Talk:Life/Draft: Difference between revisions

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{{Experimental
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|                abc = Life
|                cat1 = Biology
|                cat2 =
|                cat3 =
|          cat_check = n
|              status = 1
|        underlinked = n
|            cleanup = y
|                  by = [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 10:10, 12 April 2007 (CDT)
|            talk_archive = yes
|            approved = yes
|            auto = long
}}
==Article re-approval and version record area==
{{Approval history}}


==Suggested strategy for further revision==
==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)


Concentrate first on obvious errors and typographical inconsistencies in the first instance so that Version 1.1 folds all these in, and is uncontroversial. Consider primarily only absolutely clear cut improvements . Experience with other articles shows that these glitches are there. I can see one in Ref 1. '''Note.'''.  
: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.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 14:20, 10 March 2008 (CDT)


But for ambitious re-framing and  creative prose, our energies are now better spent on the hundreds of other undeveloped biology topics - and especially the [[cytoplasmic membrane|RED LINKS]] in [[Life]]. - [[User:David Tribe|David Tribe]] 18:57, 10 April 2007 (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.  --[[User:D. Matt Innis|D. Matt Innis]] 15:09, 10 March 2008 (CDT)


:What a task-master you are, David.
:::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.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] 16:35, 10 March 2008 (CDT)


:I would like to make a plea for substituting 'that' for 'this' when intending 'that', and 'those' for 'these' when intending 'those'.  I should think the need for ''those'' changes self-evident. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 19:13, 11 April 2007 (CDT)
::::Hi Anthony, [http://en.citizendium.org/wiki?title=Life%2FDraft&diff=100284752&oldid=100284190 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 ;-) --[[User:D. Matt Innis|D. Matt Innis]] 17:00, 10 March 2008 (CDT)


==Congratulations==
:::::Thanks again, Matt. I'll stop worrying (and copyediting). I always learn something communicating with you. --[[User:Anthony.Sebastian|Anthony.Sebastian]] 17:05, 10 March 2008 (CDT)


Well done on the approval.  The article is amazing.
==APPROVED Version 1.2==


I would like to comment on just one small thing I saw.  A sentence reads, "Self-organized systems ultimately are products of a 'blind watchmaker'."  This unnecessarily takes a specific philosophical/religious position. If you're going to say this, you should mention the other position; that's what our [[CZ:Neutrality Policy|Neutrality Policy]] requires. The other way to satisfy the policy, I think, is to say something like, "That biological systems are self-organizing in this way has led one prominent biologist to say they are products of a 'blind watchmaker'."
It appears that we have 3 to 4 approving editors with no significant outstanding issues that were not handled.  This approval can move forward.
<div class="usermessage plainlinks">Discussion for [http://en.citizendium.org/wiki?title=Life/Draft&oldid=100284752 Version 1.2] stopped here. Please continue further discussion under this break. </div>


Also, I assume that you are using British English conventions here?  Otherwise, the quotes should be double, not single. --[[User:Larry Sanger|Larry Sanger]] 21:14, 10 April 2007 (CDT)
Looking better every version!  I created a third archive as well.  If you need to bring anything back, just cut and paste. --[[User:D. Matt Innis|D. Matt Innis]] 22:11, 10 March 2008 (CDT)


::Larry, this is a bit out of my bailiwick, but my understanding is that the 'blind watchmaker' model'' is a *way* of describing something which is quite widely accepted, not a viewpoint with valid alternatives within its discipline to which the neutrality policy would necessarily apply.  There are indeed other ways of describing this phenomenon, but not really any body of science which disputes the underlying mechanism itself.  So I'd suggest "That biological systems are self-organizing in this'' way has been aptly described by [[Richard Dawkins]] using the metaphor of a 'blind watchmaker'."  Objections to the model which emanate from various religious or philosophical views could be referenced, but really do not have a bearing on the underlying science itself. [[User:Russell Potter|Russell Potter]]
== looks beautiful.  ==


:Well, it's somewhat in my bailiwick, as it happens; I've taught philosophy of religion, and "the watchmaker" refers to an analogy used to illustrate the teleological argument for the existence of God.  Dawkins is a famous atheist.  The implication is that we are endorsing Dawkins' rejection of the teleological argument.  I'm not saying that anyone ''meant'' that, I'm just saying that that is how the article reads, to this philosopher, at present. --[[User:Larry Sanger|Larry Sanger]] 22:01, 10 April 2007 (CDT)
wow.  I really enjoy the layout. [[User:Tom Kelly|Tom Kelly]] 00:37, 11 March 2008 (CDT)


::I see your point.  I have always quite admired Dawkins's book, and the "blind" in his "blind watchmaker" is a carefully chosen adjective -- implying, I think, not a total rejection of the teleological argument, but the qualified claim that increasing biological complexity does not require -- and yet does not exclude -- an element of intelligence in its design.  If [[Life]] is primarily an article within philosophy or religion, then it certainly should not endorse Dawkins's or any other view (and within both fields there are many others), but if it is primarily a scientific article, it seems to me that one *could* use this metaphor (with citation) to describe the tendency toward complexity of living systems without raising any neutrality issue.  But the article is quite strong; this is a relatively minor point. [[User:Russell Potter|Russell Potter]]
== Article of the Week - March 11, 2008 ==
This article was voted "Article of the Week" on March 11, 2008.  Congratulations to all of the authors and editors for hashing out this fine article. [[User:David E. Volk|David E. Volk]] 13:50, 11 March 2008 (CDT)


Truly incredible work, all!  Wow! &mdash;&ndash;[[User:Stephen Ewen|Stephen Ewen]] 21:56, 10 April 2007 (CDT)
== old pictures ==


I've blogged the approval: http://blog.citizendium.org/2007/04/10/life-affirmed/ --[[User:Larry Sanger|Larry Sanger]] 22:01, 10 April 2007 (CDT)
There are some images from older versions that are not in the current version. Do you think we could put the images in to a gallery subpage so that we can still easily find the images. The one that comes to mind was a picture of a man holding his hands out, I think he was an "evolutionist." [[User:Tom Kelly|Tom Kelly]] 21:52, 1 June 2008 (CDT)
:: Re Blind watchmaker metaphor. I'd argue that we don't ascribe to all Richard D's opinions just because we use the same metaphor for a well accepted biological interpretation. Its very apt too for self-organised systems. If they were organised by some entity outside the system, "blind" would not be appropriate, but that possibility's  not part of the topic "self-organised". Also since its an article about biologist's interpretation of life the metaphor is apt.


:: Re quotes: Thanks. One more item for V1.1  [[User:David Tribe|David Tribe]] 03:02, 11 April 2007 (CDT)
== Tiny typo ==
==Dawkins rears his ugly head (well metaphoricaly) -he's really good looking women tell me==
The question at issue is not what our opinions about what we are endorsing are, but ''how we can be reasonably interpreted'' by the well-informed reader.  And, as I said, the current wording ("Self-organized systems ultimately are products of a 'blind watchmaker'.[30]") can be thus reasonably interpreted as rejecting a role for God, particularly since it simply ''asserts'' that self-organizing systems are the products of a "God who is not there," citing a well-known atheist. --[[User:Larry Sanger|Larry Sanger]] 08:24, 11 April 2007 (CDT)


I agree with that reasoning- but that's not the reason I'd be happy to see the phrase go. I just didn't understand it in context. A blind watchmaker makes perfectly fine watches using his or her other senses- you don't ''need'' to see to perceive a classic mechanical watch's reading-you can feel the position of the hands - and ,especially if you are a watchmaker-it's a trivial deal to snap off the covering lens, blind or not.  The sound of the gears and the feel of the parts also are enough to make the watch, given sufficient expertise. So it just didn't make sense to me. It seemed to refer to something that I didn't know about, and whether or not the writer of the words in the article intended it that way- I guess it did. Taking it as it is- without outside references, for it to make sense you have to actually know very little about either making watches or what blind people are routinely capable of, and then I guess you might assume a blind person couldn't possible make or read a watch any more than a monkey. False, to put it mildly. [[User:Nancy Sculerati|Nancy Sculerati]] 08:54, 11 April 2007 (CDT)
This paragraph in the Molecules paragraph contains a weird fragment: "For the possibility of extraterrestrial life based on inorganic matter see novel proposal of physicists Tsytovich et al. A mass of charged particles — like a swarm of bees — exhibiting features similar to Earth-type living systems". Is this the right way to bring attention to this? [[User:Joshua Choi|Joshua Choi]] 03:02, 29 March 2009 (UTC)


::Sounds as though Dawkins's book is not as well-known as it once was -- probably another good reason not to allude to it in this particular article, as it may well create a point of puzzlement rather than enrichment.  It is also, I must admit; somewhat dated in this respect; looked at from today's point of view, "blind" is probably an unfortunate choice of adjective; Dawkins doesn't mean literally "deprived of one sense" but rather "directionless, not volitional."  The best solution here might be to create an entry on Dawkins and/or his book; once CZ users can click on a direct link, the allusion would function properly, which it clearly does not at present.  Still, I think it is much too facile to dismiss Dawkins's notion as false on this account.  I might mention at this moment that Dawkins is currently the Charles Simonyi Chair for the Public Understanding of Science at Oxford University. [[User:Russell Potter|Russell Potter]] 09:08, 11 April 2007 (CDT)
== Approved? ==


Well, if what is meant by "blind" is operating randomly, then it does make a lot of sense - as a concept. But the user of this CZ article LIfe will only read the word "blind" that way if he or she is fully familiar with Dawkins and his use of the word. That is part of my previous objection to making this into the "great man" (a la Galen) worship- fine to have an article on Dawkins, fine to link it, fine to actually quote scientists and philosophers, but that's the limit. Not fine to imply that instead of thinking for ourselves we will survey the great thoughts of the great men and marvel at their great wisdom. [[User:Nancy Sculerati|Nancy Sculerati]] 09:14, 11 April 2007 (CDT)
Citation 35 seems improperly formatted, it shows up as
:"<nowiki>Cite error: Invalid <ref> tag; no text was provided for refs named darwin1859</nowiki>"


::Dawkins may or may not be a 'great man' -- I agree that we should not fall down at the feet of ostensibly ''great'' thinkers and just cite their thoughts as though they were self-evidently brilliant -- but I do think his views on life and evolutionary biology are significant enough, just judging from the enormous impact they had at the time within the field, that within a reasonable notion of neutrality in articles, they can and should be "noted", though not necessarily here at this point in this entry.
It is from the section titled "Evolutionary aspects of 'living'". [[User:David Finn|David Finn]] 11:20, 8 November 2010 (UTC)


::Given that CZ places a great value on expertise ''qua'' expertise, certainly Dawkins is an expert, even though (and because) some other experts may disagree with him.  At the same time, he is also known as a very activist sort of atheist, a fierce critic of religion in general, and for this reason his name alone raises hackles in some quarters, even though his theories about biology can (and I think should) be considered entirely apart from his other views.  [[User:Russell Potter|Russell Potter]] 09:23, 11 April 2007 (CDT)
Thanks, fixed[[User:Gareth Leng|Gareth Leng]] 12:24, 8 November 2010 (UTC)


Russell, be that as it may-and I've taken the liberty of translating the wikipedism in your post into "neutrality in articles", this page is about the article Life, and how it can be improved- and my objection to the "blind watchmaker" is that it does not make sense unless it is placed in the context of an individual's contribution to the field, and a survey of the individuals - rather than strictly the ideas, is problematic. For example, the ideas of Aristotle are applied to living systems in a way that makes sense, and is-of course-linked to a great referemce. The idea of the "blind watchmaker" as presented in the article makes no sense- unless the reader has the background to know that the word blind is being used strictly as its fourth (or fifth or sixth)  meaning instead of its first. Maybe I am wrong about it refering to Dawkins, per se, and so maybe the idea of the "great men" is misplaced, but even if it is a phrase in some form of traditional philosophy- it does not stand by itself as clear without a full explanation of what is meant by "blind", except to those who are ignorant of the high end of abilities of the visually blind.  We are after truth here and not the appearance of political correctness. I like to think that truth is eternal. Of course, I liked to think that about love,too. And so, I may well be wrong. Regardless, I stand ''my'' ground against changing text on the vague and shifting grounds of ''the possibility'' of raising hackles, through popular (or as you say-even relatively obscure) associations that might upset some political or religious or scientific subgroup. Those kind of things might be life, as Anthony is fond of punning (God help us all), but it is ''not'' [[Life]]. This article must be as true as we can make it. That's all.[[User:Nancy Sculerati|Nancy Sculerati]] 09:39, 11 April 2007 (CDT)
== Definition discussion ==


Don't see the problem: blind watchmaker is in quotes that should display the fact that it's not intended literally, and the adjacent footnote gives the full explanation. It's also true I think that ''any'' purported mechanistic explanation of life may raise hackles; it goes with the turf.[[User:Gareth Leng|Gareth Leng]] 11:23, 11 April 2007 (CDT)
An article on definitions of life. [http://www.jbsdonline.com/product-p18287.html] [[User:Sandy Harris|Sandy Harris]] 01:10, 13 February 2012 (UTC)


::Sebastian butting in:  Though I agree completely with Gareth, I say we give Larry's concerns the benefit of the doubt re misinterpretation and neutrality, and change to the wording he suggests.  It does not detract from the point. And, Nancy, since people commonly use phrases such as "blind fate", "blind faith", "blind date" and "blind alley", readers should not be blind to the metaphorical uses of "blind". Nevertheless, since I introduced the term, I will look again carefully in response to your concerns and the comments of others. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 17:09, 11 April 2007 (CDT)
:Great find, Sandy. I found the 20 comments on the Trifonov article even more interesting.


: Larry's useful comment has to be put through scholastic tests of relevance, scientifically tested validity, style, and conciseness. They are in my opinion, worth rejecting on all four grounds. The interpretation Larry alludes to of the "blind watchmaker" phrase is not necessary, nor taken or implied  in the [[Life]] passage, the non-scientific interpretations raised by his argument are irrelevant to the passage in question, carry no authoritative or accepted argument or scholarship about biology, and will mar the style and clarity of the passage. But wait. There's more. Nancy arguing his (Dawkin's) metaphor will be misunderstood by many. Hmmm. That's something we cannot dismiss.
:What thoughts do you have re 'defining life'?


The Blind watchmaker words are only justified because they were efficient at communicating the concept of how self-organisation was generated, who said it first (great woman or flawed man, atheist or Lutheran) is irrelevant other than to provide a checkable source. Maybe I am fooled because I've read his books and enjoy them despite some irritating abrasiveness (except the God Delusion which is, IMHO a waste of energy).
:Intriguing: "Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution." (Orig Life Evol Biosph. 2010 Apr;40(2):221-9. Epub 2010 Feb 19. What is life? Defining life in the context of emergent complexity. Weber BH.)


If Nancy is right that the metaphor is not accurate or clear , then let's find a better one. It's quite a challenge in two words. A Rose by any other name would smell as sweet.
:I keep thinking: Because living systems hasten the pace to maximizing the entropy of the universe, whenever/wherever energy-matter conditions permit, living systems perforce will emerge.  Systems that generate more disorder in the system plus surroundings than the order they generate in themselves.  The universe longs for its 'heat death'. [[User:Anthony.Sebastian|Anthony.Sebastian]] 04:22, 13 February 2012 (UTC)


I thoroughly agree with Nancy's "Great man" argument, and would indeed live happily live with the elimination of eminent names. I have been uneasy about them: Schroedinger, Mayr, Dawkins, Kaufmann. Darwin we can hardly avoid, but hero worship has no place in neutral statements.  
::Also see ref 35 in the current [[Life/Draft]]. [[User:Anthony.Sebastian|Anthony.Sebastian]] 04:32, 13 February 2012 (UTC)
[[User:David Tribe|David Tribe]] 23:51, 11 April 2007 (CDT)


:David:  Your points, well-taken.  I had already edited the paragraph as follows.  It doesn’t seem to damage the message, especially given the unchanged footnote, which also follows:
== Disambiguation, or whatever ==


<blockquote>The patterns of structure and behavior in self-organized systems need no behind-the-scene 'master controller', and no prepared recipes that specify the structure and dynamics of the system. Instead, those patterns emerge from the interactions among the naturally selected components of a system, dictated by their physical properties, and dynamically modified by the emerging organization, which is itself modified by the environment. Thus the single-celled zygote self-organizes into a multicellular living system as the genetically encoded proteins interact, responding to changing influences from the changing environment generated by growing multicellularity — becoming a network of many cell-types working cooperatively. That biological systems self-organize in that way has led one prominent biologist to say they are products of a 'blind watchmaker'. [31]</blockquote>
This is obviously the primary topic for this title, but I was wondering how to deal with the game. Then I can't find an article here under Games, Mathematics or Computers. [[User:Peter Jackson|Peter Jackson]] ([[User talk:Peter Jackson|talk]]) 06:01, 1 November 2022 (CDT)


<blockquote>31↑ Dawkins R. (1988) The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. New York: W.W. Norton & Company, Inc. ISBN 0393304485 Excerpt from Amazon.com review: “The title of this 1986 work, Dawkins's second book, refers to the Rev. William Paley's 1802 work, Natural Theology, which argued that, just as finding a watch would lead you to conclude that a watchmaker must exist, the complexity of living organisms proves that a Creator exists. Not so, says Dawkins: "the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way... it is the blind watchmaker." Physics, of course, includes non-equilibrium thermodynamics.</blockquote>
:Yes, there needs to be a disambiguation page--but, what to name this one?  I'll look at Wikipedia and mull options. Any ideas? [[User:Pat Palmer|Pat Palmer]] ([[User talk:Pat Palmer|talk]]) 08:29, 1 November 2022 (CDT)


:Let’s not go up any blind alleys.
::I have begun [[Life (disambiguation)]]; it needs a lot of work.[[User:Pat Palmer|Pat Palmer]] ([[User talk:Pat Palmer|talk]]) 09:02, 1 November 2022 (CDT)
 
:I hope CZ will not place restrictions on biology articles to always mention the creationist view.
 
:Regarding Nancy’s ‘great man’ argument: I find it really a ‘straw man’ argument.  We give credit where due, and we encourage readers interested in named author’s words to follow up in the citations.  When I give an author’s name, I have no intention of performing an act of worship, but of performing an act of including the names of the those who have played a role in the endeavor to understand living things.  Carol Cleland, whom we mention, does not qualify as a man.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 14:01, 12 April 2007 (CDT)
 
Anthony, I'm not making it because I'm worried we are not worshiping women ;) - it's that the ideas should be emphasized and well enough explained that they stand alone, optimally, anyway. Of course, references and quotations are important, but I'm claiming that -in our articles- it's better (optimal) to present the attributed explanations and thoughts as "X exists because Y splits Z", not and" The Great Man (or Great Woman-either way) "attributed X to the influence of Y and Z". In the one case, if the explanation is clear, the argument really explains and stands alone. In the other case, the reader (user) either has to already know the argument to really understand the explanation, or take it as a given that if so and so said it, then its true and no further explanation is really needed. I think this blind watchmaker reference is the only example of this in the text. Personally, I would like to see it (that metaphor) either (1) concisely expanded so that the argument is made clear even to somebody who does not already know it or (2) dropped. Even with the examples you give, blind date etc, "randomly operating" is not so clear. But it's not a life or death edit for the article -;)- just a comment. [[User:Nancy Sculerati|Nancy Sculerati]] 14:41, 12 April 2007 (CDT)
 
==Fly in the ointment-Browser Issue?==
Ive tried printing the article on two different systems using the latest Firefox/ Windows XP. Printing stops at page 12.  However IE prints out the full article OK. 21 pages. Any advice from the technically savvy? [[User:David Tribe|David Tribe]] 02:49, 11 April 2007 (CDT)
 
== Wondering about accuracy of statement re Silicon ==
 
Can someone allay my concerns about the following in the approved article:
 
"Silicon, carbon's close relative on the periodic table, also forms bonds with itself, but they readily disassociate at the temperatures that are compatible with life as we know it. That is not true at much higher temperatures, and so it is possible to imagine biochemical reactions, more or less as we know them, occurring at, say, 400 degrees Celsius with silicon taking the place of carbon. If they do, one would expect that they too could form structures of such variation in size, shape, charge and composition that might be used to contain and organise information."
 
As I understand it, the Si-Si bond energy has a much lower value than the C-C bond energy, which suggests that at higher than earth life temperatures Si-Si bonds would have little stability, or not form at all.  In that case, stable Si-Si bonds require low temperatures, not the high temperatures of 400 degrees Celsius.
 
I may have my chemistry wrong, and stand ready for correction.  I do not know if silicon people will feel hot or cold to our touch.  --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 16:26, 11 April 2007 (CDT)
:The key ref is the one that cites the 400 degrees Celsius figure. i admit when i rewrote that section i did not fact check. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 16:44, 11 April 2007 (CDT)
 
::Chris: Could not find reference to silicon polymers in [[Life]], re temperature of stability of Si-Si bonds. The following article talks about silicon life only at very cold temperatures: “Many Chemistries Could Be Used to Build Living Systems”, WILLIAM BAINS. ASTROBIOLOGY Volume 4, Number 2, 2004 http://www.liebertonline.com/doi/pdfplus/10.1089/153110704323175124.
 
::I’d sure like to read the primary reference for stable Si-Si bonds at 400 degrees Celsius.  Maybe it fell out in edits. I’ll check the history. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 18:15, 11 April 2007 (CDT)
 
:::: Anthony I think you'll find the Si chemistry refs here in this section of  Talk Life http://en.citizendium.org/wiki/Talk:Life/Draft#carbon_chemistry
 
[[User:David Tribe|David Tribe]] 00:02, 12 April 2007 (CDT)
 
::David, your link above doesn't seem to get me there.  Do you have the primary reference about the stability of Si-Si bonds at 400 degrees Celsius?  Hate to keep kicking a dead horse. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 14:38, 12 April 2007 (CDT)
::I can confirm even after a literature search i cannot find a cite for this either. Admittedly it was not an exhaustive search.  Most references belabor the point that silicon is not ideal, mainly since it does not readily form double or triple bonds.  None mention other conditions where this may be different. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 14:43, 12 April 2007 (CDT)
 
== good job ==
 
just wanted to say amazing job all, especially the ones who put in tons of time writing this articles.  You are very cherished by all.  [[User:Thomas E Kelly|-Tom Kelly]] [[User talk:Thomas E Kelly|(Talk)]] 00:05, 12 April 2007 (CDT)
 
==Another Scientific concern about Life Version 1.  LUCA is DEAD==
 
In [[Life]] we say
"All living things extant today descended with modification from a single common ancestor, a unicellular organism."
 
This statement is grossly misleading and about 5 years out of date. The Last Universal Common Ancestor (LUCA) concept is long dead in the water. To retain scientific credibility we need to change it.
 
Note below links to just a few of the numerous relevant current papers (which I am attentively reading in preparation for an assault on [[Evolution of cells]], as a prelude to a thrust at the [[Origin of life]]). They and others document my seemingly bald assertion:
 
* [http://en.citizendium.org/wiki/Evolution_of_cells#Community_metabolism Community metabolism]
 
* [http://www.pnas.org/cgi/content/full/99/13/8742 The Root of the Universal Tree.]
 
<blockquote>
The universal tree has no root in the classical sense (1, 21). The root is actually a Darwinian Threshold, the first point at which we can begin to give tree representation to the organismal evolutionary course. A certain "symmetry of descent" is inherent in the classical view that is totally lacking here. In a classical phylogenetic bifurcation both sister lineages and their common ancestor are in essence alike. But, at the root of the universal tree (and in the first branching of the tree) classical presumptions do not hold (21), because the root is not a classical root, the sister lineages resulting from the earliest branchings are in no sense "sisters." They differ in fundamental ways.
 
The nonclassical perspective required here takes some getting used to. We need to release all of the classical connotations of "symmetry" in these "bifurcations." That the cell type on one side of the initial bifurcation has crossed a Darwinian Threshold does not imply that the organisms represented by the other side have done so. Indeed, different cell types would be expected to reach their Darwinian Thresholds more or less independently, at different times (1). The initial bifurcation of the universal tree (Fig. 1) tells us only that the bacterial cell type has crossed its Darwinian Threshold (23). Although the archaea and eukarya are represented by a "common lineage" at that stage, this is deceptive: the two are in effect lumped by forcing tree representation on the situation. Neither has yet to establish a stable genealogical trace. Neither has crossed its Darwinian Threshold. And that is all that their so-called "common ancestral lineage" signifies.</blockquote>
 
 
* Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA.
Decoding the genomic tree of life.
Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6608-13. Epub 2005 Apr 25.
PMID 15851667
 
* Rivera MC, Lake JA.
The ring of life provides evidence for a genome fusion origin of eukaryotes.
Nature. 2004 Sep 9;431(7005):152-5.
PMID 15356622
 
The difference between this error and Si chemistry is that the Si statement  was clearly labeled as fantasy scenario, whereas we present our common ancestor sentence as a considered scientific statement. Yes I know undergrad textbooks have it all over them, but we should aim for current scientific summaries.
[[User:David Tribe|David Tribe]] 01:13, 12 April 2007 (CDT)
[[User:David Tribe|David Tribe]] 01:13, 12 April 2007 (CDT)
 
:I'm sorry, I don't understand.  I can't figure out what that quoted paragraph is trying to say.  Are you saying that two or more currently extant kinds of life emerged without any common ancestor (i.e. evolved from scratch separately)?  Or are you saying that reproduction looked different back then, so that although the two or more kinds of life were related in some sense, they were not related in the way we usually think of things being related, i.e. cell division?  There's the idea of organelles having been originally separate life forms; does that have anything to do with what you're trying to say?
 
::: It not me thats saying that paragraph, its Carl Woese, from this paper: [http://www.pnas.org/cgi/content/full/99/13/8742 The Root of the Universal Tree.]
 
:::He's not talking about two kinds of life but three kinds of life. He's also saying that reproduction was diffeent then, some 3 billions years ago. Yes the organelle symbiosis idea does have something to do with it and the details are discussed in the papers. [[User:David Tribe|David Tribe]] 07:43, 16 April 2007 (CDT)
 
:By the way, I think mitochondria have a slightly different (but very similar) genetic code compared to other life forms, suggesting both common ancestry, and changes in the genetic code itself in the distant past.  It might be interesting to mention that in the article. --[[User:Catherine Woodgold|Catherine Woodgold]] 14:31, 15 April 2007 (CDT)
 
::: I'd argue the mitochondrial event is later than the very early events the Woese quote refers to are taking about-they are the times that the three "canonical' forms emerged and thay preceded the mitochondrial symbiosis most likely. Mitochondria are clearly related to known present day proteobacteria similar to ricketsia [[User:David Tribe|David Tribe]] 07:43, 16 April 2007 (CDT)
 
:I believe that the sentence is neither misleading nor out of date, but I'm open to arguments otherwise.  Following one of the links you gave, I get the impression that what you mean is not that life evolved from scratch more than once, but that a given life form may have had more than one ancestor;  in other words, that it would not be accurate to think of all life as having evolved from a single unique ancestor in a simple way under plain asexual reproduction without mixing of genes with other organisms.  Nevertheless, the sentence does not appear inaccurate to me.  The word "ancestor" is often used to describe humans, for example, who also had other ancestors.  Perhaps the sentence could be reworded to make more clear the obvious idea that if there was one such common ancestor, there was almost certainly more than one such (e.g. a/the parent of that common ancestor).  How about ''"There were some unicellular organisms in the distant past such that each one of them was an ancestor of all life alive today."''  --[[User:Catherine Woodgold|Catherine Woodgold]] 14:40, 15 April 2007 (CDT)
 
::: The sentence has been reworked , I think by Anthony.[[User:David Tribe|David Tribe]] 07:43, 16 April 2007 (CDT)
 
==Great men==
I agree we should avoid passing judgment on people. At the same time, I think we should not lose the sense that we are talking mostly about ideas here, and ideas are the constructs of particular people, and not necessarily held by others. I've made some minor changes to remove statements that look like unnecessary adornments.[[User:Gareth Leng|Gareth Leng]] 04:06, 12 April 2007 (CDT)
:: I'm feeling good about approving the article and the blowtorch of criticism (whether or not I agree with all of it). It's making us focus on the flaws we can fix by small edits. Instead of adding and adding we are polishing and removing blemishes. Good work everyone but especially the sharp critics. [[User:David Tribe|David Tribe]] 04:23, 12 April 2007 (CDT)
 
== Topic sentence of self-organization section ==
 
The first sentence was
*''"Living systems organize themselves spontaneously."''
I've changed it to
*''"The self-organizing activity of life occurs by means of positive and negative feedback loops that occur at many levels, from macroscopic to microscopic, among the material of which life is built."'' 
Many other first sentences for this paragraph are possible, but the one I took out feels to me as if it's just repeating what had been said (or implied several times) earlier in the article;  it doesn't pull me into reading the paragraph.  A good sentence is needed here to get the reader to settle back into their armchair and sink into the text after having had a boxed quote, point form section and a couple of section headings close together; otherwise this is a likely place to lose the reader's interest. 
 
Other possibilities for this sentence might be:
*''How do living systems organize themselves spontaneously?''
*''It seems almost paradoxical how living systems organize themselves spontaneously.''
*''Self-organization emerges from the interactions of material things.''
*''The ability to organize itself sponteneously is a defining characteristic of life.'' (This one may also be too much a mere repeat of what has already been said.) --[[User:Catherine Woodgold|Catherine Woodgold]] 14:19, 15 April 2007 (CDT)
 
 
:: In my opinion, the first (original) sentence (which I didn't write) is at least simple and it is the theme. I'm not convinced that any of the alternatives are better.[[User:David Tribe|David Tribe]] 23:21, 15 April 2007 (CDT)
 
== The word "organize" ==
 
The string "organiz" appears 75 times in the text of the article.  I think it would be good to reduce the number of occurrences to give the article less of a repetitive feel.  Words or concepts which might be substituted include:
*feedback loops
*replication
*phenotypes and genotypes
*learning; experience; testing
*reacting to stimuli
*information
*damage and repair
*resource
*combination, coalescence, union, amalgamation, assimilation, mosaic, collage, joined, congregated
*intertwine, interweave
*orchestrate, self-orchestrate (already appears but only once); self-sufficiency, self-governing
*evolve (This word only appears 4 times in the article at the moment, could be increased)
*homeostasis, regulation; adjust, regulate, coordinate, stabilize, moderate
*order and disorder; orderly; harmony, balance;
*entropy
*attractors (as in chaos theory)
*synthesis, synthesize, assemble
*cascade of cause and effect
*control, e.g. maintaining a steady body temperature or a steady concentration of a substance
*antioxidants
*arrange, regularize, arrangement, disposition
*marshalling, design, plan, contrive, programme
*management, direction
*systematization, codification, synchronization
*formulation, pattern, scheme, method
*structure, form, frame, shape, array
*standardize, make uniform
*disentangle
*whole, holistic; unifying, uniting; integrating
*incorporation, embodiment, comprehend, combination
*mould, shape, rebuild
*interaction
*not "system", though:  it appears about 140 times already!  It doesn't strike me as feeling as annoyingly repetitive as "organize", though, maybe because it's a shorter word, or it just carries less weight semantically. "Information" appears about 50 times; again, maybe OK but no use increasing it.  "Emerge" appears about 15 times.  I'm not saying the word "organize" or "self-organize" shouldn't appear a lot of times in this article -- I'm just saying maybe not *quite* that many;  maybe we could cut it down from 75 to 60 or something, and I think the article would sound better.
--[[User:Catherine Woodgold|Catherine Woodgold]] 14:53, 15 April 2007 (CDT)
 
:Definitely worth looking into. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 22:10, 15 April 2007 (CDT)
 
:Catherine: I looked through the article and felt that in most cases no other word than 'organized', 'organization' etc. helped in any way in any particular instance.  'Organization' is the special form of 'order' that living things achieve in virtue of their location along a free energy gradient, given their prebiotic evolutionary history and their inherited naturally selected information base.  Sometimes 'dynamic coordination' works.
 
:'System', 'information', 'emerge' I consider theme-words, or nodes, that give coherence to the article.  Of course, that's just feeling and opinion. --[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 22:29, 15 April 2007 (CDT)
 
::There's a long list of words from Catherine that cover related concepts, but what we need is the arguments for each particular situation where the substitute is more apt, accurate, communicative and better, and part of the intended theme or thesis. That's going to take time. For instance, I'm not sure for example where antioxidants fit, and why. I personally don't have much empathy with the word system, but I'd have to argue through my general feeling on particular phrases in context. We don't just have semantics and style to worry about, we have logical structure and narrative, and Catherine is not giving us much to chew on there. On the other hand I personally think both control loops , homeostasis and evolutionary selection are not fully developed, but I don't want to go through another big phase on making the article worse in order to make it better. Being told that to make an omelette's you have to break eggs doesn't get me all excited after this long passage so far.
 
:: Can I remind people what happened with [[Biology]]. We went through a somewhat frustrating period about version 1.1.1 where small points of debate consumed the energy of many. Lets try and release that energy for the scores, if not hundreds of wimpy articles that are around.
 
:: Thus I'm continue to argue from a strategy view point we should delay this until we have the essential corrections done. If Catherine would agree to delay her edit till after V1.1 is implemented, it'd speed things up. We can then clear the decks on all the changes changes that are agreed to, and then move on perhaps to agreeing to several of hers.  [[User:David Tribe|David Tribe]] 23:16, 15 April 2007 (CDT)
 
:::I think David's counsel is spot-on, for the big picture.  This upcoming approved version is, essentially, a sort of "bug fix" (to borrow the term from the software industry).  Let's please get this version up ASAP so as to deal with the few minor although, to me, ''annoying'' things about the current approved version.  A more thorough revision can then be tackled.  Would you be agreeable to this, Catherine, so everyone can better give what you are saying appropriate attention for the third revision?  &mdash;&ndash;[[User:Stephen Ewen|Stephen Ewen]] 00:26, 16 April 2007 (CDT)
 
=="Bug" fixing==
 
===References===
I tidied up a few references.  I also combined a few; see [http://en.citizendium.org/wiki?title=CZ:Article_Mechanics&curid=100003996&diff=100081210&oldid=100073599&rcid=113810 this] for why. [[User:Stephen Ewen|Stephen Ewen]] 23:23, 15 April 2007 (CDT)
 
===British or American English?===
Another ''annoyance'' to me -- a bug that needs fixing before approval -- is this article's quirky combing of British and American style -- or am I mistaken, thus showing my ignorance of British style?  If not, which one will it be?  If American, say so and I will gladly do the honors.  If British, I will have to plead at this time for another to undertake the task. &mdash;&ndash;[[User:Stephen Ewen|Stephen Ewen]] 00:43, 16 April 2007 (CDT)
 
:That's what you get with international collaboration. Since Anthony started this article I am assuming we are going with American. [[User:Chris Day|Chris Day]] [[User talk:Chris Day|(talk)]] 01:40, 16 April 2007 (CDT)
 
: Not sure what you're referring to? Can you give an example? But yes, go with American.[[User:Gareth Leng|Gareth Leng]] 07:06, 16 April 2007 (CDT)
 
Stephen, I'm an American and I don't see it as quirky. There is a blend of spellings and styles here, just like there is a blend of ideas- and to me, that is delightful and authentic. Authentic because it accurately reflects the collaborators. Copyediting can easily change nuances of meaning and I would beg any one changing the text who does not have an ''expert'' knowlege of the subject it covers to do so on the talk page and let the editors review it. There will be disagreements even among the "experts" before it is hashed out, most likely. For example, although it may be true that the word "organize" is used more than is elegant in prose for any word to be used in the section Catherine mentions, the "synonyms" Catherine offers are not synonyms to a scientist. The English language does have different styles in different English speaking countries, and since the characteristic of being an international community is a '''cherished''' feature of Citizendium, I feel strongly that we do not want to impose an artificial style of just one or another of these countries. If a South African writes [[Infant colic]], then let it have a South African style. If an American writes another article as primary author, let others either follow suit- or, if the article becomes a real collaboration- as this one did- let the subtle varieties of style remain. A person who is intelligent and educated enough to read this article understands that there are variations, globally, in English- even if the specific conventions and how they differ many not be understood. Gender is the English language (in all its regional forms) is another mish mash that I think is better left without strict convention. The phrase "All mankind" is foolishly forbidden, when it has a grandeur that "all humankind" does not, sometimes saying ''his or her'', or'' her or his'', is good, sometimes just ''his'', sometimes alternating in the text- as is often done when writing about children, using ''his'' in one sentence and ''hers'' in the next, is good.  Citizendium is not English or American (or Australian, or South African or Canadian or Singaporean or Nigerian...) and its language should not falsely make it appear to be one or the other or the next. English language styles over the next centuries, should the human world remain in rapid communication, will likely sort out the conventions into a new hybrid style. Let it be. [[User:Nancy Sculerati|Nancy Sculerati]] 07:41, 16 April 2007 (CDT)

Latest revision as of 09:02, 1 November 2022

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 Definition:  Living systems, of which biologists seek the commonalities distinguishing them from non-living systems. [d] [e]
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 Workgroup category:  Biology [Categories OK]
 Talk Archive:  1, 2, 3  English language variant:  American English

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)

APPROVED Version 1.2

It appears that we have 3 to 4 approving editors with no significant outstanding issues that were not handled. This approval can move forward.

Discussion for Version 1.2 stopped here. Please continue further discussion under this break.

Looking better every version! I created a third archive as well. If you need to bring anything back, just cut and paste. --D. Matt Innis 22:11, 10 March 2008 (CDT)

looks beautiful.

wow. I really enjoy the layout. Tom Kelly 00:37, 11 March 2008 (CDT)

Article of the Week - March 11, 2008

This article was voted "Article of the Week" on March 11, 2008. Congratulations to all of the authors and editors for hashing out this fine article. David E. Volk 13:50, 11 March 2008 (CDT)

old pictures

There are some images from older versions that are not in the current version. Do you think we could put the images in to a gallery subpage so that we can still easily find the images. The one that comes to mind was a picture of a man holding his hands out, I think he was an "evolutionist." Tom Kelly 21:52, 1 June 2008 (CDT)

Tiny typo

This paragraph in the Molecules paragraph contains a weird fragment: "For the possibility of extraterrestrial life based on inorganic matter see novel proposal of physicists Tsytovich et al. A mass of charged particles — like a swarm of bees — exhibiting features similar to Earth-type living systems". Is this the right way to bring attention to this? Joshua Choi 03:02, 29 March 2009 (UTC)

Approved?

Citation 35 seems improperly formatted, it shows up as

"Cite error: Invalid <ref> tag; no text was provided for refs named darwin1859"

It is from the section titled "Evolutionary aspects of 'living'". David Finn 11:20, 8 November 2010 (UTC)

Thanks, fixedGareth Leng 12:24, 8 November 2010 (UTC)

Definition discussion

An article on definitions of life. [1] Sandy Harris 01:10, 13 February 2012 (UTC)

Great find, Sandy. I found the 20 comments on the Trifonov article even more interesting.
What thoughts do you have re 'defining life'?
Intriguing: "Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution." (Orig Life Evol Biosph. 2010 Apr;40(2):221-9. Epub 2010 Feb 19. What is life? Defining life in the context of emergent complexity. Weber BH.)
I keep thinking: Because living systems hasten the pace to maximizing the entropy of the universe, whenever/wherever energy-matter conditions permit, living systems perforce will emerge. Systems that generate more disorder in the system plus surroundings than the order they generate in themselves. The universe longs for its 'heat death'. Anthony.Sebastian 04:22, 13 February 2012 (UTC)
Also see ref 35 in the current Life/Draft. Anthony.Sebastian 04:32, 13 February 2012 (UTC)

Disambiguation, or whatever

This is obviously the primary topic for this title, but I was wondering how to deal with the game. Then I can't find an article here under Games, Mathematics or Computers. Peter Jackson (talk) 06:01, 1 November 2022 (CDT)

Yes, there needs to be a disambiguation page--but, what to name this one? I'll look at Wikipedia and mull options. Any ideas? Pat Palmer (talk) 08:29, 1 November 2022 (CDT)
I have begun Life (disambiguation); it needs a lot of work.Pat Palmer (talk) 09:02, 1 November 2022 (CDT)
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