Talk:Life/Draft

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)

Sorry, maybe it would have worked better if I'd discussed it on the talk page first before editing, especially now that there's an attempt to get a stable version approved. Anyway, the way it now stands looks good to me: David Tribe has changed it to "Self-organization emerges from the interaction of life's components.", which is one of my suggestions but changed somewhat. I may be busy for the next while, so if people want to change this first sentence back to the original (for the current version or more permanently) or change it in some other way, please feel free. The original sentence may look better to me if the number of occurrences of the word "organize" is reduced in the part of the article that comes before this sentence; I may make some more specific suggestions later on about how to do this as well as further discussing why. By the way, the way it now stands perhaps "self-organization" could be replaced by "it" in the second sentence. --Catherine Woodgold 07:37, 17 April 2007 (CDT)

Thanks for the feedback and for showing understanding of practical editing to an fro. As a matter of ethical principle I prefer to stay with the last edit which is acceptable in my view. We want all points of view to be expressed, and in a few hours hopefully you'll be able to go hell for leather with your suggestions and time will tell which is the best text.David Tribe 18:00, 18 April 2007 (CDT)

More importantly, Larry Sanger seems to think the Proof phase concept is a bummer. I think we should persist with getting it working and explaining why its needed NOW. A separate Proof page is a bad idea. I think, but we should continue with the process of devising a standard working procedure thats more manageable. The fact is that Nancy and myself, Chris Day , Anthony and Gareth have together had about 95% of the approval process experience of the entire wiki, and its obvious to at least Nancy and myself that the proof idea or something similar that works NOW needs to be explained and developed so it does work , until an army of enthusiastic copy-editors arrive on the scene.David Tribe 18:00, 18 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 version 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? ;) I know that can't be- but I have to say something. You know that when you write something it has to be proofed, and you know too that the publisher doessn't want to hear that you have just had a whole new insight and now you have to change it. It doesn't matter that we are publishing in pixels here- we still need to stop and proof. Nancy Sculerati 21:10, 16 April 2007 (CDT)

Idea/suggestion: A page can be created called "life/Proof", which anyone can edit but with the understanding that normally only minor changes such as spelling correction are to be made, or possibly reverting some of the last few edits to the Draft pending further discussion. Meanwhile, more extensive editing can continue on "life/Draft". On the talk page "life/Proof" people can be encouraged to leave comments like "I read the whole thing and didn't see any errors." (If true, of course.) --Catherine Woodgold 07:25, 17 April 2007 (CDT)

Catherine, an Approved Article Version n.x/proof is a great idea- if its technically possible to do so. I think you have hit on a very practical and concrete solution to the end-game problem we have been experiencing with all approved articles. That would allow both simultaneous creative work to continue on the Approved Article Version n.x /draft, while the stable versioned article is copyedited (proofed). I will bring this up on the forums (I'll copy your post and attribute it) and on the excecutive committee. We still have not figured out a copyediting process (or style book- but never mind, Rome was not built in a day, or 6 months), and so I think the details of doing the proofing will be a work in progress, but -great idea, I think anyway. Nancy Sculerati 10:43, 17 April 2007 (CDT)

Let me comment on the suggestion on the forums. --Larry Sanger 09:22, 18 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 because of the "mixing". Then again, I've used pieces with problems to do the same. :-)

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

Now I understand what you mean Stephen. Its punctuation consistency. The solution is to fix-it. Ive been doing the honours on this for other articles but haven't done it on this yet. I recommended 'xxxx' for emphasis and " yyy" only for direct quotes. I"ll make a start. David Tribe 03:09, 17 April 2007 (CDT)PS. "what is life" of course is a direct quotation, but not of an English speaker. David Tribe 04:09, 17 April 2007 (CDT)

I like the mixture of British and USA English. I think if an American or Brit is unfamiliar with a word or spelling, then it should be wiki-linked so that they can learn what it means. -Tom Kelly (Talk) 02:58, 17 April 2007 (CDT)

When teaching, why not explain why there are discrepancies in the English Language among cultures? In general, I am opposed to going American Style since we already get stereotyped as "our way or the high way." If you really must change the style, let's pick Oz-style, mate -- and we'll all learn some new phrases. -Tom Kelly (Talk) 03:04, 17 April 2007 (CDT)

I think the quotation example is a minor point and you could put a link to an article explaining the variety-- which I would read if one existed and was linked too. -Tom Kelly (Talk) 03:05, 17 April 2007 (CDT)

I agree generally with Stephen on this issue. There are various conventions (I wasn't aware of any being British particularly). A common convention is to use '..........' for quotations and "...." for quotes within quotes; this also uses '..' for scare quotes. An alternative is to use "........" for long quotations and keep '.' for scare quotes. This is what I prefer, mainly because in science we tend to use scare quotes quite often (to introduce concepts, or to alert the reader to a different use of a word), and I think it helps to distinguish between these and verbatim quotes. The guide I have to hand says that the choice is a matter of taste, and that "On the whole British publishers prefer single quotes, while American publishers prefer double quotes" (from Mind the Gaffe by Larry Raske (born NY, living in UK, Penguin books). So maybe I'm American in this? I really don't mind what convention is used, am happy that you make it consistent, and think that the important point for me is only that verbatim quotes are clearly distinguished from scare quotes that mark a 'conventional' use (as these do, indicating that I mean use according to a particular convention, rather than a customary use). But while I agree generally it can be hard in practice. In the opening it's clear that 'life' and 'living' are enclosed by scare quotes; "Life is what is common to all living beings” is a verbatim quotation. "Life on earth" and "What is life" are really neither, they are pseudoverbatim quotes, probaly closer to quotationa than to scare quotes. Gareth Leng 03:25, 17 April 2007 (CDT)

Life on earth and What is life are both well known book titles ;) David Tribe 04:11, 17 April 2007 (CDT). I've finished a "style" check, following Gareth's bold advice, as I have before, and found one or two inconsistencies. I left "what is Life" as a quote and one other pseudoquote in "vvv" form. Hope I found em all but the main problem that caught Stevens eye I think was that we were largely following a different rule to his, rather than gross inconsistency. David Tribe 06:11, 17 April 2007 (CDT)

I think we should declare style decision at the top of talk pages of big articles like this at the first draft stage to remind people what they are.David Tribe 06:11, 17 April 2007 (CDT)

I think that makes great sense, David. Folks, remember I prefaced my initial remarks in this section thusly: "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?" At any rate, I'm glad to see that those more in the know in that style have declared this thing a go.

Wait! Stop the presses! I do know enough British English and my bastardized form of the Mother tongue (just kidding--maybe) to know that organize and organise are a problem. Are there other such quirks as well?

---Stephen Ewen 02:38, 18 April 2007 (CDT)

As a general point of policy, I'm going to agree with Stephen and Gareth. It might be "authentic" (in the sense that it authentically indicates that we are of different backgrounds all working on the same article), but it will also be seen as jarring--frankly, it does to me--by most of our readers. It will also not serve our audience well not to have definite (not necessarily singular) standards that CZ articles model. Do you really want a generation of schoolchildren around the world imitating CZ articles and mixing various styles of English? I certainly don't want my kid learning a mish-mash of styles when he's writing for an American audience.

As to this particular article, I don't care (in principle) about which language is used for general topics, like "Life," but I think we should at least know what the language is. I think we should keep track of this, moreover. The question is where we should keep track of it: on the article itself or on the talk page. David suggested at the top of the talk page; I'd agree with that. This is also precisely the sort of thing that belongs on the article checklist. I could easily add a line that would spit out "U.S. English" or something else (tell me what: "Commonwealth English" perhaps?).

Well, what do you think? --Larry Sanger 09:21, 18 April 2007 (CDT)

I actually agree with you, Larry. When I made my post, the fact that the specific criticism was actually about punctuation had not been clarified. But we are still at a loss here for approving this article. It has undergone, and continually keeps undergoing, changes in content since 3 editors read the content and approved it. So how can we possibly copy edit it? We don't even know anymore what the approved article is - it's a problem. Nancy Sculerati 10:07, 18 April 2007 (CDT) see [2] proof versions of articles

Shortened deadline

Ive just shortened the approval deadline till the 18th April to clear the decks of the bugs and force us to move onto more productive things. As always, if this is the wrong call I know I'll hear about it really soon. David Tribe 06:38, 17 April 2007 (CDT)

I pointed out a-another buzzin' gnat a-beggin' fer a-squashin' just above. Stephen Ewen 02:41, 18 April 2007 (CDT)

-ize words are a problem. It's often thought here that the ize form is American, but actually it's the traditional English form for most such words, though -ise is generally an accepted alternative. So following -ize or -ise should not rationally induce a phobic reaction from Brits. Go with whatever, but go with something consistent.Gareth Leng 12:23, 18 April 2007 (CDT)

OK I've just read it through and I can't see any trace of English English left, though possibly we just read through things after a while without seeing things (sigh). Just for the record, I have absolutely no objection whatsoever to replacing anything with American English. I also have no fixed opinion on the Oxford comma. Just assume I'll go with anything consistent or anything rationally inconsistent (like the Oxford comma when it makes sense). Not aluminum; I won't go with aluminum, if aluminum is mentioned I'll go and grow cabbages. Be careful though not to alter the spelling in the titles of Journal articles or in quotations. Gareth Leng 12:49, 18 April 2007 (CDT)

Not to again be stickler -- wait, I take that back -- but this still done got problems. Here's an illustrative one:

How the system behaves as it interacts with its environment determines how these components are organized, and so novel properties of the system 'emerge' that are neither in the environment or in that set of internal components.

British "scare quote" comma usage -- 'emerge' (and I have never seen this as an acceptable American style, although I have not seen all American styles, obviously) -- with American spelling -- organized. Again, me-thinks we need a staunch British English user or American English user to go through this thing top-to bottom.

Stephen Ewen 18:01, 18 April 2007 (CDT)

I use single-quotes, e.g., 'abcdef', when I want to call attention to the word within. I might call attention to a word for the purpose of mentioning the word, as in 'black' has five letters — I 'mention' the word, or 'refer' to it. On the other hand, I might call attention to a word in order to alert the reader to my use of a special word, or my special use of a word. For example, with 'emerge' in the sentence Stephen quoted, I want to alert the reader to something special in the use of 'emerge' there, which special use the sentence partially defines.

I tend to reserve double-quotes for words or phrases or sentences or paragraphs that I attribute to someone, someone the readers knows who by the context or by a source-citation. Also, double-quotes for article titles, as "Notes of a Bird-Watcher", by Robin Feathers. Book titles like On the Origin of Species I put in italics.

"Methinks the..[gentleman] doth protest too much."

Methinks him right about 'consistency'. --Anthony.Sebastian (Talk) 19:08, 18 April 2007 (CDT)

TIME AT WHICH VERSION 1.1 DEBATE ENDs

I agree with Anthony here and indeed was alerted to somethin that Wikipedia puts well. "A three-way distinction is sometimes made between normal use of a word (no quotes), referencing the concept behind the word (single quotes), and the word itself (double quotes): When discussing ‘use’, use “use”."

These are issues of ornamentation more than punctuation (we might have used bold more instead, or italics differently); they're value is only in how within the article they help to make things clear. As I look around in different fields and different media I see different conventions applied to quotes, and many more to punctuation usage. You will certainly needlessly antagonise many authors if you seek to impose a standard punctuation convention, (believe me, I have seen pages written by academics defending their use of the Oxford comma convention and complaining at the copy editors). All the guides I have seen here express very clearly that punctuation is a convention that is subject to preference and different conventions suit different purposes differently. The purpose of any punctuation is clarity, so I suggest the consideration should be whether the meaning is as clear as it can be.Gareth Leng 03:31, 19 April 2007 (CDT)

LOL, Anthony. Am I protesting too much? Perhaps indulge me a bit more. I understand what you described is something you appear to use consistently, but is it more a personal style rather than some "standard" and published style we can point to, like Chicago and what-not?--homemade style seems the worst possible "manual of style" for an encyclopedia. I understand that in American English, the only legitimate use of single quotes is for quotes within quotes:

As Sneedmyer contends, "Someone wise once said that, when writing, we should 'choose a style that is standard' and 'be consistent with it' throughout."

Do we all realize how much librarians will freak out when they read articles with apparently inconsistent or personal style?

At any rate, to me what this issue most highlights is that CZ needs to come up with a single yet simple manual of style in these particular regards.

--Stephen Ewen 03:42, 19 April 2007 (CDT)

Question about sentence in 'Cells' section

The last sentence of the third-to-last paragraph of 'Cells' reads:

In the human genome, about 22,000 different genes guide the production of hundreds of thousands of different proteins.

In checking the webpage cited, however, I see no reference to "the production of hundreds of thousands of different proteins". Also, I do not know what "different" means in that context. Readers might wonder how 22,000 genes produce >100,000 'different' proteins.

Perhaps the citation should relocate to follow word 'genes'.

Can someone fix the aberrancy of my thinking. --Anthony.Sebastian (Talk) 18:32, 18 April 2007 (CDT)

Nothing aberrant. Originally there was no cite at all so I added one for the 22,000 figure since that is somewhat controversial. Actually i did not notice the hundred of thousands of proteins first time around (hence not in the cite). First, i assume we are talking about primary sequence in this context. If so, is there really that much alternative splicing? I think hundreds of thousands should be changed. Possibly "upto one hundred thousand" proteins. Personally i would not count postranslational modifications in the final tally for independant proteins but that type of accounting might be how such a huge figure for the proteins came about (I'd also exclude antibodies from this final figure since those are transcribed from highly specialized cells wit specific geneomic rearrangements). Hope this helps. Certainly i would relocate the cite for now. Probably there is a better cite with the current gene and protein estimates. Chris Day (talk) 18:56, 18 April 2007 (CDT)

Chris, in response to your comments, I re-wrote the sentence as follows:

In the human genome, perhaps as few as 22,000 different protein-coding genes guide the production of the variety and quantity of protein molecules sufficient to scaffold the structures and functions of a cell.

Change it as you see fit. We can always edit it further when we get a better citation for cellular protein counts. --Anthony.Sebastian (Talk) 22:13, 18 April 2007 (CDT)

I see the point; the alternative splicers around me would I think go with Chris, as they are thinking of mRNA. But for me, any example of a protein in a cell that comes to mind is the result of some translational processing. (We talk about the vasopressin gene, but the product is a prohormone cleaved to produce vasopressin, neurophysin and a signal protein.; POMC yields at least eight biologically active signalling molecules including alpha MSH, and beta endorphin that arise by differential processing), In other words when you're talking about "the protein molecules that scaffold the structures and functions of a cell, I think you are indeed talking about the posttranslational products, not the precursors.Gareth Leng 02:46, 19 April 2007 (CDT)

My memory tells me the number of proteins is several fold the number of genes , say around 100,000. I can check it easily but Im a bit tired now after a long day. David Tribe 05:19, 19 April 2007 (CDT)

Every antibody is a different protein, not a different type of protein, but a different protein none the less. What matters is what's there, the proteins that exist in a living thing, not how it got there (or how they got there)- so, of course post-translational processing counts. Nancy Sculerati 06:22, 19 April 2007 (CDT)

There are several different things to consider here and it means we need to be careful to define our terms or get a good reference (which will define the terms for us). So how are do biologists define separate proteins with respect to the central dogma? We all agree that alternative splicing will lead to different proteins from the same gene. It is the pesky post-translational products that are the problem.

Processing will allow different proteins to be formed from the same primary sequence. There are many examples, as Gareth pointed out above. But do we include all of these as separate proteins? When processing is required for the maturation we do not count it as two proteins. Examples of this are proteins with cleaved import sequences and I would also include examples of processing to activate in this category. I think this latter one is debatable and I'm not sure how the proteomics experts categorize these different forms.

Antibodies are a more complicated debate. If each antibody counts as a distinct protein, and they clearly are, then any numbers for the gene to protein count becomes irrelevant because the number of potentially different proteins from one antibody gene alone is hundreds of thousands. Does anyone know how many distinct antibodies are present in a typical human?

In summary, it does not really matter what of the above we count, as long as it is clear to the reader what is being counted. For this reason we need to get a good reference that discusses these issues. Chris Day (talk) 10:01, 19 April 2007 (CDT)

I had a quick look at the human proteome project page. They are talking about the transcriptome (100,000) and the proteome (1,000,000).[3] This might be a useful link rather than an article since it articlulates the problem well and will presumabaly updated frequently. Chris Day (talk) 11:41, 19 April 2007 (CDT)

Following Chris's lead:

To do justice to the number of possible different protein structures in a living cell, one would essentially have to discuss the alternative spicing and post-translation modification mechanisms involved in producing them according to the details, for example, Figure 1 in:

• Norregaard Jensen O. (2004) Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Current Opinion in Chemical Biology 8:33-41

We can't just introduce alternative spicing and post-translation modification mechanisms out-of-the-blue. Shouldn't we leave any such technical molecular biology discussion for the appropriate article? Seems that level of technically not needed for the Life article.

Suggest we change:

“All cells inherit digitally stored information in the form of molecules of DNA, and with minor exceptions the DNA of all use the same universal genetic code to guide production of thousands of different protein types, manufactured by tiny organelles called ribosomes. Cells use those various proteins to carry out diverse activities, including energy processing and conversion of carbon, nitrogen and phosphorous-containing materials into cellular structures. In the human genome, perhaps as few as 22,000 different protein-coding genes guide the production of the variety and quantity of protein molecules sufficient to scaffold the structures and functions of a cell.”

to:

"All cells inherit digitally stored information in the form of molecules of DNA, and with minor exceptions the DNA of all cells use the same universal genetic code to guide production of a myriad of distinct protein structures. Cells use those proteins to carry out diverse activities, including energy processing and conversion of carbon, nitrogen and phosphorous-containing materials into cellular structures. In the human genome, perhaps as few as 22,000 different protein-coding genes lead to the production of perhaps more than a million distinct protein structures that make up the variety and quantity of protein molecules needed for the structures and functions of a cell. Numerous molecular mechanisms account for that quantitative gene-to-protein amplification. --Anthony.Sebastian (Talk) 17:14, 20 April 2007 (CDT)

Style, my recent edits

OK, I've looked through this again after reading Stephen and Anthony. I have tried to apply Anthony's convention in cases where I thought it was absent, and in the process for instance put book titles consistently in italics. I have also tried to reduce the burden of scare quotes, using them as Anthony wants but s little more sparingly where I fett they might be more a distraction than a help. I found inconsistencies in reference style, some spelling mistakes, and a couple of areas where the meaning was not at all clear. My intent with the quotes edits was not to impose my preferences but to a) reduce the burden of any future changes and to remove apparent inconsistencies with the major current use. Not saying I've seen them all.

Yes a CZ style guide is needed, but one that is pragmatically liberal, and shortGareth Leng 06:37, 19 April 2007 (CDT)

chasing our tail (while spinning our wheels at the same time)

Halting a version for proofing while immediately generating a draft version allows us complete freedom. The creative author (Dr. Sebastian, I presume? ;) ) can keep right on writing in the pursuit of the great article, the copyediters and spell checkers, and Editors who need to smooth out the last idea inserted- that was agreed on in principle- can focus on refining the stable version- ONLY refining. Or, from what seems to be suggested in the forums, we can scratch the whole thing and have no stable versioning - except for "medical" articles.[ http://forum.citizendium.org/index.php/topic,831.15.htm]l Of course, to me anyway, that is the whole draw of Citizendium- that there are reliable versions that are not undergoing major construction at any given time. Are we undermining the entire approval process by our inability to work together here? Coming to terms with the Big Ideas in a collaborative process- now that will always be daunting - and rewarding. But coming up with a proofed copy of an approved article for the wiki? That should be trivial. Why is it so hard? Why can't we have a simple step by step process for that? Nancy Sculerati 07:39, 19 April 2007 (CDT)

Oh I agree Nancy. Trouble is we don't have professional copy editors here and believe me it's a tough job; I recruited those for the Journal of Physiology and worked with them extensively at one time, it's very time consuming to get details right, and virtually impossible to do so while at the same time looking at the meaning. I just don't think we can afford to worry excessively about this, at this stage it's a luxury, when we need to encourage the content givers.Gareth Leng 09:56, 19 April 2007 (CDT)

So just freeze the approved article, and let an editor, such as David Tribe, fix the mistakes using his very own sysop powers. A real editor is better than a copy editor, anyway, and a real editor can work with others to make sure the grammer and punctuation are correct English, without losing accuracy of content. When he is done, he announces-I'm done! and we all review it. The moment the approved article was frozen, a draft was generated and those who want to keep writing do not have to wait days or even hours to do so. At that same moment, the editor (David Tribe) in my example, is refining the approved version. The only problem with that is "our rules" against letting an editor use sysop privileges to edit an approved version. It's a stupid rule that demeans the honor of editors and our ability to work. If we could do that, which WAS done (in essence) with the very first biology approval, we would have no problem. Nancy Sculerati 11:50, 19 April 2007 (CDT)

We have such a rule? I must have missed that discussion. In the early days i remember DT copy editing the approved version. Was this rule in response to him doing that? I'd be happy for copy editing to the approved version as long as the edits are also made to the draft version for continuity. Chris Day (talk) 12:02, 19 April 2007 (CDT)

I suggest you bring this up, on the forums and on Larry Sanger's talk page. There is a general rule that editors who are constables should NOT use their powers as constables to work on content (editorial) issues. Nancy Sculerati 12:04, 19 April 2007 (CDT)

Nancy, regarding "Of course, to me anyway, that is the whole draw of Citizendium- that there are reliable versions that are not undergoing major construction at any given time." I would say not 'reliable' versions but 'approved' versions. And it seems to me 'major reconstruction' prejudices the issue. I prefer 'revising to improve quality'. Textbook chapters come out revised in new editions, but one has to wait, and then one still finds the material out-of-date. With CZ, one gets faster turnover, possibly more up-to-date material.

How can we have a 'proof' version undergoing copy-editing, and a 'draft' version undergoing content and clarity/coherence revision. How would the edits of the former get into the latter?

Suggest do not nominate for approval until ready for approval except for correcting solecisms, then allow two days for correcting solecisms, so we don't lose our momentum for improving the draft. The approval tag encourages working on the draft to improve the article. Let's not tie writers' hands: "Stop working on the piece for a week, while we clean up the bugs." --Anthony.Sebastian (Talk) 14:51, 19 April 2007 (CDT)

Cell types??

200 different cell types??? Nah. Depends what you call a cell type. You only get this kind of number by calling, for example, neurons a single cell type. I can probably count more than 200 neuron types without pausing for breath.Gareth Leng 11:44, 19 April 2007 (CDT)

All comes down to definition again. I use ~200 cell types in my intro lectures. And aren't all neurons the same sort of thing? The're just a fancy specialised way of integrating signals. Some organisms (plants) do fine without them!  ;) Chris Day (talk) 12:05, 19 April 2007 (CDT)

Reminds me of a rather nasty code phrase for a clinic patient so thick that patient education requires the establishment of a new art form- "yeah" says the doc," he's running on 2 Betz cells held together by a spirochete". (or she)- combined with the assessment of "an IQ just above plant life". Nancy Sculerati 12:11, 19 April 2007 (CDT) (the preceding are two examples of why we physicians are so loved by the general public. Except, of course, Dr. House, the TV doctor, who talks just that way and really is loved by the general public. Go figure.

Gareth and Nancy: Perhaps we can resolve the issue by qualifying the we mean ‘cell types’ based on the findings of histologists who study microscopic anatomy, not cell function or genotype. From Valentine et al.’s paper, where I got the ~200 number:

”As development proceeds in a metazoan, then, cells differentiate in a pattern that is controlled through an interplay of genetic and epigenetic processes. Different genes are expressed (or are expressed at different times or in different doses) in different cells to give rise to a number of distinctive cell phenotypes—the cell types with which we are concerned here. Many cells that have very similar phenotypes, and would be classified as the same cell type, have nevertheless been subjected to different control signals and have had distinctive transcriptional histories, so that precisely the same genes are not necessarily expressed in all members of a given cell type population (see Davidson 1990). Thus, in using the level of the cell type to infer complexity we are indisputably lumping cells that have biochemical and no doubt functional differences. As we are not in fact attempting to measure complexity itself, but are using cell type numbers simply as an index of complexity, this may not present a major problem so long as there is a standard degree of lumping and splitting of cell types to permit a practical ordering of complexity among organisms with different body plans….Histologists have made few estimates of the total cell type numbers of organisms, but they have established a tradition of describing cell phenotypes that has permitted comparative histological studies that have added much to our understanding of comparative anatomy and physiology. Systematists and developmental biologists, interested in the evolution of differentiation and complexity, have been able to draw upon this histological literature to estimate cell type numbers for a variety of organisms across a number of phyla.”

So, yes, Gareth, depends on what one calls a 'cell type'. So we should qualify our use, eliminate the number, or deal with the large variety of functional cell phenotypes, even among cells with the same gene expression pattern. --Anthony.Sebastian (Talk) 22:42, 19 April 2007 (CDT)

Focus on reapproval

We have been going some time without achieving version 1.1 approval. It's rather difficult for constables to interpret the commentary here, but as far as I can see, there is no obvious reason for withholding approval, and it would be good to focus editor energies right now on communicating the article's status unambiguously to the constables.

Can I ask whether anyone has any reservation about the last edited version? I note cell number remarks are referenced by the Valentine ref, and the protein numbers issue is now now referenced fully. Please be explicit in your responses because are energies are really needed elsewhere I'd say. Please act quickly to provide signatures and remarks to resolve the confusion caused by talk debate.David Tribe 01:59, 21 April 2007 (CDT)

Status is good. Approve it. Thanks for incorporating the protein number clarification and reference. Chris Day (talk) 03:13, 21 April 2007 (CDT)

Thanks Chris. Subsequent to placing this call I have worked out that legally we had a valid approved V 1.1 when April 19th passed. Subsequent arguments are irrelevant to its legality.

• This is it

But one additional signature will make this protein amendment

• this one with protein number refs and link

absolutely legal too, so it will make worth while the extra huffing and puffing of the last few days Either way we have a legal revision. either (1) The text as it stood at midnight 18 April, or (2) the best one as of now 03:29, 21 April 2007 (CDT) provided we get one more signature. David Tribe 03:29, 21 April 2007 (CDT)

David, now I'm confused. The one you link above is from the 17th April not the 19th. Chris Day (talk) 04:06, 21 April 2007 (CDT)

Chris It's deliberately from that date, the 17th, to ensure that it is a version that is legally approved by three editors. the later date might be argued to have not been approved at the time the deadline passed. You are thinking like a scientist, that is sensibly, pragmatically, trying to do things so they make sense, trying to make real progress, this is legaleses and legalistic stuff. I know it is stupid, that's the point. We need to fix the legal morass so we don't waste these days and days over nothing. At the moment the rules don't make it clear that editors are empowered to fix typos quickly. Out this jumble of opinion will emerge a clean solution. All we need to do is show clearly that we have a mess that needs a fix, and work together to ensure the fix operates.David Tribe 13:01, 21 April 2007 (CDT)

Approve it, David can work with sysop edit privileges to make sure that the approved version is letter perfect. If we are unhappy with what appears to be a mistake, we can tell him and allow him to edit the approved version accordingly. We do not have to go through the entire approval process for every typo if we agree that its ok for a constable to fix the typo. Please approve the linked version. Nancy Sculerati 08:22, 21 April 2007 (CDT)

If any book to be published depends on the lack of ONE single typo I really wonder how many great books and articles would have appeared throughout all of history. Typoes are only minor aspects of any document/article/novel - unless one is into the really ultra-details it seems a waste of time doing so. In short I second Nancy. Robert Tito |  Talk  12:40, 21 April 2007 (CDT)

Lessons from approval discussions

Can I attempt to make some points about being more efficient about copy edit type approvals?

This is just an opinion to diagnose whats going wrong. It assumes that any system that takes weeks to implement a few error corrections is totally unsuitable for the wiki we aspire to be, with hundreds of articles going through approval.

Whats going wrong?

The way I see it, one issue is editors need to understand better where the constables are placed. Perhaps the Approval area can be used more effectively to communicate with the constables.

We should make sure we clearly communicate there the last draft version to which editors have given their legal approval. Adding on extra discussion about additional points effectively voids an approval if it doesn't also include statements to the effect that version of 17th has changes are all ok by me but maybe we can add xx to improve it. What we need is a ratchet to catch the improvements before they are polluted with crud.

Any debate about the worthiness of the additions is seen as disagreement with a back-log of its copyedits that are actually ok. The context is that Larry Sanger may well be citing Life as an explicit example of a great CZ article and of the fantastic value of our approval process in a manuscript about to be published while we are needlessly holding up a batch of essential error corrections on an article that may well be visited by thousands of sceptical pairs of eyes. This is very unfortunate. We still havn't action essential corrections days past a deadline after reams of well intentioned discussion. Action would have been more valuable for CZ.

There are several solutions I can envisage (which have been the reason for my editorial inputs such as they are): 1) focus on completing the first ~95% of copy-editing revision on time to some reasonable deadline.

2) Implement as many clear cut error corrections as possible in this phase, but don't hold up the correction the first 95 percent for weeks by wait for the last 1% to be decided or for the resolution of scholastic fine points, or by re-writing key sentences to change the content. These scholastic points can easily be fixed in Version 1.2 which can follow in 24 hours.

3) Explicitly define the last stage in the edit history that all editor accept as only containing valid edits. Get the editors to sign-off on it. Create a URL pointer in the approval area linking to it called

The copy-edit ratchet.

• Last supported good copy-edited revision here URL LINK HERE

Get three editor signatures under it pronto

4) This ratchet can be updated, but but not invalidated by later changes. The editors can thus point constables to it and constables can action them.

5) Be disciplined in the talk pages during this period and make it clear to the constables what they can act on.

In my own opinion, it would be much more efficient to charge a knowledgeable editor to implement the approval and to have them use sysop privileges to make needed error correction, but for the moment we are stuck with a cumbersome system where constables basically unfamiliar with the topic are given the hard task of making decisions. This situation is what we are currently stuck with but can change if we diagnose its ills accurately. It's been in action with Biology and Biology/Draft, Life and Life/draft and has largely been responsible for huge talk archives and slow changes to the text. I remain unimpressed with it as a standard operating procedure (British irony). I still think we should change it, and try and explain to those who are not familiar with the nitty gritty of these approval why citizendium needs to do better. I'm talking about it only to try and make the nature of the problem clearer, not to add to our challenges. Fortunately during it we cleaned up a few unobvious and tangible scholastic weaknesses, and Gareth and others have done super copyediting. David Tribe 19:34, 21 April 2007 (CDT)

APPROVED Version 1.1

Congratulations once again. Re-approval complete.

Discussion for Version 1.1 stopped here. Please continue further discussion under this break.

Strategies and lessons for further approvals

My 4cents worth.

Understanding how constables operate

SUMMARY: TELL EM IN BLACK AND WHITE ONLY WHAT THEY MUST KNOW and all THEY MUST KNOW TO ACTION AN APPROVAL. RESERVE THE APPROVAL BOX FOR THIS. KEEP IT DIRECT AND SIMPLE. ie YES, editor 1, YES Editor 2, Yes Editor 3, URL here. DEADLINE IS EXPIRED WITH CONSENSUS.

Approved version 1.1 shows in my view, that the citizendium copy-editing environment is almost unmanageable, and certainly time wasting. I personally apologise to the other authors and editors for the restrictions my efforts to manage this unwieldy system have placed on their contributions. I was expecting the process to take place much more quickly.

Holding up edits of substance to allow copy-editing is only acceptable if that copy editing is done quickly and efficiently. This is not being achieved, and it is unfair on authors to subject them to such constraints for more than a minimum time period. I'm pessimistic about forum discussions solving this, but hopeful that we can get the biology editors to develop a solution in terms of agreed informal biology standard approval practices to save us all the time wasting over trivia. One of the powers we have is editor consensus and familiarity with the science and we should use it to control the legal impositions that are currently, in my view, strangling performance.

Some new problems are emerging. Before this approval event I had assumed agreement of three editors was enough to provide assurance that an unambiguous decision to approve can be put to the constables.

But new issues such as proof that silent editors are in agreement, and the possibility of one editor being a dissenter being enough to derail approvals are now being raised in discussions (see above), and these threaten to make it impossible for editors to tell a constable that the article is ready. What do others think about this gloomy assessment? I want explicit confirmation that these complications will not derail copy-editing.

In my view, these possibilities threaten to render our already cumbersome process completely unworkable, and we must try and alert other editors and authors to the urgent need for a solution to this process confusion.

I think we must tackle the copy editing issue first as it's simpler. All of the science issues raised were completely (ie cell types a protein numbers) uncontroversial and authors were only grappling with the best form of words and the best sources to cite, but it seems that healthy editorial interaction was interpreted as dissent, when it was not, in my opinion - just routine editorial work. If there was real dissent about an issue of weight, that's a different matter.

To finish for now , we just need to get organised, and treat the constable as an unknowing legal robot who does as he's told. This is OK. Constables want a simple routine job. They do not like legal head-aches. For them, all they need is editor YES YES YES , and signatures. We (the editors) just have to understand how a robot can be made to do tricks. We need to craft and use the rules to make rapid progress, and make those legalistic robots zip through the approvals.(Give them a bone and a pat if they do the job quickly) For this I think it would be good if we put all the stuff constables need to know about an approval decision in the approval area, and state explicitly to ignore discussions on the talk page itself. i.e keep it very simple and clearcut. David Tribe 04:06, 22 April 2007 (CDT)