Talk:Life/Archive 1

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Contents

Formating decisions

Citation style as per Help:Citation style David Tribe 01:25, 5 February 2007 (CST)

Other style standards?


General copy discussion

In response to Larry Sanger's request, let's go about rewriting this article. For the purposes of the article, I suggest that we take the meaning of life to be equivalent to living things, and the opposite of death, and also of inanimate things or objects. Some points to cover: (1) features of living things v. inanimate things,(2) definition of death - when is something alive no longer alive? (3) which organic molecule collections have life? which don't? why? Nancy Sculerati MD 17:38, 30 December 2006 (CST)

  • I note David Tribe working on this article. I added a subsection "Linguistic Considerations Relating to the Definition of Life". I may presume too much in this case, but it does speak to Nancy Sculerati's suggestion to "...take the meaning of life to be equivalent to living things...". Happy to delete or put somewhere else in article or elsewhere. --Anthony.Sebastian (Talk) 16:49, 3 February 2007 (CST)
  • I also re-wrote the first paragraph of the Introduction, to provide a generalization that could set the stage for describing what we know about the common characteristics of living things. --Anthony.Sebastian (Talk) 19:11, 3 February 2007 (CST)

Thermodynamics

The intro is massive and should probably be much smaller. I usually consider them more like an abstact than an intro commmonly seen in academic papers. One way around this is to move most of the thermodynamic perspectives into a new section. Chris Day (Talk) 02:01, 5 February 2007 (CST)

  • Chris: Will take your suggestion and try additional tacks to shorten Intro. Thanks. --Anthony.Sebastian (Talk) 19:25, 5 February 2007 (CST)
  • Chris: Shortened Intro, moved thermodynamic perspective to separate section. --Anthony.Sebastian (Talk) 14:34, 13 February 2007 (CST)

Re-writing per Larry's Request

I have undertaken to re-write this article from the beginning, responding to suggestions along the way. I have re-written the following sections/subsections:

  • Introduction
  • Shared Characteristics of Living Things: Systems and Thermodynamic Perspectives
  • Some Definitions of Life Resonating with the Preceding Exposition
  • Other Shared Characteristics of Living Things
  • Life Further Characterized (partial)

I will try to come to an intermediate closure soon, so the workgroup can consider the article for approval--with the idea that, like Biology, refinements and amplifications will find their way in.

--Anthony.Sebastian (Talk) 17:43, 12 February 2007 (CST)

Seeking opinions on what to change or further develop in this article

Taking this article in its current draft, what would others, in particular the Biology Group, like to see further developed or modified. I have much more in mind for this article, but would like to consider the practicality of getting out a draft that qualifies for consideration of approval. --Anthony.Sebastian (Talk) 14:31, 13 February 2007 (CST)


I struggled a bit with this article. I had several reservations, but I think my biggest problem was that this article has this exciting theme and somehow seems to reduce the grand question to almost pedantic considerations of definition.I really only saw the point at all when I came to Mayr's words.

  • Gareth: I agree about the impact of Mayr's words. I will move that section up front. Anthony.Sebastian (Talk) 22:33, 14 February 2007 (CST)
  • Gareth: In moving the Mayr Section up front, we make the point Mayr makes about terminology, echo it with other luminaries, then go on to the science. I feel we really need to educate about the misguided and misleading practice of turning processes and activities into 'things'. Anthony.Sebastian (Talk) 12:38, 18 February 2007 (CST)

I think the point is that the simplest living biological system is incredibly complicated, and explaining why they have to be so complicated (machinery for all the processes of living; sensing the environment, feeding, reproduction etc) and what that entails (simplest cell needs ? can't remember, is it 8000 genes?). I guess the question that that begs is how did life originate? It seems to me that is one possible direction for this article.

  • Genes can't serve, because genes don't code for interactions, much less co-ordinated dynamical and hierarchical interactions. Hence need a systems science. Anthony.Sebastian (Talk) 22:33, 14 February 2007 (CST)

Another possible direction would be to talk of the diversity of life, and to explain those elements that were so important for diversification. I think you need to carefully check the text, not all cells have the machinery to reproduce themselves for example (think red blood cells).

I have the flu now, I guess I was expecting some discussion of viruses and life, and a discussion that persuaded me that the question of what counts as living is an interesting question, not a dictionary question. Gareth Leng 05:17, 14 February 2007 (CST)

OK, I think each of these statements is false:

  • all cells have an inherited "blueprint" for constructing its components, and mechanisms for carrying out the construction;

No. Red blood cells dont have a nucleus or DNA. Sperm and ova don't have a full blueprint. Many differentiated cells are not able to reproduce themselves.

  • all cells have the capability to assemble and organize themselves from more rudimentary states;

No, just not true, animal cells need a multicellular environment in order to express their developmental fate

  • all cells and multicellular systems exist interdependently with other cells and multicellular systems;

does this mean anything?

  • all cells and multicellular systems eventually die. I'm not sure that there is any (non trivial) reason why many organisms (fungal organisms) must dieGareth Leng 10:02, 14 February 2007 (CST)

Fascinating work so far, but don't you think there are rather too many lists to be maximally readable? --Larry Sanger 16:13, 15 February 2007 (CST)

  • Larry: Will consider. Off the top: lists sem to make otherwise paragraphed complex topics more readable. But will re-examine. Anthony.Sebastian (Talk) 23:02, 16 February 2007 (CST)
  • Larry: Moved one section with a long list to an Appendix. Anthony.Sebastian (Talk) 12:32, 18 February 2007 (CST)

Opening

Anthony, I think the article could gain from a simpler opening few sentences. cheers David Tribe 03:49, 27 February 2007 (CST)

Title

Just a passing comment, very probably not a new thought here. I think this article should be re-titled life (biology) to distinguish from any future article such as life (philosophy)(?) and Life (magazine). Stephen Ewen 16:10, 1 March 2007 (CST)

Stephen: Yes, 'life' has many senses. But everyone will take unqualified 'life' in its biological sense. Typically, as new 'life' articles appear, a header will announce the present article as distinguishable from Life (magazine) etc. I think the other 'life' articles should qualify 'life' in their titles, leaving biological 'life' unqualified. If qualification deemed necessary, I'd suggest 'Life, or Living Systems' as title. Not sure how to format. Thanks for the thought. Hopefully others will comment. --Anthony.Sebastian (Talk) 22:04, 1 March 2007 (CST)
When I saw the article title in recent changes for the first time, my first impression was its philosophical sense - why, how, meaning, mystery, etc. Stephen Ewen 23:41, 1 March 2007 (CST)

Anthony, this article is very erudite and becoming very interesting. I've tried to simplify the text in places, I hope without losing anything, but please revert anything without hesitation.

I think I would favour changing some of the lists into prose.

The scope of the topic is of course vast and you have to select some path through, and I can see many possible very different articles on this theme. I think things that come to mind are, in chemistry, the division between organic and inorganic, and in biology, the concept of a vital spark - and maybe Frankenstein.Gareth Leng 04:40, 9 March 2007 (CST)

I cut this out: "Interestingly, in English, according to the Oxford English Dictionary, the verb 'to live' preceded usage of the noun 'life' by some 300 years." not because I don't find it interesting, it's the kind of aside I always like, but because this is about the written use of the word, we know nothing of its spoken use. ???Gareth Leng 04:59, 9 March 2007 (CST)

Gareth: Thank you for 'erudite'. I trust you refer to the content as scholarly. I have tried hard to keep the text as unambiguous as possible, to facilitate its accessibility. I appreciate you help in 'simplifying' the text, especially the consolidations.
I would like you to know some things about my writing style:
  • Whenever possible, I try to avoid using the verb 'to be' and its declensions (e.g., is, are, was, etc.). I do that mainly because I consider them weak verbs that give the sentences no force, or dynamism, or strength--the result of taking the easy way out. I prefer to find an active verb, a legitimate one or sometimes a coined one whose meaning the context makes clear. The more active verbs in a piece, the more dynamic the text gets, as I see it. In many instances, you change the verbs I used to the weaker 'to be' versions, and I don't quite see why. I think 'to simplify'. But if so, I feel we should not support that mode of 'simplicity', which one might interpret as 'dumbing down'.
  • Another reason I try to avoid 'to be' forms: They often seem dogmatic and at the same time in reality only state a partial truth. For example: "Plants are living things". But if one posits what plants 'are', one must have a longer list of the identities of plants, much longer. Depending on context, one can write more specifically. For example, in the context of the discussion of 'semantic primes', I would write: "Plants define as living things". In a context of exemplifying living things, I would write: "Plants qualify as living things". Of course, 'are' works both places, but then you lose the richer and more specifying 'define' and 'qualify'.
  • Another reason I try to avoid 'to be' forms: They often encourage using the passive voice, which often submerges the subject or agent, and tends to dull the writing.
I do not follow that standard as a 'purist' would. "To be"s have their place in my writing, but I use them sparingly. Nevertheless, I would not try to dissuade you from re-writing my sentences with 'to be' verbs, as it often forces me to rethink the sentence to find an active verb that will strike you as apposite.
Regarding your suggestion to convert lists to prose: I prefer to use lists to reduce the density of the prose. They encapsulate the messages, making it easier for the reader to get the messages and take them home with her. I plan to write a short essay: "Ten reasons for using lists in CZ articles." As time permits.
Regarding your: "I cut this out: "Interestingly, in English, according to the Oxford English Dictionary, the verb 'to live' preceded usage of the noun 'life' by some 300 years." not because I don't find it interesting, it's the kind of aside I always like, but because this is about the written use of the word, we know nothing of its spoken use."
Indisputable. I have read two histories of the making of the OED. It would surprise me if English speakers spoke the word 'life' during the 300 years in which we can feel certain they spoke 'live', yet 'live' but not 'life' found its way into writings. Knowing how OED combed the literature, not finding 'life' suggests the English didn't use the word. Still, I only try to justify, and have no real problem bdropping the sentence. --Anthony.Sebastian (Talk) 13:49, 9 March 2007 (CST)
Regarding your: "The scope of the topic is of course vast and you have to select some path through, and I can see many possible very different articles on this theme. I think things that come to mind are, in chemistry, the division between organic and inorganic, and in biology, the concept of a vital spark - and maybe Frankenstein."
I totally agree. Right now I focus my thinking on the various perspectives scientists have on what fundamentally constitutes a living system--hoping in the end to generate a synthesis. That accomplished, much else needs consideration.--Anthony.Sebastian (Talk) 13:58, 9 March 2007 (CST)

Ambiguity

"Species populations tend to grow as resources and other factors permit." Do you mean increase here or growth in body mass?Gareth Leng 05:07, 12 March 2007 (CDT)

Thanks, Gareth, for catching that ambiguity. I changed the sentence to read"
"Species tend to grow in numbers of individuals as resources and other factors permit."

--Anthony.Sebastian (Talk) 21:57, 12 March 2007 (CDT)

Pictures

PLoS biology 234x60.GIF
Tynagh Chimneys.jpg SynechococcusPhageS PM2.gif
Sperm Entry.jpg

Top left; Tynagh Chimneys, A view from above a chimney field, showing the chimneys (round black circles) and bubbles, which contain chambers. The object placed for scale is two centimeters across. These fossil chimneys were formed well after life's origin, but may be similar to those in which, according to one hypothesis, metabolism first began

From: Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks Robinson R PLoS Biology Vol. 3, No. 11, e396 doi:10.1371/journal.pbio.0030396

Top right; A Transmission Electron Microscope Image of the Synechococcus Phage S-PM2 (Image: Hans-Wolfgang Ackermann)

From: The Third Age of Phage Mann NH PLoS Biology Vol. 3, No. 5, e182 doi:10.1371/journal.pbio.0030182

Bottom left; The first polar body (the smaller cell atop the oocyte) deforms the mammalian egg away from its encapsulating zona pellucida, creating a gap.

From: The Ins and Outs of Sperm Entry Chanut F PLoS Biology Vol. 4, No. 5, e160 doi:10.1371/journal.pbio.0040160
PLoS biology 234x60.GIF
Lamellibrachia luymesi.jpg

A) Close-up photograph of the symbiotic vestimentiferan tubeworm Lamellibrachia luymesi from a cold seep at 550 m depth in the Gulf of Mexico. The tubes of the worms are stained with a blue chitin stain to determine their growth rates. Approximately 14 mo of growth is shown by the staining here. (Photo: Charles Fisher) (B) Close-up photograph of the base of an aggregation of the symbiotic vestimentiferan tubeworm L. luymesi from a cold seep at 550 m depth in the Gulf of Mexico. Also shown in the sediments around the base are orange bacterial mats of the sulfide-oxidizing bacteria Beggiotoa spp. and empty shells of various clams and snails, which are also common inhabitants of the seeps. (Photo: Ian MacDonald)

From: Microfauna–Macrofauna Interaction in the Seafloor: Lessons from the Tubeworm Boetius A PLoS Biology Vol. 3, No. 3, e102 doi:10.1371/journal.pbio.0030102

This section is designed to discuss if / which pictures should go in this article. -Tom Kelly (Talk) 18:26, 12 March 2007 (CDT)

Tom, I hope several. Suggestions? --Anthony.Sebastian (Talk) 21:58, 12 March 2007 (CDT)
Here i three images i just uploaded from PLOS. Maybe one of these will be useful? Chris Day (Talk) 14:36, 13 March 2007 (CDT)
A picture of a baby human or baby animals? maybe just postpartum? What about an egg that is hatching... like a chick poking it's beak/head through.-Tom Kelly (Talk) 18:49, 13 March 2007 (CDT)


Love all the pictures Chris. When thinking about this I wondered about an image of sperm fertilising an egg as the instant of conception of a new life. This led me to wonder -Anthony, in what sense, if any, is a single spermatazoa alive? This goes back to the question I think of whether viruses are living.....Gareth Leng 12:21, 16 March 2007 (CDT)

Glad you like the pictures. With regard to sperm, I'd say it is definitely alive. In seedless plants there are alternating generations between sporophyte and gametophyte. They represent the diploid and haploid stages. Sperm are just highly specialised. Chris Day (Talk) 14:11, 16 March 2007 (CDT)
Off the top thoughts about spermatozoa: Whether a "living system", I'd say yes, as qualified as motile bacteria, from thermodynamic perspective. Different way of reproducing itself than motile bacteria, through its parent's progeny's meiotic activity. But reproduce it does, and with meiotic cross-over variation, as in its parent's progeny. Not a lifestyle for viruses: not generated from an organism's own cells on its own behalf, has to hijack the organism's cells; no internal organization functioning to keep its organization far-from-equilibrium. Not so for a spermatozoon. --Anthony.Sebastian (Talk) 18:57, 16 March 2007 (CDT)

Prions

In the exceptions section it states that prions 'reproduce'. I am wondering if this is an accurate statement? It would seem that it is the cell that is reproducing the prion as a normal part of its program. This is unlike a virus where the cell is co-opted to reproduce virus specific proteins, DNA and RNA. There is no doubt that the prion can catalyse a conformation change in the cells own version of the protein but is this reproduction in the biological sense? Chris Day (Talk) 22:31, 12 March 2007 (CDT)

I agree, and will remove statement. Need more knowledge of prions. --Anthony.Sebastian (Talk) 23:10, 12 March 2007 (CDT)

Tough decisions time?

This article is clearly maturing towards Approval. It is already long (47kB) and short of illustrations, so some decisions should be made about where to cut or seek to edit tightly. My personal suggestion would be to remove the Mentionables (essentially a recapitulation and out of tune with a flowing scholarly essay) and the Appendix (don't really think it adds much), and edit the new section on information processing quite hard (for example the opening, that talks of the information gained from biology, perhaps sets the reader off on the wrong track. It may be better to plunge straight into the meaning of information).

Comments?Gareth Leng 08:09, 13 March 2007 (CDT)

(BTW Just to explain my last edit - I looked at that sentence because it lacked a verb, then felt that it was very tough to follow - then wondered if it was needed at all.Gareth Leng 08:14, 13 March 2007 (CDT))

Gareth:
  • I had hoped to remove the "Mentionables" section, after making sure the article covers each concept explicitly. I'll work on that soon.
  • I suggest we not worry too much about length in this case, as 'life' is a truly major topic. We should try for some degree of comprehensiveness, try to make it standard source. (I'll check 'life' articles in other sources (Britannica, Columbia, Encarta, Stanford, etc. Have avoided that to facilitate developing an innovative approach.)
  • I will try to shorten the "Information" section. Nobody really seems to know the meaning of information, or at least not everyone agrees on a definition. I really did not want to get into 'Shannon' information explicitly. Nevertheless I will give the piece a rethink. I still want to reach the serious high school student.
  • I welcome suggestions for figures, or suggestions where to look for them. Can one request permission from publishers/authors to reproduce figures from journals/books. If so, what procedure does CZ use? Can I select figures I'd like to include and have someone at CZ administration handle the requests?
  • Re sentences with no verb: Verbs, not always necessary for sentence comprehension. As in previous sentence. Only strict prescriptivists require them.
  • I still feel the need to say a few things about 'self-organization', because I feel the 'autonomous agents' section not adequate to cover the major points. Working on that offline. Studying Per Bak's 'self-organized criticality' among other works. A 'life' article without dealing with 'self-organization' explicitly would seem grossly incomplete. I feel that hole in the article.
  • Re Appendixes: We should allow them because readers can treat them as optional, yet they do not impede the flow of the narrative. In the 'life' appendix, the quotes reverberate with the narrative, and contribute to the heuristic for learning about what constitutes 'living'.
  • I would gladly agree having the article nominated for approval, but hoped to have the rest of the week to tidy up. I'll probably want to start working on the draft version soon after approval, as I feel 'life' a critical piece for CZ.

--Anthony.Sebastian (Talk) 12:53, 13 March 2007 (CDT)

Gareth: I have compressed the article by putting 'Mentionables' in an appendix at the very end of the article, after 'References'. Easily ignored. :::--Anthony.Sebastian (Talk) 13:19, 13 March 2007 (CDT)

Consider for first-draft approval?

From one perspective, we might consider this draft for approval, pending a few tweaks, with the expectation that further refinements and new areas of interest can emerge in the next draft. I would suggest eschewing pictures for picture's sake, and seek illustrations in future drafts that coordinate appositely with the text. Thoughts? --Anthony.Sebastian (Talk) 23:39, 18 March 2007 (CDT)

From a non-scientist reader's perspective, this is simply fantastic work, all. My comments are that the glossary sub-heading definitely needs to be filled in (I had to stop and add up root words with root words a few times), and a main picture would be a marvelous addition, even if by reason of dressing. Truly impressive work! Stephen Ewen 02:23, 19 March 2007 (CDT)
Stephen: Thanks for your complimentary remarks. I plan to work on the Glossary soon. --Anthony.Sebastian (Talk) 16:46, 19 March 2007 (CDT)
BTW, Stephen: Thanks for the edits, good ones. Question: how do you code a 'dash' instead of a 'hyphen'? Can one code a short 'dash' as well as a long 'dash'? I prefer the latter for within-sentence clause separation. Where do I go to learn how to put diacriticals on letters?

A good place to go is the How to Edit CZ page. Below is a sample of what that page has to offer. Chris Day (Talk) 17:33, 19 March 2007 (CDT)

Diacritical marks:
À Á Â Ã Ä Å
Æ Ç È É Ê Ë
Ì Í Î Ï Ñ Ò
Ó Ô Õ Ö Ø Ù
Ú Û Ü ß à á
â ã ä å æ ç
è é ê ë ì í
î ï ñ ò ó ô
œ õ ö ø ù ú
û ü ÿ


À Á Â Ã Ä Å 
Æ Ç È É Ê Ë 
Ì Í Î Ï Ñ Ò 
Ó Ô Õ Ö Ø Ù 
Ú Û Ü ß à á 
â ã ä å æ ç 
è é ê ë ì í
î ï ñ ò ó ô 
œ õ ö ø ù ú 
û ü ÿ

Punctuation:
¿ ¡ §
† ‡ • – —
‹ › « »
‘ ’ “ ”


¿ ¡ § ¶
† ‡ • – —
‹ › « »
‘ ’ “ ”

Commercial symbols:
™ © ® ¢ € ¥
£ ¤


™ © ® ¢ € ¥ 
£ ¤

Greek characters:
α β γ δ ε ζ
η θ ι κ λ μ ν
ξ ο π ρ σ ς
τ υ φ χ ψ ω
Γ Δ Θ Λ Ξ Π
Σ Φ Ψ Ω


α β γ δ ε ζ 
η θ ι κ λ μ ν 
ξ ο π ρ σ ς
τ υ φ χ ψ ω
Γ Δ Θ Λ Ξ Π 
Σ Φ Ψ Ω

Thanks, David. --Anthony.Sebastian (Talk) 12:45, 20 March 2007 (CDT)

I think that, prior to approval, the article needs the close attention of an annoyingly meticulous copyeditor type, such as myself, except that I don't have time right now. I also wonder what the reasoning is for the plethora of workgroups. I don't know why any groups other than Biology and maybe Philosophy should be assigned the topic. --Larry Sanger 20:59, 20 March 2007 (CDT)

The article is remarkably detailed and appears to be quite authoritative, by the way--not that I'm in a position to be able to say so. --Larry Sanger 21:06, 20 March 2007 (CDT)

Larry: I agree the article needs a copyeditor. I hope someone can jump in soon to do that. I had to concentrate on the concepts, and try to achieve clarity and coherence, that elusive ideal. I spent most of today rewriting the section on synthesizing the various perspectives on what constitutes a living thing. If a copyeditor doesn't jump in, I'll do it myself, but other work may put it beyond launch date. --Anthony.Sebastian (Talk) 22:18, 20 March 2007 (CDT)
I started Life to learn by teaching and hope to continue that process as it self-amplifies.
I cannot remember who added the extra workgroups. I'll look closely at each and try to engage with the author/editor who added them.--Anthony.Sebastian (Talk) 22:18, 20 March 2007 (CDT)
I think that this is a great article. There are a few places though where the meaning may not be clear to readers: I know what is meant by the extract below, but I think it will confuse because intuitively the randomised sentence seems more unlikely that the ordered, not less. I've thought about how to express it rigorously but can't come u with a concise alternative I'm afraid, so I'd suggest just cutting it.

"That becomes more intuitive in thinking about sentences. Sentences carry messages; they contain information. The more random the collection of words, the less certain the message. Consider that same collection of words randomized: “More the random certain the less the collection words of message the”. The more unlikely the collection of words, the more certain the message, the more information content." Gareth Leng 05:26, 21 March 2007 (CDT)

Gareth, I agree. Try this: "That becomes more intuitive in thinking about sentences. Sentences 'convey' information. The more random the collection of words, the less certain the message. Consider that same collection of words randomized: “More the random certain the less the collection words of message the”. As a random collection of words, the preceding 'sentence' conveys no message. For that collection of words to convey a message, the words must be arranged according to rules of syntax. But there are many more different ways to arrange the words randomly than there are in arranging them according to the rules of syntax. That means that randomized collections of words are more probable than syntactical arrangements, and the latter less probable. Think of each word written on a tile and the tiles shaken in a hat. Picking the tiles out of the hat blindly and arranging them in order of selection, and repeating the process many times, will give many more non-syntactical arrangements than syntactical ones. The more improbable arrangements convey information. Information has low probability." --Anthony.Sebastian (Talk) 18:30, 21 March 2007 (CDT)
Style points; I don't think we can say that organisms subject themselves to natural selection, that implies a voluntary will.Gareth Leng 05:56, 21 March 2007 (CDT)
Gareth: Reasonable. Will try another approach. --Anthony.Sebastian (Talk) 18:30, 21 March 2007 (CDT)
Gone through with a low stringency copy edit, hope I haven't disturbed anything in the process.Gareth Leng 07:13, 21 March 2007 (CDT)
Copyediting much appreciated. You've given me the em dash — thanks. --Anthony.Sebastian (Talk) 18:30, 21 March 2007 (CDT)


OK, last three edits I've just cut small sections out as I thought that they didn't help the flow of the article. However I'll stop now and let you see what I've done and revert anything. No need to explain.Gareth Leng 09:14, 21 March 2007 (CDT)

Article flows better now. Thanks again. --Anthony.Sebastian (Talk) 18:30, 21 March 2007 (CDT)


The long quotes - while uniquely worded, would it still be better to paraphrase them or portions of them? Stephen Ewen 16:34, 21 March 2007 (CDT)
Stephen: The problem for me in those instances, I cannot do better than the quotes themselves. I pick them to fit and for emphasis. I'd like the reader to hear it from the horse's mouth — so to speak. And maybe induce them to read the original. But will keep your suggestion in mind whenever I tender a long quote. "Brevity is the soul of wit." --Anthony.Sebastian (Talk) 18:30, 21 March 2007 (CDT)

Need help with image.

Trying to incorporate Biobooks6.jpg into article Life. Lead picture. Get error. Can anyone help. --Anthony.Sebastian (Talk) 22:24, 21 March 2007 (CDT)

Problem related to server work today. Fix in progress. -- ZachPruckowski (Speak to me) 23:31, 21 March 2007 (CDT)

Appears fixed. -- ZachPruckowski (Speak to me) 23:36, 21 March 2007 (CDT)

Playing with words

What a wonderful article, Anthony! My hat is off and my hands are applauding! I find myself playing with words and hope to be helping the narrative flow, but I may be ruining things instead, despite that hope. Please revert anything I do without a second thought and if it's getting burdensome to do so, let me know. Thanks for all your efforts here. Nancy Nancy Sculerati MD 07:21, 22 March 2007 (CDT)

Thanks, Nancy. I learned so much trying for a novel approach, and benefited greatly from collaborative nature of the project. The Workgroup kept me on my toes and out of trouble. Biology and Horizontal gene transfer, inter alia, always on my mind.
Please feel free to 'play with words', the ultimate Lego set. I'll cringe little at losing active voice for passive in some cases, and I try to eschew the weak 'to be' forms, but despite the losing battle I will soldier on.
I appreciate your edits. --Anthony.Sebastian (Talk) 18:27, 22 March 2007 (CDT)

Words...

1)Historical time? I think this is incorrect, as history is the human record (contrasted with prehistory) and implies time. Is there an alternative? Gould uses "geological time."

2) capable of evolving - an individual is not capable of evolving, and I think we have to be especially careful with woords here to avoid a common naive belief that individuals can evolve. Can we reword this, maybe by adding the word transgenerationally, or longer but better, "from generation to generation". Maybe this lets us skip the time problem too. Gareth Leng 10:37, 22 March 2007 (CDT)

Gareth: I changed 'historical time' to 'geological time'. In the "Self-Organization" section, I re-wrote the ending as follows:
  • The ability to remain as a compartmentalized, self-organized, functioning system, in which factors tending to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste, always operating far from equilibrium, and capable in principle of reproducing itself and of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.
I will check the other sections for need to reword.
Thanks --Anthony.Sebastian (Talk) 18:52, 22 March 2007 (CDT)


I found that the progressively elaborate definitions become progressively harder to read and understand, so I've tried to balance the elaboration of each definition with a simplification of elements that were given more fully in previous definitions. I hope this works. I think it doesGareth Leng 12:13, 22 March 2007 (CDT)

I'll look at those carefully and get back to you. I did intend the crescendo effect. --Anthony.Sebastian (Talk) 18:52, 22 March 2007 (CDT)

spotted animals image

The spotted creatures image is very cool and I remember seeing in my old biology textbook... but did we tie it in with the article well enough? (or is it good enough?) (good=adjective... well=adverb... hmmm... -Tom Kelly (Talk) 21:46, 22 March 2007 (CDT)

so to figure out the correct english, I imagine you remove the "enough" and then decide whether it should be well or good, then add the enough back in. So is my well enough correct?-Tom Kelly (Talk) 21:47, 22 March 2007 (CDT)
Tom: I agree, pic not integrated with text. I removed it. --Anthony.Sebastian (Talk) 10:55, 23 March 2007 (CDT)

Somehow an older version of Life supplanted the most advanced version

Somehow an older version of Life supplanted the most advanced version. --Anthony.Sebastian (Talk) 15:51, 24 March 2007 (CDT)

That appeared to occur when author Joe Quick purportedly made a minor edit. I cannot determine how old the version that supplanted the most advanced version, but it preceded many edits by me and others, and it preceded addition of three or four images, now missing.

We need to restore the version immediately preceding Joe Quick's edit. I have been working on that version offline, and have made many edits, including additional Citations and Notes. I could replace the current version with that offline version. However, I await Gareth Leng's input, as he also put much work into the article.

Comments? If we leave the current version, I would have to devote considerable time and effort to upgrade it, including adding back the images, and incorporating my new edits. --Anthony.Sebastian (Talk) 15:51, 24 March 2007 (CDT)

I went ahead and reverted it to the edit immediately before Joe Quick's last minor edit. I assume this is the one you want. Joe Quick probably edited an out of date version by mistake somehow. I don't see any evidence that it was a problem on the server side. If you click history, you'll see a list of every copy of the page we have saved. If someone clicks on the time in an entry for a previous edit, they'll be taken to that version of the article. If they alter that version of the article and save it, it becomes the newest version of the page. -- ZachPruckowski (Speak to me) 17:18, 24 March 2007 (CDT)

Thanks, Zachary. I believe I can work with this version. Too late tonight to check thoroughly, but will in a.m. and get back to you. --Anthony.Sebastian (Talk) 22:35, 24 March 2007 (CDT)

Images

With all due respect, this article is a little on the pedantic side - and that is emphasized with the giant picture of all the books. That's a great picture, but not enticing in the beginning. Perhaps that picture could be demoted out of the first place position and replaced with a seductive picture of living things? Like the first of the Plos biology images on this page, above? Image:Lamellibrachia luymesi.jpg One idea, for your consideration. Nancy Nancy Sculerati MD

Nancy: I can appreciate your judgement about a little on the 'pedantic' side, though I would hope you would consider a little on the 'scholarly' side as an alternative. I would guess that editor/authors will turn in science articles running the gamut from informal to formal. Styles will undoutedly differ. I hope CZ will not penalize scholarly articles, even if they do take some effort on the part of the interested reader.
No one to my knowlege has attempted a scientific multi-perspective treatment of the subject of 'life'. I just wanted to make the article a real synthesis, and as authoritative as possible in keeping with the principles of clarity and coherence. In your earlier remarks you highly praised the article and jumped in with edits of your own. I trust you do not question the factual material.
Regarding the lead image of books: I wanted the reader to get an idea of the many different aspects of the topic of life, and the feeling that by reading the article they would get a taste of what those books contain. I also wanted each of the images to relate specifically to the text, and did not feel the PLoS Biology images had any real connection. Others also made that comment to me when I earlier had the PLoS Biology images in the text. I do not think we should have images just for images sake, or for the sake of having enticing or seducing figures not strictly tied to the text. I should think that people who go to the article will have a reason to want to read it, and will not need seduction or enticement to do so.
With all due respect, I regret disagreeing with you. I hope my thoughts above will encourage you to reconsider. --Anthony.Sebastian (Talk) 13:17, 26 March 2007 (CDT)


Yes, I think it could be dropped right down to the further reading section, giving lfe (so to speak) to an inevitably dry area. I think we are missing something of a sense of the infinite grandeur of life, to misquote Darwin. The spotted composite I think was great but somehow didn't display that diversity. Maybe we need a diversity of single celled life, something to illustrate what is emphasised here, the cell as the key element in living things? Gareth Leng 12:55, 26 March 2007 (CDT)
Gareth, I can move the 'books' image to the further reading section, but it really doesn't tell a story there. Not all the books in the image are listed, or should be, in the further reading section. The idea was, to write about life, one has to synthesize a lot of knowledge from many disciplines. That's why I put it first.
However, I would not want to jeopardize article approval on the image issue. What I think a great lead image would be: a sperm fertilizing an ovum--the start of new life. I could not find one. --Anthony.Sebastian (Talk) 13:17, 26 March 2007 (CDT)

I would not withold approval over such an issue, Anthony. I'm just making a suggestion. You have written the vast majority of the text here, and I believe that the final choice of images should be up to you. Nothing for me to reconsider.:-) Nancy Sculerati 13:21, 26 March 2007 (CDT)

Thanks, Nancy. I will continue to struggle over the images issue. See David Tribe's remarks and my response below. --Anthony.Sebastian (Talk) 22:42, 26 March 2007 (CDT)


I think it is a mistake to have no attractive images of organisms. They should be at the top, if possible. The pictures of textbooks will not draw the average reader in, as I see it. Its a missed opportunity, I think, and if the text doesn't draw them in, the text should be edited to create links key images corresponding to messages about, reproduction, cells, whatever.. David Tribe 20:25, 26 March 2007 (CDT)

David: First let me thank you for your suggestion to relocate the summary before the general explanatory text, which I have now done and would like you to review and critique. I think it works well. As to your point about having "attractive images of organisms" "at the top", I want to emphasize the article is about 'what is life?', or 'what constitutes a living entity?'. What you suggest regarding images seems appropriate for Biology but not apposite for Life. Personally what I'd like to see 'at the top' is a single image that says 'life' or 'living', rather than one that focuses on 'organisms'. Perhaps a diagram of a eukaryotic cell, since cells are the basic building blocks of all living things. Or a diagram of the fertilization of an oocyte by a spermatozoon, since sexual reproduction is so common among living things. Or even the prototypical embryo. Or the 'tree of life'. Unfortunately I'm a tyro when it comes to locating free images of the type I would like--but I shall keep looking. With respect to the interior sections, I think the images should relate to the topics, as in the section on thermodynamics, highlighting the sun as the main source of energy for all life on earth--as thermodynamics explains. --Anthony.Sebastian (Talk) 22:42, 26 March 2007 (CDT)
Giving more thought to what are the best images, some that make us question what is life would be good - a bacteriophage (easy to find) and lichen perhaps?. Ill put in a phage or virus with a caption. David Tribe 16:19, 27 March 2007 (CDT)

Approval

Seems to me its time to think of approving this provided (in my view anyway) that it has appealing images of organisms or ecosystems or whatever, but LIVING things at the start. Something breathing pulsating dividing or growing (or all of the above). A froggie or a race horse or a sea horse or whatever. A shoal of fish? A forest plus deer or birds? A new born baby? Even a puppy?

What do we need to do this approval : I think a one week deadline or maybe 10 days is more than enough. Do we need more than one editor. Maybe? Please advise. David Tribe 23:51, 26 March 2007 (CDT)

David: I guess I was shooting for a 'scientific' article and not thinking so much about images not tightly tied in with the text. I wish we could put an image upfront that says 'life' generically, like the double helix or the act of fertilization or cell division. I will try Gareth's suggestion below. --Anthony.Sebastian (Talk) 18:47, 27 March 2007 (CDT)

Anthony, I think one photo you want may be here on Wiki Commons [1]Gareth Leng 09:08, 27 March 2007 (CDT)

Also in commons [2]Gareth Leng 09:19, 27 March 2007 (CDT)

I believe both those have already been uploaded to CZ. I'll hunt them down. playing devils advocate, one problem is that the egg/sperm is low quality and another is that the moving gif is a bit gimmicky and can be distracting. Chris Day (Talk) 13:35, 27 March 2007 (CDT)

Consideration of qualification to title of article

Please give consideration to changing the title of this article to Life (definition for scholars) or something to that effect. As it is such a high level article, and Anthony makes a good case for its having qualities that might be destroyed by informality, it serves a great purpose. But as the only article on Life - without qualification, it is too advanced for poorly educated readers to follow. Anthony is unapologetic about making demands on the reader :-), and that's ok -but the level of scholarship required and expected should be upfront. We will avoid criticism that way. We have previously discussed having levels of articles. I think that -with the qualified title-that this article can be approved now. Without it, there are issues of accessibility. Nancy Sculerati 12:35, 27 March 2007 (CDT)

I think this suggestion is worth considering, and then we can approve this massive effort and fine scholarship straight away. David Tribe 16:23, 27 March 2007 (CDT)
Nancy, I like the idea of qualifying the title. For this one, suggest "Life (scientific perspective)", or "Life (scientific basis)". Nancy, I think 'scientific' puts the scholarly implication upfront. With that title qualification, perhaps then we could have additional "Life" articles: "Life (origin)"; "Life (diversity)"; "Life (artificial)"; "Life (extraterrestrial)", etc. Naturally, I also like the idea of 'approval with title change', with a one-week waiting period so I can work with Chris's, David's, and Gareth's suggestions. --Anthony.Sebastian (Talk) 18:17, 27 March 2007 (CDT)

Sounds good, I have heard from Gareth recently and I know that he is inundated with "real life" work, and he has indicated that he is likely to be off the wiki for a bit. So I think your suggestion of timing is timely :-). But- the qualifier "scientific", although apropos to the article, does not serve the required function of tagging the high scholastic level of the article. It would be quite possible, for example, to have an article Life (scientific) written for older children, and hopefully, someday we will have such an article. Can you, or anyone, come up with a word that is accurate (again, scientific is accurate) but also alerts the reader to the level of the text? That is what is needed for approval, in my eyes. Nancy Sculerati 19:03, 27 March 2007 (CDT)

Agree, science for all ages and 'levels' of intellectual sophisistication. How dumb of me not realize that. Let me try again to reveal the abberancy of my thinking.
How about:
  • "Life (fundamental laws of nature)"
  • "Life (laws of nature)"
  • "Life (upper division)"
  • "Life (graduate level)"
  • "Life (physicochemical)"
  • "Life (physicochemical principles)"
  • "Life (physics and chemistry)"
  • "Life (modern scientific synthesis)"
  • "Life (basic science principles)"
  • "Life (academic)"
Nancy, keep pushing me — you are right on, and I need it.
BTW: I knew nothing about life until you and Larry got me going. (Well, not exactly 'nothing'.) --Anthony.Sebastian (Talk) 21:10, 27 March 2007 (CDT)

I can well imagine that it was not exactly nothing. :-). I think "definition" should be part of the subtitle, because that is the essential conclusion of the article- it builds until there is a definition. The entire article explains that definition, and supports it. So, for the reader who is looking for a discussion of forms of life, for example, it is clear at the outset that this article is not that. This article defines Life as ....well, read the article and see. Academic or scholastic are two adjectives that would indicate the level. Depends on what you want, Life (a graduate-level academic definition) might be fine, unless you can say it better some other way. On a pragmatic level, speaking of levels, for example , in the Biology article ,which is written in lay terms, if it starts Biology is the science of life. And if life in that sentence hyperlinks here, it will jar -but not with the parenthetical qualification. Should we ever have a lay level article, perhaps the hyperlink will be to there - or to a menu page that allows a choice. If we ever have a biology article written for graduate level scientists, then the word life in that article might link to this article by default, and allow a different choice only through a menu. But whatever happens, the future being notoriously hard to predict, if we indicate the level now, and qualify the title, it can only help us. Life (a graduate-level academic definition) works, I think. Nancy Sculerati 10:58, 28 March 2007 (CDT)\

Nancy, one way to view the article is that it builds to a definition of life, as you say. Another, is that it builds to a comprehensive explanation of the interplay of the laws of nature that characterize a living system.
Would you accept "Life (an upper-division level explanation/definition)"?
I suggest 'upper-division' because:
  • I believe upper-division university students would find the article no more challenging than other upper-division science courses;
  • I believe the article might encourage university students to pursue a biology career, seeing it as developing into a 'hard science';
  • I believe upper-division students in physics and chemistry, computer science, etc., might be encouraged to see careers in applying their sciences to biological questions;
  • I believe professors might encourage their upper-division students to read the article, discuss it, critique it, perhaps even contribute to the article's evolution.
Or, better, in my opinion, how about: "Life (a college-level explanation/definition)"? We shouldn't underestimate the intelligence of college students, or imply if they're not upper-division they won't find the article accessible.
I feel somewhat chary about going with 'definition' alone, since the article stresses not fussing about the definition of 'Life' — the noun — but about 'living' — the activity, which is not in the title.
Could we go with "Life (a college-level explanation/definition)"? That would seem to cover all our points.
If so, how do we go about getting the title changed? --Anthony.Sebastian (Talk) 15:15, 28 March 2007 (CDT)

We can change the title with a move. That can be done by a constable at approval. Perhaps it would better be entitled "Living systems (life)" and that would solve the whole issue. Living systems is not a basic concept and does not therefore require an explanation of level - just like RNA interference didn't. I don't know how you feel about that particular title, Anthony, or whether the other editors would find that acceptable, but I mention it as a possibility. Nancy Sculerati 16:46, 28 March 2007 (CDT)

I'd have no objections to "Living systems (life)", except that would mean re-writing the Introductory section and the lead-in to the first section — as they take off from "Life" as title. The new title would also mean re-writing many other sections where 'life' is the focus. You did not comment on "Life (a college-level explanation/definition)", which I would prefer. --Anthony.Sebastian (Talk) 19:16, 28 March 2007 (CDT)

I didn't love it, but it would be ok; college level is probably not strictly accurate, though not strictly false either, and definition/explanation would likely flow nicely in German, but is awkward in English, awkward, however, is not a sin-let's see what the others say. I could live with it as a title, but a better choice might be suggested by them. Meanwhile, let me ask you something important. :-) What is the significance of &mdash ??? Nance Nancy Sculerati 19:35, 28 March 2007 (CDT)

Re 'important' question: I use the em dash for a variety of reasons: appositional, long pause, conjunctional, etc. A dash of this, a dash of that — so to speak. :-) Anthony --Anthony.Sebastian (Talk) 22:59, 28 March 2007 (CDT)
Good call on the qualification to the title. Cheers! -Tom Kelly (Talk) 01:28, 29 March 2007 (CDT)

Looked over article again. How about Living systems (life) or Living systems (Life) for a title. I read it over with this title in mind, and it reads well. No change in the text would be needed, Living systems already implies the level, and so no additional qualification would be needed, the article would be included in any search using the term Life or life, as well as systems - which is what the more sophisticated reader might use as a search term, after all. What do you think? (P.S. Anthony, it's not the use of the - that I question, it;s the actual insertion of &mdash in the text, is this a word processing glitch? Or does that collection of symbols, &mdash, have a meaning? If it's just that it comes out &mdash when you paste text in instead of -, then I will gladly copyedit and make the substitution). Nancy Sculerati 10:18, 29 March 2007 (CDT)

Nancy, I'll go for "Living systems (Life)", capitalized 'Life'. Gives one the opportunity for future extensions of article to discuss (briefly) 'other' living systems (e.g., living systems embodied in non-molecular symbol structures; synthetic living systems constructed from novel synthetic polymers). If we can agree, perhaps the workgroup will okay it. Should make sure Larry agrees, but doubtless he will. Thanks for giving this the big think.
Re &mdash: should find none in text, only in the wiki-code. I'll check text to make sure; sometimes I forget the semicolon after &mdash. With semicolon, as in "—" (see wiki-code) the text should show the em dash symbol. --Anthony.Sebastian (Talk) 16:16, 29 March 2007 (CDT)

--- Nancy: Following an overnight of mulling it over, I now find myself uncomfortable with substituting "Living systems" for "Life" as the article title, however qualified parenthetically. I would prefer to go back to your original suggestion of keeping "Life" but with qualification, perhaps as to 'level' of explanation. My choices would be:

  • Life (college-level)
  • Life (general principles)
  • Life (principles of living systems)

I remain open to other suggestions for parenthetical qualifiers. Given that CZ will have other articles on "Life", with their own qualifiers, readers can choose which aspect of "Life", or what level of treatment, they want to read, or contribute to. I put my effort into writing an article on "Life" based on general principles, and really would prefer to keep it that way. --Anthony.Sebastian (Talk) 15:09, 30 March 2007 (CDT)

I think that Living Systems (or living systerms) should be part of the title, and that final title you suggest might be ok- why don't you run it by Gareth, Chris, David- get a perspective. I think that we are close to approval and that they should sign off, anyway. Nancy Sculerati 15:18, 30 March 2007 (CDT)

The theme

I have put the six themes below as they currently iterate through the article. For each subsequent version I have idicated the differences; bold is an addition whereas a strike through is a removal with respect to the previous version. There seem to be some unnecessary changes between the versions and some changes that I think are typos. I have made a few comments about some of the versions below:

version 1 subsequent to the sections titled on Systems and Thermodynamic

The ability to remain for a time as an organized, functioning system, in which factors that tend to disturb the system’s organization are opposed by built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste (disorder) — operating from an organizationally enabling state far from an ever-approaching equilibrium (the state that we call 'death')

version 2 subsequent to the section titled Evolutionary

The ability to remain for a time as an organized, functioning system, in which factors that tend to disturb the system’s disorganization meet offsetting are opposed by built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste (disorder) — operating from an organizationally enabling state far from an ever-approaching equilibrium (the state that we call 'death'), and capable in principle of reproducing itself, and of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

The addition of of dis to "disorganization" seems premature. Shouldn't this still be organisation? Also the replacement of "are opposed by" with "meet offsetting" seems more like a stylistic change than the addition of a new idea. For continuity I think version one and two should be the same both going with either offsetting or opposed.

version 3 subsequent to the sections titled Exobiological and Self organisation

The ability to remain for a time as a self-organized, functioning system, in which factors that tending to disturb the system’s disorganizeation the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste(disorder), always operating from an organizationally enabling far-from- an ever-approaching equilibrium state (the state that we call 'death'), and capable in principle of reproducing itself, and of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

Here again there seem to be changes that are more stylistic. Why not just use the phrase "factors tending to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter" in all six versions? It is confusing to see stylistic changes mixed in with "big idea" changes.

version 4 subsequent to the section titled Autonomous agents

The ability to remain for a time as a self-organized system, functioning autonomously to work in its own behalf for self-maintenance and reproduction, where system, in which factors tending to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste, always operating from an organizationally enabling exploiting its situation far from equilibrium state, and capable in principle of reproducing itself, and of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

With respect to consistency you should go with 'far from equilibrium" or "far-from-equilibrium". See next comment below with respect to the removal of enabling.

version 5 subsequent to the section titled networks

The ability to remain for a time as a self-organized system of networks of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors tending to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste, always exploiting its organizationally enabling situation far from equilibrium state, and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

This version goes back to enabling having been transiently removed in version four. The first version has the sentence:

"operating from an organizationally enabling state far from an ever-approaching equilibrium"

Isn't there one sentence that can be used in the first version that can then be in all six versions without being changed? Tinkering with this sentence throughout only serves to make the changes of substance less clear.

For the addition of "self-organized system of networks of modular robust networks," the word networks is redundant. Couldn't it be simplified to "self-organized system of modular robust networks,"?

version 6 subsequent to the section titled Information procesing

The informational content and information-processing ability to remain for a time as a self-organized system of networks of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and reproduction, where factors tending to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter, and facilitated by production and exportation of waste, always exploiting its organizationally enabling far from equilibrium state, and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

I hope these observations are helpful. Another thing is that you might want to use a boxed style for these definitions so it is more obvious that they represent a theme throughout the article. Chris Day (Talk) 13:21, 27 March 2007 (CDT)

Working backwards

In the following examples I worked back from the final product to try and get six versions where only additional content was added to build up from version 1. In this way the definition builds without stylistic changes. Does this work? Chris Day (Talk) 15:21, 27 March 2007 (CDT)

The ability to exist as an organized, functioning system, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state.


The ability to exist as an organized system, functioning for maintenance and reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.


The ability to exist as an self-organized system, functioning for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.


The ability to exist as an self-organized system, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.


The ability to exist as an self-organized system of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.


The informational content and information-processing ability to exist as an self-organized system of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.


Boxes are obviously better to read than italics which are dreadful IMHO on the computer in paragraphs David Tribe 16:26, 27 March 2007 (CDT)


Chris: I very much appreciate your careful examination of the wording consistency in the crescendo of descriptions of what constitutes a living system. I need to give your suggested changes the careful scrutiny they deserve. I might think sacrificing a tiny bit of consistency okay if clarity seems to require, but I reserve judgment until I work on your wordings. I appreciate your eagle eyes and aesthetic sensibility.
I consider the 'box' idea genius. I may ask your help if I want to suggest a background color change. --Anthony.Sebastian (Talk) 18:37, 27 March 2007 (CDT)
Anthony, the wording is up to you, my example is just that. I agree that sacrificing some consistency is OK but we should try and keep it to a minimum. If you have a colour in mind just point it out. Or i can give you a range to pick from. Chris Day (Talk) 19:54, 27 March 2007 (CDT)
Chris, thanks. I have taken your 'working backward' approach, and have started carefully rewording, with consistency paramount but not compulsory. BTW: I found the color code I like (light-blue), but I'd like to know how to indent the box slightly, and equally at the left and right margins. Can you help me with that? --Anthony.Sebastian (Talk) 15:23, 28 March 2007 (CDT)

Anthony, see the code for the box below. I changed the colour, obviously. I removed the width parameter since when 100% is used with an indent it is still 100% and then protrudes to the right of the browser window. Removal of the width parameter means the right margin is used by default. The indent parameter is margin-left, currently set at 20px. You can play with the indent to get the desired effect. Lastly, I have added some cell padding so the text is not so tight against the box boundary. Again, you can play with this parameter to get the right look. Chris Day (Talk) 17:02, 28 March 2007 (CDT)

The informational content and information-processing ability to exist as an self-organized system of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.
Very nice. Thanks Chris.--Anthony.Sebastian (Talk) 22:21, 28 March 2007 (CDT)
I just reread you comment above and realise you preferred the boxes to be indented "equally at the left and right margins". One way to do that is to adjust to the width to less than 100% and center the box, as below. If nothing else this example will add tools for your future articles. Chris Day (Talk) 23:02, 28 March 2007 (CDT)
The informational content and information-processing ability to exist as an self-organized system of modular robust networks, functioning autonomously to work in its own behalf for self-maintenance and self-reproduction, where factors that tend to disorganize the system meet offsetting, built-in self-correcting mechanisms fueled by external energy and matter. This is facilitated by the production and exportation of waste while exploiting its organizationally enabling, far-from-equilibrium, state and capable of playing a role in the transgenerational evolution of the species to which it belongs in adapting to changing environments.

Consider for an upfront image

Signs of life. Top: Spermatozoon and oocyte merge to begin a new building block for a living system. Middle: DNA, the informational basis for producing the structural components of a living system (Courtesy of the Department of Energy Gallery). Bottom: life encoded in books.

Caption change.--Aristotle

That would appear right-aligned at the level of the TOC, under the short introductory paragraph and just superior to the first section heading.

I'll put it up on the article for you to see how it looks in context. It may need some PhotoShop tweaks. --Anthony.Sebastian (Talk) 18:59, 27 March 2007 (CDT)

spermatozoon

Hey, are we back at Aristotle? How about-for the caption, "the oocyte receives the spermatozoon to begin new life" (she ain't gonna do it twice, you know, it's up to the oocyte to be penetrated, many try but only one is admitted, or so I've heard). Forgive my informal language. And why do we consider the "spermatozoon" at the end of the article rather than a "gamete", or both types of gametes, each by name? If you are mostly interested in the aspects of a cell that are minimal but anyway, we call the cell alive, why not use a red blood cell? If you want to make the point that gametes do not reproduce themselves directly, then we are back to my question of choosing only one gamete. You guys have such a predictable focus, I'm afraid. (meow) Nancy Sculerati 16:19, 28 March 2007 (CDT)

I think the gametes get confusing. The concept of life produced by sex is different from the concept of life as outlined in this article. Or am I missing something here. Chris Day (Talk) 17:09, 28 March 2007 (CDT)


Caption leading picture:Signs of life. Top: a spermatozoon penetrates an oocyte to begin new life. Middle: DNA, the recipe of life. (Courtesy Department of Energy Gallery) Bottom: life encoded in books.

End of article: Exceptions Not all entities that otherwise qualify as living reproduce themselves, although they exist as reproduced living things. Biologists call such living things 'sterile'. Examples include programmed sterility (e.g., worker ants, mules); acquired sterility (due to acquired injury (disease) to the reproductive process; access sterility (lack of reproductive fitness); voluntary sterility (e.g., human couples). Obviously living things with the capacity to reproduce may die before reaching the reproductive stage in their life-cycle. Conversely, non-reproducing individuals may still effect reproduction of copies of their genes by facilitating the reproduction of kin, who share many genes (see kin selection). Viruses would not qualify strictly as living things, but manage to 'reproduce' in living systems. One might ask whether a spermatozoon qualifies as a living entity. From the thermodynamic perspective, one might answer affirmatively, as it keeps itself ‘living’ by doing cellular work. It has a compartmentalized internal organization functioning to keep it far-from-equilibrium. In that respect it resembles a motile bacterium. A spermatozoon reproduces, but in a different way than a motile bacterium: it does it through its parent’s progeny, which the spermatozoon plays an essential role in generating. It doesn’t have to hijack a cell’s machinery to reproduce; it cooperates with another cell (an ovum) to generate cells with machinery to reproduce it. Moreover, in reproducing that way, it subjects itself to meiotic crossover variation, just as its parent’s progeny does, contributing to the variation needed by natural selection to perpetuate the process of living on an earth with ever-changing environments. [edit]

Copied the above from the caption and the last section at the very end of the article. That's what I'm referring to-and that's what you are missing, Chris. I tell you in the same spirit with which you alerted me to the optimal sizing of David, in Cosmetic Surgery, both as a serious suggestion and with a very big smile, along with an elbow in the ribs. Nancy Sculerati 17:52, 28 March 2007 (CDT)

All right, you guys, I screwed up again, so to speak (arf). I will change caption to:
Signs of life. Top: Spermatozoon and oocyte merge to begin a new building block for a living system. Middle: DNA, the informational basis for producing the structural components of a living system (Courtesy of the Department of Energy Gallery). Bottom: life encoded in books. --Anthony.Sebastian (Talk) 19:30, 28 March 2007 (CDT)
Damn, my ribs hurt. :) Chris Day (Talk) 23:06, 28 March 2007 (CDT)

As they most certainly should! (unfortunately, so does my elbow.:) ) Nancy Sculerati 10:23, 29 March 2007 (CDT)

the new first pic

I would like it better if it were on the right side and not left. Thoughts? Also, the sperm image is slightly blurry and I think it is not good to have the first picture be slightly blurry. -Tom Kelly (Talk) 01:22, 29 March 2007 (CDT)

Tom, I will move it to the right margin, though I had it there and it looked lonely. Do you know any code that would position it at the right and leave some gap between the right edge of the pic and the right margin, so that the pic does not sit flush with the right margin?
Also, re fuzzy sperm-ovum. Got that from Wikimedia Commons. Definitely want the sperm-ovum merge, but can't find a better free copy. Can you help? --Anthony.Sebastian (Talk) 12:10, 29 March 2007 (CDT)
Re fuzzy picture- that what you get with high magnification often, slight fuzzy seems no problem to me. David Tribe 01:00, 30 March 2007 (CDT)

&mdash

Nancy, found a few &mdash's where I left off the semicolon — fixed them. Dash it all. --Anthony.Sebastian (Talk) 16:24, 29 March 2007 (CDT)

Title change notices

Someone added the following to the top of the article:

Template:Possible title change: Life (college-level)
Template:Possible title change: Life (general principles)
Template:Possible title change: Life (principles of living systems)

Generally, there should be a really good reason for putting anything between the title of the article and the first sentence of the article. (This, by the way, goes for "see also" links, which belong at the bottom, not the top, of articles.) Definitely we shouldn't put templates that are primarily for the use of contributors rather than users on the article page.

As to the proposed title change, the first title implies that there might be "Life" articles within the main namespace that are written at other reader levels--which is not the case. Moreover, all articles, particularly about such "universal" topics as "Life," should be written at the university student level, i.e., they should be accessible to a university-educated person who is unfamiliar with biologists' approach to the topic of life. As to having "general principles" and "principles of living systems" as subtitles, CZ articles don't have subtitles. They can have disambiguating phrases in their titles, however. So, for example, we might have life (biology) and life (game), but not Life (general principles) --Larry Sanger 08:54, 31 March 2007 (CDT)

Re text added at top, mea culpa.
I believe the current Life article does give the "...biologists' approach to the topic of life", as attested to by the profile of biologists cited in the references and further reading. I suggest Life (biology). --Anthony.Sebastian (Talk) 20:23, 31 March 2007 (CDT)

image copyright

Anthony, as constable, I deleted the Book cover picture. I did so simply because it is copyrighted, and no permission for use was listed. I know you are a published author (in spades). I think the easiest way for us to think about copyright for images for Citizendium is to pretend that you are submitting a review article to a journal, JAMA, NEJM- any one you like. Now, what figures and images could you submit? For a copyrighted image -you would have to have a release.Now, if you were doing a book review, a picture of the book is fine-in fact, that use is specifically granted by publishers without the need for additional copyright release. To publish on Citizendium it is at least as strict to have copyright permission as publishing figures and images in a professional journal. Since we don't have a copyright licensing agreement yet, and since the site states over and over that -at this point- we are GNU Free Documentation, that means another person (as far as I can tell) could copy the image you submit to Citizendium and change it and redistribute it. That's just the sort of thing that is liable to really aggravate the copyright holder. There may be ways around that, but I am sure book covers are OUT, unless it is either a picture of such an old book that the copyright has expired, or a picture of an entire collection of books-as you have submitted, such that it is an original photograph, an original composition. If a book cover is used such that what is really being displayed is its copyrighted cover image, meaning it is used as illustration in an article that is not a book review and is not about the book as the focus,- and there is no specific release to Citizendium by the copyright holder, that's trouble. Now, I am not a lawyer, as you know I am only a surgeon - and only a subspecialist surgeon, at that. Perhaps that description of myself will help excuse my compulsion "to do" in your eyes (understanding that it is the nature of the breed), and explain why, as constable, I could not look at an image I felt sure was a copyright violation without deleting it. Forgive me, please. I know that you thought about it before you uploaded it, and I can see why you liked that image. I wish I had a great image for you. There may be a colleague at SF who could give you one? Who has an original photograph from a laproscopic image he or she might be willing to release copyright on, such that it could be shared under GNU? If I am wrong about this, I will gratefully accept correction. But if in doubt about copyright in an image, I think we must delete. Nancy Sculerati 08:57, 31 March 2007 (CDT)

Now you mention this, I'm afraid the same is true of Schrodinger's What is Life? cover. Possibly the book spines too. None of these uses could be described as fair-use. Chris Day (Talk) 11:40, 31 March 2007 (CDT)
Nancy and Chris: I understand. I will remove the front cover of "What is Life". I'll leave the spine collection shot, as I assume on can publish say a shot of oneself in one's study with bookshelves behind. As to using book jacket covers in the future, I will request permission from the publisher, explaining how CZ works under GNU. That okay? --Anthony.Sebastian (Talk) 13:08, 31 March 2007 (CDT)

I guess so-images are a problem for all of us. I agree with your opinion that the shot of your study is fine, and I think that is very defensible. Perhaps in the future some of the copyright issues will be worked out with different licensing. We had a great picture for Chiropractic that we had to delete, too. Nancy Sculerati 15:42, 31 March 2007 (CDT)

Regarding title change

Given Larry's note above ('title change notices'), I guess the Life article cannot have a 'subtitle'. And I interpret it as meaning science articles should be written for people with a university-level education.

I would then like to stick with Life and add the permitted disambiguation '(biology)'. I do not prefer "Living systems" as title in part because that's 'life'. Having 'Biology' and 'life' articles should allow comprehensive coverage, since each has plenty of subdivisions that can be called upon.

I guess someone could write an article entitled 'Life explained to elementary school students' or 'Biology explained to elementary school students'.

Could we go with Life (biology)? --Anthony.Sebastian (Talk) 20:16, 31 March 2007 (CDT)

I would very strongly suggest keeping the single word title, which is a very close description of the contents of the article. To the extent that there are other meanings, and they should be qualified as needed, such as , Life (philosophy). Biology is self-evidently the root concept, and the level of the article is suitable for general readers. This is in a sense CZs benchmark article, and I'd keep the title as direct as possible. DavidGoodman 23:01, 31 March 2007 (CDT)

This article is a systems biology definition of life, and I do not believe that it is suitable for the unqualified title. If no qualification is allowed, which is apparently the case, then I believe the entire title should be changed to Living system or Living systems. There should be room in Citizendium for another article that actually discusses Life as a biological concept from every view, rather than the systems view alone. This article is worthwhile and a fine piece of scholarship, but it is not Life, it is Living systems. It is fully appropriate for the second title but is too technical, scholarly and arcane for the first - rather than being an easily comprehensible university level general article, it is at an advanced level, rather than entry level college biology it represents a specialized view within biology- eg -systems biology, that requires a university level understanding of biology to follow, it is therefore at a graduate or at least upper division level. Yet Life is an entry or benchmark level article. With a title change to Living systems it flies. With the title Life, it will have to be entirely rewritten into easily accesible language and include all views, biologically, of life and not strictly a systems view. We can do that, but it would mean a loss of all this work. My opinion - change the title and save the article. with respect. Nancy Sculerati 12:55, 1 April 2007 (CDT)

Nancy, as you feel strongly that the article lacks discussions of Life as a biological concept from views not covered in the article, then perhaps we could resolve the issue by identifying those other views and begin incorporating them in the article.
I would gladly work with the group to identify other views to present (I have some ideas of my own), and would appreciate knowing what thoughts you had in mind. I would gladly draft the text for those other views, and integrate them in the article. I would gladly rewrite the introduction to the article to indicate the full scope of the article.
Since you feel the article is too technical/arcane, then I will gladly rewrite the text with careful attention to target it at a general audience with a university level education, rendering it less technical/arcane. I offer this despite the fact that I agree with David Goodman that the level of the article is suitable for the general reader. Writing is rewriting in my philosophy.
Incidentally, a truly technical version of this article would contain a discussion, if not demonstration, of sophisticated mathematical tools, an enormous array of which are being used by interdisciplinary biologists to explain how life works. It would also include discussions of attempts to translate the processes of living into the language of mathematics. Many believe mathematics is the language of nature, and therefore the language of life. Without the mathematical perspective, its not a very technical article.
With those proposals the article would not need a title change to save it.
In my opinion, CZ could not have a different Life article without discussing the thermodynamic principles foundational to life, without discussing how living things differ from other entities (tornados, whirlpools, lasers, candle flames) that enjoy the benefits of free-energy-driven nonequilibrium thermodynamics; without discussing how self-organization occurs; without discussing how that self-organization manifests as an overlay of networks and how networks enable homeostasis, information processing and autonomy; without discussing emergent behaviors; and without discussing how natural selection weaves into that tapestry. A different article titled Life would have to incorporate all that and more that the current article contains—otherwise it wouldn’t approach the age-old question, “What is Life?”.
The current article describes fundamental principles that enable and characterize living things. It aims to explain the approach being taken by interdisciplinary biology to answer the age-old question, “What is Life?” Anything more could be built around the core.
You feel, “This article is a systems biology definition of life, and I do not believe that it is suitable for the unqualified title.”. I cannot consider the article aiming at “a definition of life”, since I was persuaded by the first section that we shouldn’t fuss about defining life, but focus on discovering how to explain the processes that underlie what we recognize as living in entities about us and ourselves. The curiosity we have encapsulates itself in the persisting question, “What is life? It appears that to answer that question one has to study the whole living organism, the smallest being a single cell. That necessarily entails systems thinking, but that is not the focus, just the background music. The focus is how do we as living things explain how we live in a non-living world. You need open-system non-equilibrium thermodynamics to explain that, and of course, much more. So you can’t avoid some physics, you just have to find a way to explain it, and more, to poets and economists. If we must characterize the result as a “definition” of life, I think of it more as a scientific definition not specifically as a system biological definition.
If the proposals I made do not meet with the group’s approval, then I would suggest changing the title to “What is life?”, as that has always been a universal fundamental question for Homo sapiens, and it counts as a specific sub-topic of “Life”, just as “Origin of life”, “Synthetic life”, “Artificial life” do.
I recognize that we need to discuss more about what constitutes living than what enables living. What enables living also then enables marine living, underground living, symbiotic living, and living consciously. We should probably discuss the major different ways living things make (perform) their living, in a bioscience context. Fuller descriptions of marine living, symbiosis, etc., would require separate articles. CZ should end up with more biology articles than any other type, since living things have more complexity. --Anthony.Sebastian (Talk) 23:14, 2 April 2007 (CDT)

A fork in the road

IMHO there are two ways to go: 1. Scholarly, with a name change ( I think Nancy's suggestion of Living systems is good.) The article is an extension of Systems biology.

2. Introductory. A complete rewrite to make it conform to the guideline for an introduction. I think the article reaches too far to be a readable introduction to Life.


I thus question whether the the article meets CZ criteria for an introduction to life, but it does fit perhaps as an introduction to systems approaches and scholarly views about living systems.

To quote from CZ:Article Mechanics

The nature or purpose of an encyclopedia article

While the Citizendium may not (yet) call itself an encyclopedia, its aim is to build up a body of articles that serve as encyclopedia articles. Therefore, the purpose of every article (as distinguished from lists and other supplementary material) in the Citizendium is to introduce the topic named in its title. Introductions differ from mere summaries or lists of information. An introduction is an extended, connected piece of prose, meant to be read all the way through. It is not merely a list of facts. It places what facts it presents into a context that makes them meaningful to someone who presumably needs an introduction. Indeed, the very notion of an introduction carries in it the idea that the topic introduced is new to its ideal reader.

Introductory articles, to be read and used by their intended audience, must be somewhat selective and simplified in the information they present. If an article contains information presented too densely, or in too abstract a way, it becomes merely a catalog or record of what experts know--of some interest to experts, perhaps, but not to people who actually need an introduction. This does not mean that an introduction must be brief, but that it spend the space needed to make whatever it does say clear to a university-level audience that is prepared to receive an entree to the topic. In other words, a Citizendium article is an opportunity to show off not your erudition but your ability to make the difficult seem easy.

  • How well does this advice gel with "Life" as a title David Tribe 19:01, 1 April 2007 (CDT)
I heartily agree with your advisory criteria for CZ introductory articles. Why write if not to inform, and to learn the limits of one's own knowledge and explanatory skill--in order to improve them. When it comes to "What is life?", the underpinning question of the article Life, my contributions provided no opportunity to "show off" erudition, as I asserted from the beginning that I wrote to learn, expecting that in teaching myself others too could learn. As I wrote in response to Tom Kelly, collaborative articles evolve. I expect Life to evolve as contributors see holes and vistas, but I expect it to evolve as an article about Life, since it is about what is life. --Anthony.Sebastian (Talk) 23:38, 1 April 2007 (CDT)

what about Life (scientific)

Life (scientific definition)

Life (scientific explanation)

Life (scientific basis of)

I don't know, just thought I'd throw some titles out there to see if they worked. -Tom Kelly (Talk) 19:21, 1 April 2007 (CDT)

Tom, you missed Larry Sanger's post above, which nixes such parenthetic subtitles. Nancy Sculerati 19:23, 1 April 2007 (CDT) I am copying it here:

As to the proposed title change, the first title implies that there might be "Life" articles within the main namespace that are written at other reader levels--which is not the case. Moreover, all articles, particularly about such "universal" topics as "Life," should be written at the university student level, i.e., they should be accessible to a university-educated person who is unfamiliar with biologists' approach to the topic of life. As to having "general principles" and "principles of living systems" as subtitles, CZ articles don't have subtitles. They can have disambiguating phrases in their titles, however. So, for example, we might have life (biology) and life (game), but not Life (general principles) --Larry Sanger 08:54, 31 March 2007 (CDT)

ah, yes. Well... shoot. It's a darn good article. -Tom Kelly (Talk) 19:28, 1 April 2007 (CDT)
Tom, perhaps it's pretty good, but it could be much better. In the collaborative world, narratives of explanation evolve. Life I trust will evolve as contributors see misconceptions, incompletely developed conceptions, and new conceptions. Still, I expect it to evolve as an article about "Life", about that question of questions, "What is life?", still a major topic of biology in the 21st century. Nancy has questioned whether the general university-educated reader can access the article cognitively. I take that questioning seriously and plan to focus on that question in re-examining the text. It must be accessible, and more than that, it must inculcate and stimulate. "Life" offers CZ the opportunity to evolve better answers to the perennial question, "What is life?" --Anthony.Sebastian (Talk) 23:24, 1 April 2007 (CDT)


Title

First, I think this is an outstanding article, and I am ready to approve. As to the title, the issue of other articles is at present a hypothetical one. Let's disambiguate if and when we need to, and keep this as Life for now. I don't object to doing otherwise, just stating my preference, to solve problems when they arise, when the right answer might be obvious, not before we need to.Gareth Leng 03:56, 2 April 2007 (CDT)

So be it. Let there be Life (or was that light?) Let's just lighten it up-in the sense of making it easy to read, without dumbing it down. Nancy Sculerati 06:19, 2 April 2007 (CDT)

Agree. I've run through the article again now trying to simplify where I can without loss of content, especially some of the longer and most complex sentences.Gareth Leng 06:47, 2 April 2007 (CDT)

Gareth, some of the sentences definitely needed some enzymatic disassembling and reassembling. Nancy, I'll try harder to make it easier to read without dumbing down, a challenge to keep the reader challenged just enough to make her active in the learning process. --Anthony.Sebastian (Talk) 23:23, 2 April 2007 (CDT)

Problem sentences & phrases

I am submitting sentences that I have trouble following. In other words, that I really don't understand clearly even when I think about them a lot. Can these be made into simpler declarative sentences, perhaps long sentences broken into more than one such sentence?

Biologists use the term life to refer to the processes comprising the activity of living, to the entities that embody those processes, and to the interrelations and interactions among them, that together, form complex adaptive self-reproducing systems.

A bit much, I agree. It should be enough to write: Biologists use the term life to refer to the processes that comprise the activity of living, to the entities that embody those processes, and to the interrelations and interactions among those entities. --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

phrases

I am submitting phrases that either don't make sense to me, or sound very odd to me in the context used. Can these phrases be restated in simple declarative sentences or other phrases? Perhaps, where theromodynamics is concerned, we can state things in equations as well as words? I'd have an easier time with the actual equations with each term defined. I am going in order through the article. One problem is that the "summary" is presented before the explanation.

Nancy, possibly that is the main problem, "that the "summary" is presented before the explanation". Yet, that's like the Abstract of an article printed before the text. You get a summary, but you may have to read the article to learn what the Abstract's really saying. Some people like see upfront what they're going to learn about when they read the article. Then they go back and read the Abstract for the bird's eye view. Let's consider whether we want such an Abstract. It would be hard to really simplify the summary — life's not that simple. --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

information-poor energy

disorganized state of the equilibrium of randomness

Understandable in the context of the article. --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

the flow of energy and matter through living systems enables them to organize and maintain their fully-functioning system, given the basic (genetic) information that generates their structural components

That's the concept that a large section of the article discusses. The 'summary' is not intended not so as much to explain as to presage the conclusions of the main sections. Perhaps we should put it back after the 'perspectives' sections, where I had it originally.

how did they acquire information banks? This is a basic question about cells, and I honestly find it odd to place the phrase "information bank" here. Had I not read this article already, I would have no clue to what is meant by that. Maybe I'm just dumb (not blonde, unfortunately).

this information, in the form of nucleic acid macromolecules, encodes many different types of proteins that interact with themselves and with their encoding macromolecules, and thereby assemble an organization that can import energy, matter, and information from the local environment, and export waste; this seems to assume that the details of molecular biology are old news to the reader. Is this fair to assume?

Again, in the summary that should tell the reader what she'll be reading about if she reads on. --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

physicochemical ???

those laws and inherited information enable a self-organizing system that can work autonomously for survival and reproduction, and enable properties, functions and behaviors to emerge that could not be anticipated from those of the system's components alone; this is stated before systems are discussed as if the individual has already carefully read the article. We can't assume that a reader is going to read through once, having no idea what such phrases mean until they get towards the end, and then re-read the article again so that they might understand what they had muddled through initially, can we?

That relates to the question whether we should relocate the summary. Otherwise its like reading the abstract of an article. You get the summary, but you've got to read the article to understand the full meaning. Then having the abstract gives you a more bird's eye view, and a take-home message. --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

this robustness and adaptability derive from the properties, functions and behaviors of a hierarchical network of subnetworks of molecular circuits;

Perhaps we can work on these, and then I'll go on. If everybody finds these phrases obvious and clear and it's just me-please don't be bashful- just tell me. It's ok.

Nancy Sculerati 07:22, 2 April 2007 (CDT)

Nancy, I want to emphasize that the phrases you noted cannot be obvious and clear to a naive reader until she reads on past the summary and gets into the various sections they try to encapsulate. Do you think we should move the summary to the end? Eliminate it? --Anthony.Sebastian (Talk) 23:07, 2 April 2007 (CDT)

Level of text

If we are to argue that this is a college level text, rather than a graduate level text, I think we need to change the following:
When biologists try to define what constitutes a living system, they often focus on one particular perspective; for example, undergraduate textbooks tend to define ‘life’ in terms of metabolism, reproduction and evolution. In this article, we will 'unpack' those terms, and detail the several ways that biologists view living systems.
We need to explain how "undergraduate textbooks" define life rather than assume that the reader of the Citizendium article Life is fully familiar with what metabolism, reproduction, and evolution are all about, and just how these are typically presented in the undergraduate course and just how they are typically used to define life. After all, college level means at the level of those entering college, and not at the level of those entering graduate school or upper division science classes, or at the level of the person who has taught undergraduate biology courses multiple times in different institutions over the years. Or am I wrong? (wouldn't be the first time) Or perhaps I am wrong to think that this text should try to introduce the question "What is Life" to an intelligent lay reader who has a college level of reading comprehension in a manner that pulls them through from beginning to end. We are really laying down the principles of Citizendium articles at this early stage, and I am willing to admit I may have misunderstood what I think we have agreed on. I am also willing to admit that the article is tremendously thought provoking and interesting as it is- to the reader who can follow it. Nancy Sculerati 07:27, 2 April 2007 (CDT)

This is inescapably a challenging article, as you say, interesting and thought provoking. I think "college level" in fact embraces a wide enough range to include this, though I think we should here as everywhere do our best to make it as accessible as possible. I think the challenge for us is to make difficult themes accessible, not to exclude those themes that we suspect will be too tough for many.

There is a problem of course in that there must always be presumptions of knowledge, otherwise we will have to define everything again in every article on a highly complex topic; in a sense this article rests on othe Citizendium articles (on metabolism homeostasis etc) that are not yet written.

However, I don't see this article as a gateway to everything about Life, but as a select and high level gateway to a number of themes at the forefront of modern biology; it's an introduction, but an introduction to the edge.

I agree that the Summary was hard to make sense of at the beginning; I've tried to make it a bit simpler as suits its place in the article. I also agree with Nancy that we should keep looking at the very complex sentences that say more than they really need to in context, and which because of their complexity might lose readers. Better to simplify by focusing sentences on their primary purpose, and keep the reader through the flow.Gareth Leng 11:44, 2 April 2007 (CDT)

Nancy and Gareth, you both make excellent points, and I feel lucky to have such wise people to collaborate with. I agree with you Nancy that the article needs to do a better job to fit the salient features of the concepts of metabolism, reproduction and evolution. In fact the last few days I've be thinking about how to develop the concept of 'metabolism' in the article — the salient features, since we already have Metabolism. Gareth, I originally had the 'Summary' at the end, but it seem like it the reader needed a summary of what was coming, since there were a lot of perspectives to write about. Your simplifying it helps. --Anthony.Sebastian (Talk) 22:19, 2 April 2007 (CDT)

I'm not saying it has to be for this draft, but I'd love to see a discussion of carbon-the orbitals, how the variety of bonds and shapes are conducive to building structure and gradations of energy release, water and hydrolysis- I understand there are sulphur based metabolism organisms in the deep sea- and how other molecules-like silicone-might have the life conducive properties of carbon. Also I really do think the delta G equations should be here, and things not just discussed in words. Both ways.Meanwhile "mentionables" has to go Nancy Sculerati 01:53, 3 April 2007 (CDT)

I agree; the section below doesn't really gel with the rest of the article and perhaps it's better as the stub for aother new article. For now I've put it below.Gareth Leng 04:45, 3 April 2007 (CDT)

Textbook mentionables

From the several different perspectives on what constitutes a living system, discussed in this article, one can derive the list of features that biology textbooks often ascribe to living systems:

  1. Organization: A temporary organization of interrelated, coordinated, dynamically interacting hierarchy of molecular components within cells, of cellular components within organs and organisms, of organisms within species, and of species within ecosystems—each importing energy and matter, and using it to build, grow and sustain its structural organization for performing the functional activities needed to maintain that organization for reproducing itself.
  2. Metabolism: Conversion of imported energy into any or all of the various forms of energy (e.g., chemical, electrical, mechanical, thermal), needed to utilize imported matter.
  3. Growth: At certain stages of its life-cycle, cells, organs, and organisms maintain a higher rate of synthesis (anabolism) than breakdown (catabolism) of structure and increase in organizational complexity. Growth occurs largely according to a 'plan' for survival and reproduction. Species tend to increase in numbers of individuals as resources and other factors permit.
  4. Reproduction: The ability to reproduce itself, for example, the division of one cell to form two new cells. Usually the term is applied to the production of a new individual (either asexual reproduction, from a single parent organism, or sexual reproduction from at least two differing parent organisms), although strictly speaking it also describes the production of new cells in the process of growth.
  5. Gain of New Inheritable Traits: Inheritable diversity, whether adaptive, neutral or disadvantageous, is a common feature of living things, and the starting point for natural selection. (See also:[1])
  6. Adaptation: At the species level, the ability to gain traits through evolutionary processes[1] that improve the members of the species chance for reproductive success; at the individual organism level, the ability to change (e.g., through learning) in ways that improve the individual's chances for reproductive success; at the cellular level, the ability maintain a near steady-state in response to perturbations and to change functionality in response to changes in environmental conditions;
  7. Response to stimuli: A response can take many forms, from the contraction of a unicellular organism when touched, to complex reactions involving all the senses of higher animals. A response is often expressed by motion, for example, the leaves of a plant turning toward the sun, an animal chasing its prey, or neuronal action potentials traveling down nerve fibres during thought.
  8. Homeostasis: Regulation of the internal environment to maintain a near-constant state in response to perturbations; for example, sweating to cool off.

Rewrote introduction-plus need to object to the "great man" apsect of the article

As always- I will retract any of this according to reasoned discussion. I rewrote the first paragraph, it's still not smooth but it is less deadly, I hope. I think it contains every one of the ideas, at least that was my intent. In reading through the article, it so relies on the "voice of authority" in a way that I think is an anaethema to critical thinking. It is not that I am opposed to citing and giving respect to major thinkers, it is just that the ideas should be foremost and not the people, we are not disciples nor do we want to encourage that kind of precedent in science articles. My, as usual, outspoken opinion. Nancy Sculerati 14:29, 3 April 2007 (CDT)

I'd disagree, gently, because I see quotes very differently, I see them giving a more human face to knowledge and understanding, reminding us that science is about ideas - people's ideas, more than cold facts. Gareth Leng 14:41, 3 April 2007 (CDT)

I'm suggesting de-emphasizing Ernest Mahr biographical information (picture etc.) Not the quotes- the excess. Your call (all of you). It brings up the whole Galen thing in my mind. It's the reverence rather than the quotes, and it seems to be a style through much of the article. Why not branch out and devote whole articles to these people, but make full reference to their ideas here? That's really an opinion. But -although we are not strict about byte limits, we are a bit off topic and expensive in terms of space and bytes with such inclusions. And we have said nothing about the specific of carbon sp3 orbitals silica, water hydolysis sulpher metabolism- all of which, albeit not a systems approach, are essential features of a biochemical approach to life processes, and - if we are including all important fundamental views, merits inclusion. Now, as a New Yorker, I don't object to non-gentle disagreement. In fact, I'm liable not to recognize a disagreement being voiced if it's done in too gentle a fashion (here we sometimes call that fashion, "British" ;-) in fact. That's what my kids retort when I try to correct their manners, as in "we're not..." ) So, as long as we are truly respectful of each other (which I believe we all are), outright and blunt disagreement is ok. In that spirit, you (plural) are also welcome to revert intro. again-my changes-it's all just a suggestion, really. And if I'm too gruff with my suggestions, please let me know. I've been cherishing my interactions with all of you and I do not want to offend you, you especially Anthony. Nancy Sculerati 14:44, 3 April 2007 (CDT)
You cannot offend me, Nancy, by voicing your reactions, however you might characterize them. I like what you did in rewriting the introduction. I have no strong feelings about the Mayr image; people were clamoring for images and I have little talent for finding appropriate ones. I agree with you re 'reverence', but agree with Gareth on quotes. I'm blessed being in this biology workgroup. --Anthony.Sebastian (Talk) 16:41, 3 April 2007 (CDT)
me too. Several months ago, I wrote an into here. Over that time I have learned so much, mostly thanks to you, Anthony. It was a deju vu feeling to start the intro again, thinking hard all the while about what I have learned, In terms of the blunt talk, although I understand the rationale for all the pictures chosen, and who can not appreciate Leonardo? Still, too much dead baby, old man, stilted diagrams. Though Leonardo should stay, and I am rapidly turning into an old lady myself (a process I have every intention of seeing through to completion), and have no great reverence for youth, we need something more animated here. Speaking of which, animations (that animate only when clicked) would be quite suitable for illustrating the activity of living. Maybe Matt Innis can help us. Nancy Sculerati 16:48, 3 April 2007 (CDT)

A section that I am puzzling over

QUOTE Why this concern about the word? Some words have distinct meanings not definable in terms of other words, and those essential words semioticians call ‘semantic primes’. Ultimately, all definitions converge on about 70 so-called 'semantic primes' that are universal among languages. Children learn the meaning of prime words by how the society in which they live uses them in everyday language. Every other word can be defined using some combination of semantic primes.[3] The verb ‘live’ is a semantic prime, the noun ‘life’ is not. [4] Using semantic primes, 'Life' is defined as 'that which lives', where lives is understood by speakers and listeners from their own experience of how it is used. The word "death" also comes from the semantic prime of 'that which lives'. Things which live 'die' and speakers generate the word 'death' to refer to 'that which died'. Semantically, the question, then, is not 'what is life?', but 'what characterizes things that live?' Biologists act on the latter question, even as they ask it in terms of the former. The biologist, logician and historian J.H. Woodger suggested that the word 'life' can be eliminated from the scientific vocabulary, because it is "an indefinable abstraction and we can get along perfectly well with 'living organism', which is an entity that can be speculatively demonstrated.”[5] Carol Cleland, philosopher and member of NASA’s Astrobiology Institute, adds that scientists are not really interested in what the word 'life' happens to mean in our language. "What we really need to focus on is coming up with an adequately general theory of living systems, as opposed to a definition of 'life'."[6] This resonates with the remark of biologist Antonio Lazcano: "Life is like music; you can describe it but not define it".[7]

I'm thinking at this point at the article, just when the reader is moving on to discover biological insights, that the latter part of this section is too long a digression about semantic matters. I think perhaps it a mistake to venture into semantic primes in the body of the article. Its interesting yes, but I suggest the semantic detail detracts from the flow. Perhaps they should be included as a footnote David Tribe 17:52, 3 April 2007 (CDT)

I agree. We can try it, and always change it back if needed. David, can you help with a biochemical section. Wat are living things made of? Nancy Sculerati 18:59, 3 April 2007 (CDT) Also, this really doesn't mean much to me, except as a semantic point: Scientist Eric Schneider and science writer Dorian Sagan echo Mayr: "...the word is a grammatical misnomer: life is a noun, but the phenomenon to which it refers is a process. And it is vitalistic: when we say life, we think we know what we are talking about when often we have simply applied a label that allows us to categorize, rather than examine closely, the phenomenon about which we are speaking."[1] After all, living things is a noun (modified with an adjective) and that's just the point, we are trying to categorize it. (them) Perhaps we can move that too? Nancy Sculerati 19:06, 3 April 2007 (CDT)

Yes I can do the biochemical composition thing. Probably not tonight, as my brain is starting to burn out. Ive sharpened up your cell stuff a bit. Yes I agree, the general reader needs this explanation and lead upto be able to tackle some the the sophisticated stuff AS has worked up.

I'm clarifying your use of genetic code. I'm mindful the code AUG=Met etc is exclusivly an RNA affair, and avoiding calling DNA the code. Referred to it as information storage. With Leonardo's graceful drawings leading the images I'm relaxed about our images now. At some stage we could find some appropriate image ( singled celled algae or something green and non-human) possibly replacing the sperm., or as an extra, but that could easily wait till version 1.1 in my view. David Tribe 05:03, 4 April 2007 (CDT)


Bank of the above cut from article (for now) Scientist Eric Schneider and science writer Dorian Sagan echo Mayr:

"...the word is a grammatical misnomer: life is a noun, but the phenomenon to which it refers is a process. And it is vitalistic: when we say life, we think we know what we are talking about when often we have simply applied a label that allows us to categorize, rather than examine closely, the phenomenon about which we are speaking."[2]

Why this concern about the word? Some words have distinct meanings not definable in terms of other words, and those essential words semioticians call ‘semantic primes’. Ultimately, all definitions converge on about 70 so-called 'semantic primes' that are universal among languages. Children learn the meaning of prime words by how the society in which they live uses them in everyday language. Every other word can be defined using some combination of semantic primes.[3] The verb ‘live’ is a semantic prime, the noun ‘life’ is not. [4] Using semantic primes, 'Life' is defined as 'that which lives', where lives is understood by speakers and listeners from their own experience of how it is used. The word "death" also comes from the semantic prime of 'that which lives'. Things which live 'die' and speakers generate the word 'death' to refer to 'that which died'. Semantically, the question, then, is not 'what is life?', but 'what characterizes things that live?' Biologists act on the latter question, even as they ask it in terms of the former. The biologist, logician and historian J.H. Woodger suggested that the word 'life' can be eliminated from the scientific vocabulary, because it is "an indefinable abstraction and we can get along perfectly well with 'living organism', which is an entity that can be speculatively demonstrated.”[5] Carol Cleland, philosopher and member of NASA’s Astrobiology Institute, adds that scientists are not really interested in what the word 'life' happens to mean in our language. "What we really need to focus on is coming up with an adequately general theory of living systems, as opposed to a definition of 'life'."[6] This resonates with the remark of biologist Antonio Lazcano: "Life is like music; you can describe it but not define it".[7]


Progress-but rough area-lay out road to approval

I think this is starting to metamorphasize to a new level, and I am pleased with that. We need to explain the aspects of organic chemistry that allow for living systems- the actual physical chemistry of the carbon compounds that are the stuff of biochemistry. I once had some insight into that, but it's currently a dim vision from my youth. However, I know it is a key concept here. David has begun the work of bridging from there to cells, and I think that some of the concepts from Evolution of cells might get imported. In this way, we might move from cells into living systems. Once we smooth out all this, not dumbing it down but keeping the concepts full on, maybe we can just run through the rest and clarify the language. At any point-including now- you all might think that we could go ahead and approve and keep working on a draft. Nancy Sculerati 07:03, 4 April 2007 (CDT)

Care please. I'm not at all sure about the chemistry, and would rather keep it out, or to a very minimal level. I do not know what it adds to know that particular molecules contain phosphate or ribase, and to explain why I even need to know these things is too much. It seems to me that we are not simplifying and clarifying here, but adding facts as adornments, and they don't necessarily clarify the ideas; indeed, they may get in the way of the ideas, even more than semiotic primes did. For me the section on semiotic primes was fine, as it was self explanatory - it could be understood with no external referents. It is probably redundant however interesting, and may be better as a footnote. However I do not think we can bring in chemical structures, or details of cell metabolism, in a way that adds to the understanding of life, although we might be adding facts about what life is. I think we need to think very carefully about what this article is. I think it is a truly exceptional article because it focuses on the abstract understanding of "life" - the essence of life if you like, not the material accoutrements, and brings in detail only as needed to understand the abstract ideas. At present therefore I would be inclined to edit down the chemistry, unless it becomes clear why it is important to give these facts in relation to the key concepts.Gareth Leng 08:22, 4 April 2007 (CDT)

Response to Gareth: Why is life carbon based? Why not another type of atom? What is it about carbon, water, hydrogen, oxygen that go into it?

I am not conveying my thoughts clearly. No interest in a laundry list of molecules. Here's the question: Why is life carbon based? Why not another type of atom? What is it about carbon, water, hydrogen, oxygen that go into it? There are well known ideas about the electron orbitals that hybridize in a certain way around the carbon nucleus (no longer well known to me- but once, on my own very low level-understood-back when I took Physical Chemistry and Advanced Organic Chemistry). This allows for a variety of bonds that can be made with disassciation constants that are low enough to be reversible, with availble energy that can be contained in other bonds that can be broken and release enrgy without blowing everything to smithereens...and also to allow for a variety of bonds that make, depending on the orbitals used, different shapes of CH molecules that translate into different macromolecuclar structures. Then there is water, with its polarity and surface tension. Then there are lipids that form a bilayer in water and therefore spontaneously set up a compartment, and allow for subcompartments. Interfaced by two qualitatively different boundaries: polar and non-polar. Halogens important, etc. but don't need to go there. That's what I'm talking about and that has, in my opinion, EVERYTHING to do with the essence of life as we know it. That's the physical correlate to the networks and systems theory- the way it worked out here. These forms of matter have as much to do with life as photons do, as an energy source, which are already (rightfully) included. There are theoretical reasons why Si might also work, and might be found on other planets. Why are there ambient conditions under certain limits that allow life/ Why is life not thought to be able to exist -carbon water based life, that is, -outside those limits? It all has to do with the basic chemistry and physical properties of the components of life. This is relevant. Nancy Sculerati 09:35, 4 April 2007 (CDT) [3] [4] [5] [6]

Da Vinci's Views of a Foetus in the Womb

Hullo, just a brief note from an editor in another field entirely -- I really have some doubts as to whether it is wise to use the Da Vinci image as the one immediately visible on the top of the page. I suspect it will inspire a considerable amount of activity, not all of it welcome, from conservatives and Evangelical Christians who will all want to twist the article their way. As just one example of how heated this can be, I've been monitoring the article of "Theory of Evolution" at the so-called "Conservapedia" project -- it has the most hits, the most edits, the most edit wars, and has led to the se-sysoping and banning of no fewer than 14 individuals, almost all of whom did nothing worse than try to post even the rudiments of ligitimate evolutionary theory to the article.

From another angle, also, the image is somewhat athropocentric -- humans, after all, though dominant on Earth at the moment, are only one species of mammalia, and human life is only one tiny bit of the picture of "life" generally. It suggests implicitly that somehow this article will address or answer questions such as "when does human life begin," which will bring in needless, heated arguments that really ought to be conducted elsewhere, into topics within religion, theology, or (at least) bioethics.

Its quite a lovely image all the same, like all of DaVinci's anatomical drawings -- but perhaps it could be placed elsewhere in the article? Just a suggestion.

Russell Potter

I have to say I have leaning more to Russells opinion on this although I have said nothing since I did not think it was such a big deal. My gut feeling is that it does not really represent the focus of the article, and the same for the sperm. For me these bring in idea of conception, and as Russell points out the idea of "when does human life begin", whereas most of the article is on the practial features of life. Another point I have with regard to the photos is the poor quality one for the chromosome to DNA to base pair representation. Again this can be dealt with later, but it will need to be improved at some point. One possible alternative is a more complex figure that bring in the idea of the central dogma and finishs with networks. Chris Day (Talk) 10:10, 4 April 2007 (CDT)

On images, see PLoS use of a Haeckel print to illustrate interspecies networks [7]Gareth Leng 08:35, 4 April 2007 (CDT)

Actually, the more I think about it, that image is perfect. As a drawing of a fetal corpse it represents both life and death, and Leonardo is Leonardo. I understand what you are saying Russell, but that path leads to self-imposed censorship out of fear. I argue that we should discuss everything and focus on the essence of things. Nancy Sculerati 09:38, 4 April 2007 (CDT)

Points well taken, all. I would certainly never counsel self-censorship due to fear. But I take the inclusion of this image as a choice that should be fully aware of its multiple audiences -- my anxiety is not at all about the flak that such groups might or might not post, but about the time that dealing with such postings might subtract from the project in its early stages. If my concerns have solidified your resolve, though, then all the better. I, too, admire the image's deep visual ironies. Russell Potter

That's fine- if we avoid the gross concepts of life and death, and make an assumption that human life is of no particular interest, we can stick to a very technical and abstract article that will be just a little silly with its present title. We can have it ridiculed as such, but at least we won't be answering questions similar to those asked about Einstein in the article Biology on the forums in three months. I'll back out a while and let you all settle things. Nancy Sculerati 10:22, 4 April 2007 (CDT)

Great new picture! Better for lead, lively color Nancy Sculerati 13:17, 4 April 2007 (CDT)

Thanks be to Gareth. --Anthony.Sebastian (Talk) 22
33, 6 April 2007 (CDT)

Focussing on Approval

I want to try and tease out what people are thinking and see if we do have a consensus support the approval tag I put up. What is essential to change before approval if anything?. Now images are satisfactory I think. Is Gareth saying there is too much biochemistry? If so what needs to be done to the biochemistry to transition to AS's fine achievement? Are we there or do we need more change? Please edit the biochemistry I put in only in an attempt to satisfy Nancy's request but if its not right - I have no resistance to taking it out at all. David Tribe 00:48, 5 April 2007 (CDT)

I'm very happy with the content as present, I just wanted to pre-empt a "creep" of the article into detail and away from ideas; great job everyone.Gareth Leng 03:42, 5 April 2007 (CDT)

I support approval.I just intend on tweaking carbon, water, lipid oxidation reduction theme in a general way.Meaning abstract presentation of "materials".This might lead to a couple of sentences that point out (later in the article) that at higher ambient temperatures (eg another planet) , Si might be suitable for that same dance in some other ballroom. What is not done here is easily acomplished in later versions. What is done here is fine for approval. Nancy Sculerati 05:57, 5 April 2007 (CDT)

carbon chemistry

I'm not sure what this sentence means:

"Stable bonds can be formed with other carbon molecules in several ways, and energy can be either consumed or released in changing from one type to another without the loss of covalent integrity. "

Are we thinking of redox reaction, alcholol to adldehyde etc. ? Chris Day (Talk) 08:59, 5 April 2007 (CDT)

I'm trying to remember thedifferent orbitals sp 3 etc, so that a carbon molecule can remain a carbon molecule (C-C bond) through (C=C) etc- so not =OH to -OH, but the actual backbone of the molecule. Nancy Sculerati 09:08, 5 April 2007 (CDT) That's how Si and C are alike, and that's why living things have C. Isn't it? Nancy Sculerati 09:10, 5 April 2007 (CDT)

Is it the valency, carbon and silcon both have a valency of 4, you are trying to address here? Although it sounds like you are trying to suggest more. Maybe that carbon-carbon single, double and triple bonds can form, this is unique (at standard conditions) and thus can lead to the long chains or rings that allow the macromolecules necessary for life, as we know it. Chris Day (Talk) 09:48, 5 April 2007 (CDT)

I'm going to put a post from above down here, as I think it may have got overlooked. I am expert enough to know the importance of this point but no expert at physical chemistry or advanced organic chemistry- and it's basic concepts in these fields that are key. So I hoped one of you guys might be able to help out. Yes, it has to do with the atomic number because that determines the orbital e clouds, and that determines the way it can bond to itself-and other things, and the reversibilty of those bonds- and the shape of the molecules. There are a number of hybrid orbitals possible with both silicone and carbon, and that - in my own dim understanding- is why, Carbon anyway, can work out as "the atom of life". Look at the external references, please. I think I've listed them backwards, really start at the right and move left - more obvious [8] [9] [10] [11]

I just looked a the first one and i'll read the others. At present what we have seems a bit foggy. I had started writing something as follows:
Carbon based chemitry is ideal for life as we know it since at standard conditions it can form stable bonds to itself (to form chains or rings) and react with a diverse number of elements, particularly oxygen, sulphur, nitrogen and phosphorous. Consequently there is a huge variety of carbon based molecules with respect to both size and shape; essentially a building set with an infinite number of parts.
Clearly this is not there but along the lines of how I interpret your thoughts. I'm sure after I read the references this will change. Chris Day (Talk) 10:20, 5 April 2007 (CDT)

edit conflict: Yes, it does have to do with all the parts and components and substitutions but that's just the "static" part. It's much ,much more than just macromolecules, it means that a molecule can -in a sense-store energy, by having one type of bond and yet-without being disintegrated (that;'s what I meant by covalent integrity) change in energy level as well as redox and still exist. It means that the shape of the molecule- by changing the level of the bond, can change- and still contain the same number of carbon atoms and with a little energy and available components like electrons or O or H etc, change back. It's not just a question of big-macro-or a question of modular-it's a question of dynamic. Look at the external references, please. I think I've listed them backwards, really start at the right and move left - more obvious. Although all of them are oblique :-). [12] [13] [14] [15]

Anyway, I re-read what you said about the single, double, triple bonds and that is what I mean- but it's the quantum mechanics of it that captures the implications of that, the energy and shape changes. And I am not able to convey that because I no longer am well enough acquainted. But still, I know the concepts and maybe someone who is very well acquainted with the physical chemistry can polish the words. It is something that, I think, has fundamental importance in this article. Nancy Sculerati 12:02, 5 April 2007 (CDT)

. Here is a key refs for out biochemistry spiel http://www.pnas.org/cgi/content/full/98/3/805 David Tribe 21:28, 5 April 2007 (CDT)


Quote Only two of the natural atoms, carbon and silicon, are known to serve as the backbones of molecules sufficiently large to carry biological information. Thought on the chemistry of life generally has focused on carbon as unique (3). As the structural basis for life, one of carbon's important features is that unlike silicon it can readily engage in the formation of chemical bonds with many other atoms, thereby allowing for the chemical versatility required to conduct the reactions of biological metabolism and propagation. The various organic functional groups, composed of hydrogen, oxygen, nitrogen, phosphorus, sulfur, and a host of metals, such as iron, magnesium, and zinc, provide the enormous diversity of chemical reactions necessarily catalyzed by a living organism. Silicon, in contrast, interacts with only a few other atoms, and the large silicon molecules are monotonous compared with the combinatorial universe of organic macromolecules.

Life also must capture energy and transform that energy into the chemistry of replication. The electronic properties of carbon, unlike silicon, readily allow the formation of double or even triple bonds with other atoms. These chemical bonds allow the capture and delocalization of electronic energy. Some carbon-containing compounds, therefore, can be highly polarized and thereby capture "resonance energy" and transform this chemical energy to do work or to produce new chemicals in a catalytic manner. The potential polarizability of organic compounds also contributes to the specificity of intermolecular interactions, because ionic and van der Waals complementarities can shift to mesh with or to repulse one another. Finally, it is critical that organic reactions, in contrast to silicon-based reactions, are broadly amenable to aqueous conditions. Several of its properties indicate that water is likely to be the milieu for life anywhere in the universe (2).

Thanks for the reference, David-so maybe size matters, after all. I just also want to thank everyone for putting up with me and my insistence on giving carbon and the major molecules a role here. Hopefully, it is a better article. Are we approved yet? Nancy Sculerati 21:49, 5 April 2007 (CDT)


Nancy, Chris and David: I suggest we do not go into the details of the chemistry of carbon in Life. The reader interested in those details can read Carbon, which should provide those details in a chemistry context developed for didactic clarity. We cannot provide that context, as it requires too many concepts for which the section does not prepare the reader. Fixing that would take us too far adrift from our goal. I suggest that the following paragraph as in accord with the theme of our article:


Why the central place of Carbon in the chemistry of all earth’s living things? One answer follows from the fact that the chemistry of the carbon atom renders it avid to form carbon-to-carbon bonds. That chemical property facilitates assembly of long chains of carbon-to-carbon bonds (polymers, or macromolecules), consisting of several classes of small carbon molecules, such as the sugars, amino acids and nucleotides mentioned above. Each of those small molecule classes consists of diverse species (e.g., nucleotides: adenine, thymine, guanine, cytosine, uracil; amino acids: glycine, leucine, methionine and more than a dozen others). In the sequence of those carbon-to-carbon chained diverse species of small carbon molecules, cellular macromolecules can carry sufficiently large amounts of information to specify the complex and diverse kinds of molecular interactions that enable cells to grow, survive and reproduce (see section, "Information processing", later in this article). Of all the atoms with a similar chemistry to carbon (e.g., silicon), carbon’s structure renders it uniquely capable not only of bonding stably with itself but also with the other atomic elements found in living things. Those include especially hydrogen, oxygen, nitrogen and phosphorus, necessary for forming the sugars, amino acids and nucleotides that make up the appropriate sequences in the macromolecules — nucleic acids, proteins, lipids, and polysaccharides — to build the molecular-interaction networks of the cells. Included among those interactions are those that enable the importing and transforming of energy and energy-rich matter from the environment (see section, "Thermodynamic empowerment of living", later in the article), and all those that make up the cells Metabolism. Carbon chemistry facilitates those chemical reactions, for numerous physico-chemical reasons (see Carbon). Carbon chemistry also enables its compounds to readily dissolve or associate functionally with water, of which the earth has abundance, and whose unique chemical properties for a liquid allow carbon chemistry to exploit its own life-giving properties. Elsewhere in the universe, where conditions differ greatly from earth’s, other atoms may hold a central place in life. [8]


It seems to me that with those words the reader will come away with the generalities (or principles) of why carbon has a central place in earth's living things without the burden of atomic details, and they will also presage the upcoming thermodynamic and information processing sections. I will substitute that paragraph for the current one(s) relating to carbon, and see how it flies with you all.
Nancy, whoever writes the Carbon article will need a biological perspective, so you needn't fear losing all the hard work you did in thinking about the biological aspects of carbon chemistry. --Anthony.Sebastian (Talk) 21:19, 8 April 2007 (CDT)

Last call

Yes we should be approved I will shorten the deadline and ask everyone to stop adding new conceptual stuff stuff, just copy edit and grammar/expression improvement is detected. David Tribe 22:10, 5 April 2007 (CDT)

Thanks. Nancy Sculerati 22:22, 5 April 2007 (CDT)

Suggest moving 'the stuff of life' section

I like the 'stuff of life' section — we need it. But think its location does not logically follow the introduction. Suggest moving it immediately after the 'Synthesis of perspectives on what constitutes a living system' section. Thinking this: first, basic principles of what constitutes the activity of living, then what and why the particular stuff of life on earth. After all, extraterrestrial life may be made of different stuff, but likely to have same basic principles underpinning living. Didn't want to make the move unilaterally. Thoughts? --Anthony.Sebastian (Talk) 22:54, 5 April 2007 (CDT)

I see it just the other way-(of course!). I think the stuff of life is in a good position and-perhaps in future versions, the entire article will-keeping its current form, include general concepts in each section that relate the systems approach to physics, physical chemistry, organic chemistry, biochemistry etc. For example, exobiology section might actually discuss prevalence of carbon in universe, which order stars might be expected to give conditions allwing organic based life, which stars (generally) might give conditions that would allow Si, or Si-C based biochemistry.Networks might even have a distilled abstract concept of how a Si based computer system might achieve life. What would be required? General principles. Otherwise, in my view, we are back to "Living systems".Nancy Sculerati 23:03, 5 April 2007 (CDT)
The logic we should think of is the logic of what a general reader needs to understand and learn from the article. Doesn't that reader need to be taken through the concepts in "Stuff of life" before tackling the more complex ideas about them that follow. In short I sense, it should stay where it is. David Tribe 01:22, 6 April 2007 (CDT)
I agree. --Anthony.Sebastian (Talk) 22:35, 6 April 2007 (CDT)

see also section

what about evolution in see also section? -Tom Kelly (Talk) 22:54, 5 April 2007 (CDT)

Of course. Darwin would turn in his grave. --Anthony.Sebastian (Talk) 22:59, 5 April 2007 (CDT)

Need to add CZ links like crazy

I started adding [[ ]] links but a lot more should be added (unless our policy is different than WP) -Tom Kelly (Talk) 22:57, 5 April 2007 (CDT)

should we link chemical reactions? (in molecules of life section) -Tom Kelly (Talk) 23:02, 5 April 2007 (CDT)

We have a Biology link but since the chemicals of a living system has a section, shouldn't we link to chemistry main article in that section? -Tom Kelly (Talk) 23:04, 5 April 2007 (CDT)

See also Chemistry and Organic Chemistry
In molecules of life section like is found in the biology article. How is the font smaller in the Biology article for these presection links?
See also Biochemistry and Molecular Cell Biology
What about links to main articles of Genetics and Microbiology?

in the next section -Tom Kelly (Talk) 23:07, 5 April 2007 (CDT)

I have proteins linked twice in the Molecules of living things section. I don't know which is better. I linked the first time it appeared but it was already linked in the later sentence which talked about proteins in more details. Thoughts?? -Tom Kelly (Talk) 23:36, 5 April 2007 (CDT)

should the link be proteins or proteins (singular vs plural) -Tom Kelly (Talk) 23:37, 5 April 2007 (CDT)

singular Nancy Sculerati 00:05, 6 April 2007 (CDT)

Suggestion for the carbon story paragraph

In an attempt to tell the story without detailing the chemistry, I played with the following.

Why the central place of carbon in the chemistry of all earth’s living things? One answer follows from the fact that the chemistry of the carbon atom renders it avid to form carbon-to-carbon bonds. That chemical property facilitates assembly of long chains of carbon-to-carbon bonds (polymers, or macromolecules), consisting of small carbon molecules, such as the sugars, amino acids and nucleotides mentioned above. Each of those small molecule categories consists of diverse species (e.g., nucleotides: adenine, thymine, guanine, cytosine, uracil). In the sequence of those chained diverse species of small carbon molecules, macromolecules can carry sufficiently large amounts of information to specify the complex and diverse kinds of molecular interactions that enable cells to grow, survive and reproduce. Of all the atoms with a similar chemistry to carbon (e.g., silicon), carbon’s structure renders it uniquely capable not only of bonding stably with itself but also with the other atoms found in living things. Those include especially hydrogen, oxygen, nitrogen and phosphorus, necessary for forming the sugars, amino acids and nucleotides that make up the appropriate sequences of macromolecules — nucleic acids, proteins, lipids, and polysaccharides — for the molecular-interaction networks of the cells. Included among those interactions are those that enable the importing and transforming of energy and energy-rich matter from the environment. Carbon chemistry particularly facilitates those chemical reactions, for numerous physico-chemical reasons. Carbon also enables its compounds to readily dissolve or associate functionally with water, of which the earth has abundance, and whose unique chemical properties for a liquid allow carbon chemistry to exploit its own life-giving properties. Elsewhere in the universe, where conditions differ greatly from earth’s, other atoms may hold a central place in life. [9]


--Anthony.Sebastian (Talk) 20:04, 6 April 2007 (CDT)

I think what we have is much clearer.Nancy Sculerati 20:16, 6 April 2007 (CDT)

Nancy: I know you had a hard time with the clarity of some of my sections, and you did much to improve the clarity with your edits for the audience you had in mind. Surely you can appreciate the reciprocity, that I might have some difficulty with the clarity of some of your sections. I tried hard to follow the sequence of your sentences in that last paragraph on molecules, but could not infer the assumptions needed to go from one sentence to another, and sometimes could not parse meaning within sentences — putting myself in the intended reader's position. Of course, that may reflect only my cognitive deficiency. It might also reflect a communicative deficiency in the paragraph. Respectfully, your paragraph did not reach me. I feel your attempt to detail atomic/molecular mechanisms in your effort to rightly highlight the central place of carbon in earth's living things did not succeed well, though the account had no untruths. I say that as so much opinion as your "I think what we have is much clearer". I do not defend the alternative paragraph I suggest, and regret any discomfort I might have caused you by suggesting it or making these remarks. I regret also my part in creating or fostering an environment that puts other members of the workgroup in the potentially uncomfortable position of something like arbitration. I must give that more thought. A thought I had you might consider, in the interests of reaching a varied readership, in this instance, to include the above paragraph in addition to what we have now, with the introductory sentence: "Another way to approach the question why the central place of carbon in the chemistry of all earth's living things:" I stress "in this instance", as I do not think it a good precedent. By the way, I have no expertise in the area of carbon chemistry, and what I wrote was my feeble attempt to summarize for a non-chemist Norman Pace's thoughts. --Anthony.Sebastian (Talk) 22:32, 6 April 2007 (CDT)

I just gave an opinion. There is no discomfort. You are welcome to change the text as you see fit, sometimes that's the best way of seeing if a change works. Who knows? Maybe I'll agree. Nancy Sculerati 11:06, 7 April 2007 (CDT)

Thanks, Nancy. Will fly the balloon, see if it stays up. Left your current text intact. --Anthony.Sebastian (Talk) 13:30, 7 April 2007 (CDT)

I kept some of what had been there before your addition, some of what you added (I think most) and tried to make it flow, sensibly. You are invited, of course, to modify. I am going to ask the physical chemists to comment on my lay descriptions of the physical chemical aspects of organic molecules, and stand to be highly embarressed. You are welcome to watch. :-) Nancy Sculerati 14:31, 7 April 2007 (CDT)

Nancy, nicely done. Thanks for considering my suggestions. --Anthony.Sebastian (Talk) 20:43, 7 April 2007 (CDT)

If a professional's intention is to embarrass a lay I wonder what status you may give to the professionalism of the so-called professional. Brushed the commercials and some dust out of your wordings, hope it suit the living needs :) Robert Tito |  Talk  18:07, 7 April 2007 (CDT)

Anthony, you changed the wording of early paragraph of "stuff of life" to say that in cells the organic molecules are in the liquids and colloids-but this really isn't true, because in organs and bodies (*hey-you taught me about systems) there are important (as you well know as a renal guy) compartments that are not cellular-like CSF, blood, joint gook - and its still true that its living, can I change it back please? Nancy Sculerati 20:30, 7 April 2007 (CDT)

Rob, not quite following you. I thought we could find glucose and urea, things like that, dissoved in water, say, in the cytoplasm, a colloid, of course, but still with things in solution. Regarding 'living', since the CSF flows in a cell-lined compartment in functional relation to it, I suppose you could call the CSF-compartment an organ. But I don't quite get your point. Perhaps I will after you make the changes. --Anthony.Sebastian (Talk) 20:41, 7 April 2007 (CDT)

It's not Rob, Anthony-it's me-Nancy. Look at the history pages.Nancy Sculerati 20:44, 7 April 2007 (CDT)

Oops! Sorry, Nancy. BTW: Seems Rob made Life disappear! --Anthony.Sebastian (Talk) 20:49, 7 April 2007 (CDT)

Isn't extracellular the environment? Is the air in lungs living? Or the acid in the stomach? Chris Day (Talk) 21:55, 7 April 2007 (CDT)

Minor suggestions for "molecules of life"

Chiming in with editorial comment on molecules of life section at Nancy's request. A few minor suggestions:

Current text

One set of organic molecules provides the material building blocks for living things: compounds of carbon, oxygen, nitrogen and hydrogen. Those often contain other elements, such as sulphur and phosphorous.

Input: My only real concern here is providing a concise definition of organic molecules. For example, the opening sentence might lead the reader to think that an organic molecule contains carbon AND oxygen AND nitrogen AND hydrogen - when, in truth, the only necessary component is carbon. Maybe something like:

Organic molecules provide the material building blocks for living things. Organic molecules are carbon compounds which may also contain oxygen, nitrogen, hydrogen, sulfur, and phosphorous.

... except more interesting. At some point in this section it might be worth noting that metal ions (especially iron in hemoglobin) are sometimes important parts of organic molecules.

Second suggestion:

Current text

Why does carbon hold the central place in forming living materials? The physical chemistry of carbon shows it can form many different type of bonds to other elements, and, even very easily, to itself, forming carbon-to-carbon bonds.

Input: The construction here is awkward and seems to emphasize the versatility of carbon for bonding over the carbon-carbon bonding. What is unique about carbon is its ability to form bonds with itself and form chains, rings etc. while simultaneously retaining the ability to bond with dozens of other atoms. This allows you to make molecules of many shapes and sizes with lots of different functionality. Nitrogen, for example, can bond with many of the same atoms that carbon can bond with, and can even bond with itself - but it can't form a long chain.

Put differently, I think that the question asked in the first sentence does not receive a sufficient answer. The "chains and rings" aspect becomes clearer later in the paragraph but the reader needs a more lucid answer to their question sooner, to help frame the discussion to follow.

I've made a few bad attempts at reworking this myself and will leave it to another author.

Otherwise seems factually sound. Jacob Jensen 21:58, 7 April 2007 (CDT)

Thanks so much, there have been a swarm of people working and I think a lot of the narrative sense ofg that section has been lost-will put it back, and perhaps ask you for a final check. Thanks so much, Jacob-Nancy Sculerati 22:02, 7 April 2007 (CDT)

Primary backbone

I have not followed all the recent changes but I noticed that the following sentence is right at the front end of the molecules of life section,

"Organic molecules always have a primary backbone of carbon atoms. "

Since proteins have peptide bonds (C-N) and nucleic acids have phosphodiester bonds (O-P-O) as part of their repeating backbones is this accurate? Or do these backbones not count since they are part of macromolecules? Chris Day (Talk) 00:16, 8 April 2007 (CDT)

Two different physical chemistry editors passed it- but you still may be right. You know- it's hard to say just exactly what we mean by organic molecules- they are not all Carbon-H etc, as Jacob (one of the P Chemists) pointed out. I used the word "primary" just to mean the major part of their structure, and as I say-it passed X 2, but more importantly, I think the whole section needs a fresh eye. Chris, the language has gotten entirely muddled through the various versions, I'm not sure that it's readable anymore, could you "time machine" some peeks through the versions and try to fix it up? If you are willing, you'll do a good job, I know. Nancy Sculerati 00:27, 8 April 2007 (CDT) - though I'm liable to give you a hard time, anyway :)
I will look, do you think it has settled down yet? There seems to be a lot of redundancy down at the bottom, what's up with that? I'll look through it and try and pull the ideas together I may have time tomorrow. As they say (or not) "too many biologists and chemists spoil the LB broth" And Life just can't thrive with out good LB. Chris Day (Talk) 00:38, 8 April 2007 (CDT)

OK Nancy, you can see your desired "time machine" version in the my version section below. Chris Day (Talk) 02:44, 9 April 2007 (CDT)

answer

Chris and Nancy. Since the basic structure involves carbons and the monomeric bonding is by amides, phosphodiesters and other groups the overall pictures is a carbon chain. The biochemical argument is that the amount of carbon far surpasses the amount of other atoms. It for that reason can be seen as a carbon chain. Where the latter means: a chain predominantly by carbon atoms but not solely. Is this what you asked for. It is the reason I changed the top lines in C-H-N-O with extra S and P. Because C-H-N-O make up the total backbone of any macromolecule. answered your doubt Chris? Robert Tito |  Talk  00:41, 8 April 2007 (CDT)

This is what I was expecting and I certainly would not disgree with this assessment. I do worry, however, that this could cause the misconception that all biological carbon chains are uninterupted. We know that this is not true but would someone without our background knowledge notice this? Chris Day (Talk) 00:51, 8 April 2007 (CDT)

I will try to precise then to stifle your worry :) Robert Tito |  Talk 

read and shiver, LOL, this better Chris?

Much better Rob. Chris Day (Talk) 02:41, 9 April 2007 (CDT)

A concern about abstract analysis

Where's the meat?

I suggest that usage of energy generated by metabolism, and materials from metabolism for synthesis of proteins and thus new cells is a fundamental characteristic of life. Somehow, with all the latest editing thats gone on, this has disappeared from the article, How can it be that we have cleaver discussions of systems and thermodynamics and even carbon chemistry, put the basic metabolic attributing of living systems are now not clearly readable in the article. David Tribe 03:57, 8 April 2007 (CDT)

On the latest read it seems better. I noticed on checking the diffs that the matabolism statement in Cells has been kindly restoredDavid Tribe 07:10, 8 April 2007 (CDT)

David, after we have worked together to get to this point, I ask that we discuss-all of us-before making major changes, so as not to go back to the confusion that had been generated by edit conflicts. Nancy Sculerati 13:40, 8 April 2007 (CDT)

I'm now happy with how this section returned to its earlier state and then evolved further, and particularly with the bridge Nancy built to the parts that follow. Yes, before that bridge was built the flow to further topics might have been sudden and abrupt , but it was necessary to pass through that territory early.David Tribe 16:50, 8 April 2007 (CDT)

Self-organization

No metaphor is perfect, but the genome is not both the hardware and the software, not both the computer and the program. This section has somehow lost its accuracy, and no longer makes sense. Could someone who is reasonably expert in molecular biology AND computers (not me, and I'm afraid, and not Anthony, I am also afraid - somebody who actually can program well and do molecular biology expertly) please fix it. Chris, are you our man? I think you fit the bill. Nancy Sculerati 13:40, 8 April 2007 (CDT)

This has come up before and I posted an analogy to one of the talk pages. Can't remember which one now I'll see if I can root it out. Chris Day (Talk) 13:50, 8 April 2007 (CDT)
Nancy, I fixed the problem by rewriting the first sentence of the second paragraph. Thanks for calling it to my attention. --Anthony.Sebastian (Talk) 21:34, 8 April 2007 (CDT)

Information

As we have given details about information, in the abstract, concerning macromolecules in the "stuff of life section", I was hoping that Anthony could modify the following, only because it reads as if information has not yet been discussed. (Of course, when it was written that was the case). I will contact him on his talk page, as well. Bioscientists study biological systems for many different reasons, hence biology has many subdisciplines (see Biology and List of biology topics). But in every subdiscipline, bioscientists study biological systems for the proximate reason of gaining information about the system to satisfy their however-motivated curiosity, and to apply that information to human agendas (e.g., to prevent disease, to conserve the environment). Those realities attest that biological systems harbor information, at least as people usually understand the term, 'information'. To appreciate how this perspective can contribute to understanding living systems, the following questions need answers: what do we mean by information? Nancy Sculerati 14:24, 8 April 2007 (CDT)

Nancy, not sure it needs modification, as earlier mention of 'information' far above. Will look at it again. --Anthony.Sebastian (Talk) 14:38, 8 April 2007 (CDT)

We need to assume that a reader is reading the whole article and the entire article should make narrative sense from start to finish, rather than otherwise.So yes, it does need a little modification. I will do it myself, if you like, Anthony. Let me know, please. You may well have better things to do. It should only require trivial changes, and I'll be happy to supply these. Thanks, Nancy Sculerati 14:43, 8 April 2007 (CDT)

A lot depends on how we settle the 'carbon chemistry' issue. I see no need for change until then. --Anthony.Sebastian (Talk) 21:36, 8 April 2007 (CDT)

No change except copy-edits and restorations/ of agreed points, please

Repeating a plea, and echoing others made earlier to minimise departures from current text and degradation of its content, unless argued first in talk section here.David Tribe 17:06, 8 April 2007 (CDT)

I agree, but (it's always something) the article should be readable as a whole from start to finish and I intend on going through and making it so. My best intention is to leave the ideas intact and to change as little as possible, but there will have to be some tailoring if it is to work as a whole. Is that agreeable? Does anyone have any specific suggestions? Nancy Sculerati 18:00, 8 April 2007 (CDT) In support of need to do this: Narrative coherence and flow Citzendium articles should be written from beginning to end. To be most attractive to readers, they need a unifying plan, or a narrative, which lends coherence and flow and invites readers to read to the end. This means that articles should not be modular or mere collections of facts that can easily be reshuffled. quoted from[16]

David, so much in the way of content and reorganization has been done since you nominated the article for approval that we need leave to edit content and organization, even if that means removing the nomination tag. In my opinion, the current article does not meet standards. --Anthony.Sebastian (Talk) 21:25, 8 April 2007 (CDT)

My version (actually all your versions)

I just worked through the various incarnations of the molecules section. I have tried to pick the pertinent points, keep it as simple and short as possible too. Since Anthony has also made several changes i will leave his version up, in the article and paste mine here instead. See what you think and take what you like. Chris Day (Talk) 02:33, 9 April 2007 (CDT)

Why the central place of carbon in the chemistry of all earth’s living things? The physical chemistry of carbon allows it to bond with many other elements, especially hydrogen, oxygen, nitrogen and phosphorus, and, even to form carbon-to-carbon bonds. The avidity for carbon to bond to itself accounts for the formation of organic macromolecules since these different carbon bonds vary in strength as well as in 3-D conformation - but are all remarkably stable. Carbon atoms easily join into longer chains and closed rings; and the small organic molecules (such as sugars, amino acids and nucleotides) can join into huge macromolecules.
Due to the versatility of covalent bonding that exists for carbon at standard conditions a variety of large and dynamic organic molecules are possible. The standard set of bonds that carbon can form is that of a tetrahedron, or pyramid. Other types of bonds involve more than one shared electron, and for that reason are called double, and triple bonds; importantly, these different bonds constitute three entirely different geometries. Changing from one type of carbon-to-carbon bond to another type, as when a double bond is reduced to a single bond, will cause energy changes but without destroying the molecule. Such changes not only affect free energy, but also affect the actual shape of the molecule and the particular side groups attached to it. In this way, for at least some organic molecules, the "pulse of life" is represented at an atomic level.
These properties of carbon mean that organic macromolecules are capable of containing tremendous banks of information coded in their very structure. Not only can each of the constituent molecules be huge, but several categories of chemicals, like nucleotides or amino acids, that contain several different species, can be ordered such that the possible combinations are effectively limitless. All these molecules are involved in the molecular-interaction networks of cells. Included among those networks of interactions are those that enable cells to import and transform energy and energy-rich matter from the environment and that ultimately enable cells to grow, survive and reproduce.
Are there any other ways to make complex molecules with similar versatility? Yes, by using silicon — carbon's close relative on the periodic table. But whereas the bonds of carbon are very stable at the temperatures that are compatible with life as we know it, silicon's Si-Si bonds are much more likely to disassociate. 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 would be able to form structures of such variation in size, shape, charge and composition, that their very existence provides ordered information.[10]

As an epilog, i have not rewritten any of this. I have significantly rearranged the sentences and made several deletions. You should all see a little of yourselves in this version. Chris Day (Talk) 02:37, 9 April 2007 (CDT)

Oh well done Chris. I just read through the Life article as a whole with some feeling of despair, like Anthony I feel that it had lost its way, introduced detail without explanation, and words without meaning, and lost narrative coherence and intellectual cogency. This however is much betterGareth Leng 02:40, 9 April 2007 (CDT)

I've taken an axe also to the end of the cells section, as I just didn't get the point. It seemed to me that this was a case of detail creep. Gareth Leng 03:38, 9 April 2007 (CDT)

...the Aristotle bit, I think was much better before, it was clearer I think, and if not clearer then at least shorter, and it put the biology clearly first so that the Aritotelian reference could be simply bypassed.

... and the lead. The lead just seemed to have too many words yet said too little, and some things (death) that do not really come up. I thought maybe less is better. I'll stop now.

Sorry David, but the problems I think went beyond minor copy editing.Gareth Leng 03:58, 9 April 2007 (CDT)

If Chris' text on molecules is "much better", as I also agree, can we please use it? Nancy Sculerati 04:04, 9 April 2007 (CDT)

I find Chris' text good too. The intent of my comments was to try on mimimise creeping additions that make the text worse and overly verbose. I agree shorter is better. I will take the liberty of placing Chris Day's s text given above in the article. David Tribe 06:36, 9 April 2007 (CDT)

made one word edit in that text: standard conditions a variety of large and dynamic organic molecules are possible. The standard set ... changed second standard to "simplest". It's an s orbital so I think it's true. Anyway, it not repetitious. If not correct, please do away with it. Nancy Sculerati 07:03, 9 April 2007 (CDT)

a bridge too far

Gareth, I see you removed the part about status in society determining access to food, water, shelter. That's fine- but I'd like to understand the idea better- because it is through this article-prompted by Anthony, that I have been exposed to Systems Biology (which is why I applauded him, way back when, on this page). Maybe I don't understand the concept of a systems approach, after all. I want to. Forget the article for a moment, it's not about the edit-it's about the idea. If instead of human kidney, I had said canine, and the society was a pack of dogs (or wolves)- isn't that part of the whole systems way of thinking? For example, there is a wildlife biologist, who wrote "Tracking is the art of seeing" ISBN 0-06-273524-1 who talks about an island in Canada where wolves were removed, and the deer changed. Not a new species of deer, but the size, the docility, the behavior of the herd, the deer became almost more bovine - over just a few generations. His argument was that the deer and the wolf cannot be properly considered except together- along with all the other factors of the system (at the time I read the book, I didn't think of it as a "system" but he did). Isn't it literally true that -getting back to either the deer- or the wolf- that the position in the herd (or pack) literally influences each cell in their bodies? At the extreme- say in famine or drought, might that not even be the difference between life and death of the cell? Or is that not considered biology? Not part of the systems approach, but instead, politics?? Nancy Sculerati 06:21, 9 April 2007 (CDT)

Isn't that ecology? Chris Day (Talk) 08:02, 9 April 2007 (CDT)
Just stopped in and I don't know if that is ecology, but is a very interesting concept that should be written about somewhere, even if not in this article. --Matt Innis (Talk) 11:01, 9 April 2007 (CDT)

If its ecology, which I agree it can be thought of-then it's the ecology of a renal cell. So-what's that called?Nancy Sculerati 11:24, 9 April 2007 (CDT)

For a renal cell I'd call it physiology but the concepts are pretty much the same as for ecology. The cells interact with their environment. They manipulate their environment. The only difference is scale. Chris Day (Talk) 13:17, 9 April 2007 (CDT)
well, can you give me an example-concrete-of an emergent property? renal cell or otherwise?Nancy Sculerati 14:12, 9 April 2007 (CDT)
Hi Nancy, check out this review. Burggren WW, Monticino MG. (2005) Assessing physiological complexity. J Exp Biol. 208(Pt 17):3221-32. PMID 16109885 Chris Day (talk) 01:49, 10 April 2007 (CDT)
Hi, there was nothing wrong at all in what you wrote, it's just that this was introducing other novel concepts into what was meant as an explanation of the most difficult concept in the aarticle, the concept of emergence, which is central to Anthony's construct. I'm still not sure that we have really got the notion across in fact. Technically emergent behaviours can arise in large nonlinear massively coupled dynamical systems when the systems exceed a critical level of complexity (numbers of interactions). These properties are visible at one level up from the level of the components. So digressing into multiple levels of interactions loses the thread of the explanation of emergence. Indeed, for this reason it might be better to trim back further, and introduce the idea of multiple levels separately.Gareth Leng 11:34, 9 April 2007 (CDT)

Maybe you could give concrete examples that show emergence , illustrate it, like in math when a new concept is introduced. Personally- I think the molecules-cells-organs-systems-organism-ecology thing which resonates with new qualities at every level caused by the interactions of them all is just what this article is about, and what Anthony is implying in the caption for that great hummingbird illustration he came up with, and that making this difficult concept interesting with an engaging narrative -along with that final box that Matt is looking for-would really complete the article. That's all about the resonance of different levels, so taking a reductionist approach just does not seem optimal to me - multiple levels in this topic is the essence - not digression. No? I would love to read your technical explanation (above) translated into such a pradigm, concretely show the abstract concept with a worked out problem that illustrates the principles. I'd like to understand it and I am not sure that I do. Can you explain it to me?Nancy Sculerati 11:41, 9 April 2007 (CDT)

A once through

I performed my first once through since you guys started and was very impressed. Made some minor spelling edits, etc.. The blue boxes are a good idea for creating a synopsis, but two were the same (I think) I went back and forth several times to see if they were. Also, I got to where I was expecting one at the end that wrapped it all up, but it wasn't there;) The article is packed with information from start to finish and flowed well from simple to complex. There were some points where the article may lose less knowledgeable readers as it got pretty intense, but it was worth it for the more advanced to see it brought together. Overall, very good work that combines the narrative format with hard facts. Can't wait to see it finished. --Matt Innis (Talk) 11:08, 9 April 2007 (CDT)

"Molecules" too chemistry-technical

Please consider that the "Molecules" section may scare off a lot of readers who may think they will have to wade through a lot of technicality in the rest of the article. I suspect a lot of readers will get stuck in "Molecules" and give up.

I suggest we relocate to the end, and give it a major header.

The reader does not have to start with carbon molecular chemistry with the technical detail spelled out in order to receive a coherent story of the "Principles of life". Carbon chemistry could nicely serve as a coda.

If you think it absolutely necessary to have a molecular beginning, give the generalizations in a way that presages the sections to come. I gave you an example of how that could be done. The detailed chemistry properly belongs in a chemistry article on carbon, with a biological perspective included. There all the terms and concepts now appearing ad hoc can be properly contextualized.

In addition, focussing on carbon chemistry tells only part of the story. Water chemistry deserves almost as much attention in highlighting the molecules conducive of earthly living as does carbon. One could not overstate the importance of the chemical properties of water in discussing "Molecules" in the context of the stuff of life. And it is not a short story devoid of chemical and physical technicality.

Why hydrogen, why nitrogen, why phosphorus? What makes their chemistry so accommodating. Without hydrogen, no carbohydrates; without nitrogen, no nucleotides or amino acids; without phosphorus, no ATP. The section is carbon-focused and therefore woefully inadequate to the promise of the title "Molecules".

Does anyone in our group feel they could write a comprehensive article on the elements and molecules that make up the living things on earth?

I urge you to take a step back, empathasize with the intended reader, and reconsider an alternative to what I feel is a misguided section.

--Anthony.Sebastian (Talk) 17:36, 9 April 2007 (CDT)

Certainly, I am persuaded that this molecular focus early on brings us away from the intended focus on life. As well as being half baked. I agree that the porperties of water are equally important and could give us a whole new section in itself. But to do justice means adding more and that will make the situation worse with regard to drawing away from What is life, as opposed Why is life possible. Chris Day (talk) 17:45, 9 April 2007 (CDT)

Chris, you wrote that section as it appears- yet you call it half-baked? Nancy Sculerati 17:51, 9 April 2007 (CDT)

Hi Nancy, I just noticed this. Anthony has it right below. For me, the main issue is one that addresses the thrust of the article. I don't think the text itself is bad. Does that make sense? As David says below, let's fly the kite and see what it looks like. We can always go back to other versions in the history. Chris Day (talk) 00:58, 10 April 2007 (CDT)
Nancy, non-pejoratively, 'half-baked' simply means more baking needed, Chris's point. And Chris, I agree, 'to do justice means adding more and that will make the situation worse", which is why I suggest putting the section last, as a main header, so we can expand it in "Life/draft" if we so desire. We do not know that the chemistry of earth's living things applies generally to Life in the universe, but we can feel prety confident that living things will require compartmentation, energy gradients (whether electromagnetic or chemical), information processing, self-oranization, evolution, etc. are fundamental principles of living. Starting with cells, then fundamental principles, and ending with molecules seems quite coherent.

If you don't want to put "Molecules" last, I offer the following for the section. I believe most readers will follow it:

Molecules

All known living things share the same set of organic molecules: although organic molecules may contain many different chemical elements, with few exceptions they always have a predominant structure of carbon linked to itself. In living things, organic species exist in mixtures of colloidal aqueous solutions, never completely homogeneous, bounded by lipid sheets, and proteins, allowing each pool a different composition. The stuff of living things, then, consists of carbon chains, studded with other atoms, and arranged in lagoons of fat, protein, water, and salts, of differing compositions. Those compositions determine regional properties like charge, density, viscosity, and osmotic pressure. Those varying compositions form gradients that provide the basis for the generation of electric fields, fluid shifts, and transport of molecules.

Why the central place of Carbon in the chemistry of all earth’s living things? One answer follows from the fact that the chemistry of the carbon atom renders it avid to form carbon-to-carbon bonds. That chemical property facilitates assembly of long chains of carbon-to-carbon bonds (polymers, or macromolecules), consisting of several classes of small carbon molecules, such as the sugars, amino acids and nucleotides mentioned above. Each of those small molecule classes consists of diverse species (e.g., nucleotides: adenine, thymine, guanine, cytosine, uracil; amino acids: glycine, leucine, methionine and more than a dozen others). In the sequence of those carbon-to-carbon chained diverse species of small carbon molecules, cellular macromolecules can carry sufficiently large amounts of information to specify the complex and diverse kinds of molecular interactions that enable cells to grow, survive and reproduce (see section, "Information processing", later in this article).

Of all the atoms with a similar chemistry to carbon (e.g., silicon), carbon’s structure renders it uniquely capable not only of bonding stably with itself but also with the other atomic elements found in living things. Those include especially hydrogen, oxygen, nitrogen and phosphorus, necessary for forming the sugars, amino acids and nucleotides that make up the appropriate sequences in the macromolecules — nucleic acids, proteins, lipids, and polysaccharides — to build the molecular-interaction networks of the cells. Included among those interactions are those that enable the importing and transforming of energy and energy-rich matter from the environment (see section, "Thermodynamic empowerment of living", later in the article), and all those that make up the cells Metabolism. Carbon chemistry facilitates those chemical reactions, for numerous physico-chemical reasons (see Carbon). Carbon chemistry also enables its compounds to readily dissolve or associate functionally with water, of which the earth has abundance, and whose unique chemical properties for a liquid allow carbon chemistry to exploit its own life-giving properties.

Elsewhere in the universe, where conditions differ greatly from earth’s, other atoms may hold a central place in life. [11] (by Anthony)


My take on this is that although I agree with the scientific point about water (but for brevity why say more) , I don't think the present article's section on chemistry IS overly technical. I tend to agree that the silicon details are iceing on the cake (which I can live with though) and think the current top copy is written fairly well. The alternative still needs some work and is not appreciably shorter. In simple terms it doesn't take us much further (yet). That's my take. David Tribe 18:32, 9 April 2007 (CDT)
David, thanks. I'll continue to work on it as I already have.--Anthony.Sebastian (Talk) 19:40, 9 April 2007 (CDT)

Molecules

I can buy into the argument that the molecules section is too long ( but not necessarily accept its fully true in this case.) The issue is worth airing thoroughly, and verbosity and continual additions of extra material are my main worry. I'm personally not keen on extensive discussion of silicon.
David, not too long, in my opinion, just too out-of-the-blue technical. Many readers may give up at that early point. Re silicon-silicon bonds, I think the assertion of their possibility at higher than earth temperatures reflects an inaccuracy. Their bond-energy is lower than carbon-carbon bonds, so they need lower than earth temperatures for stability. --Anthony.Sebastian (Talk) 19:33, 9 April 2007 (CDT)
Yes water should be and is mentioned (I put in the aqueous comments). But this issue is not solved by moving it elsewhere in the article. I can be so'ved by saying less and saying it concisely, which is the challenge with several writes which Chris Day addressed well. As far as Life is instrinsically a matter of molecules. The central features of life features include energy metabolism via oxidation reactions, ATP coupling and protein synthesis.=
David, one could list numerous other features of living things essential and therefore qualifying as central. I don't think life has a central feature; it's a system.
The article has to mention these molecules and metabolic aspects or briefly allude to them (as I did with water - but I didn't write a whole article about it). But we doesn't have to have much more that a few key hyperlinks to the details, in my view.
David, hyperlinks important, but the technical chemical level of the section properly requires more than few. I should think keeping a flow going without potential blocks our main goal. We can stop them at the end. --Anthony.Sebastian (Talk) 19:33, 9 April 2007 (CDT)
So yes, the article should perhaps say less about these topics, and I'm still struck how Norman Pace and Carl Woese do this briefer and better that we do. But to omit any comments about molecules will be to have a abstract complex essay without grounding or connection in material physics and chemistry. Do we really want that? (Thats opinion.)
David, more than one way to say less, and get more understanding more easily. I offer one above. (Opinion) But I feel reluctant to supplant other hard work by others, even though that hard work in my opinion slows down or blocks the flow. Moving the section to the end as a main header obviates that. --Anthony.Sebastian (Talk) 19:33, 9 April 2007 (CDT)
On the other hand, I can accept a start with what we have in cells as containing adequately brief comments about the essentials of molecules and metabolism, and see what happens if we move molecules to near the end? But Isn't it better to stay with what we have. There a lot of effort going into last minute radical surgery.David Tribe 18:19, 9 April 2007 (CDT)
David, trying it can't hurt it would seem, since we can always recover. --Anthony.Sebastian (Talk) 19:33, 9 April 2007 (CDT)
Im open to try and Ill do so with minimum (or zero editing just to see the effect. Its called a kite. Doesnt do any harm even if its ugly. I'll Flag it as Anthony and Davids kite. David Tribe 22:33, 9 April 2007 (CDT)
Anthony, I have made the change, leaving what I regard a minimal initial comments about molecules (mostly non technical chemical) which allow the cells section to remain unchanged with the same segue. I am aware that the information discussion has been moved with carbon. For the moment lets just inspect what we have. Revert all changes by going back to here David Tribe 22:49, 9 April 2007 (CDT)
David, on first look, looks good. Will give closer look in a.m. (One thought: to change header to "Life as organic chemistry" since we can't really say what life is.) --Anthony.Sebastian (Talk) 23:28, 9 April 2007 (CDT)

Molecules vs. cells first

We agree on the basic building block and working unit of life (things that live): the cell. It seems fitting then to build our article on Life on that basic building block, and start the article with cells. Yes, cells are made up of molecules, but so are automobiles. Only molecules organized as cells relate to life (living things). Starting off with cells binds the article together, because all the following sections refer to cells and cell systems, since we focus the article on them — how cells make a living.

Still, we want to write about the molecules, and what properties they have that make them life-as-we-know-it-enabling. That section would make a nice way to end the article, as it ends by opening a new vista relating to life (living things): atomic chemistry and biochemistry. It also brings in the new vistas Origin of life and Extraterrestrial life. Our article on Life gives focus to those two articles, as what we describe as living is the origin's goal, and what we describe as fundamental principles most likely applies to extraterrestrials, whatever their molecules. So life propagates, generating articles.

--Anthony.Sebastian (Talk) 20:14, 9 April 2007 (CDT)

animation

what do you guys think of this- [17] Nancy Sculerati 20:51, 9 April 2007 (CDT) oooh. its aliiivee! David Tribe

Stunning

This article is looking absolutely stunning. Your work on this article, folks, is truly inspirational. When this is approved, I'll blog it and draw a certain lesson: look, world, at what experts can do when they collaborate. It's nothing short of fantastic.

Speaking of stunning, the length of this talk page must be some sort of record. --Larry Sanger 00:15, 10 April 2007 (CDT)

OK, just a few tweaks; I'm very pleased with this. Well done everyone. Think it's going to be a very hard act to follow....Gareth Leng 04:54, 10 April 2007 (CDT)

The split of organic chemistry did work out to be much better (thanks Anthony, and all)- but it would be smooth if the section on how the molecules can themselves be informative was re-titled (after all, it now follows the Information section), I gave it a first try-but I'm tired this morning. I'm not sure my choice of title isn't just plain wrong. Please look at it and fix it or polish it.Nancy Sculerati 05:47, 10 April 2007 (CDT) also- does nobody want to actually use the rotifer? [ [18]]? Maybe an illustration for for cells-multicellular organism? Nancy Sculerati 05:59, 10 April 2007 (CDT)
The rotifer is cool and should fit in nicely. I'm enthusiastic. I'm still puzzeling through if the author has given his /her real name tho. My German is almost zero. David Tribe 07:01, 10 April 2007 (CDT)

We are back to the copyright issue. Can anybody at your place, David, - or you, do a quicktime through a binocular microscope? Of something cool- amoeba even better.Then we wouldn't have to worry. Or maybe a yeast cell budding - Chis, Gareth, Tony? Let's kick it up a notch. (not that it should hold up approval- we can always use it for a linked article on say Cell which we are still lacking.) Nancy Sculerati 07:22, 10 April 2007 (CDT)

The rotifer I agree is cool, but let's lock this down and move on - there are lots more articles to write, and we've found a lot of things that can be used in those.Gareth Leng 09:09, 10 April 2007 (CDT)

would someone please make it approved NOW

I am going to ask one of the other constables to approve it now- it's clear we all agree and that further changes, which are bound to occur otherwise- will just prolong the agony. Those inclined can continue on the draft. If other editors agree with approval now, putting that agreement here below will make the constable's job straightforward.Nancy Sculerati 09:43, 10 April 2007 (CDT) agreeGareth Leng 10:20, 10 April 2007 (CDT)

I counted on April 11 as approval date. Would like to do a few final tweaks today, April 10. --Anthony.Sebastian (Talk) 15:36, 10 April 2007 (CDT)

You are adding a lot of text-we have agreed on copyedits only. Please save whole new sentences - doubling of paragraphs for the draft. Please? :) Nancy Sculerati 15:51, 10 April 2007 (CDT)

Not a lot. But I'll stop now. I agree to approval now. When can I start working on Life/draft? --Anthony.Sebastian (Talk) 17:35, 10 April 2007 (CDT)

Stephen Ewen said he'd have time to do the approval "tonight" - but I don't know his time zone. Meanwhile- why not work on a related artilce? How about Emergent Properties for example, or Emergence. Look at my talk page and at Gareth's talk page, we discussed it as a good next article- I think that would be great. If that does not appeal-how about Cell? We have so very many major articles to write. I'm not suggesting that you stop writing Life, but that you take a section of Life -this article, (any one you like) and expand that into an entire article. That would be such a great contribution -and it would link to here, so in a sense- it would be an immediate modification to this article (by hyperlink) without having to wait for the draft. Nancy Sculerati 17:41, 10 April 2007 (CDT)


Fortunately in my time zone its your tomorrow. So I'm about to request Stephen to do the approval NOW. Ill check the last edits and update the URL first David Tribe 17
49, 10 April 2007 (CDT)

APPROVED Version 1.0

This article has been Approved. I see four editors indicating approval of the text on the history date given. I see no disapprovals. Congratulations on a job well done! --Matt Innis (Talk) 18:07, 10 April 2007 (CDT)

  1. 1.0 1.1 Jablonka E, Lamb MJ (2005) Evolution in Four Dimension: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge: The MIT Press
  2. Schneider ED, Sagan D (2005) Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. ISBN 0-226-73936-8 excerpts of several chapters here
  3. Wierzbicka A (1996) Semantics: Primes and Universals. Oxford England: Oxford University Press ISBN 0198700024
  4. See list of semantic primes at this site: Goddard C, Wierzbicka A (2006) Semantic Primes and Cultural Scripts in Language: Learning and Intercultural Communication
  5. J.H. Woodger (1929) quoted in Barbieri M (2003) The Organic Codes; An Introduction to Semantic Biology. Cambridge University Press. Appendix. DEFINITIONS OF LIFE. (Author notes: From Noam Lahav's "Biogenesis", 1999; from Martino Rizzotti's "Defining Life", 1996; and from personal communications by David Abel, Pietro Ramellini and Edward Trifonov, with permission)
  6. Carol Cleland on "What is Life?"
  7. (Lazcano A (1994), cited in Popa R (2004) Chronology of definitions and interpretations of life. In: Popa R, (ed.) Between Necessity and Probability: Searching for the Definition and Origin of Life. Berlin: Springer-Verlag 2004
  8. Pace NR (2001). The universal nature of biochemistry. Proc Natl Acad Sci USA 98:805-808 Link to Full-Text
  9. Pace NR (2001). The universal nature of biochemistry. Proc Natl Acad Sci USA 98:805-808 Link to Full-Text
  10. Cite error: Invalid <ref> tag; no text was provided for refs named pacepnas01
  11. Pace NR (2001). The universal nature of biochemistry. Proc Natl Acad Sci USA 98:805-808 Link to Full-Text