Talk:Life/Draft

Article re-approval and version record area

Article re-approval and version record area

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Approval process for Life Reserved for a log of re-approval events for Life article See here for help. Version 1.0 approval One editor approval possible on the grounds that Tribe has had insignificant and mundane author involvement David Tribe 08:44, 4 April 2007 (CDT) Updated URL David Tribe 05:54, 5 April 2007 (CDT) Updated URL David Tribe 21:19, 5 April 2007 (CDT) Updated URL David Tribe 01:12, 10 April 2007 (CDT) Updated URL David Tribe 05:42, 10 April 2007 (CDT) shortened deadline to 1 week from first tagging. David Tribe 22:11, 5 April 2007 (CDT) Updated URL to last version with out substantial change from agreeed final form http://en.citizendium.org/wiki?title=Life&oldid=100075828 http://en.citizendium.org/wiki?title=Life&oldid=100075828 DOUBLE CHECKED OK David Tribe 18:03, 10 April 2007 (CDT) There is multi-editor demand for actioning approval now so deadline set to now after very long editing process. David Tribe 17:56, 10 April 2007 (CDT) Verified 4 editors agreed none disagreed. --Matt Innis (Talk) 18:26, 10 April 2007 (CDT) With Leng support we would have three editor approval also . Leng has given support below. David Tribe 05:55, 5 April 2007 (CDT) You have Sculerati support for approval. Nancy Sculerati 05:55, 5 April 2007 (CDT) Version 1.1 approval The purpose of this approval is to fold in minor corrections to the obvious typos and errors in version 1.1. That is all the uncontested uncontroversial minor revisions. For such a change I am putting up a 4 day deadline as being adequate. The points also included are (i) a slight revision of the Blind-watchmaker quote, (ii) making the great men theme less intrusive,(iii) a single common ancestor scientific simplicity softened. (iv) finalise the exact re-wording of the Si-chemistry statement. The last point (iv) should be the focus of a collaborative re-edit but the mechanics of editing it in light of later edits are complicated by due process for discussion, so it may have to wait till that due process occurs. (strikethrough after taking up one of Catherines alternatives slightly modified)David Tribe 17:51, 16 April 2007 (CDT) Tribe judge's he has tacit support for this act from from Sculerati, Leng, Day and Sebastian from various discussions. Confirmation here would be appreciated.David Tribe 18:59, 15 April 2007 (CDT) David, I did a few fixes today, re silicon and evolution of cells (latter in Appendix), and some minor text tweaks. With those, I support the upgrade. --Anthony.Sebastian (Talk) 22:36, 15 April 2007 (CDT) That is, I would like to see those fixes incorporated. --Anthony.Sebastian (Talk) 22:39, 15 April 2007 (CDT) Updated URL Incorporates above mentioned fixes, supported also by Day in Tribe user talk, with thanks David Tribe 00:04, 16 April 2007 (CDT) Updated URL http://en.citizendium.org/wiki?title=Life/Draft&oldid=100081336 David Tribe 07:26, 16 April 2007 (CDT) URL updated http://en.citizendium.org/wiki?title=Life/Draft&oldid=100081731 David Tribe 17:51, 16 April 2007 (CDT) URL updated after style check http://locke.citizendium.org:8080/wiki?title=Talk:Life/Draft&oldid=100082093 SHORTENING APPROVAL DEADLINE TO CLEAR THE DECKS OF BUGS, GET THE SHOW ON THE ROAD David Tribe 06:33, 17 April 2007 (CDT) URL udated last time before approval http://en.citizendium.org/wiki?title=Life/Draft&oldid=100082364 David Tribe 07:17, 18 April 2007 (CDT) URL updated again http://en.citizendium.org/wiki?title=Life/Draft&oldid=100083248 David Tribe 05:32, 19 April 2007 (CDT) UPDATED URKL http://en.citizendium.org/wiki?title=Life/Draft&oldid=100084516 Punctuation issue resolved, cell number issue resolved; protein number issue resolved incorporating A Sebastien latest text which is scientifically uncontroversial and documented by added references. No issues seen by D Tribe that amount to disagreement with text that hasn't been fixed. Deadline exceeded. David Tribe 23:42, 20 April 2007 (CDT) David, I see that the approval date is passed for version 1.1, but am unclear as to whether we have other editors ready to approve. The talk page seems to reflect some confusion about whether to approve. Can you get me another head count? --Matt Innis (Talk) 21:10, 19 April 2007 (CDT) Constable All issues of content at the time of the April 18 deadline are corrected by edits. Protein numbers are fully addressed by AS text introduced by D Tribe by pasting from the talk page. There are no outstanding issue with the text at the time the April 18 deadline passed and subsequent matters are legally irrelevant and in any case insubstantial. David Tribe 03:12, 21 April 2007 (CDT) I CONFIRM http://en.citizendium.org/wiki?title=Life/Draft&oldid=100084516 is approved by three editors and is the Last supported good draft . I ALSO CONFIRM THAT FOR SOME DAYS NOW THE APPROVAL PROCESS HAS BEEN CUMBERSOME AND ILL ADAPTED FOR CORRECTION OF OBVIOUS TYPOS ON A PREXISTING APPROVED VERSION THAT SHOULD HAVE BEEN FIXED PROMPTLY AND THIS PAGE PROVIDES CLEAR EVIDENCE THAT EDITORS SHOULD BE PROVIDED WITH TOOLS THAT ALLOW THEM TO ACT. ALL IS REQUIRED IS TRAINING and CONSENSUS FOR AN AGREED PROCESS WHICH IS TECHNICALLY STRAIGHT FORWARD. ANY AGREED PROCESS WILL WORKDavid Tribe 12:33, 21 April 2007 (CDT) David, I will cease all editing until v1.1 approved and new draft started. I support approving v1.1 as it currently stands. --Anthony.Sebastian (Talk) 13:31, 21 April 2007 (CDT) We now have TRIBE SCULERATI DAY AND SEBASTIAN SUPPORTING THIS SO ANY CONSTABLE CAN ACTION APPROVAL David Tribe 17:24, 21 April 2007 (CDT) Thanks David, for your efforts to clear this up. Combining the following comment from above: We now have TRIBE SCULERATI DAY AND SEBASTIAN SUPPORTING THIS SO ANY CONSTABLE CAN ACTION APPROVAL David Tribe 17:24, 21 April 2007 (CDT) And one on my talk page: Preferably wait for triumvirate since the difference between the two versions above includes many copy edits from Gareth. It would be good to get those in the approved version. Chris Day (talk) 04:03, 21 April 2007 (CDT) It appears that we have three editors that approve the article in its current version. We have one, Chris Day, that agrees that it is the best version, but is concerned that the fourth editor is not here to approve. The fourth editor, Gareth Leng, is apparently unavailable. Using the following approval standard: Group approval. If there are at least three editors, all of which are expert in the topic of an article, and all of which have been at work on an article, then any one of them may approve of an article with the concurrence of the other two (or more) expert editors. After lengthy evaluation of the above rule, I can only conclude that it appears that the rule expects that if three editors were working on it, then three are needed to approve it. By the same token, the placement of the words "at least" and "(or more)" tells me that if there are ten editors working on it, all ten are needed to approve. Using this interpretation, we would need to wait. On the other side of the coin, Professor Leng has not shown any sign of disapproval. However, there have been significant changes since his last edit. Barring any further clarification of the rules, I must wait before considering this article approved for the current version. --Matt Innis (Talk) 22:58, 21 April 2007 (CDT) Matt, apparently, that bit needs to be rewritten. A minimum of three out of however many editors at work on an article may approve it. If some other editor disagrees, that's another matter, however. --Larry Sanger 23:31, 21 April 2007 (CDT) Thanks Larry, in light of that new information. I see that we have the necessary three editors to approve. I will start the process immediately. --Matt Innis (Talk) 23:48, 21 April 2007 (CDT) Discussion for approval process for Version 1.1 stopped here. Version 1.2 Gareth Leng nominated this version of this article for approval. The Biology Workgroup oversaw this approval and the article was approved on, or around, 10th March 2008. The above Approval included that version indicated by Gareth Leng with 5 additional copyedits by Anthony Sebastian that became this version.

Suggested strategy for further revision

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..

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 RED LINKS in Life. - David Tribe 18:57, 10 April 2007 (CDT)

What a task-master you are, David.

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. --Anthony.Sebastian (Talk) 19:13, 11 April 2007 (CDT)

Congratulations

Well done on the approval. The article is amazing.

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 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'."

Also, I assume that you are using British English conventions here? Otherwise, the quotes should be double, not single. --Larry Sanger 21:14, 10 April 2007 (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. Russell Potter

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. --Larry Sanger 22:01, 10 April 2007 (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. Russell Potter

Truly incredible work, all! Wow! —–Stephen Ewen 21:56, 10 April 2007 (CDT)

I've blogged the approval: http://blog.citizendium.org/2007/04/10/life-affirmed/ --Larry Sanger 22:01, 10 April 2007 (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 David Tribe 03:02, 11 April 2007 (CDT)

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. --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. Nancy Sculerati 08:54, 11 April 2007 (CDT)

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. Russell Potter 09:08, 11 April 2007 (CDT)

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. Nancy Sculerati 09:14, 11 April 2007 (CDT)

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.

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. Russell Potter 09:23, 11 April 2007 (CDT)

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.Nancy Sculerati 09:39, 11 April 2007 (CDT)

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.Gareth Leng 11:23, 11 April 2007 (CDT)

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. --Anthony.Sebastian (Talk) 17:09, 11 April 2007 (CDT)

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.

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).

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 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. 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:

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]

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.

Let’s not go up any blind alleys.

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. --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. 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? 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. --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. 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. --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

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. --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. Chris Day (talk) 14:43, 12 April 2007 (CDT)

Chris, I know this from Physical Chemistry-or think I do (it's been a few years- but its basic stuff). The references given do discuss the fact that Si-O bonds are more stable at that temperature, but again perhaps you could ask a Chemistry editor to review the statement again (PS:they already have, X2 different editors although they did not comment specifically on that statement, and I guess it is possible that they both overlooked it?). Nancy Sculerati 07:59, 16 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. -Tom 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:

• Community metabolism

• The Root of the Universal Tree.

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.

• 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. David Tribe 01:13, 12 April 2007 (CDT) 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: 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. 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. --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 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." --Catherine Woodgold 14:40, 15 April 2007 (CDT)

The sentence has been reworked , I think by Anthony.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.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. 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.) --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.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.

--Catherine Woodgold 14:53, 15 April 2007 (CDT)

Definitely worth looking into. --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. --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. 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? —–Stephen Ewen 00:26, 16 April 2007 (CDT)

What is the big picture, really? I think it has to do with the need for a formal convention of a copyediting stage after approval - a proof. This was discussed in forums [1] after the Biology article was first approved. It was accepted then that an editor could take over to copyedit an article - with that final version agreed on by the other editors involved in orginal approval, rather than leave the endpoint of the article a moving target, in which both copyedits of the approved version, and changes in content like new wordings and concepts were all being added simultanously on the wiki. For anyone who has published, the notion of "a proof"- and what is and is not allowable for changes in a proof, is understood. That's what we need here- not a new approved version, simply a proofed copy of the approved version. I think this article offers a good opportunity for us to settle on such a process of "proofing" an approved article. The very first approved Biology version was proofed, but the next approved version lost that stage. And, as David says, it was a difficult process to manage. Nancy Sculerati 08:28, 16 April 2007 (CDT)

Nancy: I do not view the approved version of Life as requiring only 'copy-editing', though one can interpret that activity somewhat broadly. I would like to continue to work on the content of the article, as we receive feedback, and personally as I continue to learn more, from reading and discussion and reflection, about what goes into the process of living. And how best to communicate it. I might choose to invest much of my energy into further development of the article, risking the charge of not dong as much to further CZ in other areas. I doubt I will obsess to that degree, as I have a long list of subjects in Biology and other workgroups that I want to contribute to as best I can. I see Biology and Life as hubs connecting to all articles the Biology Workgroup produces, and for that reason I think we should regard them as unfinished symphonies, not 'proofs'. In my opinion, of course. --Anthony.Sebastian (Talk) 19:05, 16 April 2007 (CDT)

Of course, Anthony. But that is EXACTLY why we need to have a simple proof- because everyone wants to expand, and although that is a good-even a great thing, we can never get a proofed stable versdion unless we approve a version and then allow a proof to be made. Once the proofed approved version is up, the draft continues. When it gets approved, it too will need proofing, and so on. Do you see? Or is it that extra X chromosome that accounts for my vast superiority in this matter? ;) Nancy Sculerati 21:10, 16 April 2007 (CDT)

"Bug" fixing

References

I tidied up a few references. I also combined a few; see this for why. 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. —–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. 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.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 in 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. Nancy Sculerati 07:41, 16 April 2007 (CDT)

I agree with Nancy on this one. Let's call it CZ style. Welcome to a smaller world, I like it. In fact, I think I'm starting to sound a bit British myself. --Matt Innis (Talk) 08:44, 16 April 2007 (CDT)

...with a southern accent? It's good to agree with you Matt- we usually do, I think.Nancy Sculerati 09:15, 16 April 2007 (CDT)

hehe.. Ya'll know it sounds good, and I do enjoy kibbles-n-bits, or is that fish-n-chips, or eggs-n-grits. Anyway, yes Nancy, we always agree even when we agree to disagree! --Matt Innis (Talk) 10:48, 16 April 2007 (CDT)

I feel as Nancy does, ceteris paribus. --Anthony.Sebastian (Talk) 19:12, 16 April 2007 (CDT)

Ya'll, I was told I speak like a Boston Yankee by a southern gentleman from Missoora (he said), but I not sure if it was a compliment. Also I thought grits was spelt greeeyutz, but I stand corrected by an expert. BTW in NZ they say fush-n-chups David Tribe 19:22, 16 April 2007 (CDT)

Grits? There was this Yankee vacationing in Louisiana. So he stops at the local Greasy Spoon for breakfast. He sees grits on the menu. So he asks the waitress, "Ma'am, I've never had grits before. Can you bring me out just one first so I can see if I like 'em?"

(Sorry, couldn't resist). ;-)

An example, Gareth? Sure, first paragraph, intro. We have 'life', "life on earth", "what is life?", 'life', 'living' and “Life is what is common to all living beings”. And so forth. We also have quotations that cannot decide whether the period goes before or after the ", hence, ." and ". And that sort of thing. I still think one or the other is the way to go.

Let me say that inconsistency in style reduces educational value. I use well-written things to help teach grammar and writing. I could never do that with this piece. Then again, I've used pieces with problems to do the same.

—–Stephen Ewen 20:35, 16 April 2007 (CDT)