Talk:Biology/Archive 1

Article Plan, Policies, and Decisions

• Here we need to summarize the conclusions arrived at in the archived discussions, in a bulleted list.
• This set of policies should go at the top of the talk page.

Folks, can you fill this in? I.e., in bulleted points, what should I glean from the discussions so far? What have the editors decided?

• Talk:Biology archive 1

Readings

This needs some more: 1 or 2 standard textbooks, possibly some more general books. Though they may fit into other sections also, at least 4 or 5 should be given here, and possibly some more diverse outside sites. But perhaps you are about to do it. DavidGoodman 13:27, 30 November 2006 (CST)

Please give suggestions. Nancy Sculerati MD 16:14, 30 November 2006 (CST)

Images

see [1] Check out [2] especially [3] re Darwin Gareth Leng 14:38, 30 November 2006 (CST)

I also found this, but it is not credited to Leeuwenhoek? --D. Matt Innis 22:03, 30 November 2006 (CST)

Oh but it is just so perfect!! Please put it inGareth Leng 08:40, 1 December 2006 (CST)

Your wish is my command:) --D. Matt Innis 10:15, 1 December 2006 (CST)

The EM Epstein Barr picture to the right was from #2 above. I can get any of the other ones that you might want as well. --D. Matt Innis 22:26, 30 November 2006 (CST)

This electron microscopic image of two Epstein Barr Virus virions (viral particles) shows round capsids—protein-encased genetic material—loosely surrounded by the membrane envelope

Does anyone have any photos of their own that they might be willing to donate? I don't, I'm pretty pitiful as a photographer. Also- can anyone program the DNA image so that it's still unless clicked? I think the animation is great - but distracting on the page if you try to read on-line. Nancy Sculerati MD 16:16, 30 November 2006 (CST)

I'm never satisfied with my photos either and I could not see any way to stop the DNA animation. I think someone would have the right software to reprogram it. --D. Matt Innis 22:03, 30 November 2006 (CST)

I think we have to use this!! Image:Sperm-egg.jpg|right|300px|thumb|A spermatozoon fertilising an ovum On Nancy's point, we could maybe replace the animation with a still but give a link to the animation?

I'll work on that too. --D. Matt Innis 10:15, 1 December 2006 (CST)

What about some Vesalius? Not sure. http://blpc.bl.uk/learning/images/bodies/illustrations/vesalius-st.jpg or Galen? http://www.karlloren.com/images/Medieval_Anatomy_1.JPG Oh, 'please check this out [4] (One of the most fascinating features of sea urchins is 'Aristotle’s lantern'. This complex device for grinding food consists of an elaborate musculature and 40 calcareous plates, and was first described by Aristotle)

doesn't take much to make you happy does it? its a sea urchin;) --D. Matt Innis 10:18, 1 December 2006 (CST)

My you are busy:) --D. Matt Innis 10:15, 1 December 2006 (CST)

The mitochondrion picture is great - can anyone rescale it to be a bit smaller? Gareth Leng 07:13, 1 December 2006 (CST)

The scaling feature in CZ doesn't work yet, but I can shink it and redownload... However, when I did that I couldn't read the words:) Still want it smaller? --D. Matt Innis 10:15, 1 December 2006 (CST)

I don't think it is a good idea to upload a small picture because the scaling does not work. Especially if the text becomes illegible. The solution, for now, is to just link to the picture image:mitochondria.jpg without it being visble. I am assuming it is trivial to get the scaling to work. Chris Day (Talk) 13:41, 1 December 2006 (CST)

I agree, especially with text. We could do this, too:

• The mitochondria is the powerhouse of the cell.

Though, it means they have to click on it. Not quite the same as seeing it automatically. --D. Matt Innis 14:34, 1 December 2006 (CST)

Hey thanks Matt, so good to be working with you again, the homunculus is just great. Mitochondria - well you know, what can I say, bigger better for now.Gareth Leng 11:22, 1 December 2006 (CST)

I like the idea of being able to click on some things to get images - is there any way that our own legend can appear with the image when we do that?Gareth Leng 06:52, 2 December 2006 (CST)

Every picture that we link too could be our own. All we have to do is upload the picture and write our own description. Uploading our own versions is probably a requirement for other reasons. To make a montage that fits tightly together the pictures need to have the correct aspect ratios. For the images to have the correct impact some will have to be cropped. So the first requirement is to pick the pictures we think best represent the topic. I had started selecting some of the best from wikicommons here following Nancy's earlier requests. There are two spots free that require some cropping of pictures. I have my eye on a beautiful SEM of pollon grains and a toadstool. The only problem then is that bacteria are not represented, I could not find a suitably dramtic photo. Nancy had requested an attacking lion and that one in the linked montage is the best available. It would be better, in my mind, if we had one that included the lion's prey in the picture too, unfortunately there is nothing in commons. This is a start, however, I suggest we choose the photo's we think are the best available and most topical before creating the montage itself. Chris Day (Talk) 11:36, 3 December 2006 (CST)

Here is a copy of the montage I have put together in wikicommons using some of their better photos. As I mentioned above, it can be seen here and each photo can be clicked to link to the original. Unfortunately, since the resize photo feature in CZ is non functionale, the code I used to write that photo-table montage does not work in CZ.

Can you add in text box, below the photo-montage, the name of each organism? You can add something of the kind present in Wikipedia's Biology article: "Biology studies the variety of life (clockwise from top-left) E. coli, tree fern, gazelle, Goliath beetle". Thanks. Yuval Langer 13:50, 13 December 2006 (CST)

That was the idea although i was waiting for the picture scaling bug to be fixed before continuing. At present all the images in this article are substitute images. Plus the final montage figure has not really been finalised, although with the current approved version I guess it has been finalised. Chris Day (Talk) 14:16, 13 December 2006 (CST)

I hadnt been reading the talk page and this is after the event but I actually rescaled the mitochondrion a few days ago. Glad to learn that soft-rescaling is not yet operational, saves me time trying to learn why Im makeing coding errors!. If you are after bacterial images I can find a few. We have them by the zillions in my teaching department. David Tribe 15:32, 12 December 2006 (CST)

With regard to the content, one problem is that we are lacking a picture of bacteria. I am thinking a hot spring might be a good one for that example, similar to this one in Yellowstone NP. I'll probably be messing around a bit more to try and incorporate it if others like the way this is going. Any other must have pictures you have seen? Chris Day (Talk) 23:54, 3 December 2006 (CST)

Wow, Chris, that looks great! I like it. Even if we went with it the way it is. --D. Matt Innis 16:28, 4 December 2006 (CST)

Anthony.Sebastian recent [12/01/2006] edits

Some references to "3rd pgraph" really 4th pgraph.

Some concern about early introduction in article of science vs. religion controversy.

Consider article as a whole a tour de force.

Welcome, Anthony. I've avoided your phrase 'On Earth' just to avoid possible distraction re extraterrestrial life. I don't think we should get deep into the religious controversy but just acknowledge it. Maybe we should link into a footnote to reference Dawkins book? Gareth Leng 06:43, 2 December 2006 (CST)

Thanks, Gareth. I had intended the phrase "on Earth" to do double duty, focusing on life on Earth, as currently biology restricts itself to Earth's living things, and as an idiom referring to 'among all the possibilities', as in 'How on Earth did you find that outfit'. A little double entendre with the second meaning slightly humorous.

I don't think we should introduce the science vs. religion at all, especially early on in the article. It requires a more extensive and balanced treatment, either as a separate section or separate article. --TonySeb 11:59, 2 December 2006 (CST)

Agreed. It will appear in several topics as well as of course evolution. For evolution, we probably will need for clarity an article on the modern theory of evolution, presenting it as the scientific consensus is, without the debate. Then we do need articles both on the 19th century debate, which is reasonably well covered by the present WP article on Darwin, as well as the contemporary controversy, which in WP is dealt with very poorly (in my opinion) in a number of places. And then we need one on Philosophy of Biology, which [perhaps should be done in conjunction with the philosophy group. For this article, I'd just put links to a few such obvious places.

Links

What's our policy on wikilinks here? My feeling is that we should be conservative, link only to good articles that are directly relevant or which might be needed for understanding - so for example I wouldn't link to mathematics etc Any views on this?Gareth Leng 07:03, 2 December 2006 (CST)

Linking is often wildly overused, but I think just a little more linking than you suggest is a good idea, namely also linking to a) related areas (so I would include mathematics, as another science) and b), to be vague, a limited amount of areas of genuine interest that readers might not be aware there are articles on. For example, from this article: "At some point, probably somewhere in the fertile Nile delta ...". Knowledge of the Nile delta is not really necessary for understanding the article, but it is nonetheless something that might catch a reader's interest and linking it gives them the opportunity to pursue it further. Generally, I would say that linking is not only to help readers understand the article's topic, but also to accommodate the browsing reader (which is quite a large proportion of readers, I would say). (But emphatically not any article that happens to exist). Also, I think it is best to link each article once, the first time it's mentioned. Damien Storey 08:23, 2 December 2006 (CST)

---

My opinion:I think that links, like references, should be minimized in the text. They are generally distracting and often superfluous. Now, if a word or phrase has an obvious meaning then I'd argue that just because we can find an internal link does not mean we should. For example, unless mathematics links to a show case article, why stick in a hyperlink? Same for 'mankind'. On the other hand, if the link is for a word like DNA or Darwin, that would send the interested reader "down the rabbit hole" to a pertinent fund of knowledge, then I think that's good. Also, a reader who is very familiar with either will probably choose to read on, where as a person who really isn't sure what those words mean can find out. Personally. one aspect of WP that works against its content (to me anyway) is the apparent contest among readers to stick a hyperlink and reference to practically every word. That is a style CZ can best eliminate rather than emulate. If anybody who speaks English fluently understands the words, and there is no considered reason to point them to the article, then no reason to have the text change color. Similarly, I don't think the second line of this article needs a footnote to bring us down to Etymology. Why not let Etymology just stand on its own as the last, or near last, section of the article? [User:Nancy Sculerati MD|Nancy Sculerati MD]] 08:43, 2 December 2006 (CST)

In general I agree with the Nancy. Consider some of the newer WP articles eg WP:Napthaleneto see the use of links, which in general is more restrained than it used to be. Remember that links are normally made only at the first mention of a word, unless there's a real need to link again to a subtopic when it's discussed again later--so they should normally not be very heavy later down.

But remember we are writing for readers who do not nevessarily know about changing the way links appear.

There has been an ongoing issue between religion and science for hundreds of years that still concerns millions of people. In the US there are several school districts that are concerned about exactly how biology is taught for those reasons. There are scientists who are 'faith based athiests' and vigorously object to notions like 'the soul', and there are religious individuals who believe that teaching evolution undermines the student's possible salvation. There are plenty of references to both in the world's literature, including such journals as Nature and newspapers like The New York Times. It is important to offer a conciliatory view and its inclusion is one of the better features of the article.

Matt, I love your pictures. I'll look into the programming over the next weeks. Chris, I do like that collage you came up with, it's odd that it has so many of the images that I had mentioned as possible. I'd never seen it.

Gareth, I'd like to change the word 'enigmas' in the intro back to something more street-wise, you silver-tongued Brit. By the way, I like the whole Human Genome thing, meaning I like how you worked it in. I do think we should move on though, and start on some new articles.

David, I think you hit the nail on the head with your phrase Collaborative writing. That's what we seem to be doing, and it's fun, because we all learn, plus it enables the article to have a voice. It's not easy and it's impromptu rather than rule-bound. It's like a scholarly jam session for those who take pleasure in thinking about these subjects.

Damien, for browsing, I think we can figure out a way to put internal links at the bottom of the article in a separate section instead of having interference of the flow of text.

Nancy Sculerati MD 08:43, 2 December 2006 (CST)

I'm not sure about that: for example, should the link to Nile delta be put at the bottom of the article? Damien Storey 08:50, 2 December 2006 (CST)

IMHO The purpose of wikilinks is multi-fold: At the basic level, they provide expansion of difficult words or terms used. They are also used to point to logical extensions on the subject of the article for linear follow on reading. Sideways addition reading on parallel or sister subjects should also be provided.

The linked terms should not be too high brow. While an adult may know that Botany and Zoology are subsets of biology, links should also be provided on low brow terms, piped to the relevant article, so that younger readers can make use of the site. (e.g. I paraphrase, 'Biology includes the [ [Botany|study of plants] ].')

Links should still be made if the targeted article is of poor quality or even if the article does not yet exist. The red link or prominent low quality page should prompt other authors to write or improve the bad page. Omitting the link will result in the loss of the potential for improvement of the bad article.

The visual appearance of a large number of links is to some extent irrelevant. While the current default link colour is bright blue, this can be changed. It is also within the scope of each individual CZ user to set his own individual preferences.

In general, I don't like long lists of links at the end of articles. A article should finish with the same boldness as it started. It shouldn't whimper away into excessive listings of trivia at the end as is so common on WP articles. Derek Harkness 10:34, 2 December 2006 (CST)

The place to put the trivia is nowhere, in WP its a way of avoiding edit wars on th main content. But the external links and the references-- where else can we put them? The end is where such things go in books. It's good having them together.DavidGoodman 19:15, 2 December 2006 (CST)

I personally like the links in the body of the article. Certainly it sometimes leads me in directions that I did not intend, but I always learn something and that is what makes electronic media so interactive and draws us in. We can go where we want when we want. I know it might put the onus on the author to keep the readers attention to the end, but if the reader doesn't know what one of the words means, they probably aren't ready to comprehend the rest of the article. After awhile, we all stop seeing the blue anyway, but it's nice to see it when we are questioning our own knowledge. The red is another story, but Derek makes a good argument for building purposes. I don't see any reason why we can't take a link off if it seems to be redundant or unnecessary. --D. Matt Innis 22:18, 2 December 2006 (CST)

WRT David's comments, There is no rule that says external links must go at the end and internal links must go in the text. There's nothing to prevent you linking to an external site in the prose of the article. At the end you may want to mention a few sites or pages that provide additional reading. However, this could be done as prose with comments introducing those sites/pages rather than just listing URLs.

As for references, there is an on going discussion on the forums about how to better reference our articles. The current system, inherited from WP, is not the best but we have to live with it for now.

To finish, two general comments about links: We should avoid making links within section headlines. (e.g. don't do = = [ [Section title] ] = =) Apparently the wikimedia software has a bug and links in the section titles messes with the article's menu system — And lastly, remember to check pages that you are linking to so as not to point to a alternative spelling (leaving a red link that should be blue) or to a disambiguation page that could only confuse the reader. Allot of time is waisted on WP fixing links that point to disambiguation pages. Derek Harkness 22:49, 2 December 2006 (CST)

Terminology: "life" vs. "living things"

I would like to make a pitch for substituting "living things" for "life" whenever possible in the Biology article.

When we say biologists study "life", we really mean they study "living things". The word "life" nominalizes, or technically, reifies, the processes that occur in living things that enable them to remain alive. One cannot answer the question, "What is life?, without answering the question, "What processes constitute the activity of living?

We cannot attribute to biology the science of life, because its science does not investigate an abstraction. It studies the tangible, the proceses that occur in living things.

For the sentence "Biology is the science of life", I substituted "Biology is the science of living things". No reason given for changing it back.

"Life" has no specificity. We even speak of inanimate things as having life, as in the useful life of a car or battery. Biologists do not study cars or batteries, although some living things transport other livings and others generate electricity.

Some will say I quibble. That's life. Anthony Sebastian 15:23, 3 December 2006 (PST)

I wanted this article to convey the sense of excitement and challenge, and biology is about the differences between living things and non-living things, and that's life. I guess I thought that the 'science of living things' didn't convey this for me, it sounded a bit flat, as though its about the things and that they happen to be living is almost incidental. We do much more than study the things, but go beyond to ask the abstract ot higher level questions, like what makes this alive? and this I saw as a question that catches everyone's imagination as being an eternal and enduring challenge to understanding. What makes what a biologist do different from what a physicist does? I think it is in part these big, abstract questions that lurk beyind all we do. However, I'm easy, I'll go with whatever consensus there is.Gareth Leng 05:19, 4 December 2006 (CST)

Gareth, you seem reluctant to advance beyond the "received" terminology--received from as early as 1200 A.D. according to OED, which at any rate defines "life" in terms of "living" matter as opposed to non-living matter: "The condition or attribute of living or being alive..."; "The property which constitutes the essential difference between a living animal or plant, or a living portion of organic tissue, and dead or non-living matter...". Perhaps "Biology is the science of living matter" would appeal to you more, getting, as it does, away from "things". That definition would seem to cover biology in its broadest sense. The question, not "what is life?", but "what makes it that matter can live?" You said it: "what makes this alive?" --Anthony Sebastian 13:54, 9 December 2006 (PST)

As an author, I agree that when I read "life" it opened a much bigger door, after all, wasn't that really how biology started - looking for that "spark" of life? I think it is more than semantics, it does mean more. The question is whether you editors want it to mean more. --D. Matt Innis 07:40, 4 December 2006 (CST)

Matt, yes, looking for the 'spark' of life. As if a 'spark' or 'force' or 'spirit' needed. We don't need to respect the origins of biology by acceding to its outmoded thinking. Now we look for the physical processes that distinguish living matter from non-living matter. Michaelangelo could bring life out of a marble stone but he couldn't make it a living thing. ----Anthony Sebastian 14:08, 9 December 2006 (PST)

I see where you're coming from and it certainly simplifies things, but, isn't biology still looking for the physical/chemical 'spark' that defines life?. IOW, doesn't biology also include the sciences that study why we love, we hate, we marry and we feel a need to believe (things that define "life" more than just living)? If not, then it would follow that biology is just accepting that there was a 'spirit' that guides these factors. Certainly these things can be explained in ways other than 'spiritual'. Though it is safer. --D. Matt Innis 17:30, 9 December 2006 (CST)

And are viruses alive or not? Scientists can't even agree on this, so it might be worth giving it a nod in the article. Chris Day (Talk) 08:09, 4 December 2006 (CST)

---

Nancy:

Your defining biology as the science of life in no way disaccords with conventional views or terminology. In my defining biology as the science of living things, or as I now prefer, the science of living matter, I wanted to try to move beyond conventional thinking and introduce a more rigorous terminology. I took my lead from a respected biologist, Ernst Mayr, “one of the 20th century's leading evolutionary biologists” (Wikipedians 2006).

Ernst Mayr, in his last decade as a centenarian, wrote a book called This is Biology: The Science of the Living World (Mayr 1997). One might have considered the title presumptuous had it not come from someone the likes of Ernst Mayr. I believe in his subtitle he chose to ‘define’ biology as “the science of the living world”, rather than as “the science of life”, because in his opening chapter, What Is the Meaning of “Life” [his quotation marks], he states:

"To elucidate the nature of this entity called "life" has been one of the major objectives of biology. The problem here is that "life" suggests some "thing" -- a substance or force -- and for centuries philosophers and biologists have tried to identify this life substance or vital force, to no avail. In reality, the noun "life" is merely a reification of the process of living. It does not exist as an independent entity. One can deal with the process of living scientifically, something one cannot do with the abstraction "life". One can describe, even attempt to define, what living is; one can define what a living organism is; and one can attempt to make a demarcation between living and nonliving. Indeed, one can even attempt to explain how living, as a process can be the product of molecules that themselves are not living." (Mayr 1997, page 2).

I suggest taking Ernst Mayr’s lead, defining biology as the science of living matter, adds precision and rigor of terminology to CZ’s article, “Biology”, and modernizes thinking about the nature of biology as a science.

With that said, I still feel completely comfortable deferring to your and the groups’ judgment, and remain impressed with the work you did to rewrite the article from scratch.

References

Mayr, Ernst (1997), This is Biology: The Science of the Living World (Cambridge, Mass: Belknap Press of Harvard University Press)
Wikipedians. Ernst Mayr. http://en.wikipedia.org/wiki/Ernst_Mayr . 2006.

---Anthony.Sebastian 19:51, 11 December 2006 (CST)

Getting close

Good idea Chris - made me think, perhaps we can get this and some other thought provoking questions into the legends of the composite images? On Approval - this is an article written by experts at a popular level and maybe its approval should be gauged by how well it meets that ambition - perhaps we should invite Larry Sanger to oversee the approval of this article, especially as it may well be the "first" to be approved, so why not let him judge how well it meets his hopes for CZ, when we think we're ready. I think we'll be ready to ask when we have the images, and then we can move on?Gareth Leng 10:20, 4 December 2006 (CST)

Since we are the first group to have an article ready, I suggest we first have a formal approval by 2 of us, as is presumably going to be the pattern. They could then ask Larry to collaborate. Testing it with less experienced people would also be a good idea, if they decided to do that. (As I originally had a totally different conception of the article, I'd rather not be one of this group)DavidGoodman 14:08, 4 December 2006 (CST)

I'll make up some sort of temporary approval template in the next day or so. --ZachPruckowski 15:27, 4 December 2006 (CST)

OK, we now have an article approval template. To see it in use, check out my user page (which is obviously a demostration for testing purposes, and not an actual approved article). It currently isn't "locked" in any way (someone who has sysop can do that later, after it's "finished"), and it needs to be cooler looking, and ideally also easier to use. --ZachPruckowski 16:34, 4 December 2006 (CST)

Aristotle

I removed the following sentence:

"It might also have come from examining the seeds of some trees, where the entire immature plant is contained within the husk, and springs into independent life as a young tree once planted."

I can see how this might have inspired him to think of the concept of the homunculus, but, at present, this does not seem to be the emphasis. Currently the paragraph seems to emphasise the woman vs male contribution more and so I deleted it out for now. It is also confusing since if Aristotle did use the plant for inspiration, it was based on a misconception. The analogous idea, from the perspective of a plant, would be that the plant equivalent was in the pollon, not in the seed. Chris Day (Talk) 23:56, 4 December 2006 (CST)

Consistency

What date format will be the final one here? Currently we have "20th century" and "Twentieth Century" styles intermingled throughout. Chris Day (Talk) 00:04, 5 December 2006 (CST)

So far there has been little discussion on manuals of style other than to say "we need one". For consistency with other articles, I'd say we should follow the WP manual of style pages until we decide on something better, later. So for dates with centuries, use 1st, 2nd, 3rd, 4th and "century" with a small "c". E.g. "20th century". For years, use numbers like 1984. There is no need to append AD. For dates BC, you should append like "246 BC." If the date is approximate, use c. or circa e.g. "c. 246BC" For exact dates to the day, use month day, year or day month, year. e.g. "January 1st, 1984" or "the 1st of January, 1984"

It may be that this style is changed at sometime in the future, should be decide to depart form the WP style manual. But at least by sticking to the WP manual for now we can possibly automate any alterations later.

I agree with this approach. It is the only feasible way to start, remembering that some subjects will differ. Even there, I would follow the established conventions of WP for such fields for the time being. DavidGoodman 19:13, 5 December 2006 (CST)

I say Biology is Science of life is the way it should be in approved version

Come on, guys, do you seriously believe that Biology is not the science of life? Or that the phrase "living things" is indisputably more accurate than the word "life"? Sorry, it ain't so. I strongly object to the change, especially since it markedly degrades the literary quality of the piece for no unambiguous reason. I really object to this new opening. Nancy Sculerati MD 08:09, 9 December 2006 (CST)

Also-can we put that collage of Chris' that's here on the talk page in the beginning of the article? Is it possible to put it to the right of the contents box- in that blank space? Nancy Sculerati MD 10:14, 9 December 2006 (CST)

I put a scaled down version in where you were asking so you could get a feel for what you want until Chris gets back. When the scaling feature gets fixed in CZ, then we can go back to the first verion and get exactly what you want. You can move it around anywhere you want by cutting and pasting from there. The article is looking really good. I like life vs living things. --D. Matt Innis 12:35, 9 December 2006 (CST)

For those interested there are two other possible montages to be seen. Not to mention many other very good photos that are not included in any of the current montage choices. I particularly like the SEM of the drosophila eye. The tigers roar might be more dramatic than the current lion. See what you think. Chris Day (Talk) 21:59, 9 December 2006 (CST)

religion and science

"conciliatory view was mentioned. I do not think we should intend to offer a conciliatory view. I think we intend to offer an objective view, which in this particular case may not be the same thing at all. For some such contentious topics--even ones with less emotion involved-- the difficulty of present a fair view in a sentence or two is extremely difficult, and the solution is to defer the discussion on more detailed pages. I can't imagine a reader who would not know to look at the evolution or the Darwin article as a place to start. DavidGoodman 15:16, 9 December 2006 (CST)

I personally know a number of people, adults, who are very bright and successful in business, finance and sports who would not have a clue. Years ago, I had a friend running for the U.S. Senate who was suprised to find out that my cat had a heart. It amazes me, too. Still, many people, even if they are not religious themselves, have a popular notion that science is against God. There really are people out there who are literate and bright enough to follow the text we are writing here, and yet honestly will be learning because they are not really sure what biology is. Isn't that who we should be writing for? Others can use it too, but I think it should include everyone and not assume knowledge.Nancy Sculerati MD 09:01, 10 December 2006 (CST)

I like the way that religion is introduced here, and think it's handled well; I see the approach taken as being objective, rather than conciliatory; the secular position is described unapologetically, but without being confrontational. I think that an interesting article need not shy away from indicating areas of wide interest, and yes of course this needs to lead to articles of greater depth.Gareth Leng 12:03, 10 December 2006 (CST)

links

Many apparently absurd WP links are made for a purpose. The links from years is a way of getting a list of all things that happened in that year. Many of the links from places are meant to give a list of everything relevant to the place. I am not quite sure we will want to do either one of them. If we do, although they cannot really be added properly by a bot, it would not be hard to do manually. People wanting such list can always go to WP. Linking the divisions of a subject or cognate subjects is an obvious use. Linking to biographical articles, though it can look very dense, is the only way to indicate them, since not every name mentioned will have an article. The sort of absurd links to ordinary words that happen to be used in an article is, of course, absurd, and I'm even seeing less of it in WP than I used to find.

Links versus see also: Even in paper encyclopedias &c. there are sometimes bold face links in the middle of text to indicate related articles. Given hyperlinking, I think the users will now expect them. There's a convention (often not followed) in WP that see also's are given only for terms not linked, under the assumption that the link was sufficient. The alternative is to have something like the traditional library: Broader subjects: Related: Narrower: with narrower and broader going only 1 level down or up. I mention these just to list the possibilities--I am not sure what style is best. DavidGoodman 15:16, 9 December 2006 (CST)

subdisciplines and Biology today

There has been discussion in the forums about the bio article. Zach and Chris, and David Goodman and others have pointed out the lack of "biology today" as compared to "development of biology" and the advantage to a sort of central spot for the article in a reference sense. I had replied: in earlier versions, there was a clickable outline of biology to follow the essay part. A sort of reader's guide that helped the user explore more on biology in CZ. I remember that you had filled a lot of that in, Zach. When it disappeared, I was quite sorry to see it go. I am not sure why there is that length message of the byte limit. I do understand that in WP many articles end in silly lists, but for an article "covering" a huge field, like this biology article, there is value to having an explicit reader's guide included in a formal section towards the end. That's the kind of feature where uniformity does have value, and might be repeated in all similar articles on giant subjects that have whole sets of subdisciplines. When I was kid, I inherited a set of ancient (WW II era) Compton Encyclopedia. The last volume was an index that had short entries, so it was readable rather than just a list of names and subjects- but it referenced the whole set in that index.I think the way we had it, the "Fields within Biology" list, helped guide the reader the same way that old index helped guide me. We might even expand it so that there were two or three sentences about each sub discipline instead of just a phrase. I open that to the group. I found that the list was moved to a separate page. I moved the contents back. Do you think it is better this way? Should we expand the descriptions a little? If we keep it this way, we need to fix the links and delete the orphan page. Or is it better the other way? Nancy Sculerati MD 19:40, 11 December 2006 (CST)

Thanks,Chris for those last changes. Are we there yet? Can we vote on approval?

Personally, I think that the article is "good enough" to be approved. Since I made the plan, I don't think I should push the "approve" button. From the Forums, it seems that Larry is happy if 3 editors agree to approve. If you do, please record that approval here. If you don't, please state what aspect of the article PREVENTS its approval. So we can fix it. Nancy Sculerati MD 10:43, 12 December 2006 (CST)

My view is that Nancy has put a lot into literary style, and that her judgement is good. Much of the qubbling is argually true in some sense, but the changes mooted detract from the aesthetics and the arguments to do so are not compelling. Weve got a LOT of articles to do so it time to move on. Sorry if I dont have style and tact but Im a three fingered slow typist! Thanks Nancy David Tribe 15:49, 12 December 2006 (CST)

I agree we need to move on, but while I have this article on my mind there are some phrases and sections that I felt need to be imporved. I have attempted to fix as much as I can today so you can move on with the approval process with my support. Much of my editing may seem semantic, but, I do think it is as important that the articles here are written accuratly as well as with style. Chris Day (Talk) 16:00, 12 December 2006 (CST)

Ive made about three word changes. Used particulate in describing Mendels genes, instead of "sort of binary". Ova instead of ovum for reasons of grammar. Two substantive points 1. There is a warming that 36 k is too big for some browsers. As the words are so good (and should be kept IMHO), can this be fixed with shrinking images or eliminating one image! 2. The only substative addition I think might add something is a mention of the RNA world or RNA based catalysis, or RNA regulation as a acklnowledgenent of a major change in concepts. I can craft a few word, dont think it matters eactly what, as long as it provides a glimpse of this previously uncharted territory. Mabe as a link in Further reading? Give me a few (scores of minutes) hours and Ill find a way.

THAT SAID, It has my vote for approval as an editor that did not contribute much at all. As was said earlier, I think, its a tour-de-force. I read it word by word and it held my interest, and I've been reading this stuff since the mid-sixties.

We need to move rather than quibble as we have about 5,000 more fish to fry.

David Tribe 16:44, 12 December 2006 (CST)

Hundreds

• Currently this article says:

"Not only was that vast project, involving hundreds of laboratories in many different countries, completed ahead of schedule"

Were there really "hundreds" of labs involved the HGP? That means over 200, but I'm not aware it was that many. How are we defining '"involved" in this context? Chris Day (Talk) 15:07, 12 December 2006 (CST)

Change it to "scores" OR "scores, if not hundreds" and be done David Tribe 15:53, 12 December 2006 (CST)

I can live with scores. For reference, the HGP sequencing consortium involved 20 sequencing centres in six countries. [5] Chris Day (Talk) 16:03, 12 December 2006 (CST)

I added in a few words that make hundreds OK but take em out if you want Nancy David Tribe 16:29, 12 December 2006 (CST)

• Another point. i'm not too keen of the sentence:

"but use this genomic information to trace our own distant ancestry to more primative life forms"

No extant species can be described as primative in the true sense of comparing genomic sequences. They are all modern species. Chris Day (Talk) 15:38, 12 December 2006 (CST)

---

I think that's Gareth's stuff. But I'd say that even if a lab sent in a sample- that's "involved".I added the word hundreds back in, because I thought it provided more of an image for those who are not personally familiar with laboratory collaborations. I see your point about "primitive", and agree. There probably is a smooth ay to say "to life forms that appear to have evolved such that they are morphologically similar to primitive life forms, and, allow us to infer more detailed hypotheses about the specific path of our own descent - if we make the assumption that genotypic change has been as limited as that of their morphological phenotype." but I can't think of it, offhand. I'd like to make sure I understand your point about biology turning the tables on technology (in a sense) and acting as a catalyst in the human genome project. What specific technological advances were made? Nancy Sculerati MD 16:04, 12 December 2006 (CST)

Actually i was not meaning that biology turned the tables on technology, although that is an interesting perspective. I was trying to elude to the fact that the biology was being driven by the new technology. It would not have happened without it.

I was thinking along the lines that big biology has become possible due to the following; all provided from outside the field of biology.

1. The ability to sequence massive amounts of DNA cheaply and yet reliably. Applied Biosystems sequencers revolutionised the science along with the automated robots that were developed for the more tedious tasks.
2. The computer programming skills that allowed the assembly of the sequences and the gene annotation to be automated. The database programming that allowed huge amount of information to be accessible to biologists.
3. With regard to biological research, the nanotechnology is allowing genome wide northern blots using various ingenious technologies. Also, genome wide analysis of chromatin conformation.
4. Real time growth kinetics and 3D reconstructions that could only have been dreamed of before the current computer power became available.

It's possible you misinterpreted my original version? I'll let you change it to how you see fit. Chris Day (Talk) 16:16, 12 December 2006 (CST)

So, with Gareth that's 3. I'll e-mail Larry

I'm assuming that Gareth approves, although I have not got him to respond today - he was happy with it in the recent past. I'll e-mail Larry, and we'll put it up. I'm sure it will still have things that could be said better, but as David said, we've all got a lot of other work to do here. Thanks, every one. Nancy Sculerati MD 17:10, 12 December 2006 (CST)

Review

This is an amazingly well-written article. It does not attempt to introduce every aspect of biology equally, but by being selective--focusing on the definition and scope of biology, and then surveying its main areas via its history--it does provide exactly what is wanted from an encyclopedia article about biology, namely, a general introduction that conveys a rough general understanding. A survey of the main areas--alphabetically, say--would convey more information about those areas, but would very probably not do nearly as good a job at introducing biology as a whole. So, thanks, folks, for helping prove the viability of the general premise behind CZ.

The next thing to do--because I want to use this article to illustrate the proposed approval process--is to make the relevant templates. Also, I won't be able to protect the main page until I can make subpages, and I can't make subpages until subpages are turned on. I've already asked the tech guys to turn them on, and since I told them it's top priority, hopefully it will be done by this evening. --Larry Sanger 18:10, 12 December 2006 (CST)

I added near the end (see history) In 2006, not only can we map out how chromosmes have evolved across species, but use these genomic resources to trace our own distant ancestry to other life forms, even so far as the enigmatic traces of a preceding world .

We can cut it to just one reference We are at 37 kb

In 2006, not only can we map out how chromosomes have evolved across species, but use these genomic resources to trace our own distant ancestry even so far as the enigmatic traces of a preceding world [18] [19] [20]. However, for all the advances that have been made in the study of living things over the centuries, biology remains a science that has only begun to provide a basis for understanding life. The genome projects, so far from answering all our questions, instead opened up many new ones. One of the biggest surprises was the realisation of how few genes it takes to make a human being - just 28,000 or so, not many more than is needed to make simple animals, and fewer than the number of genes in many plants.

There that cleaner, even if I did write it myself, it even bypasses a previous quibble! David Tribe 18:30, 12 December 2006 (CST) Ill see what image fiddling can do

David Tribe 18:20, 12 December 2006 (CST)

Approval template

Nancy Sculerati MD has nominated this version of this article for approval. Other editors may also sign to support approval. The Biology Workgroup is overseeing this approval. Unless this notice is removed, the article will be approved on 20061212.

I've switched this to the last page in the history that Nancy edited. If you want to nominate a later version, please do so (and discuss). I.e., convince me that you're all comfortable with David Tribe's latest edits...which I haven't even looked at myself, so I have no opinion, I am just the janitor. --Larry Sanger 18:59, 12 December 2006 (CST)

These edits were directed at file compaction. I did discover they give scope for providing better presentation of links.

The Idea of Key pointers to XXXX , oriented to learning is useful as a subpage concept for main subject area in general, rather like an analogy to Ecyclo Britaanica Micropedia.

• BUT My Firefox browser gives no indication of having problems with the file size at present, and as they say, if it aint broke, why try and fix it?

I'm absolutely delighted with Nancy's and others' efforts (gentle pushing) , and the approval process, and look foward to the next biology approval (maybe Barbara McClintock ? which we'll work with via the workgroup forum David Tribe 19:47, 12 December 2006 (CST)

I would point out that some issues discussed and agreed to above got missed by finalising with Nancy's last edit. I made quite a few changes which i think others agreed to, including repairing typos. David's further edits also tightened the article a lot and I really like the solution to the lists at the end. So I would endorse David Tribe final edit here as the best version to date. Chris Day (Talk) 20:47, 12 December 2006 (CST)

Aha, then the procedure would be to remove the {{ToApprove}} template above and insert it again here with new information. Then either we wait at least 24 hours, or two more editors approve as well. --Larry Sanger 20:54, 12 December 2006 (CST)

Since Nancy approved the template above, I will leave it to her to make the decision to extend to David's last version. Chris Day (Talk) 21:15, 12 December 2006 (CST)

Post Approval Copyedit Final Version Plan by Nancy

Please give me 36 hours to come up with a final version that incorporates Chris and David's stuff. I think I understand what is needed. The last version that I edited is not the one that should be frozen long term for this article. That version is actually not quite written yet. It's just that it never will be written if we keep going, because we hit edict conflicts and we are in a sort of infinite series of half-lifes to the end point (so to speak). I think that we have managed to come together as a team, and I propose that the article is "provisionally approved", which means that it should be frozen now - as I hope it is. On Thursday I will post a version of the last section (the continuing story)on the talk page here and we can all take a look, and make changes on the talk page, agree on that section. Meanwhile, every one should look over the article for typos and double words and that sort of problem. Post your findings here on the talk page. I'll then ask Larry to remove the template and put up the final article, with all those things fixed. Nancy Sculerati MD 21:23, 12 December 2006 (CST)

Nancy, I would suggest you continue to work with the current draft version rather than posting here on the talk page. The way I see it, these approvals just hold a stable version (vandalism free :) ), but the draft remains organic so it can, and should, improve with time. I am assuming there is no final version here if editors agree to new changes.

Larry, on a related note. Now I have see the frozen version with the template, I realise that the template is quite prominent. I was imagining something a lot more subtle. Could we at least have it invisible in the print version? Chris Day (Talk) 21:33, 12 December 2006 (CST)

Chris, everybody changes the draft page and I'm new at the wiki, I just get confused. Don't worry. I think it will work this way. Nancy Sculerati MD 21:40, 12 December 2006 (CST)

Hi Nancy, just to be clear, I think Chris meant this page: Biology/Draft. The policy is that new versions of the article can be developed on that page, while (post-approval) Biology is reserved strictly for approved versions. --Larry Sanger 21:53, 12 December 2006 (CST)

Biology/Draft, is what i was referring to since there is a link to that draft version in the approval template. Besides there are many edits that David and I made that did not make it into the final version. You can see the differences looking at the history here. I feel these are more than just a few typos (the primative discussion above for one) and to do this on the talk page seems to go against the editing mechanisms that are being proposed here in CZ. Chris Day (Talk) 21:57, 12 December 2006 (CST)

Chris, that's exactly what I will include. Just please give me until late Thursday, I am not available today to work. Yes, we need to incorporate those changes and we will. This is not just a proof. Meanwhile, please do a proof on what is published as the approved version - leaving out the last section. Put your findings here on the talk page. I promise that by Friday you should be happy.Nancy Sculerati MD 06:40, 13 December 2006 (CST)

Just to transparently go over this: I wrote to Larry (just before approval) Larry, take a look at the biology article talk page - several editors now approve Biology. Can you make it so that only I can edit it if you agree? I just want to copy edit it and tweak a few words as we have gone over in the discussion page. I'd like to get it done and move on, as David Tribe said- "we have about 5,000 more fish to fry" and if it's open I get into edit conflicts that slow me way down. Please let me know, best, Nancy (meaning not perfect, but generally all right ;)) I wrote that because, as we were working, as I am no expert at "merging" (mean I plain can't do it) conflicting versions when an edit conflict comes up, I was not able to fix it with it on the open wiki. I had no idea that Larry would go back to the last version I edited and approve that one, but I can see -re-reading my e-mail- why he did. It is true that the last section needs a couple of sentences fixed. David Tribe's "compressions" are in the record, and although nice, we apparently do not have a browser problem without them. What I propose -remember this a test case in the approval process- is that we AGREE on a last section, fix the typos, and in some organized fashion, put up the very final approved article- which will be >95% what is up there now. If I go back to the draft- which is open (properly) to every one - instead of trying to fix this through the talk page over 48 hours (or less), then I (and I argue no one) can keep abreast of the changes. That draft page is the incubator for the next article, or perhaps another article. Nancy Sculerati MD 07:03, 13 December 2006 (CST)

As Ive said elsewhere, having been through this 1.5 times I now see how we can develop a workable procedure.

A little Approval process dynamic flexibiliity is no big deal and we can easily revert. We can both keep moving and accomadate the last minute details if we devolpe workable patterns of interaction.

Let me try and explain:

The To approve tag gives us the flexibility (suggested by Larry) to update the link shown in bold in this model:

ToApprove|editor=Nancy Sculerati MD|url=http://pilot.citizendium.org/wiki?title=Biology&oldid=100012065%7Cgroup=Biology%7Cdate=20061212

in the provisional time af a day or so before it takes effect,I think we should leave it up to the nominating editor to choose the version thats best, provided they dont involve substantive changes

In any case if the "approved" version misses out on important improvements we can , in a dynamivc fashion empower the editor to Action a second To approve tag and just ask her for a reasonable justification that huge issues are not involved before allowing it to go through unimpeded.

Thanks Larry for the next comment which was drafted as I wrote this! David Tribe 15:47, 13 December 2006 (CST)

David makes good points here. I would like to suggest that the draft version should be the canvas where we "develop our workable patterns of interaction". With its built in history and the ability to compare different versions quickly, it is by far the most powerful editing environment. The talk page is obviously important for discussion that is more complex and that requires more input than an edit summary. But, in my view, it is a poor substituite for the actual editing. Chris Day (Talk) 16:50, 13 December 2006 (CST)

Well done everyone. Can we get rid of the WP disclaimer? certainly not appropriate hereGareth Leng 10:56, 13 December 2006 (CST)

I'm drafting a reply to Nancy's latest on the forum, which requires that we basically solve the endgame problem. Gareth, I asked the tech guys re the disclaimer and they say it's automatically tacked onto every article. It's going to require some extra coding to make it turn-offable. --Larry Sanger 15:38, 13 December 2006 (CST)

Seeing how well this went, and anticipating some WP type adversarial editing in the future. What is to stop three other editors from coming along and approving a new draft the next day? And then we would have group edit wars? This group worked well together, but I can see some difficulties with an article like homeopathy for instance. If this has already been answered, just feel free to point me in the right direction. --D. Matt Innis 16:23, 13 December 2006 (CST)

See this forum page. We have no shortage of problems--use your creativity to think of solutions. --Larry Sanger 19:18, 13 December 2006 (CST)

Congrats

Please accept my heartiest congratulations for approving the first article in CZ. I feel guilty in not having been able to try my hand in this article owing to time constraints. However, I hope to make up for that in near future. Supten 21:26, 12 December 2006 (CST)

Comment on approved vs current draft

Here is a summary of the edits in the last paragraph made AFTER the approved version was set. The bold text highlights the differences between the versions and underneath the grey box is the justification for the edits. This is only some of the changes made. There are other changes that were made that I will try and document later. Chris Day (Talk) 16:50, 13 December 2006 (CST)

Before Not only was that vast project, involving hundreds of laboratories in many different countries, completed ahead of schedule After Not only was that vast project, drawing on the inputs of hundreds of laboratories in many different countries, completed ahead of schedule

The Human Genome Project sequencing consortium involved 20 sequencing centres in six countries. [6]. David made the edit above that seems to solve the problem by making the claim of hundreds more vague.

Before In 2006, we can not only actually map out how chromosmes have evolved across species, but use this information to trace our own distant ancestry to the most primative life forms After In 2006, not only can we map out how chromosomes have evolved across species, but use these genomic resources to trace our own distant ancestry to other life forms.

I made the following edits:

"we can not only actually" is hard to read. I have simplified it.

"chromosome" typo corrected.

"information" sounds too dry

"the most primative" is incorrect when comparing genomes since all are from extant modern species.

David then went on to substitute other with the following text even so far as the enigmatic traces of a preceding world. I think this is a thought provoking idea that does tie into to a quote made earlier in the article. Three different references are given and may be excessive.

• http://nobelprize.org/nobel_prizes/chemistry/articles/altman/ The RNA World
• http://nobelprize.org/nobel_prizes/chemistry/articles/cech/index.html Exploring the New RNA World
• http://www.pnas.org/cgi/content/abstract/86/18/7054 Modern Metabolism as a Palimpsest of the RNA World

Only the last reference really addresses how the genome project could help reveal the RNA world; ironically it was published (1989) before the genome projects started. I am assuming there is a better more up to date reference that incorporates genomics into the discussion.

Before The human genome project, so far from answering all our questions, instead opened up many new ones. One of its biggest surprises was the realisation of how few genes it takes to make a human being After The genome projects, so far from answering all our questions, instead opened up many new ones. One of the biggest surprises was the realisation of how few genes it takes to make a human being

This section was rewritten so it focuses on the concept of genome projects rather than the HGP alone.

Before Understanding And so we come full circle, After And so we come full circle,

Clear typo here was removed.

Thus the final text would look like the following:

By the end of the 20th century, progress in molecular biology had given rise to the Human Genome Project, an ambitious vision to sequence the DNA of every single human gene. Not only was that vast project, drawing on the inputs of hundreds of laboratories in many different countries, completed ahead of schedule , but we now also have the DNA sequences of many other species with which to compare the human genome. The purposes of these gene sequencing projects have required close collaborations with both engineering and computer sciences, and those efforts have provided new technological tools. In a sense, technology has now been advanced by modern biology (returning the favor).

In 2006, not only can we map out how chromosomes have evolved across species, but use these genomic resources to trace our own distant ancestry even so far as the enigmatic traces of a preceding world (new reference here for RNA world/genomics) However, for all the advances that have been made in the study of living things over the centuries, biology remains a science that has only begun to provide a basis for understanding life. The genome projects, so far from answering all our questions, instead opened up many new ones. One of the biggest surprises was the realisation of how few genes it takes to make a human being - just 28,000 or so, not many more than is needed to make simple animals, and fewer than the number of genes in many plants.

However, it seems that identifying the sequence of our DNA is not enough, to really unravel our genetic code, biologists must start the difficult process of understanding all the ways that these genes can be processed and just how they interact with each other. And so we come full circle, again relying on the traditional fields of biology to unravel the secrets that are not apparent from knowing the genomic sequences alone.

The following sentence "In a sense, technology has now been advanced by modern biology (returning the favor). " also needs to be reworked due to a mix up between nancy and myself discussed above.

---

RE enigmatic traces of a preceding world, which I definitely think is work arguing for, one reference is enough and http://www.pnas.org/cgi/content/abstract/86/18/7054 Modern Metabolism as a Palimpsest of the RNA World

is very good, highly relevant, and I can't resist the poetry of Palimpsest in the title.

The concept is from the pre-genomics era and I think it's pointless to link it to genomics David Tribe 18:57, 13 December 2006 (CST)

There is no doubt that the PNAS one is the best (by a large margin). But don't we already link it to genomics in the above sentence? "use these genomic resources to trace our own distant ancestry even so far as..."

I do like the addition since it relates well to the sentence much earlier in the article that refers to the primordial soup paper in Nature ("It is now widely believed that almost four billion years ago, before the first living cells, life consisted of assemblies of self-reproducing macromolecules".[12]". It adds a little more continuity to the article (similar to the baby theme). Chris Day (Talk) 19:13, 13 December 2006 (CST)

1)If we say hundreds of scientists instead of hundreds of laboratories it will be true without changing the rhythym of the words.

2) I'm not sure that the Human Genome project actually did change technology. That might have been my misunderstanding of something Chris Day wrote. It might be more accurate to bring up the technology theme in this way: That unexpected speed was another boon from technology.

3) We need to come up with a sentence that leads into the the last sentence of the article- which I think should remain there. Nancy Sculerati MD 21:27, 13 December 2006 (CST)

I agree with point one. With regard to point 2, I had never intended to say it changed technology, the emphasis of what I wrote got corrupted from subsequent edits. What I originally wrote was: "In a sense we have seen modern biology catalysed by technology" i.e. it would not have been possible without the modern technology. So we are on the same page here. Finally, the last two sentences should definitely stay i made a copy and paste error above but have resotred them. My original lead in sentence was:

"The scope of these projects is to focus on whole systems and has required close collaborations with both engineering and computer sciences to establish new technology. In a sense we have seen modern biology catalysed by technology. However....."

This has now moved up but something along the lines of:

The scope of these projects has been to focus on mining the genomic data for the blueprint of life. However it seems that identifying the sequence of our DNA is not enough, to really unravel our genetic code. Biologists must now start the difficult process of understanding all the ways that these genes can be processed and just how they interact with each other at the level of whole organisms. And so we come full circle, again relying on the traditional fields of biology to unravel probe the secrets that are not apparent from knowing the genomic sequences alone.

New stuff (or recycled) is in black. This might set the scene for big science vs small science and hint at the balance that must be met to move forward. Chris Day (Talk) 22:37, 13 December 2006 (CST)