Talk:Life/Draft

Formating decisions

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

Other style standards?

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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).

• Yes. I had not got that far in editing the article. Anthony.Sebastian (Talk) 22:33, 14 February 2007 (CST)

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)

• • Yes. Needs work. Anthony.Sebastian (Talk) 22:33, 14 February 2007 (CST)

• • Re flu: get well soon. Anthony.Sebastian (Talk) 22:33, 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

	File:Synechococcus Phage S-PM2.gif

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

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?