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==APPROVED Version 1.1==
Congratulations once again.  Re-approval complete.
<div class="usermessage plainlinks">Discussion for [http://en.citizendium.org/wiki?title=Life/Draft&oldid=100084516 Version 1.1] stopped here. Please continue further discussion under this break. </div>


==Strategies and lessons for further approvals==
My 4cents worth.
===Understanding how constables operate===
SUMMARY:
TELL EM IN BLACK AND WHITE ONLY WHAT THEY MUST KNOW and all THEY MUST KNOW TO ACTION AN APPROVAL. RESERVE THE APPROVAL BOX FOR THIS. KEEP IT DIRECT AND SIMPLE. ie YES, editor 1, YES Editor 2, Yes Editor 3, URL here. DEADLINE IS EXPIRED WITH CONSENSUS.
Approved version 1.1 shows in my view, that the citizendium copy-editing environment is almost unmanageable, and certainly time wasting. I personally apologise to the other authors and editors for the restrictions my efforts to manage this unwieldy system have placed on their contributions. I was expecting the process to take place much more quickly.
Holding up edits of substance to allow copy-editing is only acceptable if that copy editing is done quickly and efficiently. This is not being achieved, and it is unfair on authors to subject them to such constraints for more than a minimum time period. I'm pessimistic about forum discussions solving this, but hopeful that  we can get the biology editors to develop a solution in terms of agreed informal biology standard approval practices to save us all the time wasting over trivia. One of the powers we have is editor consensus and familiarity with the science and we should use it to control the legal impositions that are currently, in my view, strangling performance.
Some new problems are emerging.
Before this approval event I had assumed agreement of three editors was enough to provide assurance that an unambiguous decision to approve can be put to the constables.
But new issues such as (if I read it right) proof that silent editors are in agreement are now being raised in discussions (see above), and these threaten to make it impossible for editors to tell a constable that the article is ready. Surely this is overkill to allow error correction to take place? What do others think about this gloomy assessment? I'd want explicit statements in approval rules that such complications will not derail copy-editing. We would wait ages for all editor to check in
In my view, such possibilities threaten to render our already cumbersome process completely unworkable, and we must try and alert other editors and authors to the urgent need for a solution to this process confusion.
I think we must tackle the copy editing issue first as it's simpler.  All of the science issues raised were completely (ie cell types  a protein numbers) uncontroversial and authors were only grappling with the best form of words and the best sources to cite, but it seems that healthy editorial interaction was interpreted as dissent, when it was not, in my opinion - just routine editorial work. If there was real dissent about an issue of weight, that's a different matter. Seroius objections have to be listened to, but lets devise a error correction process thats faster and efficient.
To finish for now , we just need to get organised, and '''treat the constable as an unknowing legal robot''' who does as he's told. This is OK. Constables want a simple routine job. They do not like legal head-aches. For them, all they need is editor YES YES YES , and signatures. We (the editors) just have to understand how a robot can be made to do tricks. We need to craft and use the rules to make rapid progress, and make those legalistic robots zip through the approvals.(Give them a bone and a pat if they do the job quickly) For this I think it would be good if we put all the stuff constables need to know about an approval  decision '''in the approval area,''' and state explicitly to ignore discussions on the talk page itself. i.e keep it very simple and clearcut. [[User:David Tribe|David Tribe]] 04:06, 22 April 2007 (CDT)
::David, dear, you - of course- ''are'' a constable, and so your comparisons to Robots is all in the family. Hopefully, there will be a position for an Editor to help co-ordinate these matters, I have applied for one - but the job description will have to be, rightfully, agreed upon in Executive Council. You have done a heroic job here.We thank you for it.  [[User:Nancy Sculerati|Nancy Sculerati]] 08:06, 22 April 2007 (CDT)
::: Thanks Nancy. Yes I wear different hats. As an editor I'm different to a constable, and an author. At CZ we are evolving towards having different roles which provide checks and balances, and thats good. Authors want facts, creativity freedom and an audience. Editors want style, quality, verification of contention, themes and readability. Constables want legality and due process -they hav'nt got the time or skill to be editors as well (I think that's what Matt Innis is saying too)[[User:David Tribe|David Tribe]] 16:14, 22 April 2007 (CDT)
:::: PS I have just learn't with pleasure that Nancy Schulerati has been appointed to a Managing editor role which will tackle and almost certainly resolve the issues just listed. We now thankfully take our lead from Nancy, and the above thoughts, are, well, just thoughts that Nancy will factor in to her judgments and activity. The solution has arrived and we work with Nancy on this. A great decision by Larry. [[User:David Tribe|David Tribe]] 16:38, 22 April 2007 (CDT)
Yep, David, I agree with you 100%.  When a constable is asked to come to a page, it would be much easier if you editors had all your ducks in a row editor 1,2,3 all signed off in the same place, whether in the approval area (which sounds like a good idea) or at the bottom of the page.  Constables, by definition, are not allowed to make judgements about content - whether the change appears like a copy edit or not.  Lord knows that changing one word can change meaning, I sure don't want a constable to assume anything that important, do you?  That is up to the editors.  I think Nancy's solution of Editorial Manager is just the ticket to be able to make simple copy edits now. --[[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|(Talk)]] 21:12, 22 April 2007 (CDT)
:Here's a way it could work.  Each working group could work out among themselves the details of how they approve articles and what types of changes can be made at the copyediting stage.  Then, one editor can check the final, copyedited version and check that all the approval rules are satisfied, and can tell the constables, "I certify that this particular version meets the criteria and has been approved, and that the article can be considered approved by editors 1,2 and 3."  Editors 2 and 3 may have approved a slightly different version, and editor 1 is certifying that there were only minor copyediting changes since then.  (Some editors might want to specify that when they approve an article, they're approving only the very specific version and that they would have to look again after any copyediting.  The certifying editor would have to be aware of any such restrictions among their working group.)  --[[User:Catherine Woodgold|Catherine Woodgold]] 18:30, 23 April 2007 (CDT)
::: Thats similar to what we've just attempted to go through, Catherine. I acted as the editor go-between, but unfortunately from my point of view, the dialogue with the constable went round and round in circles for various reasons. Despite me saying that there existed an approved copy with legal support, he kept on being worried there was dissent even though if you looked hard at the record, an approved version had passed the deadline with no adverse comments. The worries expressed after the deadline prevented the earlier approved version from being activated. It didnt really matter whether the worries were irrelevant to the approval that we had spend many days working hard to finish, or whether the worries were trivial, the worries were there.  I had to peer closely at the talk page records for some hours to try and clear through the confusion. The constable wasn't able to.
:::There is a big gap between what we all want to do (which is close to what you are suggesting), what ''seems'' straightforward, and what actually happens on the wiki. The current solution is to get a intelligent person to make a decision (Nancy) and take responsibility for it, rather that relying on the complex interaction with the wiki software of several people who are each unsure what the rules allow them to do. I think it will work, but well all have to work together to ensure Nancy has procedural (legal) support to do the copy-editing. That's very important, so that we establish an efficient, workable fast copy-editing process. [[User:David Tribe|David Tribe]] 19:58, 23 April 2007 (CDT)
::::David, I think you did a great job co-ordinating the approval.  It looks as though there still seems to be some misunderstanding about what happened, though.  I followed every one of your comments, but from my point of view, your problem was the inability to show three editors agreeing on the NEW version.  I could have actioned the 18th version at any time, but was asked to wait till you had "a triumverate"[http://en.citizendium.org/wiki/User_talk:D._Matt_Innis#Life_Version_1.1_approval_Legal].  The problem was that the date that was in the box to be approved was not the 18th, it was the 21st.  With the way the rule was written, I still would not have okayed it, because Chris (an editor) suggested that the changes were more than just copy edits.  Larry's last minute change of the rule is what allowed it to go through for the 21st, otherwise I'd still be waiting for Gareth. --[[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|(Talk)]] 20:25, 23 April 2007 (CDT)
:::::I believe it's technically possible for anyone to create a page "life/Proof" or to create a page in their user space e.g. "User:Catherine Woodgold/life (Proof)".  This may or may not be a good idea.  I think it was Larry who pointed out that the page history would not all be in the same place.  For that matter, the first time an article is approved, it may make sense to move (rather than copy) the page to "pagename/Draft" so that the edit history from the beginning is all in one place, at "pagename/Draft".  --[[User:Catherine Woodgold|Catherine Woodgold]] 18:40, 23 April 2007 (CDT)
==Glitch in the printed versions of Life==
When I print out Life with IE on a Windows XP to a Laser printer, the Image of the Leonardo sketch obscures text in the autonomous agents section. Possibly the Image should be coded or positioned differently. With Firefox browser still only the first 12 pages print. Possibly the issue is file size related [[User:David Tribe|David Tribe]] 19:38, 22 April 2007 (CDT)
==The word "organize" ==
If the word "organize" is really a technical term with a specific meaning in this context, then I think it would be worthwhile to provide a definition for it in the article.  I think, though, that it is rather a word whose meaning is closely related to the answer to the question "what is life?", an answer which emerges from the article as a whole and cannot easily be pinned down in a short definition.  Therefore those who have an idea of what it means in this context experience a feeling of understanding every time the word is used, while perhaps those who haven't gotten the message yet merely see the same poorly-defined word used over and over again.
It reminds me of something B.F. Skinner wrote.  Apparently he had been criticized for using the word "contingency" too often.  He argued that he used the word that often because what he was writing was ''about'' contingencies, and that if he had been writing about mushrooms, the word "mushroom" would have appeared as often.  In my opinion, a well-written article about mushrooms might use the word a fairly large number of times, but not as often as Skinner was using "contingency".  Pronouns and other devices would be used to reduce the repetition of the word.  Ways would be found to occasionally use more general or more specific words instead, or words for the organisms at particular stages of development, incidentally giving the reader information about taxonomy and vocabulary while reducing repetition.
The use of the word "organize" in this article gives me the same feeling as Skinner's use of the word "contingency":  it seems to me that the word is being used as a one-word thesis or as an anchor in the sense of Neuro-Linguistic Programming:  that the word is being asked to carry an amount of meaning usually carried by a sentence, paragraph or perhaps a whole essay, rather than what is appropriate for a single noun or verb to carry.  When this is done, it becomes more difficult to analyse and criticize what is being said.  Clarity of thinking suffers.
When I provided a list of alternative terms above, I was not claiming that these terms are synonyms for "organize" that can be substituted into the article with no change in meaning.  Actually, the only one that looks to me like a really good synonym for "organize" is "orchestrate", and I think it will feel overly repetitive if it's used more than one to three times in the article (two might be too many).  Rather, I was suggesting that we might spend less time talking about organization and more time talking about other aspects of the answer to the question "what is life?"  There may not be an equally apt way to say the things that are being said with the word "organize", but there may be other things that can be said instead that would be more interesting to a reader who might feel he or she has heard enough about organizing for now.
I note that the philosopher of science D.M. Walsh quoted in the article (see below) doesn't seem to share the sentiment that the use of the word "organize" is absolutely necessary to get across these particular ideas.
:''Philosopher of science D.M. Walsh puts it this way: "The constituent parts and processes of a living thing are related to the organism as a whole by a kind of 'reciprocal causation'."<ref>Walsh DM (2006) Organisms as natural purposes: the contemporary evolutionary perspective. Stud Hist Philos Biol Biomed Sci 37: [http://dx.doi.org/doi:10.1016/j.shpsc.2006.09.009 771-91]</ref> In other words, the organization of the components determine the behavior of the system, but that organization arises from more than the set of its internal components. How the whole system behaves as it interacts with its environment determines how those components organize themselves, and so novel properties of the system 'emerge' that characterize neither the environment nor that set of internal components.''
In the above section of the article, I would like to cut down the use of forms of the word "organize" from three down to two or one.  I note that the fact that the word "organization" appears twice in one sentence is not due to a semantic necessity in this case, but is only necessitated by the way the sentence is &mdash; ahem &mdash; organized.  :-)  So I suggest saving one use of the word by changing the sentence to:
:''In other words, the behavior of the system is determined by the organization of the components, which in turn arises from more than just the set of those internal components.''
Alternatives for ''"how those components organize themselves"'' in the sentence after  that one in the above passage include:
:''how those components arrange themselves''
:''how those components are arranged''
:''how those components inter-relate''
:''how those components mutually interact''
:''how those components position themselves with respect to one another''
:''the pattern of interaction of the components''
:''the pattern of interaction that is set up among the components''
:''which sets of states are accessible via the chaotic interactions of the internal components''  (I like this one -- it brings in "chaos" which I think is not mentioned often enough in the article -- in fact, the word doesn't appear once in the article itself, although it appears twice in titles in the bibliography etc.)
:''which feedback loops become established among those components''
:''into what internal structure those components formulate themselves''
Later I expect to come up with specific suggestions for reducing occurrences of the word "organize" (and/or increasing occurrences of other concepts such as "chaos") in other parts of the article. --[[User:Catherine Woodgold|Catherine Woodgold]] 17:45, 24 April 2007 (CDT)
::Catherine: I regard your persistence commendable. You have forced me to realize how critical for us to explain to the reader precisely what we mean by 'organization'.  I have operated too cavalierly in thinking the reader could draw from experience to appreciate the appositeness of the word as applied to living systems.  Therefore I have written a lower level section to inculcate the reader.
::Once done, and done properly &mdash; it may need work &mdash; we no longer have to concern ourselves over the repetitiveness of 'organization' or its derivative forms than we have to over the repetitiveness of 'living' or 'life' or 'organism' or 'system'.  We must not, in my opinion, marginalize or deemphasize 'organization', once clearly contextualized, because living things do not 'self-order' as much as they 'self-organize' &mdash; the 'order' enjoys the special feature of functional goal-oriented dynamic coordination.  We must, in my opinion, instill the reader with 'organization' in that sense as a defining characteristic of living systems.
::The principle of parsimony applies here.  We want to explain living systems as 'organized' systems, and say what we mean by 'organization' as applied to living systems.  Let us do that.  Check out the new subsection.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 21:45, 25 April 2007 (CDT)
:::The new section adds 17 occurrences of the word "organize" bringing the total in the article to 90.  This is the opposite of what I was recommending.  In my opinion it increases the tediousness of the article and adds little or no useful information.  In the new section you say ''"'Dynamic', 'coordinated', and 'goal-directed functionality' characterize 'organization' in biological systems. The words 'organize' and 'organization' should invoke those properties."''  A better way to present this information without boring the reader would be to delete this new section, and replace some of the other occurrences of the word "organize" with "dynamic", "coordinated" and "goal-directed functionality". 
:::It's OK to repeat words such as "the" large numbers of times;  that doesn't bore the reader.  Repeating a phrase such as "goal-directed functionality" more than about 3 to 5 times in the article would sound overly repetitive and bore the reader.  The word "organize" lies somewhere between the two.
:::The idea that life emerges by means of organization only needs to be said ''once''.  --[[User:Catherine Woodgold|Catherine Woodgold]] 17:37, 26 April 2007 (CDT)
::::Catherine, I begin again by commending your persistence.  We ignore the wisdom of ''pluralitas non est ponenda sine neccesitate'' at our peril, the 14h century thinker William of Occam advised.  We do not wish to bore the reader, the reader can only find herself bored &mdash; the reasons, situational and personal.  'Organization', ''''as contextualized in the article'''', especially with the new section motivated by your comments, must become as familiar to the reader as 'energy', evolution', and 'molecular' &mdash; if the reader wishes to explain 'living' from the perspectives of the article.  Repetitio mater memoriae.  You have made a real contribution in motivating the new section that tries to highlight the word's centrality and explicate its specific meaning as applied to living systems.  In advancing your argument based on word count by boosting the count with the clarifying effort only serves, in my view, to weaken it.  The extensive enlightening literature on the principles underlying the activity of living emphasizes 'organization', as we do.  I would love to hear your views of those references and of our article's organization.  Cheers. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 19:57, 26 April 2007 (CDT)
:::::We have a dispute here.  I oppose the new section, for the reasons stated above, and I object to the great increase in occurrences of the word "organize" after I had already suggested decreasing it.  I had no intention whatsoever of motivating an increase in occurrences of the word "organize", and I dislike having my comments described as "motivat[ing]" such an increase.  (I did not wish to motivate the author in this way;  the author can only find himself motivated, for reasons situational and personal.)
:::::I doubt that the word "organize" appears as densely in as long passages in the material listed in the bibliography as it does in this article. If it does in a few of the bibliographic references, then I suggest:  have one section of the article, one to three paragraphs, which attempts to explain the marvelous, fascinating and difficult-to-explain relationship between organization and life, and have the word "organize" appear as densely in that section as it does in the references (or as densely as most of the authors of the article agree is necessary).  And then stop.  The rest of the article can be about other aspects of life.  Otherwise, the reader, male or female, may be left thinking, "Why am I having difficulty focussing my attention on this article when it's about such a fascinating topic?"  There is no need to go on at length about one topic in an encyclopedic article, which is supposed to be a summary.
:::::By the way, usually when supplying a definition one does not feel compelled to repeat the word being defined 17 times.  I take this as further evidence that it is difficult to explain what is meant by the word -- that the meaning of the word is being built up by using it in a variety of very similar contexts rather than by stating its definition, and therefore that it does not have a specific, technical definition but is being used as a repository for a complex of ideas being built up in the reader's mind.
:::::I don't understand why my argument seems to you to be "weaken[ed]" by adding the 17 new occurrences of the word in the new section intended to define it.
:::::In my opinion, the quote you supply from Occam seems to suggest reducing the unnecessarily large number of occurrences of the word.  --[[User:Catherine Woodgold|Catherine Woodgold]] 07:43, 27 April 2007 (CDT)
::::::In my opinion, this seems to be a content, rather than copyediting, disagreement. Both sides have been very well-argued. I would tend to have a bit more sympathy with Anthony's point-- sometimes a spade is a spade, and despite concerns about repetition we should call it a spade. But that's my non-expert view. Can we get an uninvolved biology editor to weigh in here? --[[User:Mike Johnson|Mike Johnson]] 12:06, 27 April 2007 (CDT)
:::::::Mike, I think you are correct as to the fine point here.  Rather than Catherine making edits (as she is certainly allowed to do), she is asking if there are places where another word ''would be considered a copyedit'' so that she does not disturb the ''content''.  Perhaps a closer look by Anthony could find a few spots. --[[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|(Talk)]] 12:32, 27 April 2007 (CDT)
I do not think the word organized is at all "overused" in context. Anthony's ideas are subtle and intruiging, not to mention frequently brilliant,  and I hope that he will not have his muse stifled by readers counting the number of times he uses ''any'' word and calling him to task for it, repeatedly. Now, of course---the ideas ''themselves'' are always worth a good argument. That's what we all live for, I expect. En garde! :-) [[User:Nancy Sculerati|Nancy Sculerati]] 12:34, 27 April 2007 (CDT)
:Functioning as an author here as I have done in the past. In my reading of the article with its use of "organize" (and words from that root), it is ''useful'' and  ''needed'' to have repetition of the word as it provides a continuity of theme that makes the article easier to follow.  If this were a biography, or a novel, or some such, repetition of wording is ''and should be'' avoided. But copyediting for such things is not like copyediting for science materials, which carries a set of unique concerns.  In an article about science, variation ''must'' be conceded to the primal need for use of the ''precise'' language of science and the meanings ''assigned'' to words. We simply, and forthrightly, must concede to Dr. Sebastian's extremely knowledgeable assertion that "'Organization', 'as contextualized in the article' ... must become as familiar to the reader as 'energy', evolution', and 'molecular' — if the reader wishes to explain 'living' from the perspectives of the article. ''Repetitio mater memoriae''."  In science, less, and parsimony, is more.
:Idea: we need a '''Science''' Copyeditors Workgroup.
:---[[User:Stephen Ewen|Stephen Ewen]] 15:44, 27 April 2007 (CDT)
::Thank you, everyone, for your opinions.  I accept that the word "organize" is not considered overused by (apparently) anyone other than myself.  I would like to point out, though, that I don't agree with Matt Innis' interpretation of my comments.  Rather, Mike Johnson correctly understands that I see this more as a content issue than a copyediting issue.  I would still like to see some things covered in more depth (or at all), for example, chaos and attractors;  the relationship between natural selection and the tendency of organisms to regulate their internal and external environments;  and antioxidants, which are an important part of how organisms maintain their state of being far from equilibrium;  equilibrium in our oxygen-laden atmosphere being little but CO2 and water.  I would also like to see more information that the typical reader would not have known before reading the article.  I think there's only one clear example in the article of something I didn't know before reading it:  that is the bit about there being two different kinds of membranes.  I'd like to see more interesting tidbits like that.  Possibilities might include:  how many phyla are known, and when was the most recent discovery of a new one?  How does the genetic code of mitochondria differ from that of other parts of a cell?  How deep inside the Earth is life known to exist, and how far up into the atmosphere?  What is the longest-living known multicellular organism?  Better yet, more interesting and surprising things that biologists know that I don't know yet, if they can be fit smoothly into the article here and there.  --[[User:Catherine Woodgold|Catherine Woodgold]] 19:20, 27 April 2007 (CDT)
:::Catherine, Mike is a constable (as am I, but ''not'' in this article because I have contributed to it as ''an author'') and was meaning that that this is a dispute that the Constabulary has no authority to get involved in.  For the Constabulary, copyediting, or any sort of matter related to wording, ''is'' a content issue; thus, constables have no authority over such things (except in ''blatant'' cases, e.g., articles that ''to nearly all'' constables would ''obviously'' not be encyclopedic; "edit warring" over content - obviously, neither an issue here).  Any and all ''content'' disputes that cannot be resolved by dialog of involved editors and authors needs to be decided by an uninvolved editor of the Biology Workgroup.  That's the the way CZ does conflict resolution over ''content'', and it is tightly summarized [[CZ:Introduction_to_CZ_for_Wikipedians#Handling_content_disputes_without_.22edit_warring.22|here]].  [[User:Stephen Ewen|Stephen Ewen]] 03:57, 28 April 2007 (CDT)
::::Well said, Stephen. And Catherine, I also *really* enjoy those little interesting tidbits. Reading an encyclopedia article can and should be fun. Re: the additional things, if you could enumerate what things you'd like integrated into the article, perhaps we could discuss your suggestions and gear up to write them into the next draft?
::::Just a short digression- I think we'll soon (if not already) have the best article on Life that anyone has written... ever. Speaking pragmatically, I'm ''very'' happy to see that, though we may be quickly getting into the realm of diminishing returns here. There are a lot of important article plots yet laying fallow. But as the first rule of wikis seems to be to encourage people to write about what they're excited about, I'll just cheer about the progress here and start planning the article I've been meaning to Citizendium-ize. :) --[[User:Mike Johnson|Mike Johnson]] 13:20, 28 April 2007 (CDT) Edit: I see the "Suggestions for additional content" section has beat me to it.
This article is not ''about'' the Biosphere, it is about the ''concept'' of living. No wonder you are disappointed Catherine! A reader may certainly prefer a different article, and perhaps the best way to have biologists write one is to request it. here. [http://en.citizendium.org/wiki/CZ:Requested_Articles] [[User:Nancy Sculerati|Nancy Sculerati]] 13:39, 28 April 2007 (CDT)
:I should add, you may also start one yourself here: [[biosphere]]. :) --[[User:Mike Johnson|Mike Johnson]] 14:25, 28 April 2007 (CDT) Absolutely! Even better! [[User:Nancy Sculerati|Nancy Sculerati]] 14:29, 28 April 2007 (CDT)
==Function==
Id like to suggest that the article lacks a theme about function and physiology. I see it is alluded to, say in Systems, but its a <s>cell</s> key concept in living behaviour and I suggest it could be developed. What do others think? [[User:David Tribe|David Tribe]] 08:13, 27 April 2007 (CDT)
:David, I agree we need more function and physiology.  More specifically, a little metabolism, too.  One thing we might include: the Smith/Morowitz cogent argument for the universality of the ''reductive'', or ''reverse'', TCA cycle and its implications for free-energy capture by chemiautotrophs situated in a redox free-energy flow (Smith E, Morowitz HJ. (2004) Universality in intermediary metabolism. Proc Natl Acad Sci U S A 2004;101:13168-73. http://dx.doi.org/10.1073/pnas.0404922101).
:: This fit in with Orign of Life or Evolution of cells better I think.[[User:David Tribe|David Tribe]] 06:11, 28 April 2007 (CDT)
:Did you have some specific points re function/physiology you think we need to make?  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 18:14, 27 April 2007 (CDT)
== Suggestions for additional content ==
Now that we have a core article on 'Life', we can begin thinking about additional content that says within the theme of the article, or that resonates harmoniously with the theme, namely the principles that render systems alive and able to stay alive and to perpetuate life.
David Tribe suggests we expand on 'function' and 'physiology'.
Catherine Woodgold suggests discussing:
:*chaos
:*role of natural selection in homeostasis and niche construction
:*special role of antioxidants
:*more taxonomy
:*mitochondrial genetics
:*distribution of living things in the biosphere
:*life spans
The challenge, I think, especially as others suggest their ideas: what stays on theme or resonates coherently with theme, what deserves its own article?  ''Some ''leaning toward new articles, which 'Life' can touch upon as appropriate and coherent &mdash; new articles contributing to CZ growth.
--[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 20:00, 27 April 2007 (CDT)
We need more articles. Most of all. For example, we have not yet worked on [[Physiology]] - ''forget about'' "function". [[User:Nancy Sculerati|Nancy Sculerati]] 20:16, 27 April 2007 (CDT)
:: I think Ive gotta agree with Nancy. Ill focus my efforts on other articles [[User:David Tribe|David Tribe]] 06:09, 28 April 2007 (CDT)
== Whether life evolved separately more than once ==
Anthony Sebastian said in an edit summary: "Catherine, you edited a direct quote from Professor Woese's paper. I reverted back to the original, as I do not want to put words in his mouth".  Oops!  That was careless of me.  Sorry about that.  Thanks for catching it.  Nevertheless, the quote seems to be saying that life evolved separately in 3 distinct lines, while the abstract of the paper referenced to the quote seems to be saying that all life was interconnected by horizontal gene transfer, i.e. that life extant today did not evolve from scratch in more than one separate line. Perhaps a few words could be added after the quote to clarify. --[[User:Catherine Woodgold|Catherine Woodgold]] 22:31, 28 April 2007 (CDT)
:I took a long look at it, and I believe this may be moved to (and expanded within) the "Evolutionary aspects of 'living'" section. Once we delve into the nuances of and controversies in life's evolutionary past, the clarity of the bullet-point-style of this section suffers. --[[User:Mike Johnson|Mike Johnson]] 12:08, 29 April 2007 (CDT)
== I made a mistake ==
I mistakenly edited the approved version of [[Life]], "organic chemistry as informatics".  When I discovered my error, I restored the approved text.  Then I made my desired edits on the draft version.
Why can someone edit an approved version, anyway?
--[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 17:43, 13 May 2007 (CDT)
:When you became an Editorial Personel person, you were given SYSOP privileges. You need these to make new accounts and to make users editors. SYSOPS can edit protected pages. Just be careful. I made a mistake too. I copied some code of an image in the [[Dog]] article to use it to place a thumbnail picture of a different image in Contraception (medical). I had a couple of windows open in my browser, and somehow I saved the wrong one- managing to put a picture of French oral contraceptives in the puppy section of Dog. Before I figured it out, Chris Day-always vigilent!-demanded to know why I was changing an approved article without even'' mentioning'' it on the talk page. That alerted me to the fact that something was up. Once he saw the image, he figured it out. Total mistake. I corrected it, too- and I'd say no harm done. Lesson learned. :) [[User:Nancy Sculerati|Nancy Sculerati]] 18:15, 13 May 2007 (CDT)
::Demanded? I asked, prior to realising it was a mistken edit, "[[Talk:Dog#Problem|Are these changes even allowed to go through without a 'toapprove' template?]] " This wasn't a fair question? Certainly no harm done, but sysops do need to be more alert, especially when deleting pages. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 10:39, 14 May 2007 (CDT)
==Nice image==
*http://www.flickr.com/photos/b_g/169456947/ [[User:Stephen Ewen|Stephen Ewen]] 13:49, 8 June 2007 (CDT)
*Cool photo, but I think this article already has the perfect amount of images already. --[[User:Charles Sandberg|Charles Sandberg]] 15:04, 20 June 2007 (CDT)
==changes to date==
[http://en.citizendium.org/wiki?title=Life/Draft&diff=current&oldid=100102529 Changes since last approval]. We might want to consider a update approval soon. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 14:35, 20 June 2007 (CDT)
:Chris, the subpage template appears odd.  ??  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 13:04, 1 August 2007 (CDT)
==Approval time==
Since the last approval there have been a significant number of changes. See [http://en.citizendium.org/wiki?title=Life/Draft&diff=current&oldid=100150079 this link] for the current updates. I know I want to modify the plant development note. If anyone else sees changes they are worried about now is the time to make comments or edits. I'll hold off adding the ToApprove template until I have read all the changes. But I'll place it soon. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 04:34, 14 August 2007 (CDT)
== Inconsistent spellings and language usage ==
As this is likely to be Article of the Week, could someone please copyedit it into American English? For example, the picture by da Vinci is described in the undertext initially as a Foetus, and in the next phrase as a fetus. This is SO obvious when the words are almost adjacent, and looks very unprofessional. --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 01:59, 17 August 2007 (CDT)
:I'd be happy to do that, but first need the input of a principal American author on this article's usages of 'single quotes' and "double quotes".  I know of no American style that uses 'single quotes', except for "making 'quotes within quotes', as such".  But this could mean nothing more than that I am not aware of the style.  Please advise. &nbsp;&mdash;[[User:Stephen Ewen|Stephen Ewen]]&nbsp;[[User talk:Stephen Ewen|(Talk)]] 12:48, 20 August 2007 (CDT)
::Hmm, well maybe the quotes style is British, but most of the spellings are US. We have to set the style first, but is it so difficult to change all the single quotes? If so, then make it UK English... and I suppose a British person should copyedit it! --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 13:02, 20 August 2007 (CDT)
:::As a very minor American author, and a zealous copyeditor of, at least, my own stuff, I'm 99.99% certain that double quotes are always used for quotations, with a single quote for a quotation within a quotation.  The Brit system is, generally, the reverse.  So all you have to do is decide (decisely) which system you're gonna use, then apply it throughout.  (See an old John Barth story told entirely in dialogue [about Ulysses, I think], in which the dialog ended up as " ' " ' " ' " ' " etc. etc., quotations within quotations within quotations about 7 layers deep. Just Barth showing off....) [[User:Hayford Peirce|Hayford Peirce]] 13:12, 20 August 2007 (CDT)
I use single-quotes, e.g., 'abcdef', when I want to call attention to the word within.  I might call attention to a word for the purpose of ''mentioning'' the word, as in "'black' has five letters" &mdash; i.e., I ''mention'' the word, or ''refer'' to it.  On the other hand, I might call attention to a word in order to alert the reader to my use of a special word, or my special use of a word.  For example, with 'emerge' in a sentence, I want to alert the reader to something special in the use of 'emerge', which special use the sentence implies or partially defines.
I tend to reserve double-quotes for words or phrases or sentences or paragraphs that I attribute to someone, someone the readers knows who by the context or by a source-citation. Also, double-quotes for article titles, as "Notes of a Bird-Watcher", by Robin Feathers, when stated in the text.  Book titles like, ''On the Origin of Species'', I put in italics when stated in the text.
::"Methinks the..[gentleman] doth protest too much."
I use italics for emphasis without necessarily calling attention to the italicized word itself.
I would like to keep that convention.  I could put an explanatory footnote about the usage of single and double-quotes. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 15:25, 20 August 2007 (CDT)
If consensus against that, I would change single quotes to italics (or to bold non-italicized) for calling attention to the word, and use bold italics for emphasis. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 15:39, 20 August 2007 (CDT)
== Final adjustments needed for revised Approval ==
If your quotations are all in double quotes, then that is the US version. I don't have a problem with single quotes [when the quotation style is double quotes] or double quotes [when the quotation style is single quotes] for picking out words or phrases. Nor do I think it so unusual that it needs any footnotes to explain the convention.
So, if there is no dissent, could you put this completely into US English, Anthony? We need this for the next approval, which is also needed for the Article of the Week approval! --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 01:39, 29 August 2007 (CDT)
::How about moving the appendices to subpages?[[User:Gareth Leng|Gareth Leng]] 04:24, 29 August 2007 (CDT)
::::Yes. Certainly this is needed. Maybe even some of the content could be reallocated to subpages. I note that the format is also wrong in this article: we need the horizontal form template to be inserted. Any offers to do this? [I don't know how] --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 04:34, 29 August 2007 (CDT)
:::::I changed the subpage template to subpages9 template ont he Draft version to let you see what it looks like.  I think we have to do it on all the subpages as well, but eventually it will change to just plain ole subpages (without the 4 or 9). --[[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|(Talk)]] 16:30, 29 August 2007 (CDT)
::::::Switched to subpages9 on all the pages.  Let me know if it's missing something.  This is my first time switching this. --[[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|"(Talk)]] 20:05, 2 September 2007 (CDT)
Martin: I will make sure that all quotations use double-quotes, all 'calling-attention-to-specific-words/phrases' use single-quotes, italics used for emphasis, bold-italics for stong emphasis.  That seem okay? --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 15:24, 2 September 2007 (CDT)
::sounds good. can you also remove any britishms that might lurk there? Then the very last thing is for someone to move text to subpages, but let's deal with the language style first. --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 16:08, 2 September 2007 (CDT)
:::I asked Chris where to put the appendexes, as "Appendexes to Main Article" not listed in Unused Subpages.
:::I would hope no content need be moved to subpages.  I'm working hard to keep the article coherent.  The TOC should enable readers to navigate as desired.  Life's a major topic with many important issues to deal with.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 22:50, 2 September 2007 (CDT)
==Reading through it now==
"We take as non-fiction risk of considering molecules sine qua non for living." ??[[User:Gareth Leng|Gareth Leng]] 04:09, 3 September 2007 (CDT)
This is a massive article, vast in scope and a real challenge. I think the appendices can go to subpages without a problem, but I suggest that this article really needs a wholly new subpage - a lay summary of the article as a whole.[[User:Gareth Leng|Gareth Leng]] 11:44, 3 September 2007 (CDT)
:That would be the scope for the Student Level subpage. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 12:01, 3 September 2007 (CDT)
::I like the idea of a Student Level subpage.  Sounds challenging.  What level to pitch at: 8th grade, 10th grade, 12th grade? --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 16:44, 20 September 2007 (CDT)
That sounds like an insoluble riddle:-) Also it might have infinite permutations, like "We carry the unreal certainty of viewing molecules as being essential for life", or "there is a real danger of thinking that molecules are needed for everyday living", ad infinitum... :-)) Does this mean anything in fact? --[[User:Martin Baldwin-Edwards|Martin Baldwin-Edwards]] 15:13, 3 September 2007 (CDT)
::Martin, I tried to fix the problem.  See what you think.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 16:44, 20 September 2007 (CDT)
==Approval==
It's daunting to review such a massive article. However it's clearly an advance on the already impressive Approved article, and on that basis I support reapproval[[User:Gareth Leng|Gareth Leng]] 10:59, 22 January 2008 (CST)
:Thanks, Gareth.  And thanks for the thorough review and many helpful edits.  --Anthony.Sebastian 13:53, 22 January 2008 (CST) [[User:Anthony.Sebastian|Anthony.Sebastian]]
::Yes it's an advance in some respects, but I think as general observations:
1/the two sections on  systems biology and on thermodynamics have been enlarged disproportionately to the rest of the article. 
2/ The total absence of some sort  of systematic discussion of what types of living things there are is a little remarkable, both in the older version and the present one. Life is about living organisms, after all.
3/the organic chemistry as informatics section at the end is not adequate integrated in either version. Some of it is a simple duplication of the section on molecules, some of it  probably goes up with informatics, to explain the physical substrate that is actually being discussed
4/ "Identifying the different scientific perspectives seems a parallel article, or an alternate way of arranging the article,  but I think it was intended as a summary.
Is the current version perhaps intended as an intermediary version until the other portions can be expanded? If so, do we really want such a long article as that would be? Instead of mainly adding to the original content, perhaps we should be thinking of concision. [[User:DavidGoodman|DavidGoodman]] 18:56, 22 January 2008 (CST)
----
In the CZ-biology mailing list, David Goodman writes:  “Philosophy of biology to me is less important than actual biology, but then I'm a biologist not a philosopher. What life ultimately is and how life is exactly  defined cannot be intelligently discussed until you know what its physical structure consists of.  I'd move all the philosophy to a separate article as subsidiary. The main article on the subject should be about life as biology.” 
“This is too important an article to proceed without some time for thought about it. “
I agree with David Goodman that “The main article on the subject ‘Life’ should be about life as biology.”  Since CZ has defined biology (in its [[Biology]] article) as the “science of life”, one might argue that that biology article, and those related articles it links to, should cover the subject of “life as biology” -- as they appear to do.
I believe we need, in addition, as emphasized in the [[Life]] article, an article that focuses on life as the processes that enable the activity of ‘living’, with the theme, “''Life is what is common to all living beings''” (Christian De Duve).  Namely, the theme what fundamental processes characterize living things that distinguish them from non-living matter?
The discovery of those fundamental processes clearly have led to a deeper understanding of the biology of life.  To take one example from the article:
a) Living things sustain their biology in virtue of their location within the downhill stream of a flowing energy gradient, whether that gradient consists of photons emitted by the sun, electrons transferred from reduced mineral compounds in hydrothermal vents, or energy-rich matter generated by other livings.  We must understand that before we can make sense of the “physical structure” comprising living things (on Earth).
b) Living things build their physical structure in virtue of their ability extract a portion of that energy flowing past them and to utilize it to do the work of creating and re-creating the ordered (low-entropy) state that constitutes their physical structure.
c) Living things can accomplish that work of self-fabrication and re-fabrication in virtue of their ability to maintain a state far from the equilibrium (high-entropy) state of randomness.
d) They accomplish the maintenance of a far from equilibrium state in virtue of their ability to export into their surrounding a more degraded, less usable form of energy than they extracted, in quantities that create more disorder overall -- system plus surroundings – according to the dictates of the Second Law of Thermodynamics.
e) In doing that, they hasten the rate of dissipation of the energy gradient they lie in, hastening its distribution toward maximal randomness, a disposition that energy gradients possess  by nature.
Those considerations, of the driving force of energy gradients and the constraints imposed by the Second Law of Thermodynamics, reveal fundamental aspects of the commonalities of the biological basis of living things, despite their diversity of physical structures.  They seem to me more germane to a Science of Life than to a Philosophy of Life.
Nevertheless, the point of the request to replace the currently approved version of [[Life]] with the nearly year-long redrafting, [[Life/Draft]], resides in the fact that, though the theme of the article has not changed, the development of the theme has proceeded to the point where the draft version improves on the CZ approved version.
I personally would not know how to proceed with an article entitled, [[Philosophy of Life]], but I doubt it would bear much resemblance to our [[Life]] article.
On the Talk page of [[Life/Draft], David also comments as follows:
“::Yes it's [[Life/Draft]] an advance in some respects, but I think as general observations:”
“1/the two sections on systems biology and on thermodynamics have been enlarged disproportionately to the rest of the article.“
A.S response:  Yes, I can see how the systems biology section could be shortened.  Its main message is about a fundamental aspect of living organisms, namely the ‘emergence’ of levels of organization with novel properties not predictable from the parts.  I can see shortening the section, possibly re-titling it to refer more specifically to emergence, and reconsidering where I should be located in the article.  I will work on that.
I will re-examine the length of thermodynamics section.  The concepts there may be difficult for many readers and therefore may require a more lengthy discussion than the other sections in the article.
“2/ The total absence of some sort of systematic discussion of what types of living things there are is a little remarkable, both in the older version and the present one. Life is about living organisms, after all. “
A.S response: Yes, I agree, “Life is about living organisms.”  But, on a deeper, more fundamental level, life is also about the commonalities of the processes, shared by all living organisms (on Earth), that underpin the activity of living itself.  We have taken that as our (stated) theme for the article.  So the article is about living organisms after all.  Perhaps what we need to do to get to the level of the taxonomy of living organisms is to link to the appropriate articles in CZ that do that, or to write a separate article that deals with the diversity of living organisms on Earth.
“3/the organic chemistry as informatics section at the end is not adequate integrated in either version. Some of it is a simple duplication of the section on molecules, some of it  probably goes up with informatics, to explain the physical substrate that is actually being discussed “
A.S Response: I agree, and will rework the section in response to David’s  observations.
“4/ "Identifying the different scientific perspectives seems a parallel article, or an alternate way of arranging the article, but I think it was intended as a summary.
A.S Response:  Yes, it was intended as a summary, but also one that arranges the sequence of the article differently, to give the reader a reprise in a novel way that hopefully encourages reflection.
Is the current version perhaps intended as an intermediary version until the other portions can be expanded? If so, do we really want such a long article as that would be? Instead of mainly adding to the original content, perhaps we should be thinking of concision. “
A.S Response:  Naturally, some topics in CZ will require more text than others.  With a topic as large as ‘Life’ (no pun intended), perhaps such is the case.
--Anthony.Sebastian 21:03, 23 January 2008 (CST) [[User:Anthony.Sebastian|Anthony.Sebastian]]
=="Quantum coherence in photosynthetic systems"==
Perhaps later, it would be great, IMHO, to include a discussion on the following:
[http://www.nature.com/nature/journal/v446/n7137/abs/nature05678.html Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems]. Nature 446, 782-786 (12 April 2007)
My point is that issues debated in the field of [[quantum biology]] are relevant to the discussion on emergent properties, coherence, and points a) and b), above (A.S: "... Living things sustain their biology in virtue of their location within the downhill stream of a flowing energy gradient, whether that gradient consists of photons emitted by the sun, ... We must understand that before we can make sense of the “physical structure” comprising living things (on Earth)."). Photosynthesis would be quite a good place to start, wouldn't it?
:Very interesting, Pierre-Alain.  Perhaps you might incorporate those new findings in the photosynthesis article, and then we can refer to it in the life article in the appropriate places, and also in the emergence article.  I'll check out the Nature article.  [[User:Anthony.Sebastian|Anthony.Sebastian]] --Anthony.Sebastian 12:30, 24 January 2008 (CST)
:: I realized that there is no CZ [[photosynthesis]] article yet. However, the [[metabolism]] article (which is approved) has a concise and detailed description of [[Metabolism#Phototrophic | phototrophic metabolism]]. I wonder if it would be a good idea to integrate these considerations in the new [[Metabolism/Draft | metabolism draft]]. I suppose it will have to be quite short in order to remain in the tone of the article. Another issue is that there is no reference section. The introduction of quantum coherence, of a "''spooky action at a distance''", in such a high quality article might deserve some explanations and references, considering that many will take this as pure speculation (I suppose). IOW, the credibility of the article might unnecessarily suffer from this addition, if it is too short.  And finally, if we want our [[Life/Draft | Life]] to be approved ( ;-) ), making internal links to unappoved drafts might delay the process.
:: My wish: invite CZ specialists and members of the [http://www.cchem.berkeley.edu/grfgrp/ Fleming group] (who worked on this phenomenon for years) to write a [[photosynthesis]] article communicating the enthusiasm that is apparent in, for instance, [http://www.bio.ic.ac.uk/research/barber/ps2microsite/overview.html An overview of Photosystem II: The Engine of Life], a page written by another related group of researchers.
:: Once again, this may take some time. Last resort: import the [http://en.wikipedia.org/wiki/Photosynthesis WP photosynthesis article]. But it's written in encyclopedese (IMHO), and it appears that some basic notions are not well addressed (see [http://en.wikipedia.org/wiki/Talk:Photosynthesis talk page]). I can't tell.
:: [[User:Pierre-Alain Gouanvic|Pierre-Alain Gouanvic]] 15:02, 26 January 2008 (CST)
BERKELEY, CA -- Through photosynthesis, green plants and cyanobacteria are able to transfer sunlight energy to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency. Speed is the key - the transfer of the solar energy takes place almost instantaneously so little energy is wasted as heat. How photosynthesis achieves this near instantaneous energy transfer is a long-standing mystery that may have finally been solved. ...
"We have obtained the first direct evidence that remarkably long-lived wavelike electronic quantum coherence plays an important part in energy transfer processes during photosynthesis," said Graham Fleming, the principal investigator for the study. “This wavelike characteristic can explain the extreme efficiency of the energy transfer because it enables the system to simultaneously sample all the potential energy pathways and choose the most efficient one.” ...
"The classical hopping description of the energy transfer process is both inadequate and inaccurate," said Fleming. "It gives the wrong picture of how the process actually works, and misses a crucial aspect of the reason for the wonderful efficiency." ...
Engel said the duration of the quantum beating signals was unexpected because the general scientific assumption had been that the electronic coherences responsible for such oscillations are rapidly destroyed.
[http://www.eurekalert.org/pub_releases/2007-04/dbnl-qso041207.php Quantum secrets of photosynthesis revealed], eurekalert.org
[[User:Pierre-Alain Gouanvic|Pierre-Alain Gouanvic]] 02:54, 24 January 2008 (CST)
==Long series of edits==
I'm sorry, I've made a lengthy series of edits intended to tighten, trim and clarify. Most impotantly, the boxed definitions I really found hard to read or follow, and in aspects wordy. (A gradient is a gradient, uphill or downhill...).... while (at the same time)...
I think it's very important that these boxed elements appear clear and pithy. They are profound, but the excess of words maakes them seem pretentious.
Anyway, revert my changes as you will - they're good intentioned but maybe some are ill conceived :-)[[User:Gareth Leng|Gareth Leng]] 15:59, 26 January 2008 (CST)
:Gareth, thanks for putting in the time and effort to "tighten, trim and clarify".  Right on edits.  I take your point on the boxed definitions; I will work on them.  -- [[User:Anthony.Sebastian|Anthony.Sebastian]] 19:30, 26 January 2008 (CST)
== Editing in response to comments by David Goodman and Gareth Leng ==
In responding to recent comments by David Goodman and Gareth Leng, to whom I express my gratitude for their thorough reading of [[Life/Draft]] and their insightful critiques, I have extensively edited the draft, reorganizing sections, eliminating material, and re-writing each section's blue summary box, among many other edits.
David and Garth, when time permits, please give it another look.
As I believe we have now a more mature and nuanced version, I would hope we could soon replace the okay but somewhat exiguous currently approved version.
--Anthony.Sebastian 18:24, 28 January 2008 (CST) [[User:Anthony.Sebastian|Anthony.Sebastian]]
:Thanks also to Chris Day for enhancing the epigraphs, and Stephen Ewen for tidying up the images. [[User:Anthony.Sebastian|Anthony.Sebastian]] Anthony.Sebastian 18:21, 3 February 2008 (CST)
==Quotes==
I notice that some of the quotes are in a dark red and other are purple.  Is there any significance to these colours?  If not we should go with one color or the other. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 13:40, 1 February 2008 (CST)
:Thanks, Chris.  I changed all to "purple".  --Anthony.Sebastian 14:12, 1 February 2008 (CST) [[User:Anthony.Sebastian|Anthony.Sebastian]]
::Chris, why does the 4 tildes not save as link to my user page? I have to add by hnd [[User:Anthony.Sebastian|Anthony.Sebastian]] to show link. (see edit)
:::Go to the preferences and fix your nickname.  You have have what ever you want in your signature. Let me know if you need more help (make sure the raw signature box is ticked)  [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 14:20, 1 February 2008 (CST)
::::Could find no box for "nickname" in My Preferences.  Username = Anthony.Sebastian (doesn't need "fix".  Real name = Anthony Sebastian (correct).  Raw signature box checked.  Always worked before; recent problem.  Still flummoxed.  --Anthony.Sebastian 15:45, 1 February 2008 (CST)
:::::Interesting.  There used to be, there must have been a change to the media wiki that caused that choice to be lost.  However, the field must still exist since my signature is customized. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 16:18, 1 February 2008 (CST)
::::::Anthony and Chris, the nickname feature was taken out months ago.  The only reason Chris still has his is that he hasn't made any changes to his preferences.  A couple of months ago I updated my time zone and lost my (talk) link :-(  So now we are stuck with our user names. [[User:D. Matt Innis|D. Matt Innis]] 11:54, 18 February 2008 (CST)
==Thanks Anthony==
Thanks for being so conscientious in your revisions Anthony. I am willing to approve this tour-de-force. It's too big and complex ever to be perfect, but it's certainly something to be proud of[[User:Gareth Leng|Gareth Leng]] 10:20, 18 February 2008 (CST)
:Thank you, Gareth. I have no excuse for [[Life/Draft|Life/Draft's]] prolixity, except to say that 'Life' encompasses everything in 'Biology'. I look forward to spending more time getting [[Systems biology]] to a state meriting consideration for approval, and fleshing out [[Homeostasis (Biology)]] and [[Evolutionary medicine]].  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 13:30, 18 February 2008 (CST)
== general comments ==
First, I want to avoid doing any editing in this article, so that if ever needed, I could be an approver later.  So, I will just add some comments. 
:First, the use of 'quotes', "double quotes" and ''italics'' is '''grossly''' overused.  When you stress everything, you stress nothing.
:The article is too long, because of rambling sentences, questions and other items that are not necessary for the article and which provide no information.
Example from article: Particular collections of such molecules somehow manage to generate symbols forming metaphors that attempt to explain themselves as constituting living things.
::This is colorful language that gives me no information. 
Life is fundamentally about the ability to reproduce, yet this concept is nowhere near the top of the article. The fundamental unit of life is a cell, but this category is also too far down the page.
Sections that should be removed or placed into separate articles:
* Thermodynamics of life
* Notes on organization
I need to really read this over better before making comments, but I would certainly like to see some of these issues raised be addressed by the authors. [[User:David E. Volk|David E. Volk]] 08:58, 28 February 2008 (CST)
::David, thank you for your thorough and thoughtful comments. I will try to address all of them.
::*I will re-examine the use of quotes, double quotes and italics, regarding their possible excessive use, and try to remedy any excess that seems counterproductive.  Regarding double quotes, I personally think them unnecessary when using the 'blockquote' format.  I think those we could eliminate.  I use single quotes not for emphasis but simply to call attention to the word more or less as a word, not to place emphasis on the word to clarify the meaning of the sentence.  Nevertheless, I will scrutinize all three formatting categories you mentioned and try to minimize. I hope others will comment now and after further editing.
::*I will look for "rambling seentences"', recognizing my "Isaiah Berlin" tendency to longer sentence stucture.  I suspect much could be done to enhance ease of reading and clarity of exposition.  Will work on it. 
::*Regarding items "not necessary for the article and which provide no information". I will look for them. Sometimes a writer will include sentences that are not strictly informational but serve to make the reader think about aspects of the topic that go beyond the immediate purpose of the paragraph, sometimes even to inspire wonder.  The sample you gave,
:::<blockquote>Particular collections of such molecules somehow manage to generate symbols forming metaphors that attempt to explain themselves as constituting living things.</blockquote>
::::appeared in this context:
:::<blockquote>On Earth, everything alive teems with vibrant molecules of myriad types and sizes, too small for the naked human eye to see, but numerous enough to come into view as a flea or a giant sequoia tree (up to 4.5 million pounds of molecules).[6][7] Particular collections of such molecules somehow manage to generate symbols forming metaphors that attempt to explain themselves as constituting living things.</blockquote>
::::To me, it seems truly something of wonder that particular collections of molecules can, in the form of living things, actually generate symbols (words, sentences), in the form of metaphors, with which they use in an attempt to explain themselves as living things.  Imagine, living things, comprised of molecules, recognizing themselves as living things, processing symbols, generating metaphors to try to understand the wonder of it all.  In writing about life, I hope Citizendium can inspire wonder and awe, when appropriate, in addition to simply conveying facts.  Nevertheless, I will take another look at the sentence and try to improve it.
:::: Regarding above: You have just provided the information that was lacking in the single sentence I pointed out.  Now I understand you are saying humans are creating symbols, languages, metaphors and are self aware.  So rather than the one sentence, expand it to something like you have just stated above.[[User:David E. Volk|David E. Volk]] 16:07, 28 February 2008 (CST)
::*Regarding your comment: "Life is fundamentally about the ability to reproduce, yet this concept is nowhere near the top of the article. The fundamental unit of life is a cell, but this category is also too far down the page."  I tend to disagree that "life is fundamentally about the ability to reproduce."  In your terms of "fundamentally about", I would argue that life is fundamentally about sustaining the activity of living, which for life on Earth, the ability to reproduce constitutes only one aspect of sustaining the activity of living. Other no less fundamental aspects of sustaining the activity of living are free-energy harvesting, self-organization, exportation of entropy, and self-fabrication of the components that self-organize into the very system that fabricates those components. Without those activities, living things could not reproduce themselves to sustain the activity of living.
::*I agree that the fundamental working unit of living things is the cell, and that that fact needs emphasis early in the article. But cells are made up of molecules, making it difficult to describe their fundamental role without first a word about their molecular basis.  That is why the section on cells follows immediately the section on molecules.
:::: Regarding chemicals, almost everything (not protons, muons, etc), like rocks, plastics and planets, are made of chemicals.  It is the living cell that distinguishes life from non-life, not the presence of chemicals.  The chemicals section should probably be incorporated into the [[cell]] article if not already there. [[User:David E. Volk|David E. Volk]] 16:07, 28 February 2008 (CST)
::*Regarding your comment: "Sections that should be removed or placed into separate articles: Thermodynamics of life; Notes on organization."
::::The section on Notes on organization has a long history too boring to recount here. I think the points it makes do help the reader, but perhaps do not need to be located where they are in the article.  I will see if I can tighten the text and locate it in a footnote.  That should avoid distracting the reader and giving her the option to skim or skip it.  I'm glad you brought up the issue.
::::The section on the thermodynamics of life, in my opinion, is critical to the goal of the article stated in the last paragraph of the Introduction:
:::<blockquote>This article focuses less on 'life', than on 'living', on what essential activities living entities perform to enable their living — specifically, on the fundamental processes of living, those that underlie the complexity of all living things, the "common denominator that allows for the discrimination of the living from the non-living",[2] as inferred from the study of living things on Earth in the light of science.[3]  It takes, as its theme, “Life is what is common to all living things on Earth” (Christian De Duve).[4]</blockquote>
:::: re: Thermodynamics, Gibbs free energy, enthalpy, metabolism, catabolism, etc are important considerations that are inter-related.  Perhaps a slimmed down version would be better, with an expanded separate article as well? [[User:David E. Volk|David E. Volk]] 16:07, 28 February 2008 (CST)
::::I do not believe one can understand the nature of living systems without understanding the basics of the Second Law of Thermodynamics as applied to open systems in a quasi steady-state far from equilibrium. I believing putting that section in a separate article would destroy the coherence of [[Life]].
::*I do hope, as you do, that we will hear from other members of the relevant workgroups.
::*Thank you again for taking the time to give [[Life/Draft]] a thorough review and for your many helpful suggestions.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 15:27, 28 February 2008 (CST)
:::: In regards to the carbon atom drawing, I suggest rewording to avoid using the word want with regards to the desires of a carbon atom.  Wanting is a trait that animals have.  Instead use terms like highly energetic state, more stable, lower energy, etc.  In addition, you might talk about electronegativity, EN, (in the paragraph, not the image), since EN values range from about 0.8 up to 4 (in my old textbook), and the EN of carbon is 2.5, smack in the middle of this range.  Because of this, carbon can covalently bond very favorably with a great many elements, with positive and negative oxidation states.  Elements on either end of the EN range have limited covalent bonding and are more likely to form salts.  [[User:David E. Volk|David E. Volk]] 14:24, 28 February 2008 (CST)
:::::David, I struggled with explicating the concept of the greater quantum stability of atoms with their valence shells filled to capacity. I decided not to say that atoms ''wanted'' to complete their valence shells.  Instead I said explicitly that they behaved ''as if'' they ''wanted'' to complete their valence shells.  That is true, is it not?  They do behave as if they wanted to complete their valence shells.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 15:39, 28 February 2008 (CST)
What you really mean is "to a '''human being''', it appears as if the carbon atom wants to fills its valence shell".  A dog or plant would not think so.
:Yes, I agree.  It appears to us humans that a carbon atom behaves as if it wanted to fill its valence shell. I offer that the reference to humans as the observers of that putative carbon atom behavior goes without saying, however. To whom else would it so appear?  Surely not to dogs or plants. But what do I know, I'm not a dog or a plant, though I have occasionally dodged expletives to that effect hurled at me. --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:53, 28 February 2008 (CST)
== example intro ==
I would like to see the intro start out with something along these lines:
The definition of '''life''', its [[origin of life|origin]] or [[evolution]], and the nature of living things have been the subject of much debate throughout the history of mankind.  The definition of life at any given moment in history, even today, is naturally limited to mankind’s knowledge at that time.  Presently, all life can be categorized as animals, plants, bacteria, yeasts or fungi, but an entirely new life form could be discovered at any time, including extraterrestrial life.  This article discusses the basic characteristics shared by all known life forms, including the cell, which is the basic unit of life, and the many processes they have in common, including boundaries, metabolism, communication, (re)production from parents, self-defense, adaptation or death, and a sense of the outside world.
(note: not all living this are reproductive, but they all must come from one or more reproductive parents.  This covers, for example, sterile hybrids of animals and plants, castrated animals, non-reproducing (not the Queen) bees and ants and the like. [[User:David E. Volk|David E. Volk]] 15:18, 28 February 2008 (CST)
== suggestions for Molecules section ==
In paragraph #2, fix these links which are incorrectly set to the plural form:
*change <nowiki>[[amino acids]] change to [[amino acid]]s</nowiki>
*[[nucleotides]]
*[[monosaccharides]]
*[[nucleic acids]]
*[[polysaccharides]]
In paragraph #3, change molecular species to molecules
In the "informatics section:
Reformat the leading question to make a real sentence, ie
* Why do carbon atoms play a central role in life?
Also add wikilinks for methane, carbon dioxide and hydrogen cyanide (hydrocyanic acid). [[User:David E. Volk|David E. Volk]] 16:46, 28 February 2008 (CST)
::Thanks, David.  I made the changes, though some remain red links. --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:26, 28 February 2008 (CST)
== thermo section ==
I like the thermo section the more I read it, but there is one mistake in it twice, the "jar-filled water vapor".  Presumably you mean the water vapor-filled jar.
:David, good pick-up. I made the change.
:Glad to learn the thermo section growing on you.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:28, 28 February 2008 (CST)
== evolutionary aspects of living ==
This sentence needs fixing - ie remove the bolded 'the' shown below:
The variations occur due to chance variations (e.g., mutations) in the inherited genetic database (genome) that the organism draws upon to '''the''' help it self-construct and self-maintain its organismic traits (phenotype), and also to various natural experiments (e.g., symbiogenesis) that lead to emergent genotype-phenotypes.
:David, couldn't find '''the''', but made sure sentence read clearly.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:30, 28 February 2008 (CST)
== self-organization section ==
* The link for [[Van der Waals forces]] needs fixing
*change adaption --> adaptation? [[User:David E. Volk|David E. Volk]] 17:49, 28 February 2008 (CST)
:Done. Thanks again for your thorough reading.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:35, 28 February 2008 (CST)
==Delayed approval==
I have put back the date of approval for another week to allow further changes to be made; if it is clear that the draft version is then ready I will change the version number to the then current one and allow another 24 hours. I will leave the approval notice though to alert editors that approval is being actively addressed[[User:Gareth Leng|Gareth Leng]] 05:53, 29 February 2008 (CST)
== new layout, nice ==
I really like the present layout much better, the corrections by [User:Anthony.Sebastian|Anthony.Sebastian]], and the recent rephrasing done by [[Chris Day]].  I still would prefer to have the cells category above the molecules section, but it appears other disagree so let the majority rule.  Well done everyone. :) [[User:David E. Volk|David E. Volk]] 15:50, 3 March 2008 (CST)
:I've made an attempt to reorganise the molecules and cells section as one called "building blocks". Essentially I have just rearranged what we already have with a couple of linking sentences to bring bring more prominence to cells.  See the text at [[Talk:Life/Draft/Building_blocks]] and see if that or a similar structure would be a useful way to present it? Note: the text in the molecules and cells section is unchanged.  I have rearranged the preamble from the current molecules section and added it immediately after the building blocks heading on the experimental page linked here. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 17:21, 3 March 2008 (CST)
::Chris, I think it works fine the way you did it. But, personally, I prefer teaching the molecular ABCs first, then their organization as cells.  Perhaps I'm too focused on the abiotic-to-biotic transition during the origin of life.  Nevertheless, the story gets told and the citations remain. Just a difference in style. Substance more important.
::Thanks for working so diligently to get a finished product out, and thanks to David Volk for thoughtful prodding. --[[User:Anthony.Sebastian|Anthony.Sebastian]] 20:02, 4 March 2008 (CST)
==Approval==
==Approval==
OK, I've updated the version number, and don't see any dissent from approval, so at the end of today, this article will be approved unless there is a last minute objection.[[User:Gareth Leng|Gareth Leng]] 06:05, 10 March 2008 (CDT)
OK, I've updated the version number, and don't see any dissent from approval, so at the end of today, this article will be approved unless there is a last minute objection.[[User:Gareth Leng|Gareth Leng]] 06:05, 10 March 2008 (CDT)

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Approval

OK, I've updated the version number, and don't see any dissent from approval, so at the end of today, this article will be approved unless there is a last minute objection.Gareth Leng 06:05, 10 March 2008 (CDT)

Thank you, Gareth. In the new version number, I still see a typo or two, and a few wikilinks needed, but I will not edit the current version, so you will not have to update the version number again today. I understand an editor can make minor copyedits to an approved version, but I'll check policy on that if I decide such edits necessary after today's (hopefully) approval. The curse of the perfectionist. --Anthony.Sebastian 14:20, 10 March 2008 (CDT)
Anthony, if you want to go ahead and make the changes that you see I will incorporate them into the re-approved version tonight as long as they are not 'content' edits. Spelling and linking are definitely allowed. I'll just make a note of them on the Approval page. --D. Matt Innis 15:09, 10 March 2008 (CDT)
Thanks, Matt. I made five history-page-recorded edit series since 21:00, after Gareth updated the version number for approval; all corrections of typos or additions of wikilinks. I appreciate your offer to "incorporate them into the re-approved version tonight", but if that means your inserting the edits yourself manually, that seems too much. I'm happy to edit the re-approved version after its up, tomorrow say, assuming I have authorization to do such a thing, and assuming an approved version once up is editable by an editor. If so, you can monitor my edits afterwards. Save you the work. --Anthony.Sebastian 16:35, 10 March 2008 (CDT)
Hi Anthony, those edits are all copyedits, so I will just copy the current draft page over to the approved version with those edits with it. That is no harder than copying the other version, so no problem. You can still make copyedits afterward, too, as the nominating editor. And as always, I look out for anyone changing the approved versions, as you pay me to do ;-) --D. Matt Innis 17:00, 10 March 2008 (CDT)
Thanks again, Matt. I'll stop worrying (and copyediting). I always learn something communicating with you. --Anthony.Sebastian 17:05, 10 March 2008 (CDT)

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