Talk:Biology/Archive 1

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• 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.

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)

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)

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)