone is both arrogance and nastiness, and it didn't start with me.  Gnixon 14:25, 14 April 2007 (UTC)


 * As for content. In my experience, someone who swims in details without being able to organize their thoughts or explain them clearly is in fact showing that they don't really undertand the "content" all that well.  Someone famous has a pithy quote about it.  For all the time you spend boasting about your teaching experience (that'd be a few years as a grad student and a year or two as a postdoc by my count), I'd think you would have by now learned something about presentation.  Gnixon 14:25, 14 April 2007 (UTC)


 * 6 years in grad school and 5 as a postdoc, 3 of the last 5 which I've spent teaching Evolution specifically. I also write and publish in Evolution, and have written grants for Evolutionary research that were funded by the National Science Foundation. Writing and teaching are *all about* presentation.  How about you, Gnixon?  What's your experience in presenting evolutionary content in a way that lets you keep your job?  Look, I really have no need to post my resume here, other than to show that you're mistaken, and I have never *boasted* about teaching experience -- I just refer to it a lot because it is completely relevant to what we're trying to do.  Quit the attacks, as they are quite juvenile.  Focus on the task at hand. TxMCJ 16:26, 14 April 2007 (UTC)


 * I need to stop attacking you? Sorry for being wrong about the length of time you've spent in grad school and your postdoc.  I agree your teaching experience has great potential to be useful here.  Gnixon 17:01, 14 April 2007 (UTC)


 * Saying "I think you would have by now learned something about organization" based on your failed attempt to discredit me by making an incorrect calculation about my experience, is a failed attack. And it wasn't the first attack.  As Orangemarlin has said before, "I know what you're doing, and others will too" TxMCJ 17:05, 14 April 2007 (UTC)


 * In good faith, I'll work on your list if you'll return the favor by suggesting any changes that are needed in my broad outline above, then suggesting content that would be included in each of the major topics.
 * Gnixon 03:05, 14 April 2007 (UTC)


 * I would be more than happy to rethink your outline, since as I've said, an organizational scheme without any prior consideration of *what you are organizing*, is a completely backwards approach to *anything*. TxMCJ 06:28, 14 April 2007 (UTC)


 * Just trying to help out, since you seem incapable of organizing anything. See my above comment about the implication.  Gnixon 14:25, 14 April 2007 (UTC)


 * See my comment above about what constitutes meaningful organization. You need to know what the "anything" is, before you can attempt to organize it TxMCJ 16:03, 14 April 2007 (UTC)


 * Okay, I'll agree you know more about this subject than I do, if you'll agree you can't write well or organize your thoughts. Maybe then we can stop this stupid bickering and each look to others to fill in where we're lacking.  Gnixon 16:09, 14 April 2007 (UTC)


 * Are you joking? You want me to agree that I can't "write well"? (please compare my contributions to the article with your own)?  I write professionally about evolution, and I have also won two specific literary awards (both previously won by Ralph Waldo Emerson and John Updike as well) that are *specifically* awarded to essay-writing geared to a layman audience.  I am not bragging about this, I am just saying that any attack on the quality of my writing is nothing more than a simpering attack on your part.  And you want me to agree I can't "organize my thoughts"?  Buddy: you've got to have the thoughts before you can organize them.  My thoughts are plenty organized in that I am able to organize, to an order of magnitude more effectively than you can, what the key concepts and topics in Evolution are, and how to group them into a logical sequence (grouping + sequencing = organization.)  Please, man.  Your little statement above is the silliest little jab I've seen here, second only to your little tirade about "worshipping authority". TxMCJ 16:20, 14 April 2007 (UTC)


 * I was referring to choices like this one to detail natural selection in the lead (with an odd choice of formatting). But you're right.  Whether true or not, it was a petty jab and I apologize.  If we meet someday in real life, we can discuss the quality of each other's professional and personal capabilities, but I'll drop it in this forum from now on.  I'd appreciate some measure of similar effort on your part, but this isn't a quid pro quo---no more personal critiques from me.  Gnixon 16:33, 14 April 2007 (UTC)


 * A previous attempt at describing selection was already in the lead, my dear. The edit you link to was my attempt to make it more accurate.  I was not the one who chose to try to explain selection in the lead -- all I did was correct and improve the pre-existing presentation.  If you think that the mechanism of selection needs to be removed from the lead and inserted further down, fine -- that's not a point I am particularly passionate about debating one way or the other. TxMCJ 16:47, 14 April 2007 (UTC)


 * Please don't address me with diminutives. I've managed to avoid calling you names, and I don't think it'd be hard for you to return the favor.  Gnixon 16:50, 14 April 2007 (UTC)


 * You may not specifically call names, but you sure spend a lot of time calling me arrogant, googling who I am and posting your findings in an (unsuccessful) attempt to discredit me, and saying that I "boast" about things and "spit on others", and then you try to make an (unsuccessful) attack on my writing skills, et cetera et cetera, not to mention posting your extremely transparent and stupid comment on my talk page about "experts shouldn't expect to have their holy authority worshipped"... while all this time, providing almost no contributions to this article or our goals in terms of information, content, or actual WRITING. If you want me to cool down, then you'll need to BACK down. TxMCJ 17:02, 14 April 2007 (UTC)


 * I googled you long ago in an effort to support you on this page and after you thanked me for discussions with you, provided your full name, and invited me to email you. I'd point out that you never made any attempt to correct me when I overstated your credentials; instead, you've used your credentials like a weapon to support your ideas on this page, and in my opinion, you've implied that they're stronger than they are in factfor all those reasons, I felt it was proper to get the facts on the page.  As for attacks, we've both provoked each other---I'm sorry for my share of it, and I'll try to do better.  I'd love it if we never communicated again, but given our different opinions about this article, I doubt either of us will be able to resist responding to what the other posts here.  We could try to be more civil and less combative.  I'm willing to try.  Gnixon 17:16, 14 April 2007 (UTC)


 * Here's your big chance! 1.) When have you overstated my credentials, which I "let slide" in my sneaky attempt to ratchet up my credibility quotient around here?  Please provide details so that I may publicly apologize for my slimy, self-serving oversight.  and 2.) Where have I implied my credentials are stronger than they are?  Please provide details, so that I may publicly apologize for those slimy, self-serving falsehoods.  If you cannot do either of those two things, then all you have said above constitutes an attack, and worse than that: fabrication of things that never happened, in order to support your vague argument (whatever it is).  JUST STOP IT.


 * I don't use credentials like a weapon, I use them as defense against your attempts to trump scientific knowledge with your personal wiki-politics and rhetoric. Such a statement on your part is nothing more than an anti-elitist reaction (like your comment about "holy authority"), to the simple fact that I *do*, simply and factually, have more experience in these topics than practically anyone else I've seen edit this page since I've been here.  That does not mean I think I'm always right.  That does not mean I think I'm the boss.  That does not mean I am full of myself, or that I want to rule the roost or run the show.  It only means that I have quality content and knowledge to contribute, and that you, for whatever reason (I think it's article ownership) seem very threatened and dismissive of it.  If you want the article to grow, you'll cut all this B.S. out. TxMCJ 17:22, 14 April 2007 (UTC)


 * I twice called you a "professor" in prominent places on this page. As for implications of stronger credentials, perhaps there's just a misunderstanding because we have different ideas about the intellectual authority of grad students and postdocs---now that you've kindly provided details about your positions, there shouldn't be much room for misunderstandings.  I don't mean for that to be rude or have any subtext, by the way.  My opinion is that you don't have sufficiently more experience to command greater authority than the several advanced bio grad students and bio Ph.D.'s I've seen editing here---write back if and when you get tenure at a major institution.  No disrespect to your accomplishments so far.  Others can judge your authority for themselves.  I'm done discussing the issue.  Gnixon 17:37, 14 April 2007 (UTC)


 * Calling me a "professor" does not constitute an overstatement, because although I do not hold a professor's *appointment*, it is common practice for the instructor of university courses to be called the professor within that context (students do it, the administration does it, etc.), so that was not a glaring overstatement that I somehow "allowed you to make" in order to bolster my position. Also, at no time have I tried to argue that I'm a better authority than anyone else working in my field.  I will be the first to agree that Graft (an apparent Ph.D. student?) has posted some of the most thoughtful and meaningful content to these talk pages.  But I will maintain that evolutionary biologists of any professional rank (and I do include advanced grad students) are the people who should be taking the lead writing this article.  Not hobbyists, not "facilitators", not "organizers".  People in the field, of whatever rank.  If any person assumed that I thought I was the only one qualified to write here -- that person was you.  And if "tenured professors" is the only authority you will ever respect, then you are likely to wait until Doomsday before any of them shows up to waste time around this dense and frustrating environment.  Even tenure *track* professors don't have time for the debating and bureaucratic swimming that is required around here.  If you have even the slightest interest in the article itself, you should be somewhat grateful that I *do* have the time (and limited patience) for this.  Most of my peers do not, and tenured professors *most assuredly* do not.  As a last note on this, I would like to post a little sentence that Filll kindly posted on my talk page: "it is too painful to edit articles in areas in which I am an expert and have to deal with assorted morons and dufuses".  I'm not calling anyone here a moron, but whereas most experts apparently flee from that "pain" and go edit other articles, I have chosen to stick around (for the time being).  I apologize if I come across as abrasive, but I am *not* an elitist, and any snappy tone I adopt only comes from the frustration that Filll eloquently described, which I've posted above. TxMCJ 18:02, 14 April 2007 (UTC)

Err, this is all nice and everything, but could you guys please take this to a user talk-page or not do it at all? Graft | talk 18:00, 14 April 2007 (UTC)


 * Point taken Graft... But when attacks and bad arguments are presented here on the article talk page, in what I view as a clear strategy to "own the article", I am compelled to respond to them on the article talk page, so that such ownership does not occur. I will be the first to agree that it wastes a huge amount of space and time, and the first to invite any future such garbage to the user pages. TxMCJ 18:06, 14 April 2007 (UTC)

Discussion of structure 2
Britannica:
 * Introduction
 * General overview
 * Evidence for evolution
 * History of evolutionary theory
 * The cultural impact of evolutionary theory


 * The science of evolution
 * The process of evolution
 * Species and speciation
 * Patterns and rates of species evolution
 * Reconstruction of evolutionary history
 * Molecular evolution

Total article length is 73 pages. All subtopics under General overview and Science of evolution have further sub-subtopics. Gnixon 02:53, 14 April 2007 (UTC)
 * Additional reading


 * OK, now I'm really confused, utterly and thoroughly confused. Does you posting this outline mean (following your above insistence that we are writing an *encyclopedia article* and not a textbook, and thus 17 sections is "far too many"...) does you posting this Britannica report mean that you think we should model our article to be somewhere along the lines of 73 pages, since (as you insist) it is an *encyclopedia article* and not a textbook?  I am now thoroughly bewildered at what your position on length could possibly be.  Do you prefer the above "encyclopedic" model over my outline because it only has 12 headings instead of my 17, even though the Britannica article takes up 73 pages?  I have to say, I really thought we could write ours in far fewer pages than that. TxMCJ 06:28, 14 April 2007 (UTC)


 * I'm not sure what's so hard to understand. You asked for the Britannica outline.  It has four first-level headings, then 4-6 subheadings under each of the two main subsections, each of which has further sub-subheadings.  This is the essence of organization.  I would certainly hope that the entire content of our Evolution article and its subtopics would cover over 70 pages.  Luckily, though, we have the advantage of providing links to sub-articles to make our ("entire") article easier to navigate.  By linking to long subtopics, we should have no trouble keeping this article to around 10 pages.  "Summary style" may be useful for such a deep subject as this.   Gnixon 14:14, 14 April 2007 (UTC)


 * All right, I've done as asked, and here's my report.
 * Gnixon suggests four categories: observations, theory, research, and social impact.
 * After the lead, I agree that something akin to an "Observations" section is a good way to start (#2 in my list), but I think calling the section simply "Observations" is a little obtuse. Straight up "Evidence for Evolution" is a fine title for this section, and it is basically an "observations" section including the kinds of things I've listed above, and more.
 * I have a problem with the next section, simply "Theory", 1.) because as a section title, that's a loaded word for most readers, and so we should be smarter about its use in the article... but I also have a problem with a single "Theory" section because 2.) under a 4-part article as Gnixon suggests, this is the only section to place the bulk of the scientific concepts (my points 3 through 15, if we were to use them all.) An article built the way Gnixon suggests may only have 4 sections, but this second one will be the biggest one, and I kind of feel that it needs to be subcategorized quite significanty.
 * I also have a bit of a dilemma with a "Research" section, not because it's a bad idea (it's not a bad idea, it's a good one), but because there are so many possible research projects and programs that could be mentioned here. I mean, there are literally thousands of evolutionary research projects going on right now, as we speak... projects in systematics and selection and evolutionary ecology and phylogenetics and molecular evolution... so what belongs in this section?  It's not very clear.  And I have a strong sense that any inclusion of a "research" section may result in swift deletion because it kind of gets away from the point.  It's not like there are 3 or 4 active research projects in evolution right now.  There are thousands.
 * Social Impact -- as some have voiced, this section may not even belong in this article at all. I won't argue that point one way or the other.


 * So, in summary, while I like beginning with something like an "observations" section, and then going immediately into a description of the theory, concepts, and mechanisms (albeit without calling that section a straight-up one word title "theory" because 99% of readers can't define that word correctly), the problem that remains is that there is too much information that makes up evolutionary science to just lump and cram into a single section, and thus that second section would have to be huge. The proposed 3rd section (Current research) is not a bad idea, but I'm not sure what projects we'd pick, or why we'd pick ithem, or how much to include, or how much to leave out, and honestly a lot of such a "research" section may come across as being trivia and only tangentially related.  An alternative way to integrate current research into the article is just to provide frequent links to recent papers, and mentions of recent or ongoing studies throughout the article. Social controversies:  I'll take that section or leave it... there are other articles for most of that, right?TxMCJ 07:28, 14 April 2007 (UTC)


 * Thanks. I'm not tied to the "Observations" title, but I don't want "Evidence" to become "proof that evolution exists."  It's certainly as loaded a word as theory.  I think that section could be broader than you imply, because as you've pointed out, there's tons of evidence for evolution, but beyond that, there are lots of observations supporting and verifying all aspects of the theory.  The human genome project, for example, might be worth discussing there.  I'm also not tied to the title "Theory," but it seems like any science can be usefully divided between "observation/experiment" and "theory."  I'd point out that most of the things that might be confusing under "theory," such as speciation, common descent, timeline of history of life, would fit better under "observations" (or maybe "evidence"---see the difference?).  Of course "theory" would have many significant subsections, and I probably should have filled in the next level in the hierarchy.  Simply explaining "research" in the appropriate other sections might work well, but for such a big subject as evolution, I would have thought research could be divided into subfields whence having a section devoted to that classification would be useful.  As for "Social impact/controversies," I've pointed out before that many readers of this article are more interested in that topic than in genetics, so I can't support cutting it.  I'd point out that Britannica saw fit to include it after "evidence" and "history", but before any of the "science."  I'll fulfill my half of the bargain later this weekend.  Gnixon 14:14, 14 April 2007 (UTC)


 * I'm sorry, but your above distinction between "observations" and "evidence" doesn't make any sense to me at all. When you say observations, do you mean something like "controlled experimental data"?  Even if that's what you mean: experimental data fits directly into the broader heading of Evidence (whether you use the word "evidence" or not, is not my point.)  It is also not clear to me how the Human Genome Project fits into a section about evidence/observations.  Or why you'd pick the "human" genome project when there are a number of other genomic models that have been sequenced. TxMCJ 16:12, 14 April 2007 (UTC)


 * I meant "observations" as a broader and less charged word than "evidence." It's really not a big deal to me.  But Sweet Baby Jesus!  Who cares which genome project I mentioned?  The human genome project has been in the news a lot.  Substitute drosophila if that makes you happy.  Gnixon 16:17, 14 April 2007 (UTC)


 * Mainly I don't know how ANY genome project fits into that section. Please clarify. TxMCJ 16:21, 14 April 2007 (UTC)


 * Surely a complete gene sequencing can elucidate the evolutionary history of an organism, but let's not get hung up on one example. I was just trying to illustrate the possible breadth of an "observations/evidence" section, i.e., how much of interest to this topic can be discussed before getting into details of the theory.  Others can disagree, and I'm not really interested in defending my brief thoughts against good faith objections.  I was just trying to start a discussion about the overarching organization of the article.  I thought it would be a simple matter to reorganize what we already have without getting into some protracted, rebuild-from-the-ground-up debate, but clearly I set off your "don't let this jerk have a say" button.  I'm sorry.  That wasn't my goal.  Gnixon 16:40, 14 April 2007 (UTC)


 * Do you mean a complete *genome* sequencing? To answer your question: no, a complete genome sequencing says nothing about the evolutionary history of an organism.  A sequenced genome is one single data set.  Evolutionary history is determined through comparisons with other organisms.  So whereas *comparative evolutionary genomics* might fit exceedingly well into a section about "evidence", citing a single genome project in isolation without any further context is kind of meaningless.  And by the way, I do not have a "don't let this jerk have a say" button, but I do have a hair-trigger reaction to people who waste a lot of time talking *around* issues instead of about them. TxMCJ 16:55, 14 April 2007 (UTC)


 * Thanks for catching my typo. It's good to have people keeping a sharp eye out for things like that.  I opened my post yesterday with "In hopes of provoking a better organization of the article, here are some thoughts on the major sections."  I guess I at least succeeded in provoking discussion.  Gnixon 17:06, 14 April 2007 (UTC)


 * Although there is another typo in your sentence above: Even a complete genome sequencing *cannot* elucidate the evolutionary history of an organism (not "can").  Evolutionary history can only be reconstructed via comparisons between taxa. TxMCJ 18:14, 14 April 2007 (UTC)


 * Actually most of the genome sequencing papers (maybe not the human one) had something to say about evolution. The mouse genome paper, for example, had an important bit of comparative genomics - it included an estimate of the fraction of the genome under selection. Graft | talk 18:02, 14 April 2007 (UTC)


 * Right, but that's *comparative genomics*, looking across species. A single genome in isolation provides no information about evolution. TxMCJ 18:07, 14 April 2007 (UTC)


 * That said I agree with TxMCJ that a genome project paper might not be the most appropriate - there are likely specific analysis papers that would be much better. Graft | talk 18:03, 14 April 2007 (UTC)


 * It was really just an example, guys. Cheers, Gnixon 18:10, 14 April 2007 (UTC)


 * Thanks for the suggestion -- but it's not a good example unless you discuss comparative genomics. That's my only point. TxMCJ 18:15, 14 April 2007 (UTC)

Scientific Controversies
A request to see more information about "scientific controversies", a rebuttal, and a redirection to the FAQ.

I Noticed that there was not a section for scientific controversies. Even though it is taught in most schools that there is no opposition to this theory in the scientific community I found some articles even here on wikipedia about controversies surrounding evolution. I created this section to cover those topics and tried to develop a small paragraph addressing theses arguments from a neutral perspective.B89smith 18:31, 14 April 2007 (UTC)


 * The fact that Evolution -- like any science -- is a field where hypotheses get tested and supported (or rejected) and concepts and ideas sometimes change, does not imply that there is scientific "controversy" as to whether Evolution is true (as we define anything to be "true"). There is no controversy among scientists that all life evolved from shared ancestry, via mechanisms of selection and population dynamics as outlined in part by Darwin, Wallace, Fisher, and the Modern Synthesis.  Like any science, controversy sometimes exists on smaller points, such as the actual structure of a phylogenetic tree, or whether or not sympatric speciation can occur in sexually reproducing organisms.  But those controversies do not mean that phylogenetics is under scrutiny, or speciation does not occur. Normal scientific debate about specific topics does not mean that the core structure and tenets of the science are under any debate whatsoever. TxMCJ 18:56, 14 April 2007 (UTC)


 * This issue is addressed in the /FAQ. You may be interested in Objections to evolution.  Cheers, Gnixon 18:34, 14 April 2007 (UTC)

I still think it should be included on this wiki since social controversies is a section. It would be inconsistent to not include scientific controversies. As soon as we remove this section from the wiki we remove the objectivity of this article and replace it with a subjective opinion on evolution. This greatly lowers wikipedia's credablity down from a encyclopdia to a chat forum discussing what wikipedia members think about evolution.B89smith 18:45, 14 April 2007 (UTC)


 * As everyone here will attest, I am very interested in the problem you are having inserting this material that is fully attributed to many Reliable Sources. :))  Would you agree to the principle that the evolution page should contain only material that satisfies the standard of "Verifiability, not truth"?  --Rednblu 19:16, 14 April 2007 (UTC)


 * You may want to propose revising the FAQ. Gnixon 19:19, 14 April 2007 (UTC)


 * Apparently, it is not safe to have this discussion in the public square. Therefore, let us disappear while we yet can and reconvene in the safety of the Role of truth page.  --Rednblu 19:50, 14 April 2007 (UTC)

Going in the right direction
I like TxMCJ's and Slrubenstein's content suggestions (both see the weakness in the current History section and the opportunity to relay history, evolutionary thought, and theory for example). That should be the first priority-what to put in the article. How to fit it into some Wiki format may be an issue, but I would hope the goal is to produce a superior article on the subject. Face it, most encyclopedia's bite. It would seem an excellent opportunity to build a better encyclopedia article-informative, up-to-date, and not watered down drivel. I think many readers are looking for something more than your average encyclopedia article. I think one of the reasons that this subject generates so much controversy is naivety of the subject-fundamentalist, general public, and many scientists (even educated people who believe and support evolution are ignorant of the facts, and most scientist's education become restricted to an expertise). Rather than talk about social controversy lets help make it disappear with an article that is "Gee-whiz that does make sense, seems obvious, and those arguments are difficult to deny". Just a suggestion. GetAgrippa 14:00, 14 April 2007 (UTC)
 * I'm not opposed to those content suggestions. I'm just suggesting we consider first reorganizing what we already have in a more reasonable way.  Gnixon 14:32, 14 April 2007 (UTC)


 * I think Slrubenstein's way is wonderfully reasonable. TxMCJ 16:33, 14 April 2007 (UTC)
 * Be aware, though, that too much "fluff" at the top of the article - geeneral discussions of evidence, and so on, and you end up with a vicious cycle in which the lead has to get more and more detailed to give the background needed. Also, I have to ask whether the history and evidence is really the most important discussion in the article. I'm inclined to think that mosrt readers wouldn't really care much about the history, and might not be able to understand the evidence until after basic processes asnd mechanisms are explained. Adam Cuerden talk 01:03, 15 April 2007 (UTC)

By evidence I meant evidence - not a general discussion of evidence, but an account of the history of life as best we understand it relying on concrete evidence. I hav eno objectin, in principle, to putting the mechanisms first and the story of life/evidence second, but I also see no reason why opening with a story - necessarily selective (with links to other articles) - of the actual evolution of life and species cannot be a compelling and fascinating way to draw people into the article. Slrubenstein  |  Talk 11:26, 15 April 2007 (UTC)

Just a thought....
Thinking again about issues of organization and problems of language (e.g., theory/fact), what about these as the two sections with most of the meat?


 * Observations and inferences
 * (overview)
 * Homology
 * Fossil record
 * Genetics
 * Speciation and extinction
 * History of life


 * Mechanisms
 * (overview)
 * Variation and mutation
 * Heredity
 * Natural selection
 * Genetic drift
 * Gene flow

Subtopics were chosen from the current TOC (mostly). Additional sections might include "Research" and/or "Social impact." My hope is that this layout would clarify the difference between the "facts" of evolution and the inferences that immediately follow (e.g., speciation, common descent), versus the scientific "theory" that explains them. Putting things like speciation/extinction and history of life in the first section avoids associating them with "theory." I likely left out some subtopics, and subtopics may not be optimally ordered---just trying to get the broad ideas. I suggest untitled "overviews" beginning each main section so that subsections can be detailed without confusing the general reader.

These are just suggestions---nothing I'm tied to. If they won't work, I'll take no offense if someone improves upon them; if they're not acceptable for some reason, fine. Just my two cents. Gnixon 05:18, 15 April 2007 (UTC)


 * What's the difference between an inference and a theory? Aren't theories inferential? In what sense are variation, mutation, and heredity not "observations" or "inferences", while genetics and the history of life are? Also, doesn't it make sense to present facts and their respective explanations in the same sections, so that many readers don't only learn about the puzzling phenomena and then stop reading the article before they get to any of the actual meat&mdash;that is, how and why those phenomena occur? -Silence 08:46, 15 April 2007 (UTC)


 * I would say an inference is something that follows directly from the observations/evidence without significant theoretical structure. Thus the "fact" that all galaxies are moving away from us can be inferred directly from their redshifts, and one can also therefor infer that space is expanding.  However, the theory of big bang cosmology isn't mere inference---it has a logical structure that explains how and why space is expanding (among many other things).  Gnixon 13:03, 15 April 2007 (UTC)


 * Likewise, evolution as change over time of populations and even the history of life are simply observations or direct inferences, but the processes of variation/heredity along with the mechanisms of natural selection/genetic drift form the structure of a scientific theory explaining in detail how and why things evolve. (Thus variation/mutation/heredity can be observed, but the fact that through natural selection and genetic drift they result in evolution constitutes the theory.)  Gnixon 13:03, 15 April 2007 (UTC)


 * My point is exactly that the subtopics under that first section are a big part of the meat, and I think its useful to understand the facts about what happens via evolution before worrying about why evolution happens. Gnixon 13:03, 15 April 2007 (UTC)


 * Regarding readability, I think overviews beginning each section should provide all the material someone would want on a first reading, and I think readers would naturally skip through details and go to the next overview if the article was reasonably structured. Gnixon 13:03, 15 April 2007 (UTC)


 * Thanks for your questions. Hope this clarifies what I meant.  By the way, "Evidence and inferences" seems like it would work just about as well.  Best, Gnixon 12:58, 15 April 2007 (UTC)

Revising "Theory"-->"Mechanisms" since "theory" seems unpopular and "Mechanisms" probably works as well. Gnixon 19:28, 15 April 2007 (UTC)

If we want to provide the evidence for the theory, how should we lay out the article?
The recent push toward rewriting this article in a way that not only explains, but also evidentially justifies, the various aspects of evolutionary theory is a very interesting and compelling new idea. However, I find it strange that this push has not been accompanied by a move away from artificially dividing the article along lines like "Observation/Theory". Instead, the reverse has been the case: people are suggesting more than ever an "Evidence/Explanation"-style article sectioning. Yet surely such a division would have exactly the opposite effect than what is intended in giving readers the evidential basis for evolutionary ideas?

Look, for example, at Evolution, a section which already (at least in part) explains the exact reasoning behind many of the basic ideas of heredity, thus achieving the desired effect of giving a grounded, reasonable justification for the theory rather than simply stating the theory authoritatively and moving on. Now consider how much less effective this section would be if we tried to artificially segregate the "theory" from the "observation": half of the first few paragraphs would need to be moved to "observation", where they would remain unexplained until many pages later, when the "theory" section gives a justification for them. This clearly wouldn't be an effective way to go about things; we should, instead, provide evidence in every single section if it's our goal to give the basis for evolutionary theory here, grounding each section's theory with concrete observations.

A consequence of this is that we can probably simply delete the section Evolution, instead distributing the evidence according to what it's specifically evidence for. We could, for example, change "History of life" to "Common descent" (and the two subsections into one section explaining the current reconstruction of life's history) and move much of the "evidence for evolution" contents there, explaining, for example, how anatomical and molecular homology (e.g., from genetics and fossils) support common descent, before exploring the consequences of common descent for life's history.

Another consequence, at least in my view, is that we probably want to begin (rather than end) the article with a discussion of the history of evolutionary theory, since this will provide a suitable "background" section for explaining where many of the subsequent examples are coming from. This will be particularly useful if we draw upon actual historical examples of evidence used by biologists for evolutionary theory, such as Darwin's finches and Mendel's peas, since this will tie the whole article together nicely&mdash;whereas mentioning Darwin and Mendel and the like throughout the article before their importance in the context of the history of evolutionary thought is explained will leave many readers confused regarding why these strange people keep getting mentioned. -Silence 09:21, 15 April 2007 (UTC)

Incidentally, since a lot of other people have been suggesting new layouts, I'll throw one out there:


 * 0. Introduction
 * 1. History of evolutionary thought
 * 2. Heredity
 * 3. Variation
 * 3.1. Mutation
 * 3.2. Recombination
 * 3.3. Gene flow
 * 3.3.1. Hybridization and horizontal gene transfer
 * 4. Speciation and extinction
 * 5. Mechanisms of evolution
 * 5.1. Genetic drift
 * 5.2. Selection and adaptation
 * 5.2.1. Competition and cooperation
 * 6. Common descent
 * 6.1. Homology
 * 6.2. History of life
 * 6.3. Phylogeny and systematics
 * 7. Modern research
 * 7.1. Academic disciplines
 * 8. Social effect
 * 8.1. Controversies
 * 9. Notes and references
 * 10. External links

The basic idea is to move from a general overview and background look at the core ideas and history of evolutionary theory, then to explain, in a step-by-step process, (1) how variation is passed down from generation to generation (heredity); (2) what causes this variation (mutation, etc.); (3) the long-term results of this variation (speciation) and how it terminates (extinction); (4) what causes certain variants to become more common than others (natural selection and genetic drift); (5) the evidence (homology) that all life is related (common descent); (6) a brief overview of the informed reconstruction of the many speciations and extinctions through evolutionary history; (7) the scientific study of evolution; and (8) the social effect of evolutionary theory. Feel free to ask questions about or criticize the proposal, especially if I made an error in one of my categorizations of sections or if I overlooked an important section. -Silence 10:58, 15 April 2007 (UTC)

Response from Slrubenstein
I hate to screw with what you are doing by raising a too-specific point, but I think it is important: I would put selection and extinction before selection and adaptation. One of the most common misunderstandings of evolution (even by non-creationists) is that "adapt" is something species actually "do." One of the things that makes Darwin so brilliant is that he makes nature the actor, rather than the species: nature acts by killing off the less-fit. Whatever is left is "adapted." I know natural selection is not the only cause of extinction, my point is that it is because natural selection acts primarily by causing individuals to die or under-reproduce and adaptation is the literally unintended outcome of a process of elimination. Slrubenstein  |  Talk 11:31, 15 April 2007 (UTC)


 * I know all that already. But why is that a reason to put speciation and extinction before natural selection? Actually, I see why you'd say that, and the very last change I made to the above list, right before I posted it, was to switch the order of 3.2-3.4 (originally it was Heredity, then Speciation and extinction, then Selection and adaptation, then Genetic drift), but I decided that genetic drift made more sense following heredity, that natural selection and drift should be grouped together, and that speciation/extinction was an excellent way to "transition" from natural selection to common descent. What order, specifically, would you propose they be in instead? -Silence 11:57, 15 April 2007 (UTC)

Sorry I was not clear. I do not think we should put speciation and extinction before natural selection. The fact is, I misread what you wrote (your outline, above) so this may just be a big misunderstanding ... I guess it depends on how we execute your (or the final) outline. My mistake: I thought after genetic drift 3.3 was "speciation and adaptation" and 3.4 was "speciation and extinction." - in other words, I though you were dividing natural selection into these two topics. I just misread what you wrote. But to see if I can salavage my point (and my dignity!) let me just ask - thus a kind of thought-experiment - how it might work if 3.3 were selection and extinction and 3.4. were speciation and adaptation? Here is the difference: your current proposal (now that I read it correctly) introduces two important concepts - selection and adaptation - first, and then two concrete manifestations of these concepts - exitinction and speciation. I am suggesting that perhaps there may be more sense in linking concept to concrete manifestation, so first introduce the concept of natural selection and show how at a large scale it can lead to extinction, and then introduce the concept of adaptation and show how at large scales adaptationas accumulate to manifest themselves in new species. As with my earlier suggestions I myself am not sure this is better, I am just raising the possibility to see what ideas it sparks. Sorry for my initial misundersrtanding. Slrubenstein  |  Talk 12:14, 15 April 2007 (UTC)


 * Ah, I see; when you listed "Speciation" two times, I thought it was just a typo. Anyway, your revised point is a good one, actually: it is true that going from the more concrete (speciation) to the more abstract (natural selection) makes sense, and it's also true that it would be very difficult to discuss natural selection without using the examples of speciation and particularly extinction. But still, I'm loathe to not have genetic drift and natural selection side-by-side for the sake of comparison, and I also still like the idea of speciation being a "bridge" between natural selection and common descent. But perhaps the original order (heredity, then speciation and extinction, then selection and adaptation, then genetic drift) is better, then? Though if we go along with the below post and remove "speciation and extinction" from the "mechanisms" section (and presumably move it higher up the page), then perhaps we can just have the three mechanism sections be "heredity", then "genetic drift", then "selection and adaptation", since that'll allow us to go from the concrete to the abstract more generally. I suppose what I really want to know is: which of the sections in my outline can and can't fairly be called "mechanisms of evolution" without being arbitrary or inconsistent? -Silence 17:27, 15 April 2007 (UTC)


 * I think "heredity," "natural selection," and "genetic drift" are good answers. I might also include "gene flow" to discuss issues like population bottlenecking, etc. (but perhaps that goes under something else).  Gnixon 17:43, 15 April 2007 (UTC)


 * Great discussion. A couple of comments: 1.) I think it's a little backwards to describe speciation before you describe selection, drift, and gene flow, because selection, drift, and reduced gene flow are the processes that drive genealogical divergence in populations that are undergoing reproductive isolation before speciation.  I really think you need to lay out the basic principles and mechanisms early in the article: heritable variation results from allele variation; allele frequencies change as a result of selection, drift, and gene flow/migration; and then you can get to describing more complex mechanisms like speciation.  Otherwise new readers won't really understand how speciation happens, until they get further down into the article and read about mechanisms.  Seems like just recently there was a comment/objection from some (likely creationist) user who was perplexed about where species come from.TxMCJ 20:21, 15 April 2007 (UTC)


 * It's really a catch-22. Basic principles without concrete examples are vague, ethereal abstractions; concrete examples without an overlying structure or reason are arbitrary, trivial factoids. Either scenario will confuse readers. That's a large part of the reason why I'm advocating including evidence for theories in the same sections as the theories themselves: isolating either from the other renders both frustratingly hollow.


 * I see what you mean -- thus the 1-2-3 structure I also mention below (1. observations you can make today without any understanding of mechanisms or history; 2. mechanisms; 3. evolutionary histories that explain the observations in (1).) TxMCJ


 * In this case, if we address natural selection before speciation and extinction, we won't be able to expect our readers to understand how species arise and die out, which is a very valuable thing to know before natural selection is explained. On the other hand, if we explain speciation and extinction before natural selection, our readers won't understand why certain species survive and others don't until they reach the natural selection section. Of these two, I currently think the former is preferable (it's easier to describe speciation/extinction without explicitly refering to selection than it is to describe selection without explicitly refering to speciation/extinction), but the counter-argument that we should explain the most important aspects of evolution (e.g., common descent, selection, drift) as early as possible is a strong one, especially considering the simple fact that most people won't read very far into the article.


 * Well in this case I would have to disagree, strongly. Selection happens in populations and species in complete isolation of other populations or species.  Thus even if you only ever studied ONE SPECIES ever, you would find that selection occurs.  No understanding of speciation and extinction is required (selection against individual phenotypes is not the same thing as species extinction.)  Thus I would strongly argue that understanding selection DOES NOT require any understanding whatsoever of speciation or extinction.  And on the contrary, describing the mechanism of speciation *absolutely, without exception* requires an understanding of how 2 reproductively isolated populations differentiate from one another.  Selection is fundamental to that (along with reduced gene flow and drift).  I'm not trying to argue, I am just saying that I believe that the exact opposite of what you're saying, is the case. TxMCJ 21:09, 15 April 2007 (UTC)


 * Ultimately this reader laziness is just something we have to live with; we can't put everything important at the top of the article and everything less important at the bottom or the page will be unbalanced and disjointed. We shouldn't sacrifice the value of this article to in-depth readers in order to appease the largely disinterested. However, the simple fact that many people don't bother with most of the article is a large part of the reason I've been pushing to keep an entire paragraph on natural selection in the lead section: because it makes up for the fact that we might not get into the in-depth explanation for that process until halfway through the article, simply because there's so much ground to cover (e.g., basic genetics) first. Hopefully having those brief explanations in the lead section and at the start of basic processes (now "variation") will help make up for the fact that common descent, selection, and drift are being left until much later in the article; it's not ideal, but I think it's by far the best compromise so far. -Silence 20:39, 15 April 2007 (UTC)

Response from Gnixon
In this outline, I like having "History" first, because it can also serve as an introduction and overview. Is "Speciation and extinction" a "Mechanism" or a result? I might have put it under "Common descent." This outline doesn't distinguish between evolutionary facts (e.g., common descent) and evolutionary theory (e.g., the mechanism of natural selection), which I prefer, but I think it's reasonable. I also like that we could easily rearrange what we already have to match your layout. Gnixon 13:48, 15 April 2007 (UTC)


 * How is common descent an evolutionary fact, in any sense in which natural selection is not? -Silence 17:27, 15 April 2007 (UTC)


 * Common descent is an almost direct inference that one can make from, e.g., homology (morphological and genetic). Natural selection is an explanatory mechanism for how and why organisms evolve the way they do.  If "evolution" means "change in populations' traits over time," then I'd say common descent is one aspect of evolution, whereas natural selection explains how it works.  Clearly the distinction is somewhat semantic since one can also infer natural selection from the data.  But when I think of TxMCJ's argument that natural selection results from basic facts and has significant consequences, it seems clear to me that it's part of a scientific-theoretical structure.  Perhaps the experts around here could comment on how the terms are used within the field.  Gnixon 17:39, 15 April 2007 (UTC)


 * I don't see how common descent is "almost direct" in a way that natural selection is not; if anything, I'd say that natural selection is completely direct, while common descent is merely "almost direct". After all, it is quite common for people to say that natural selection is almost self-evidently true; in contrast, there are many ways to explain homologous-seeming structures (including horizontal gene transfer, convergent evolution, and simple coincidence), and common descent is only a reasonable inference because we lack any other way to explain the sheer number of homologous systems. The line of thought required to reach common descent seems to me to be much more complicated than even just "we observe similarities between all life, therefore we can conclude beyond all doubt that common descent is true"; and even though common descent is so well-supported that it might seem like simple "fact", it is simply misleading to characterize it as such when it is based entirely on theoretical reconstruction, not direct observation. Inferring shared ancestry from similarity is not any more "direct", or any less theoretical, than natural selection.
 * Common descent is not an "aspect of evolution" (at least, the process of evolution; it is certainly an aspect of the theory of evolution), because if organisms weren't all related by common descent, evolution would still work in the exact same way; the evolutionary history of organisms would be completely different, but the actual process would work in just the same way, still operating under natural selection, etc. It is much fairer to describe natural selection as "one aspect of evolution" than to describe common descent as such, such natural selection describes how evolution must work, whereas common descent describes how the evidence strongly implies it has happened to work in the past. -Silence 18:52, 15 April 2007 (UTC)


 * That's fair, and my words (or thoughts!) have probably been unclear. Maybe a better way to put it would be that common descent is simply an inference (at some level of depth) from the data and what we know about evolution---it's a result.  Natural selection is an explanatory mechanism for how evolution works (as well as an inference).  Gnixon 19:15, 15 April 2007 (UTC)


 * Although I need to revise previous comments, the cosmological expansion of space and the big bang keep coming to mind:
 * 1) observe redshift-distance relation (homology or fossils)
 * 2) infer expansion of space (speciation/extinction and branches on tree)
 * 3) infer further that there must have been a "big bang" (common descent, LUCA)
 * 4) general relativity is an explanatory mechanism for how space expands, forming part of the theory of cosmology
 * All these things can in some sense be "inferred" from the data, but the first three are inferences about what happened, while the last item is an inference of how they happened. Admittedly, those distinctions are somewhat arbitrary in this language, but the confusion is exactly over the distinction between theory as inference and theory as scientific explanatory structure.  Gnixon 19:15, 15 April 2007 (UTC)


 * I agree with everything you said above. What we're saying, then, is that common descent is a theory for how evolution actually happened to occur, whereas natural selection is a theory for how evolution always occurs. Both are theories, but one is necessary for (Darwinian) evolution to occur at all, whereas the other, common descent, isn't. In this sense, natural selection is exactly analogous to the Big Bang theory, just as you note: it's an extremely plausible inference from the evidence/observations, but it's not the evidence/observation itself. -Silence 19:28, 15 April 2007 (UTC)


 * I might argue, contrary to the above, that given the self-evident facts of selection, drift, and the behavior of alleles within populations, that even speciation necessarily follows when sexually reproducting organisms undergo reproductive isolation for extended periods of time. And speciation histories is what leads to histories of common descent (despite how many "original ancestors" there were.  In every lineage there will be traceable patterns of shared ancestry and descent.)  I think when you take evolutionary mechanisms as a whole package, that speciation (and thus shared ancestry of a lineage) are also *self-evident*, although not immediately evident to someone who doesn't understand how speciation works.  Thus, perhaps another article to present microevolution (population based mechanisms) before macroevolution (species-based mechanisms).  I don't know why this makes Gnixon go "egads" (below) -- macro/micro is a fair and scientifically sound distinction to make here. TxMCJ 20:34, 15 April 2007 (UTC)


 * Perhaps, but reproductive isolation may not be a necessary aspect of developing life, and sexual reproduction certainly isn't. Moreover, by "common ancestry" we were really discussing "universal common ancestry", something that certainly wouldn't necessarily have to be the case for any planet's lifeforms; it's entirely possible for two species to live in the same habitat that have no common ancestor at any point in the history of the universe. In this sense, universal common ancestry is not "self-evident" even given speciation, selection, drift, etc. Common ancestry is only "self-evident" for species within a lineage&mdash;that is, for species that have a common ancestor! Clearly this is only trivially true. -Silence 20:47, 15 April 2007 (UTC)


 * I agree with your first point, but not sure that it is the task of this article to come up with a framework that allows for all conceptual versions of life or evolution that have not yet been discovered on alien worlds. I am not being flip by that statement -- my point is, we should focus on describing what we DO observe and what we DO know, instead of what we merely can imagine (which complicates our task greatly and needlessly).  Also, I see what you mean about the UCA vs. "common ancestry" and I get your point, but as I said above -- regardless of how many CA's there were on Earth, you would still necessarily get histories of shared ancestry and descent within each of those lineages (as you also say above).  Anyway... not sure exactly how this bears on the writing of the article, but in general, I do see your points.  I'm just not sure whether these "hypothetical worlds" should really guide our writing too much here.  It is interesting, though. TxMCJ 20:59, 15 April 2007 (UTC)


 * I don't think the question is something a "mechanism or result" is helpful. Causes and effects are known to us via evidence (and a story of this evidence would constitute a "fact" or "evidence" or "history of life" section.  "Theory" or "model" is about the relationship between causes and effects.  Now, we can describe the theory of evolution (or the model that is called the modern synthesis) in terms of concepts, mechanisms, processes, whatever ... but all the elements of the model or theory are ultimately claims about the relationship between causes and effects ... not "causes" in and of themselves. Slrubenstein   |  Talk 14:51, 15 April 2007 (UTC)


 * Sure, I didn't mean to suggest a false dichotomy. However, I think "speciation and extinction" isn't really a mechanism of evolution (i.e., something explaining why/how populations change over time).  Rather, I think it's sort of an extreme aspect of evolution---sometimes populations evolve so much that they're new species or are selected against so strongly that they vanish.  That's why in my outline, speciation and extinction fall under "observations and inferences," whereas in Silence's outline, I'd suggest speciation falls under "common descent," whereas extinction may fit there or under natural selection.  I don't feel strongly about these things, but I'm glad we're discussing the language.  Gnixon 15:27, 15 April 2007 (UTC)


 * Well, I think you are getting into semantics. Speciation and extinction are events that leave evidence and as such can be explained by processes - but you can also say speciation and extinction are the very processes by which evolution.  If evolution is (as some say it is) a change in gene frequencies, speciation and extinction explain why the gene frequencies have changed.  Saying this does not mean that speciation and extinction themselves do not have explanations.  I think you are wrong to think that there is an "extreme" version of evolution (unless you mean macroevolution, which is different from microevolution only in scale - is this what you mean by extreme, a change in scale?).  Slrubenstein   |  Talk 16:36, 15 April 2007 (UTC)


 * Egads! The last thing I want to do is raise a distinction between macro-/micro-evolution!  Still reading the rest of your post.  Gnixon 17:45, 15 April 2007 (UTC)
 * Explanation: getting this article too much into micro-/macro- could encourage confusion about their equal acceptance. Gnixon 00:05, 16 April 2007 (UTC)


 * If you see my comment above, from 12:14, I am suggesting to Silence something similar to what you are suggesting now. Like you, I don't feel terribly strongly about my suggestion.  But I think the issue is this: do we have one section where we discuss different observable/observed phenomena (such as speciation and extinction) and another section where we discuss elements of the theory that explain/make sense out of the date (such as adaptation and selection)?  Or do we have one section where we link one element of the model to that part of the phenomenal world it accounts for (selection and extinction) and another section where we link another element of the model to another part of the phenomenal world it accounts for (adaptation and speciation)?  This is an editorial discussion and I think the decision should be based on how well it reads/clarity of explanation.  However, whichever way we choose to go, we need to make it clear that (1) there are observable facts, and these facts feature changes in genotype and phenotype over time and at different scales (2) there is a theory that accounts for the facts i.e. a model of what causes lead to what effects, and (3) there is a recursive relationship between fact and theory namely observing facts led to the development of the theory; the theory leads us to look for and helps us make sense of new data; the new data leads to refinements in the model, and so on. Slrubenstein   |  Talk 16:36, 15 April 2007 (UTC)


 * I agree with your analysis of the alternatives. Gnixon 17:47, 15 April 2007 (UTC)


 * Gnixon's point that speciation and extinction are more "extreme aspects of evolution" (i.e., consequences on a larger scale of things like natural selection) than mechanisms explaining how evolution occurs (this is particularly true in that they cannot, in themselves, account for any aspect of microevolution) is a good one, and reason enough to remove it from the "mechanisms" section (though, another question: is it acceptable to have "heredity" there? and are there any glaring omissions of mechanisms, in the context of the layout I provided?). But I don't really agree with adding it to the "common descent" section, since that would imply that speciation and extinction are somehow based on common descent, when in reality they're just observations; plus placing them lower than "natural selection" would fail to address Slrubenstein's earlier concern. So right now I'm tempted just to put it in a section on its own.
 * I'm also gonna try putting "Heredity" in its own section, either before "Variation" or before "Speciation and extinction", depending on whether it's better to deal with the basic topic of heredity before addressing things like gene flow and recombination under "Variation". I'm gonna put it at the beginning for now, on the grounds that it'll be a great way to introduce important basic ideas about genetics in a concrete way (e.g., from the "peas" example), which will in turn allow those ideas to be clearly explained in the "Variation" section. -Silence 17:27, 15 April 2007 (UTC)


 * Certainly speciation and extinction aren't based on common descent, but I think they can either be considered an aspect of it or at least closely related to it. The issue of heredity is interesting.  In my observations/theory divide, I like putting stuff about the peas into observations suggesting heredity, whereas the theory would probably consist of a discussion of how genetics works.  My point is that there are two aspects of it, and only one aspect is a mechanism (genetics).  Gnixon 17:53, 15 April 2007 (UTC)


 * I don't think it's fair to consider speciation or extinction to be "aspects" of common descent; both could occur even if there was no common descent, and likewise common descent could hold true even if nothing ever speciated or went extinct. Speciation and extinction certainly play a major role in understanding common descent and its role in the history of life, and it is only in this sense that they can be considered "aspects" of common descent; however, in this sense natural selection, genetic drift, mutation, and a host of other mechanisms are also aspects of common descent, because they all play a role in how life descended from a common ancestor. I think that's one of the reasons I love having common descent be the last big section concerning what the science of evolution tells us; common descent and the history of life tie together all the past themes that will have been discussed in article's other sections, providing a coherent narrative in which all the previously-discussed actors, from heredity to extinction to selection, play a part. They are the stage upon which our evolutionary dramatis personae play out their various roles; it's an eloquent and meaningful way to explain evolution to laypeople, I feel. But although speciation and extinction are certainly "closely related" to this narrative, playing a major part in it, that doesn't mean that we should categorize them under the "common descent" section, which should be reserved for things that provide direct evidence for common descent (morphological and molecular homology) or are based upon common descent (the reconstructed history of life, phylogenetics, etc.). Just like many things play a role in "variation", but I tried to reserve the subsections of Variation for things that generate variation. -Silence 19:37, 15 April 2007 (UTC)


 * I object, somewhat, into complicating our task (writing the article) by getting too caught up in philosophical speculations about situations that never existed on Earth, and in my mind cannot really logically have existed under Darwinian and population-based mechanisms (common descent without without speciation; speciation without common descent.) Whether or not you agree that those things can happen without the other, I'm not sure what the point of such a discussion is.  The history of life on earth, and the mechanisms responsible for it, are clear.  Evolution texts and courses (designed to present evolution to non-experts, which is also the goal of this article) are fairly straightforward in describing 1.) Incontrovertible "observations" you can make here and now that do not require an immediate understanding of mechanisms or history (e.g. homologous structures, nested hierarchical order of taxa, geographic ranges, vestigial traits); 2.) the mechanisms responsible for organismal evolution (heredity, variation, reproduction, selection, changes in allele frequencies from generation to generation) and 3.) the long-term histories and events that result from this, and thus account for (1) above (these events would include things like speciation, extinction, coevolution, adaptive radiation, etc.)  To me (and I might add to the majority of writers and teachers on the subject), the above 1-2-3 flow is a time-tested one that works, and is really quite uncomplicated. Perhaps the distinction (one which is made in Evolution all the time) is the distinction between PATTERN and PROCESS. TxMCJ 20:46, 15 April 2007 (UTC)


 * This is the organizational principle I think we've been groping for: 1-2-3. Straight-up observations, processes and mechanisms, long-term histories.  Credit to TxMCJ.  Gnixon 22:02, 15 April 2007 (UTC)


 * Well...thanks, but if you look at my 17-point proposal, it is also organized in this same logical sequence. Group things how you want to, the order of presentation is still the same.  Either way -- I really think this is the best structure TxMCJ 22:19, 15 April 2007 (UTC)

I'd also point out that having a serious History section up front probably means social impact and controversy need to be addressed there, too. That could be a problem. Gnixon 14:43, 15 April 2007 (UTC)


 * I don't think we need to address social impact and controversy at the top of the article (at least, not in more than a sentence or so), because the top deals only with the history of scientific thought on the matter, as a way of introducing the science of evolution; its social impact is explicitly distinguished from this. -Silence 17:27, 15 April 2007 (UTC)


 * I just want to make sure we are clear - sometimes we talk about "history of evolutionary theory" (and I agree with Silence here, I think controversy can and should be dealt with separately because the main controversies never really had an impact on the development of evolutionary research or theory) and "history of life" which (unlike the current version) I think ought to largely be an evidence-based narrative. For clarity's sake, can we avoid using "history" alone and always specify, history of theory versus history of life?  That said, i think there are major areas where Gnixon, Silence, and I agree - this has been very productive.  I am content to let Silence mull over my comments and Gnixon's and then revise (and at this point, flesh out a bit more) his proposal accordingly, if he is willing. Slrubenstein   |  Talk 18:50, 15 April 2007 (UTC)


 * Agreed. Of course, comments from others would also be helpful.  Gnixon 18:56, 15 April 2007 (UTC)


 * What do you mean by an "evidence-based narrative"? The current narrative is "evidence-based"; do you mean that we should explicitly detail the evidence supporting each and every major development in the history of life? Because I'm very wary about going into that level of detail; I put a lot of effort into trying to keep the current narrative as short as possible because it's so exquisitely easy to go into too much depth with such a fascinating account as the history of life. This isn't the article for that, though. So, I'm open to revising the section in question to try and make it more clear, reasoned, and intuitive to readers (rather than just "one damned thing after another"), but I'm very wary about going into too much detail regarding the evidence for specific occurrences in the history of life.
 * (In contrast, I think providing plenty of evidence for the basic idea of common descent itself is an excellent idea; that's what I plan on having the entire "homology" section consist of, by trimming and adapting the current "evidence of evolution" section into the homology section. I also am proposing to the editors at Evidence of evolution that that article's name be changed to Evidence of common descent, per the concerns of myself and some other editors who find the current title ambiguous and defensive in its implications. See Talk:Evidence_of_evolution for the discussion.)
 * And, I've made a few revisions to my above proposal (mainly to the "mechanisms" section), but feel free to suggest any other changes you think would be helpful! -Silence 19:16, 15 April 2007 (UTC)


 * I didn't read Slrub's comment as a call for more detail---I thought "evidence-based" was just an adjective used in passing. Surely we can distinguish between "History of evolutionary thought" and "History of life," at least for purposes of this discussion.  Thanks for continuing to work on this stuff.  Gnixon 19:22, 15 April 2007 (UTC)

YASO (Yet another stupid outline)
I couldn't resist. Having perhaps come to see the wisdom of history first and mechanisms before observations, here's another proposed outline. I've tried to get all the topics from the current article.


 * 0) Lead
 * 1) History of evolutionary science
 * 1.1) Lamarckism
 * 1.2) Origin of species
 * 1.3) Mendel's genetics
 * 1.4) Modern synthesis
 * 1.5) Current research


 * 2) Mechanisms
 * 2.1) Genetics
 * 2.1.1) Phenotypes and genotypes
 * 2.1.2) Heredity
 * 2.1.3) DNA
 * 2.1.4) Chromosomes and alleles
 * 2.1.5) Mutation
 * 2.1.6) Other lifeforms
 * 2.2) Natural selection
 * 2.2.1) Superfecundity
 * 2.2.2) Adaptation
 * 2.2.3) Extinction
 * 2.3) Genetic drift
 * 2.4) Reproduction
 * 2.5) Speciation
 * 2.5.1) Migration
 * 2.5.2) Gene flow
 * 2.5.3) Hybridization
 * 2.5.4) Horizontal gene transfer


 * 3) Observations and inferences
 * 3.1) Homology
 * 3.1.1) Morphology
 * 3.1.2) Cellular processes
 * 3.2) Fossil record
 * 3.2.1) Extinct species
 * 3.2.2) Transitional fossils
 * 3.2) Modern speciation and extinction
 * 3.3) History of life
 * 3.3.1) Common descent
 * 3.3.2) Phylogeny
 * 3.3.3) Abiogenesis


 * 4) Social impact

Not trying to supersede the very good progress being made in discussion topic above. Just my current thoughts. Presumably some of the lowest-level topics wouldn't need section headings and thus wouldn't clutter the TOC. Gnixon 20:22, 15 April 2007 (UTC)


 * Why "mechanisms before observations"? I would think that the reverse would be more helpful: give an observation, then explain it with a mechanism. Then move on to the next observation. Also, I don't think all molecular homology consists of cellular processes, per se...
 * A lot of interesting ideas here, but a few comments: (1) it seems strange to discuss reproduction so much later than genetics; (2) it seems strange to discuss extinction so much sooner than speciation; (3) migration, hybridization, and horizontal gene transfer are all examples of gene flow, not of speciation, and I'm not sure why gene flow is grouped under speciation; (4) "the history of life" is not an observation, and if it is an inference then so are all the "mechanisms"; (5) countless observations are left out of "observations/inferences" (not to mention countless inferences), including genetics, speciation, extinction, and reproduction; (6) what is a "transitional fossil"? more to the point, what isn't one?; (7) are you actually proposing that each of these numbers be a distinct section, or is this a way of laying out what topics to cover in some depth? For example, many of these proposed sections seem to me to deserve a few sentences or a paragraph, but not a whole section (particularly the subsections in the "history of evolutionary science" and "genetics" sections). -Silence 20:59, 15 April 2007 (UTC)


 * This is probably moot after your recent edits and mine. Evidence before genetics and mechanisms seems like the way to go, with broader aspects of evolution (speciation/extinction/common descent) coming after them.  Gnixon 21:31, 15 April 2007 (UTC).
 * On second thought, most of what isn't in Variation or Mechanisms fits well under Common descent. Gnixon 23:38, 15 April 2007 (UTC)
 * I don't see how anything fits well under common descent other than the evidence for common descent (formerly "evidence of evolution") and the consequences of common descent (phylogenetics and the reconstructed history of life). Nothing else quite fits, as far as I can see. -Silence 23:52, 15 April 2007 (UTC)
 * Continued under TOC discussion below. Gnixon 00:02, 16 April 2007 (UTC)

Outlines
Since there have been 7 different outlines mentioned so far (3 from me, sorry), I've put each of them on a separate subpage so we can see their tables of contents.


 * Gnixon's broad outline
 * TxMCJ's textbook/course-based
 * Britannica
 * Slrubenstein
 * Gnixon's two main sections
 * Silence
 * Gnixon's lengthy one

I tried to make them represent the original intents, but they may need to be improved. Gnixon 20:50, 15 April 2007 (UTC)


 * I've (evolution is fake) e greatly; it now includes a paragraph-by-paragraph breakdown of every topic to be covered even within s (evolution is fake)(This, of course, will need to be heavily revised, but it should (monkey man darwin) ea of the topical layout envisioned.) -Silence 21:43, 15 April 2007 (UTC)

Changes
Silence recently moved some sections around (with some rewriting): Basic processes cut; History of thought, Heredity, Variation moved to top. I then combined Heredity/Variation into Genetics and put Evidence before Genetics/Mechanisms, but Speciation and extinction after them, before Common descent. Gnixon 21:23, 15 April 2007 (UTC)

I think this layout does a nice job by going
 * History
 * Evidence
 * Genetics
 * Mechanisms
 * (Broader aspects): Speciation/Extinction and Common Descent
 * Current research
 * Social Impact

The overall result is to make Genetics and Mechanisms central, with other topics arranged logically around them. Gnixon 21:32, 15 April 2007 (UTC)


 * The only reason I didn't include "genetics" in any of my layouts is because it simply seems too vague to me. What aspect of evolution isn't, on one level or another, "genetics"? For example, why is gene flow "genetics", while genetic drift is not "genetics"? Dividing the article between genetic and non-genetic topics seems misleading to me; plus I suspect that more laypeople will be able to quickly grasp the scope of "heredity" or "variation" than "genetics". -Silence 21:41, 15 April 2007 (UTC)


 * True, genetics spans most of evolution. Perhaps "Heredity" would be a better title for combining those sections, but the totality of that section is essentially about the nature of genetic information and how it is transmitted (and that description doesn't apply directly to the other sections).  I think the other sections can be reasonably separated from "Genetics."  (Genetic drift being the only problematic sub-section I notice.)  Gnixon 21:49, 15 April 2007 (UTC)


 * Genetic drift isn't the only problematic section; natural selection is one of the most important concepts in population genetics. I don't see a lot of value for our readers in bothering to point out that topics X, Y, and Z are all "essentially about the nature of genetic information and how it is transmitted"; that's a suitably vague oversectioning as to not convey any useful information about the relationship between the subsections. -Silence 22:01, 15 April 2007 (UTC)


 * Heredity, then? (As opposed to mechanisms influencing what gets inherited.) Gnixon 22:04, 15 April 2007 (UTC)

another proposal
I am not going to argue forcefully for the following - here are just two suggestions and my hope is that even if people criticize it it will help us clarify what we do want to do.
 * 1) statement that evolution refers to the fact that species change over time and that different species are related, as well as concepts/models that explain how and why species change over time and are related
 * 2) evidence that species change over time/history of life (this would include MCJ's 7, 8, 12, 13 - the story of life and the evidence are infused)
 * 3) evidence that species are related (see paranthetical above)
 * 4) basic genetics, assortment, mutation all explain how, even were all life descended from a common ancestor, life can take so many different forms
 * 5) natural selection and drift explain why some forms endure and others do not
 * 6) special cases: sexual selection, kin selection
 * 7) historical background: the move away from Linneus and Lamarck to Darwin and Wallace to Mendel to Fisher, Dobzhansky, Sewell, Wright, Simpson, etc, to present. Can we tell this story in a way that emphasizes the recursive relationship between observation (and when appropriate experimental data) and theory?  I think we should try.
 * 8) recent developments: coevolution, evo-devo
 * 9) social controversy
 * 10) misconceptions

Like I said, just an idea - working on the fine work Silence and MCJ have done, and considering Gnixon's thoughts. Slrubenstein  |  Talk 11:31, 14 April 2007 (UTC)


 * Hooray Slrubenstein! This is a fantastic contribution, and an example of good organizational thinking, since you refer to the actual topics.  Merging an outline like yours with the key topics I've posted above (and Silence's earlier to-do list which focuses on fine-tuning the content) should be a fairly simple task, and is the right direction to move in. TxMCJ 16:32, 14 April 2007 (UTC)
 * Looks good to me, in particular the point of presenting "explanations" rather than talking about "theories" (a much misunderstood term) .... dave souza, talk 19:29, 14 April 2007 (UTC)
 * I can understand wanting to avoid "theory" to avoid misunderstandings, but to me it diminishes the scientific stature of evolutionary theory to call it an "explanation." For me, common descent is an "explanation" of the fossil record, but evolutionary science also has a full-blown scientific theory.  To make an analogy, the discrete spectrum of atomic transitions is "explained" by the idea of quantum energy levels, but to refer to quantum mechanics as an "explanation", not a full theory, would seem to be somehow detracting from its significance.  Maybe just semantics.  Gnixon 20:53, 14 April 2007 (UTC)


 * 1. That species change over time (i.e., evolve) is a fact; that all species are related is an explanation for the similarities between organisms and for the distribution of species in the fossil record. I don't see a need to call the theory/explanation of common descent "evolution" when we already have the word "common descent" to refer to it, and using the word loosely will only lead to ambiguity when we speak of "evolution" later on. The theory of evolution states that all known life has developed through the process of evolution from a common ancestor; we should use "evolution" to refer to the process, but "theory of evolution" to refer to the explanation, and "common descent" to refer to an aspect of the explanation.
 * 2. The "history of life" is a reconstruction of how species probably developed, on the basis that they are related and change over time; it is not "evidence that species change over time", anymore than the Proto-Indo-European language is evidence that languages change over time.
 * 5. I'm not sure that's the best way to put it. Extinction is what really explains why some forms survive and others don't; natural selection and drift just account for differential fitness (which 4 is also essential to explain).
 * 7. It will be difficult to do so without leaving anything important out and without letting the section grow too large yet again. I endorse an attempt to try and improve the history section in the way you mention, but don't be surprised if we end up needing to shorten it some more afterwards; ultimately, it may be most valuable to work on trying to improve History of evolutionary thought in the way mentioned, and then simply try to encapsulate the most essential ideas there here. We can't include everything interesting in Evolution, after all.
 * 10. Are you proposing a separate section for misconceptions? Why? -Silence 21:07, 14 April 2007 (UTC)


 * I agree with Silence here, whose points are quite clear. I would add, though, that I also support a section for misconceptions, because misconceptions about Evolution run rampant in popular culture.  Misconceptions I would add are: Evolution is generally gradual; evolution is generally directional; evolution is generally optimizing; evolution is generally complexifying; life is a ladder/great chain, rather than a phylogeny; most traits are adaptations; "theory" means "hypothesis"; etc. TxMCJ 22:02, 14 April 2007 (UTC)
 * I think these concerns are best addressed (in the context of an encyclopedia) by presenting information that rebuts them (e.g. presenting a phylogenetic tree instead of a ladder, discussing exaptations, etc., in the appropriate context. Graft | talk 22:13, 14 April 2007 (UTC)


 * I agree with Graft that it may be best to address some of the misconceptions as they arise, but there is also a developing Misunderstandings about evolution article that can be linked to address the subject in more detail. Since there are a lot of experienced editors, it would be nice to create a final draft proposal,plan, constitution, for a road map to build and keep the article on track. Face it, everyone has an opinion or perspective on evolution and people constantly want to change the article (it would be frustrating to finally build a solid article with sound reasoning and with experts bothering to contribute and then have it morph into drivel). Perhaps a well thought constitution to address the building, content,and reasoning behind the article will discourage vagrants from mucking with things, or at least a conscientous editor can read the plan and repair any damages. Controversial high turnover articles can discourage qualified editors because of such antics of digress rather than progress. There seems a good mix of editors to reach critical mass here. GetAgrippa 22:42, 14 April 2007 (UTC)


 * Personally I think that we should not only address misunderstandings in their respective specific sections rather than grouping them all under a "Misunderstandings" section (for example, misconceptions about speciation belong under "Speciation and extinction", not stuffed at the bottom of the page under "Misunderstandings"), but that we should apply the same principle to articles: delete Misunderstandings about evolution and use various topic-specific articles to address any valuable information that's there. The first section there can be dealt with at Evolution as theory and fact, the second at Biological devolution, and the third at survival of the fittest. I see no value in having such a redundant page, when Evolution should already serve to summarize any important misconceptions, and the topic-specific daughter articles are the best think to link people to who want more information on any of those topics, since those articles can deal in much more depth with their respective issues. -Silence 08:50, 15 April 2007 (UTC)


 * From a scientific and rational standpoint, I agree with you, that there's not a great reason to group "Misconceptions" into their own section... EXCEPT FOR THE FACT, that this is not really a purely scientific and rational article, in that it is targeted towards "the masses", where those misconceptions exist quite strongly and soundly. The value of a "misconceptions" section is that it accomplishes two things: 1.) consolidates, in one place, incorrect (but popular) ideas about Evolution that pervade its understanding among people with a genuine interest in it, and 2.) consolidates, in one place, incorrect (but popular) ideas about Evolution that are continually cited by creationists as scientific flaws.  I'm not saying the article should be targeted to one type of demographic or another, only that it should be targeted for "the masses" (since it IS an encyclopedia article -- people "look it up" because they need to).  And I think you could really kill a lot of birds with one stone by providing a "Misconceptions" section like that in an article like this. TxMCJ 20:54, 15 April 2007 (UTC)


 * You mention two groups who would benefit from a "misconceptions" section. The first is "people with a genuine interest" in evolution who happen to have popular incorrect ideas about it; I would think that the best way to fix this problem would be to simply create as good, clear, and informative an Evolution article as possible! If someone is interested in evolution, he's more likely to read up on how evolution works than to assume that he's mistaken about evolution and go looking for a "Misconceptions" section; in the process of having evolution explained to him, the person will have his misconceptions cleared up as well, so two birds really will be getting killed with one stone&mdash;not only with the misconception be cleared up, but actual new information that is not erroneous will replace it. This not only eliminates current misconceptions, but also makes it less likely that future misconceptions will crop up! In contrast, focusing on telling people what's wrong, without intermingling that with examples of what's right, just leaves them just as susceptible to misunderstanding evolution the next time around (and thus just as susceptible to the next creationist argument that pops up).
 * The second group you mention is "creationists". Leaving aside for now the issue of whether we should really be tailoring our science articles to the misconceptions of creationists, I think this issue is already taken care of by an article I created expressly for this purpose: Objections to evolution. This article not only addresses countless creationist misconceptions, but also does so in a neutral fashion, since it doesn't frame the exercise in a biased way to begin with by characterizing a certain ideology as misunderstanding-based. (Which it is, but saying that with a "Misunderstandings" page would exhibit bias, whereas simply showing it through an "Objections" page makes the intended point quite clear.) -Silence 00:52, 16 April 2007 (UTC)


 * I spearheaded the first Misconceptions section in Evolution; it eventually grew and then was split off and renamed the Misunderstandings about evolution; disconnected from Evolution and with a mess of templates up top. Not exactly what I had in mind. I think my point being, there are a lot of misconceptions out there... keeping such a section short/tight/focused enough to keep within Evolution as a sub-section, I believe, is asking too much. As such I think a new lead for the Misconceptions article should be crafted, which would then be replicated in Evolution as a sub-section. Of course with its future in limbo with a proposed merge, that needs to be sorted out too. - RoyBoy 800 03:38, 16 April 2007 (UTC)

Condensing the TOC
===Heredity=== Would it make sense to include the current version's "Variation" section under "Heredity"? Gnixon 22:30, 15 April 2007 (UTC)

That section would become
 * Heredity
 * Variation
 * Mutation
 * Recombination
 * Gene flow

assuming hybridization and HGT could be trimmed to fit under gene flow without subheadings. Gnixon 22:32, 15 April 2007 (UTC)

Speciation and Extinction
How about putting "Speciation and Extinction" in with "Common descent," which has turned into a major topic in the article? The section seems very out of place between "Variation" and "Mechanisms." Gnixon 22:30, 15 April 2007 (UTC)


 * In what way is it out of place there? It explains the eventual consequences of variation right after "variation", and that species have differential survival rates right before "natural selection". It's a pretty clear transitional section. -Silence 23:49, 15 April 2007 (UTC)
 * Again, heredity, variation, selection, drift are fundamental processes of (micro-)evolution. Speciation/extinction are not---they derive from those more basic processes.  Thus they disrupt the flow of the fundamentals and fit better under the broader theory of Common descent.  Gnixon 00:01, 16 April 2007 (UTC)
 * There is no flow of the fundamentals! If those 4 sections happen to be more "fundamental" than speciation/extinction, that's purely a coincidence; the deliberate arrangement was not to arbitrarily place the most "fundamental" topics at the highest hierarchy, but rather to simply present information in an order that cumulatively expands on the reader's knowledge in an intuitive and clear way. And common descent and variation are not "processes", so I don't see how they're any more deserving of top-level notice than "speciation and extinction". But none of that matters, because speciation and extinction simply do not fit in the "common descent" section; there is no logical connection whatsoever, because speciation and extinction are not dependent upon common descent, nor vice versa (whereas homology and common descent are mutually dependent, as are phylogenetics and common descent). So even if we'd like it if we had a convenient top-level section to place them in, we don't; and it is especially absurd to try to pack speciation/extinction into such an ill-fitting oversection immediately after removing genetic drift and natural selection from a relatively nicely-fitting section, "mechanisms"! How can we be so strict in our standards for genetic drift and natural selection, and so arbitrarily loose in our standards for speciation/extinction? -Silence 00:26, 16 April 2007 (UTC)


 * Surely you agree that Common descent of today's species from a LUCA (the whole thing) can't happen without massive amounts of speciation and extinction? Gnixon 00:35, 16 April 2007 (UTC)


 * First, that's irrelevant. Common descent of today's species from a LUCA also can't happen without every other section in this article on the science of evolution; if merely being necessary for Earth's current biodiversity to arise from a UCA is sufficient to justify including that thing in "Common descent", then every section of this article should be put under "common descent", with the exception of the history-of-science and social-effect ones.
 * Second, common descent can be true without any speciation or extinction occurring or ever having occurred; this was certainly the case at one stage or another in the history of life on Earth. So clearly, although speciation/extinction and common descent are related, they are important for entirely different reasons, and do not depend in any way upon each other. If every organism on the planet was the same species, that wouldn't imply that common descent was untrue; likewise, if lots of different species lived on the Earth, but they shared no homologous structures or other evidence of common ancestry, it wouldn't be fair to leap from speciation to common descent. The relationship between speciation/extinction and common descent is the same as the relationship between heredity and common descent, natural selection and common descent, mutation and common descent, etc.: the former plays an important role in the evolution of life under the latter, but is not restricted to common descent in its scope of importance or relevance, making it inappropriate to include any of the former as a subsection under the latter. -Silence 00:43, 16 April 2007 (UTC)


 * I think I'm somehow failing to get a point across, but I'm afraid I can't discuss it further tonight. I'll try to continue tomorrow.  Gnixon 00:49, 16 April 2007 (UTC)


 * In the meantime (and this isn't meant to be rude), maybe have a look at some of the comments from Silence and I over the past few days, and think about how you may be complicating the process (and frustrating editors) with too much emphasis on neat-and-tidy organization and categorization of everything. The problem is not as opaque as you seem to think it is.  We've laid out the topics, there seems to be consensus for an article structure that goes Lead, Pattern, Process, History of Life, then "other" (history of the field, misconceptions, social controversy, etc.)... so I suggest we just do that reorganization and let any other fine-tuning come after that.  We know what the "boxes" are and what topics to put into them.  Progress need not be postponed based on despair of not knowing how to label the boxes. TxMCJ 00:59, 16 April 2007 (UTC)


 * Even if you don't intend to be rude, please appreciate that I'm not disposed to take personal advice from you right now. It hinders my ability to read the rest of your comments, which appear to be reasonable.  Gnixon 02:35, 16 April 2007 (UTC)


 * Well in all honesty and politeness, the above suggestion is really the best one I've got for you (specifically) right now. Although I do appreciate the edits you've done to the article itself today, and I'm about to go have a look through those in high hopes that they were in line with the progress we've all made on this talk page. TxMCJ 08:25, 16 April 2007 (UTC)

Homology
In the current version, morphological and cellular homology are included in common descent---after "Mechanisms." This doesn't follow the observations-explanations-implications layout suggested by TxMCJ. Do these work better under "Common descent" (after mechanisms) or before Heredity and variation are discussed? I personally prefer keeping them under Common descent, but then for consistency, I think Speciation and extinction belongs there, too.Gnixon 22:37, 15 April 2007 (UTC)

Added Speciation/Extinction to Common descent for consistency. Gnixon 23:03, 15 April 2007 (UTC)


 * How does that help consistency? Why does speciation/extinction have any more to do with "common descent" than heredity or natural selection do? This doesn't make any sense at all to me. For the last time, the general processes of speciation and extinction are neither evidence for common descent, nor crucial aspects of common descent, nor consequences of common descent! -Silence 23:42, 15 April 2007 (UTC)
 * Also, when did anyone ever suggest putting "speciation and extinction" at the start of the article?! There's been no support for stuffing all the evidence at the very beginning of the article; you misunderstand what an evidence-before-explanation model means within sections, assuming that anyone who agrees that we should put the evidence before the explanations think that we should put every observation first, followed by every explanation, when clearly it makes vastly more sense to put all observations immediately before their respective explanations. I just spent hours explaining exactly why it makes 0 sense to split up evidence from what it's evidence for, and you respond by doing exactly the opposite without any discussion?
 * "Speciation and extinction" fits well before "natural selection" because it provides the observations, and natural selection follows this up with the explanations and the general theoretical model. Moving it into common descent serves no purpose and makes the "natural selection" section (as well as the "common descent" section) much less valuable and coherent. -Silence 23:48, 15 April 2007 (UTC)


 * Strongly agreed with your initial point regarding odd and arbitrary classification of topics. But please see my detailed objection above (under "response from Slrubenstein") to placing speciation before selection (because understanding how speciation occurs requires an understanding selection; while the reverse is not true). Speciation is not really an "observation", although extinction (as implied by fossils) might be. But other than the order of presenting speciation and selection (selection needs to come first), I agree with almost everything else you've said, Silence.  Thanks for being vigilant. TxMCJ 00:20, 16 April 2007 (UTC)


 * Doesn't Speciation/Extinction disrupt the logical flow from Heredity and Variation to Genetic Drift and Natural Selection (since those are fundamental processes)? It also fits well within Common descent because Homology-Speciation/Extinction-History of life makes a chain from direct observables to processes to the broad history.  Speciation/Extinction are necessary processes for evolution to get us from a LUCA to a small set of highly-evolved, homologous species.  I apologize if I jumped the gun on those moves.  Gnixon 23:57, 15 April 2007 (UTC)
 * Your typical reader couldn't care less about "logical flow" that verges on OCD like wanting all the "fundamental processes" (whatever those might be) in a continuous chain. "Logical flow" that will really matter to readers is flow of ideas; how we arrange the sections matters very little compared to how the information with each section helps one get a better grasp on the next one, and it's with that in mind, more than with any abstract aesthetic notions of inherent orderliness, that we should be organizing the article. An article is fundamentally something to be read, not something to sit there and look pretty and organized. I can understand and sympathize with the impulse to value consistency above utility, but order for its own sake is not what encyclopedia-building is all about. Just because we might think that speciation and extinction are somehow less "important" or "fundamental" than the other top-tier sections doesn't mean that we should go out of our ways to shove them into an oversection that they don't fit very well into, and that disrupts the flow of ideas in the "common descent" section, and in the article as a whole. Also, it is incorrect to say that "Homology-Speciation/Extinction-History of life makes a chain from direct observables to processes to the broad history"; homology and speciation/extinction are both direct observables (albeit both influenced significantly by our understanding of processes and theories), they're just observables for different things (homology directly supports common descent, by its very definition; speciation/extinction does not, at least any more than any other aspect of evolution). -Silence


 * Couldn't agree more -- except for only one single point, that speciation is not really directly observable, and thus belongs later on in the flow of arguments, not before selection. Otherwise, Silence, you are absolutely correct about all of this. TxMCJ 00:23, 16 April 2007 (UTC)


 * It seems to me to be directly observable in the same way that homology is; you can compare two organisms that share a common ancestor to identify a homologous structure, just as you can compare ancestor and descendant organisms to identify a speciation. I'll certainly concede that the latter is a lot more difficult and tricky than the former, though. -Silence 00:29, 16 April 2007 (UTC)


 * Aha! I see what you're saying now.  Only problem is: you can't compare ancestor and descendant organisms, you can only compare organisms that are equally descended from ancestors.  The ancestors are long, long gone.  Even with fossils, scientists rarely argue strongly for naming a particular fossil taxon the "ancestor" to some modern group, mainly because the fossil record is so piecemeal, that it's more parsimonious to view the majority of fossils as extinct cousins rather than direct ancestors.  Anyway... no big deal, I just wanted to say that I do understand what (I think) you mean, but the only problem is we really *can't* compare ancestors and descendants, without already having other models in place (such as phylogeny) TxMCJ 00:54, 16 April 2007 (UTC)

(undent) Speciation and extinction are processes that logically depend upon more fundamental processes (or at least speciation, and extinction goes with it), so they have to go after the other things---not because they're less important, but because they rest upon them. Gnixon 00:44, 16 April 2007 (UTC)

Given that the process has to come later in the article, what direct observations support it? Answer: modern observations, homology-->phylogenetics and the fossil record. In the story of common descent of today's species from a LUCA, speciation and extinction are the processes that link the macroevolution from the LUCA to today's small number of species. Gnixon 00:44, 16 April 2007 (UTC)

I'm not trying to be OCD about organization, just following TxMCJ's suggestion about observation-process-story and applying it to universal common descent. I think that paints a consistent story that will be more readable than throwing Speciation/Extinction in the middle of no-man's land. Gnixon 00:44, 16 April 2007 (UTC)


 * Thanks for your support, but I'm afraid I have to concur that you are pretty OCD about organizational themes. TxMCJ 01:05, 16 April 2007 (UTC)


 * That reads to me as sarcasm, and if so, I don't appreciate it. If that wasn't your meaning, I apologize for being oversensitive. Gnixon 02:32, 16 April 2007 (UTC)


 * Not sarcasm at all. I was concurring with Silence above (who first mentioned "verging on OCD", and if that wasn't HIS meaning, I apologize for misunderstanding it. TxMCJ 08:22, 16 April 2007 (UTC)

Balance
It seems like the current TOC is unbalanced according to the significance of its sections. Does Variation need so many sections when Mechanisms is so sparse? If, as the intro to variation says, evolution consists of two processes, variations and mechanisms, shouldn't Mechanisms have roughly equal coverage? Can we condense Variation? Gnixon 23:03, 15 April 2007 (UTC)


 * "Balance", as you mean it, is completely unimportant. The fact that evolution consists of variations and mechanisms doesn't imply that the two are equally important, and even if it did, two equally important things rarely merit the same coverage, because coverage is not based on a "merit system" ("the better the topic is, the more it's covered"), but rather on how much information is needed to coherently explain the topic. For example, the only reason "natural selection" is longer than "genetic drift" is because giving a basic-level explanation of the former takes longer than the latter, not because either one is necessarily more important. However, I do plan to condense "Variation"; it happens to have more now because it had more before any of the reorganizations to article layout were made. Balance between number of sections is 100% irrelevant, but the raw length can certainly be made a bit more balanced if we cut most of the information out of "hybridization" and "horizontal gene transfer", and some of it out of "mutation", which is exactly what I'd planned to do. -Silence 23:39, 15 April 2007 (UTC)
 * Surely having lots of subsections suggests the section is long. I didn't mean to get in the way of you trimming Variation---more power to you.  I started on hybridization by cutting some extraneous details about mules and wheat.  Gnixon 23:53, 15 April 2007 (UTC)


 * Silence: I couldn't agree more. Some vague criterion of "balance between sections" is totally irrelevant and has nothing to do with the information and goals of the article. TxMCJ 00:24, 16 April 2007 (UTC)


 * Indeed. Gnixon is correct, though, that sometimes an excess of subsections can imply excess focus or bloat in a certain area. We should just be careful not to assume that all imbalance is bad; sometimes certain topics simply deserve more attention than others. Balance is only relevant when it implies that a certain section has received too little or too much attention relative to the information content needed to explain it and relative to its importance for the topic in question. -Silence 00:33, 16 April 2007 (UTC)


 * Agreed, sorry for the misunderstanding. Gnixon 00:46, 16 April 2007 (UTC)

Phylogeny
Suggest adding a subsection on Phylogeny to Common descent between Speciation/extinction and History of life. Gnixon 23:13, 15 April 2007 (UTC)

Speciation and extinction 2
First of all, apologies. I think I got a little overexcited to see the article finally taking on some sort of logical structure. I've moved the Speciation/Extinction section out of Common descent so that it is immediately following Natural selection and before Common descent. I think that's where others wanted it. I know that saying this is going to expose me to labels of being a sly creationist under deep cover here, but I'll maintain that it seems useful to me to include Speciation and Extinction among other topics pertaining to the broader evolution of life on Earth---the macroevolution. All the topics under Common descent depend, of course, on the fundamental processes of evolution, but Speciation and extinction do too, and most importantly, Speciation and extinction are the additional key processes that glue together universal common descent from a LUCA to the species we have today---you've gotta have both tons of speciation and tons of extinctions. That's why it makes sense to me to give Speciation/extinction the same centrality in a discussion of common descent that we give to genetic drift and natural selection for the article as a whole. Call it OCD organization if you will, but I find that complex scientific explanations are much easier to follow---particularly for a non-expert general reader---if they're very well organized upon a logical structure. On the other hand, I can see a good argument for keeping Speciation/extinction in close proximity to Natural selection and in a place where it displays as a general phenomenon, not as some piece of Common descent. I hope my recent move of the section resolves any disagreements. The bottom line is that I'm very happy about the recent changes to the article's organization, and I think they immensely improve its overall quality as well as the likelihood that it will continue to get better. Cheers, Gnixon 02:49, 16 April 2007 (UTC).


 * ...but now, Silence, I can't understand why you're insisting on putting Speciation/Extinction in between Variations and Mechanisms! Gnixon 02:54, 16 April 2007 (UTC)  Under the assumption that it was part of an edit conflict mistake, I've put it back after Mechanisms.  If someone moves it again, I'll leave it be.  Gnixon 02:59, 16 April 2007 (UTC)


 * "Didn't we all want this after Mechanisms?" The thing I understand least about this entire exchange is how you can so consistently and unwaveringly misrepresent what everyone else wants. It shouldn't even be possible to misunderstand what structure people are advocating or trying out, when those people have explicitly listed their entire article layout proposals in ToC form! How could anyone look at Talk:Evolution/Outline6, for example, and interpret this to mean "speciation and extinction should come after mechanisms"? However, while your misunderstandings are baffling, your point is well-argued. I don't especially care whether we list "Speciation/Extinction" before or after the mechanisms, as long as we don't list them as a subcat of "Common descent". I'm certainly willing to try out the before-common-descent organization. -Silence 03:10, 16 April 2007 (UTC)


 * And this is precisely why I am not involved with this article any more. Gnixon has an agenda that would probably garner some support if he only would explain what his agenda is.  You are infinitely more patient than I.  But I cannot believe what has happened to this article.  Samsara apparently was so frustrated he made a huge revert, and I rarely agree with his edits.  The article is almost to the point where it needs to be rewritten from top to bottom.  But I hope a few rational editors can grab a hold of it, and get it back into shape.  I'll help as long as I am not in an edit war with Gnixon.  Orangemarlin 21:06, 16 April 2007 (UTC)


 * Silence: I admire the good faith and credit you continue to show. Orangemarlin and I have also wondered how Gnixon can "so consistently and unwaveringly misrepresent what everyone else wants" as well.  It is a well-tuned art it seems.  I wish I had your patience with it. TxMCJ


 * Sorry for the misunderstanding. TxMCJ clearly argued for putting it after Natural selection, and I thought you assented.  Gnixon 03:13, 16 April 2007 (UTC)


 * ...or why it's worth having so much of History of life be about abiogenesis, and so little about what we actually know. Or why we need to mention the Hox gene.  Gnixon 02:57, 16 April 2007 (UTC)


 * I don't think that a paragraph on abiogenesis is too much to ask, when one considers that probably over 90% of the people who do a Google search for "evolution" will be expecting an extensive discussion of the origins of life in the article. If only to help allay common misconceptions about abiogenesis and evolution (such as that abiogenesis is a part of evolution!), it seems worthwhile for purely informational, practical purposes. As for the Hox gene, if the Hox gene caused the single greatest explosion in genetic diversity in the history of life, it seems noteworthy enough to mention; weren't you just saying that we should include more of the things we actually know? -Silence


 * Sure, but I was taking from the total length of that subsection that we didn't have much space to devote to History of life, so I thought we should make room for other parts of the timeline. If we're willing to expand the rest of the section, I can live with keeping that much info on abiogenesis.  Is the Hox gene really notable (in that context)?  It just sounded like WP:OR to me, and the article on the gene says nothing about the Cambrian.  Gnixon 03:17, 16 April 2007 (UTC)


 * There is no "the" Hox gene, which I'm surprised isn't better known here. The HOX gene *cluster* is a tremendously important cluster of tandemly duplicated genes which have duplicated even further throughout vertebrate evolution via whole-genome duplications, and the HOX genes are largely responsible for the great structural diversity of animals as they play a huge role in developmental genetics and evolvability.  The Hox story goes nicely hand-in-hand with the Cambrian story... but again, this is only in terms of the evolution of ANIMALS and not "all of life".  I strongly suggest that the Hox clusters and the Cambrian Explosion ought to have prominent places in the article. TxMCJ 08:35, 16 April 2007 (UTC)


 * ...and in full awareness that I'm reinforcing my OCD organizational image over a minor point, I'd suggest swapping the order of Genetic drift and Natural selection, since one is closely related to Variation, whereas the other is closely related to Speciation/extinction. Wording that depends on the order could be easily altered.  Gnixon 03:30, 16 April 2007 (UTC)


 * What? Did an editor of this article really just write *that*?  It would be utterly fascinating to read any attempt at an explanation of how Drift has more to do with variation (or speciation/extinction) while selection has more to do with speciation/extinction (or variation).  Or any arrangement of those terms, any way you'd like to slice them or mix them up.  I'm sorry, but that comment/logic (or whatever it is) simply shows very, *very* little understanding of any of those concepts.  Please, though: is it that you think Drift has more to do with Variation, or with Speciation/Extinction?  And that Selection has to do with the other?  Or do I have it backwards?  Would you mind elaborating on this concept? TxMCJ 08:44, 16 April 2007 (UTC)


 * Perhaps Gnixon means that since natural selection has a stronger presence in large populations than genetic drift, and speciation/extinction are essentially macroevolutionary, it makes sense to transition from seemingly "smaller" to "larger" processes, especially considering that the section after speciation/extinction deals with the largest ("most macro-") evolutionary topic of all, the history of life. I think Gnixon's point is a fair one, and further I do have a preference for discussing genetic drift before natural selection in "mechanisms" because I think it's the easier way to explain both topics (and it's the way that the topics were presented in the lead section as well, prior to your recent edits). -Silence 16:54, 16 April 2007 (UTC)


 * Hmm... YOUR point makes sense, Silence, but I can't make the logical connection between what you've just said here, and Gnixon's statement immediately previous. Also: I don't mind discussing drift first.  I'd probably have it the other way myself, but it's a trivial preference. TxMCJ 23:07, 16 April 2007 (UTC)

And on that note, I'm going to try and enforce a few days break from this article---so much stress to get anything done around here! Thanks to good work by Silence and others, this article is better now than it was when I started being a pain-in-the-neck about organization. I'm sure someone has an unkind retort ready for that---she's welcome to the last word. Gnixon 03:30, 16 April 2007 (UTC)


 * Thanks! And here it is: Rosebud.  ;-)TxMCJ 08:19, 16 April 2007 (UTC)