Talk:Biology/Archive 1

Proposed Article Plan

a) purpose: a true and accurate explanation of the subject that is an inspiring introduction for an interested user to explore the topic both on (1) CZ and (2) the web. To introduce a few selected major issues in biology -like (1) evolution as opposed to belief in religion's depiction of creation of man.

b) style/intended readership level. Simple but elegant language. As a flagship entry point into Biology, this article should be written at a consciously lay level. Keep jargon out and use natural language wherever possible. Maintain a consistency and coherence of style within this article.

b) length. Short and sweet; An essay that is readable and enjoyable alone, and which looks good when printed out.

c) things needed urgently: suggestions for illustrations, or for particular examples, interesting in their own right, understandable to lay readers, illustrative of the excitement about biology, from different perspectives (impact of biological science on our lives and the environment - the Green revolution? cloning? molecular biology and understanding the building blocks of life? Ecosystems, evolution, genetic engineering, brain imaging?

This article cannot and should not attempt to be comprehensive. It doesn't matter what is left out, only that what is included is interesting and inspiring to a lay audience, accurate for an expert reader, beautiful in words, images and layout to both, and that paths to follow are signposted. How this is to be done is not clear, I personally do not like lists; I'd rather see a link to a list here, and would still rather see a link to a "map". As this article should contain nothing seriously disputed, the need for references is minimal. Gareth Leng 06:06, 10 November 2006 (CST)

Talk

Dr. Sculerati--that's quite bold, to simply dive in and rewrite the thing from scratch. I like it!

However, there is one problem, that anyone (not just you) could help with. It is that there are many links from the original biology article that no longer exist. That doesn't necessarily mean that the pages linked-to are orphans, but what it does mean is that there is no longer such an easy way into those topics from the article. What I suggest, then, if we completely scrap an old article, is that we keep a list of old links at the bottom of the article, and make sure they are incorporated into the article as appropriate. (Of course, some links probably don't need to appear anywhere on the page at all. But the names of subdisciplines, yes.) --Larry Sanger 02:40, 1 November 2006 (CST)

Fields list

I'd like to comment, but I do not know how far developed you consider this to be. Your list of fields is partial, but is it more helpful to contribute more now or to wait until you have done s--in what will undoubtedly be a more systematic way?20:47, 2 November 2006 (CST)

Style

I have made quite a few edits and have a few points to address regarding those edits. First, what is citizendium planning on doing with respect to style issues? I noticed this page has already started drifting away from those established in wikipedia. Was that intentional? I have made some changes to the titles that conform to the MoS in wikipedia. I have also established a reference section at the bottom so citations can be added.

I add some content back, such as the classification section. I hope that is OK. Along those lines, I have also restored many of internal links that were lost during the initial reorganization. Maybe we do not want to discuss homeostasis or even link to it but we can see how the article develops with time.

With respect to the lists I am not sure which is the best way to go. For the topics have add all three possible routes in the one section, we need to decide the best way to present such information. Three possible choices include: 1) having a footer template and nothing in the article; 2) Having a comprehensive list in the article; or 3) having a narrative on the topics with a reference to a separately maintained list on a different page. Chris day 05:02, 7 November 2006 (CST)

Biology and philosophy

I moved the following paragraph from the introduction:

Biology asks some of same questions found in religion and philosophy, questions such as "How did life begin?", and "What features seperate something that is alive from something that is not alive?". The biologist approaches these questions using the scientific method. Therefore, the biologists answers to such questions differ from the answers found in philosophical and religious works. Whether scientific thinking about such great issues as the origin of life on earth is compatable with religious doctrine is itself a contentious issue. Some great thinkers, such as the physicist Albert Einstein, have found no real conflict on the varying teachings in science and religion, but consider Divinity and the Natural Universe to be one and the same (see Albert Einstein for detailed discussion with references).

This seems to be a little off track for the introduction but as the whole article is not currently layed out I cannot tell how it will relate to future content. To me it seems like material that should be in the body of the article itself. Also, biologists barely touch on the subject of "how did life begin", so it seems a little too much weight for an overview article (assuming you are planning to flesh this out in the main text). Chris day 13:38, 7 November 2006 (CST)

Chris, I find the paragraph on the philosophy of the biological approach, elegantly written. After all, what separates biology from intelligent design or religion? I am new to CZ so please forgive any lapses in protocol. What inspired Watson & Crick was an attempt to understand what constitutes life. So this is engaging, and inspiring to the reader. So just as where did the universe evolve from inspires the physicist, the understanding of what constitutes life is the ultimate question in Biology. As Feynman stated, I wonder why, I wonder why I wonder.

Biology asks some of same questions found in religion and philosophy, questions such as "How did life begin?", and "What features seperate something that is alive from something that is not alive?". The biologist approaches these questions using the scientific method. Therefore, the biologists answers to such questions differ from the answers found in philosophical and religious works. Whether scientific thinking about such great issues as the origin of life on earth is compatable with religious doctrine is itself a contentious issue. Some great thinkers, such as the physicist Albert Einstein, have found no real conflict on the varying teachings in science and religion, but consider Divinity and the Natural Universe to be one and the same (see Albert Einstein for detailed discussion with references). Arnold R. Rabin,MSEE,M.D. --Arnold Rabin 04:23, 8 November 2006 (CST)

My problem is that it romanticises biology into something it is not. Very few biologists ask "How did life begin?" or "What is life?" What they routinely ask is how does it work. Or with respect to watson and Crick what is the structure. I know this sounds boring but it is the reality of the work. Chris day 08:28, 8 November 2006 (CST)

Many do not subscribe to the idea that biology is boring. An analogy might be that computer science is boring because most programmers write code or algorithms to solve discrete problems. Much of it is mundane. However in the hierarchy of CS is Kurzweil, von Neumann. So when I look up computer science, it can read a) the study of the hardware and software used to solve problems that would take enormous amounts of time if done manually. b) the study and application of circuits and algorithms to engage in problem solving; the ultimate goal of which is to achieve a level of problem solving than is not possible by man alone. I understand your difficulty with "What is life?" in a practical sense. We certainly ask "What is life?", when looking at phage, DNA , RNA viruses and now Preons, we rethink what is life.

Chris, I agree that this is a matter of style. Can we be engaging without seeming to be unrealistic or trite. In fact, in my opinion, it is engaging writing that can set CZ apart. "I looked up --- the other day and was blown away by the elegance and incite of its editors. Since Larry's goal is to set CZ apart because of our expertise, these discussions are powerful. With editors with great expertise, this can be the most accurate and the most engaging and welcome source. Maybe we can get Larry Sanger's input on style as well as that of science editors. After all it is iteration that will make CZ a great reference. In addition, the author cites Einstein inaccurately. What Einstein implied was that the mystery of life or creation of the universe was not incompatible with belief in a higher entity, he did not subscribe to religious dogma. As an aside, Einstein also stated "God does not throw dice" when confronted with quantum theory. He was wrong.--Arnold Rabin 14:58, 8 November 2006 (CST)

I am definitely not implying that biology is boring. How a cell functions and reproduces itself is fascinating and mind boggingly (is that a word?) elegant. On the other hand we need to keep the intro based in reality. When biologist ask a question such as "What is life?" is it really any different to the philosphers? We are in awe at the biology but I don't think we are using the scientific method to specifically address that question. And if we are going to cite a physicist, I would have thought Erwin Schrodinger would be more appropriate. I will add, i am not trying to black ball this paragraph but I think it needs to be discussed and through collaboration it can be improved. Chris day 15:30, 8 November 2006 (CST)

I think articles should have a personality and be interestingly written. It's possible to have a neutral article that is written in a lively way. --Larry Sanger 15:43, 8 November 2006 (CST)

I agree with this sentiment, I just thought the way it was written was a little too much (just my opinion of course). While you here, is there a manual of style? I am noticing editors here changing the stardard style of wikipedia. An example would be capitalising all words in section titles. I have nothing against that style, however, since all these articles have been scrapped from wikipedia changing that style will entail changing every article to be consistent. Have you decided how to address this issue yet? Chris day 15:58, 8 November 2006 (CST)

After poking around a bit i found the following in the forums http://textop.org/smf/index.php?board=24.0

So from what i can gather there is no set style manual in place. Is that correct? Chris day 16:20, 8 November 2006 (CST)

Intro Changes

I am by no means a biology expert, but from a layout perspective, I feel like the etymology doesn't belong at the top of the page. I tossed it atop the history section, because it seems like it should be there. I feel like the intro should be something simpler, something completely straightforward and clear to everybody, and the "Biology is the science of life" paragraph does that perfectly. I also added the third sentence to fill it out a bit, and because I think it is worth noting that Biology is a major field of science. --ZachPruckowski 15:23, 8 November 2006 (CST)

The reason I changed the prose was because I found the original hard to understand. So i would debate whether they are clear and more interesting. I am not trying to be negative but bring a new perspective. This is meant to be a collaborative effort afterall. The romanticised part I pasted to the talk page. Why wouldn't Schrödinger's "What is Life?" treatise be more appropriate for the intro with respect to big picture thinking? Einstein seems to be several steps away from biology with respect to his comments. Chris day 19:33, 8 November 2006 (CST)

That is true but there is no reason we cannot discuss the current content too. Chris day 20:51, 8 November 2006 (CST)

Nancy, I agree with should work together but this series of edits you made is not furthering the progress of this page. You have reverted back to your original version and in the process lost many stylistic changes that are important. Wikilinks are gone for one. I think these are early days here and there is little traffic but you should be willing to discuss differences on the talk page. Just reverting things back to your old version is not very inviting from a collaborative perspective. Personally, I am not particularly bothered to fight this one out but as more people get involved you will find that other editors will change your edits too. This is encouraged and usually after a few back and forth edits the articles are better not worse.

With respect to portraying an average biologists perspective that is hardly the issue here. The changes i made were minor with respect to the wording. Admitedly I cut the religion paragraph but that is because I think it is not suitable for the introduction. What is the intention of this article? To give an overview of biology or to debate the philosophy of biology?

It may be true that Einstein rings a bell across the planet, but what does that have to do with biology? Don't you think it will confuse people more than get them excited?Chris day 21:14, 8 November 2006 (CST)

Article planning

I don't pretend to have a view on what's being discussed above, but I would like to say that an essential function of CZ is for editors to come to agree upon a set of guidelines for particular articles. This article is illustrates the need to focus on that function, because the article will be examined and changed (probably) by many authors and editors. Some clearly-stated principles are, therefore, desperately needed, or else the article will be endlessly changed endlessly by people with very different ideas about the function of this sort of article. It seems to me the efficient way to agree on a set of guidelines is to separate out various contentious questions, discuss them individually, and agree to reach an agreement, i.e., discuss with a view to developing a consensus. We ought to make use of a "dispute resolution" process only as a last resort, I think. By the way, I think every article should have a threaded forum attached. What we might do, in lieu of that, is set up the CZ Forums with a bunch of discipline-specific boards, and then let people link from talk pages to those boards.

Over the coming weeks and months, I propose that we draft some succinctly-worded policies that describe our best practices. The jumping-off place for finding those policies will be CZ:Project Home. --Larry Sanger 00:36, 9 November 2006 (CST)

Comment on Approach

Congratulations to Nancy on diving in and starting afresh; I think a start like this is exactly what is needed to focus the issues. I think it will be easier for others to chip in if we can see where the article is going. I'd suggest maybe that Nancy proposes on this page an article plan, stating the purpose as she sees it, but including perhaps the following -

a) purpose: to act as a gateway into other articles? To advertise high points from other CZ articles with selected links and images?

b) style/intended readership level. As a flagship entry point into Biology I think it's appropriate to keep this article at a consciously lay level. Keep jargon out and use natural language wherever possible?

b) length. Short and sweet? An essay that is readable and enjoyable alone?That looks good when printed out? It might therefore be that the links and references should be kept sparse.

c) things needed urgently suggestions for illustrations, or for examples?

Maybe the only links should be to the next hierarchy of articles, or maybe the hierarchy should be displayed here as a box with links, and excluded otherwise?. WP loves links, but they clutter an article, and maybe this should be kept as clean as possible. I especially feel that this particular article should not include external links - this is a gateway to CZ biology, not the world. Leave the external links to the subarticles.

I think this draft goes too fast from the lay to the technical, and that Classification should definitely go elsewhere. I like the idea of selecting a few examples (maybe some historical, some contemporary technological perhaps -transgenics?- some molecular (DNA structure), and yes in particular examples there might be technical terms, but so long as the examples are self contained (i.e. skippable), then they don't need to be fully explained for the article to make sense.

It might be worth considering giving the article a little different focus; too many of the introductory remarks sound too trite, even for a lay readership. I think that what has fascinated people and what makes this fascination different from their interest in say cars, rocks or alcohol, is their fascination by life itself - the enduring big question is, what is life? Gareth Leng 04:06, 9 November 2006 (CST)

Comparing first paragraphs

CZ:

Biology is the science of life. Biologists study all aspects of living things, including all of the many life forms on earth and the processes in them that enable life. These basic processes enable living things to harness energy, to synthesise the many different materials that make up their bodies, to assemble these materials to build organs and structures, to correct errors and repair injuries, to sense their environment and to make sense of it, to reproduce themselves, and to communicate with others.

Life forms have been of interest to all peoples throughout history, and the roots of biology go back to earliest known mankind. Curiosity about the human body and about the bodies of plants and animals remains active in every human society. Much of the interest in living things stems from a wish to better exploit natural resources and to improve health, and has yielded detailed knowledge about plants and animals used to improve the standard of living. Not all plant and animal lore is biological science, however. Biology differs from simple interest in plants, animals, and the human body in using a systematic approach to study, that incorporates an understanding of mathematics, physics, chemistry and other sciences. Importantly, not all interest in gaining knowlege about living things comes about from a desire to apply it, whether or not that interest comes from within biology or elsewhere. The core of that desire is sparked by the need to understand the human condition and the nature of the world.

WP:

Biology (from Greek βίος λόγος, see below) is the branch of science dealing with the study of living organisms. It is concerned with the characteristics, classification, and behaviors of organisms, how species come into existence, and the interactions they have with each other and with the natural environment. Biology encompasses a broad spectrum of academic fields that are often viewed as independent disciplines. However, together they address phenomena related to living organisms (biological phenomena) over a wide range of scales, from biophysics to ecology. All concepts in biology are subject to the same laws that other branches of science obey, such as the laws of thermodynamics and conservation of mass.

At the organism level, biology has partially explained phenomena such as birth, growth, aging, death and decay of living organisms, similarities between offspring and their parents (heredity) and flowering of plants which have puzzled humanity throughout history. Other phenomena, such as lactation, metamorphosis, egg-hatching, healing, and tropism have been addressed. On a wider scale of time and space, biologists have studied domestication of animals and plants, the wide variety of living organisms (biodiversity), changes in living organisms over many generations (evolution), extinction, speciation, social behaviour among animals, etc.

The CZ article shines by comparison. What's the difference? The CZ article is really an attempt to explain the subject, to introduce it to someone who actually needs an article about the subject. The WP article, by contrast, reads like a student's report, regurgitating unexplicated facts, often without rhyme or reason. Consequently, the CZ article (these paragraphs anyway) are actually readable in a way the WP article isn't. As many people have observed, WP articles and its system seem to be set up for the benefit of contributors, while we want to be oriented toward users.

Think of this now: imagine this sort of authoritative, yet readable treatment being given to every subject (or, anyway, hundreds of thousands) in Wikipedia. The result will be, frankly, embarrassing for WP. There won't be any contest. I hate to say it, and this is the first time I've said this or even really thought it, but if we do this well, WP might as well give up.

--Larry Sanger 04:14, 9 November 2006 (CST)

No question, Nancy has made a great start. Style query - the article avoids the first person - personally I prefer to say "the need to understand ourselves" rather than "the need to understand the human condition" etc ?? I think Larry is right - and although all articles will be collaborative, yet we should wish them to be swans not camels, and so each needs a "voice" of its own, and so needs someone to "set the style" in a coherent way. Delighted for Nancy to do that here. Gareth Leng 09:09, 9 November 2006 (CST)

and just as we follow date or spelling styles already set by the aricle, we sould certainly ry to do additions and changes in as close tothe sle of the article as we can, & I hope Nancy wil upgrade if we fall short.DavidGoodman 09:43, 9 November 2006 (CST)

My impression of CZ after 48hrs

Larry, I think you are missing my point. I am not saying that Nancy's paragraphs are worse than WP's. I am saying that they can be copy edited and improved. Apparently Nancy did not agree since she reverted my edits back to the original version.

Nancy, you say that you did not revert "I never "reverted", by the way. I just went to an older version to retrieve language I thought was good and copied it and pasted it back in so it wouldn't be lost.". But this is essentially a revert, actually it's worse, since you lost all the hyperlinks along the way.

Nancy, in multiple places you have stated that you are trying to keep it simple but inspiring:

"inspiring and simple language that might serve as an introduction for an interested user" On this talk page

"I think we need to pull together in format and plain language style in order to be a better reference, more user -friendly." At Citizendium Forums

I think this is a good goal too. And my copy edits were trying to achieve that goal. Look at some of the things you changed back without discussion in one of the sentences.

My version was:

Biological studies of animals fall under the field of zoology, where as the biological study of plants is called botany. Medicine and the health sciences apply biology to understand and improve health, and to cure and alleviate the effects of disease.

Your latest version:

Biologic studies of animals fall under the field of zoology, where as the biologic study of plants is called botany. Medicine and the Health Sciences apply biology to understanding and improving health, and to curing and assuaging the effects of disease.

I have four points here:

1. Can biologic even be used in this context?
2. I don't understand how the use of assuage could be regarded as more simple than alleviate.
3. All the hyperlinks are gone.
4. You have added capital letters where they are not required (IMO).

I'm not going to go into other changes in detail since it is boring, but in other places you added back typos (knowlege) and you ignored my request for a citation to your claim that "the roots of biology go back to earliest known mankind". I have not heard this claim before. Is it possible you are referring to the beginning of agriculture, but that is a long time after "earliest known mankind"?

Immediately after you "cut and pasted" over my edits you posted the following on the notice board.

"Is your User page filled out? Please put something there if you are active on the pilot wiki. We are not anonymous here, but members of a real community (a welcoming one!)." [1]

I am not sure if this was inspired by me, although, as a new editor I had not edited on my user page or talk page. Nancy, a welcoming community would have addressed my newbie questions on this page above Talk:Biology#Style. It would also be nice if you would have been more thoughtful about my edits before "cutting and pasting". Finally, you could have commented on my talk page and explained to me a bit more about your outline for this page.

I would suggest there needs to be more discussion. If there is a vision for an article it would be helpful if there is an outline. Experts disagree all the time, this is the normal process of editing. Chris Day (Talk) 12:05, 9 November 2006 (CST)

guinea pigs

Knowing Nancy a litte, I expect she is willing for this article to be used as an trial example. We will gain more by working this way with a number of the intial articles than by any amount of theoretical discussion on the list. WP articles start in various styles, some rather formal, some rather flowery, and many rather drab. I haven't the least preconception of what extent we should keep to a uniform style, or of what it should be (other than not drab. I'd suggest--and I only mean suggest--that normally the beginning of an article should contain an representative very brief introduction to the major themes of the article. For example, Philosophy of biology is probably appropriate for an article of its own, probably jointly written; it should be represented by a section in the general "biology" article, which in turn should be represented by a sentence or two in the lead paragraph(s). Possibly philosophy of life should be another--and similarly religious views about life are not at all the same thing as religious views about the science of biology.

So I tried to change a few phrases myself to make it more exact, trying to use more consistent language, but just to see.

The etymologies are goingto be a problem. Perhaps something could be said in a few words, but a full etymology, afrter the fashion of the OED, takes longer. Which raises the question of the source for the etymologies. We cannot simply copy or slightly abbreviate the OED-- but for many of us, there is no other way to get the information. Perhaps we need an etymology squad.

Style in working is another problem. Some of us, like myself & Nancy, have only a little experience only with WP;some will have none; some have a great deal. Our attitudes to WP conventions will also vary, and our resulting standard of etiquette wsill have to be worked out. Some parts of the prior discussion here seem to reflectthe WP dificulty of separating discussions of substance from discussions of method. To adapt a WP phrase, don't bite each other--we're all newcomers here. DavidGoodman 22:07, 10 November 2006 (CST)

Appropriate?

The third sentence currently reads (my emphasis in bold):

These processes include the making and harnessing of energy, the creation and duplication of the materials that make up the body.

What is meant by making and creation in this sentence? Neither seem suitable in this context. Making should probably be removed since as written it seems to contradict the first law of thermodynamics. Personally, I think synthesis is more accurate than creation. Chris Day (Talk) 23:41, 10 November 2006 (CST)

synthesize

1. To combine so as to form a new, complex product.
2. To form or produce by chemical synthesis.

create

1. To cause to exist; bring into being
2. To give rise to; produce

I'm sorry you think my edits are less than constructive. I agree that this should be exciting to read but this should not be at the expense of accuracy. While I agree I am nitpicking on word usage, my aim is that they are edits to improve the accuracy of the article.

Please excuse the insertion with the request for a reference, after watching you edit this article I had assumed such insertions were your modus operandi. I certainly prefer to discuss things on the talk page too and agree that editorial comments in the article inhibit the flow of the existing text. That is why i pasted your two editorial comments above from the article to here. So lets start again. Chris Day (Talk) 10:47, 13 November 2006 (CST)

One way to avoid being interrupted is to work off-line. This can be problematic in active topics in WP, with multiple daily confusing edits, but should be more feasible here.DavidGoodman 00:00, 14 November 2006 (CST)

---

In the introduction there is a sentence that reads as follows.

"Living organisms have been of interest to all peoples throughout history, and, accordingly, the roots of biology go back to earliest mankind."

Is there a citation for the claim that "the roots of biology go back to earliest known mankind"? I have not heard this claim before. Is it referring to the beginning of agriculture, but that is a long time after "earliest known mankind"? It is not clear to me how far back this implies. What is the evidence they were studying their environment as opposed to being at one with their environment? User general information template

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Useful links for Userinfo System development edit

Instructions: CZ:Userinfo System - CZ:Userinfo System Documentation Group and workgroup tables: CZ:Group Status (demo) - CZ:Anthropology Workgroup/Status (demo) Group table technical innards: Template:GroupInfoTable - Template:GroupInfoTableLine - Template:GroupInfoTableCell - Template:GroupInfoTableCellLinked - Template:WorkgroupInfoTableCell - Template:WorkgroupInfoTableCellLinked Individual table (userplan): User:Larry Sanger/Userplan (demo) - Template:Userplan-all - Template:UserplanAllToWorkgroup (used in the latter) - Template:Userplan-all-workgroup - Mediawiki:Common.css Group data and examples: Template:UserinfoSystemUsers (everybody listed) - Template:UserinfoSystemUsers/Anthropology (anthro workgroup members listed) - CZ:Userinfo System Workgroup Member Lists (list of workgroup user lists in the system) - Template:WorkgroupCodeToFullName (interchanges workgroup codes and "pretty names" of workgroups) Individual data examples and templates: Template:User/Larry Sanger (demo of individual data page for all of CZ work) - Template:User/Larry Sanger/Philosophy (demo of individual data page for a workgroup) - Template:User - Template:User/Template1 (general data) - Template:User/Template2 (workgroup data)

No reference is required, the statement is self-evident. Human beings eat plants and animals. The phrase "the roots of biology" does not mean study, per say, but could mean even interest, note the word "roots" modifying biology. Human beings by their very nature are interested in what sustains their own life, eg, their food. User general information template

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Instructions: CZ:Userinfo System - CZ:Userinfo System Documentation Group and workgroup tables: CZ:Group Status (demo) - CZ:Anthropology Workgroup/Status (demo) Group table technical innards: Template:GroupInfoTable - Template:GroupInfoTableLine - Template:GroupInfoTableCell - Template:GroupInfoTableCellLinked - Template:WorkgroupInfoTableCell - Template:WorkgroupInfoTableCellLinked Individual table (userplan): User:Larry Sanger/Userplan (demo) - Template:Userplan-all - Template:UserplanAllToWorkgroup (used in the latter) - Template:Userplan-all-workgroup - Mediawiki:Common.css Group data and examples: Template:UserinfoSystemUsers (everybody listed) - Template:UserinfoSystemUsers/Anthropology (anthro workgroup members listed) - CZ:Userinfo System Workgroup Member Lists (list of workgroup user lists in the system) - Template:WorkgroupCodeToFullName (interchanges workgroup codes and "pretty names" of workgroups) Individual data examples and templates: Template:User/Larry Sanger (demo of individual data page for all of CZ work) - Template:User/Larry Sanger/Philosophy (demo of individual data page for a workgroup) - Template:User - Template:User/Template1 (general data) - Template:User/Template2 (workgroup data)

When I first read the current sentence I had tyhought there was an implication of an event that sparked the biological interest in humans only. But now I read your explanation it would appear that the roots of biology is fuzzy and go back much further than mankind. May be we could modify it to prehistory as suggested by David Goodman? Chris Day (Talk) 10:47, 13 November 2006 (CST)

Suggestion

1) I strongly suggest that we move on. The introductory paragraphs are great for now, but the rest of the article needs to take shape. Then we will certainly need to revisit with a final check and copy edit, but it seems to me that we are leaving the big issues aside, and when the whole shape of the article is clearer we may think differently. The first paragraphs have established a voice and a level that now needs to be extended. The third section on History needs to trace some selected path of the many possible, but I like the idea of picking on one stream of technological change - microscopy - to show how increasing sophistication in our ability to measure things has changed our understanding in fundamental ways.

2) Keeping then to the theme that Biology is inspired by a wish to understand what life is, what are the milestones that we should choose here? Amongst these might be:

• Viruses and bacteria at the e m level?
• Images of chromosomes? - Fragile X syndrome?
• X-ray diffraction alongside a double helix?
• Imaging of calcium changes in an egg at fertilisation? Video anyone?

3) Then what? ..a grandeur in this view of life..?

3) Then - Classification I think should just go into another article.

4) I don't like the idea of lists within this article - we could just shift the lists to a subarticle and link to them. For now they're a diversion and I can just see them becoming an unwieldy, arbitrary selection that is a source of unproductive controversy.

Let's remember, this article is a gateway, so the snippets we mention here must have somewhere good to go. This article is just the start.Gareth Leng 03:58, 14 November 2006 (CST)

I rescued the classification stuff from the original article since I cannot imagine an article on biology that does not discuss the kingdoms of life. The current section is practically unchanged from the wiki version but i left it all since it gives some insight to the other content here. Likewise the list was just global links that I harvested from the deleted version. Some of these can be incorporated into the article. For now they are just there for context with respect to other content in CZ.

Just out of interest, are we going with templates or similar? The ones such as the Biology footer certainly gives a lot of contextual links in the minimum space. Much of this depends on how the article are to be classified in lieu of categories. The other viable option, as I discussed above, is to reference to a separately maintained list, for example List of biology disciplines. I agree the lists in this overview article are the least desirable option.

As far as milestones, classification wrt to Linnaeus is the foundation for much of modern biology and the diversity of life is still one of the major themes in undergraduate education. Obviously Mendel and Darwin's contributions should be regarded as milestones. With respect to the modern era, many of the milestones have been from a technological perspective. Starting with sequencing proteins and DNA to whole genomes. More recently the huge impact of GFP from an imaging perspective and PCR from a recombinant DNA perspective.

I agree all these milestone are important but at some point the relationships between the different fields of biology should be discussed, especially how the lines of demarcation are becoming blurred. I'm not sure the priority for this article should be to document the history of biology but rather explain the discipline, preferably with as much reference to modern biology as to the nostalgic milestones. A nod to the current trend of BIG biology is probably appropriate too. Chris Day (Talk) 13:44, 14 November 2006 (CST)

Classification is important of course, but this article is just the popular front page of what should become a series of deeper and deeper focussed articles. Here I'd like to see just enough hint of the interest in the kingdoms of life to attract a reader to an article on just that - maybe a snippet about extremophiles?. Similarly with the other "tasters" - and yes, a couple of things at the very forefront would be great.

My own preference is for an article that could be printed off and look good; so I prefer as little clutter as possible. I like the idea of a separate article that is maybe an annotated list, or a map of biology. I wonder if we can't do something imaginative for this on CZ - even just being able to collapse and open sections of a map to see subfields. Footers, I guess the policies on these are up for discussion.

Any number of graphic indexes can be added after we have the articles. They are not mutually exclusive. The only real difficult is the need to keep them up to date and consistent with each other. DavidGoodman 22:39, 14 November 2006 (CST)

This is not really an issue if templates are used (the biology footer is such a template). One change to the original template will be reproduced on all pages that include (transclude) the template. This makes maintenance quite easy. Chris Day (Talk) 22:55, 14 November 2006 (CST)

I wasn't referring to style or wording, but rather to the addition of new topics, which must be assigned a place in each classification scheme where placement is not automatic. WP has not done very well on that score.DavidGoodman 19:42, 15 November 2006 (CST)

Now i get you, I think. In WP, the main problem seems to be that people don't know how to use categories, or should I say, there is no consistent use of categories. Not sure how this will end up here. Specifically, what do you have in mind with respect to problems in keeping them consistent with each other? Is this with respect of how they are labelled or placed in the hierachy? Chris Day (Talk) 02:25, 16 November 2006 (CST)

Who are we aiming at exactly? I guess I have in mind an article that would interest the school student who's just deciding whether to follow a path in Biology to University, and which would be looked on with some pride by anyone who calls themselves a biologist as a suitable advert for their calling.Gareth Leng 16:33, 14 November 2006 (CST)

About the image homunculus.gif, in this site is written: "All content and images on this site are copyrighted by The Evergreen State College." R.Versuri 05:27, 18 November 2006 (CST)

Hi Nancy,

I would be more then happy to try to help you out. I just looked at the first image and it looks like it’s a custom photo from this teacher:

http://academic.evergreen.edu/v/vivianoc/

I highly doubt that it is copyrighted. At the bottom of the page it said the website was last updated in 2000 so that is another reason why I don't think they would care. However, I sent an email and asked for formal permission anyways.

As for the other picture they say that you may use their pictures just as long as you are teaching science and give proper attribution in their terms of use here:

http://www.hometrainingtools.com/faq/our-company/q69.html

I don’t know if this applies for an online encyclopedia however. It looks like a promotional shot for one of their microscopes which would probably make it copyrighted. I do think they would let us use it so I asked for formal permission and I will let you know about the response.

Feel free to just brown the net and don’t be scared to find high quality photos that you want and I will review the copyrights for you. Just let me know if you need anything.

Eric Pokorny 00:31, 20 November 2006 (CST)

Hi Nancy, have you seen the animation in the WP article on DNA? http://en.wikipedia.org/wiki/DNA I'm envious, should we use it here?Gareth Leng 10:17, 22 November 2006 (CST)

Biology editors-take a look at article discussion please

Yes, Gareth - it looks great, but I'm not able to stick it in the article- can you? Also, I've been slowly trying to fill out the "development" section by using points provided by what others had listed in the "major themes in biology". It's still raw, and much may not yet make clear sense, but I'm hoping I can turn it over to you all in a fairly short time. Do you, or anyone interested, have additional suggestions? Chris? David? Could you tell me your ideas here in discussion? It's hard to maintain a "voice" in the narrative tone of the article with multiple authors editing the text, but certainly you are welcome to make contributions there as well. If you read it at least initially without modification, I hope that you'll see that many past suggestions have been incorporated. It takes me a long time, with many revisions, to get it down - but new suggestions would also get incorporated if chosen to be made here in discussion.

Looking forward to hearing from youNancy Sculerati MD 11:19, 23 November 2006 (CST)

comments--DG

Nancy, you've asked me for general comments. The summary and first paragraphs are in your personal style, and I am not sure how many others will do similar. I do not consider this a problem or disadvantage, because in my personal view there should not be one uniform style; I do not know how others will feel. But I'd certainly defend doing it this way for any similar general article--even though I intend to do nothing of the sort myself.

For the rest, what needs to be done is to outline the different fields, and the different dimensions in which they vary; plant/animal/micro-organism, historical/biographical. etc , and I think this is what you are trying to do. It may be better to do some of this after the next level articles are written, because what you are saying about the early history of biology, for example) must match to some extent what the writer of that article will want to do.

Most of the rest you've written is history of biology. (I think after that, all the different subjects must be at least mentioned and interconnected, and I am not sure you are planning to do so.) I think you give too much detail is some parts, and that you will not be able to sustain the entire article at this depth. I am not sure that all of it is balanced. Aristotle's views on embryonic development are interesting, not least because he got it wrong, and all of this should be explained in a separate article.

To try to accurately summarize historical developments in a sentence is tricky, as I 've found in other subjects, and takes much experimentation at various hands until it comes out correct and understandable--this is one of the areas where the multiple reader of WP sometimes help --and of course sometimes turn into mush. It is in particular very tricky indeed to summarize the meaning of classification and similar subjects. It is even tricky when philosophical roots or historical influences are treated. Writing like "Science is always influenced by past ideas. No scientist can consider any idea, or analyze experimental results without using his or her mind. That mind is both consciously and unconsciously stamped with the culture that produced it." need to be well integrated, not mentioned as asides.

I am not saying that I or any of us could individually have done better. Please don't misunderstand that. This article is merely being used as a convenient example, for it is the first of the science articles to be written from the beginning. DavidGoodman 22:52, 24 November 2006 (CST)

I think this is a great draft, a strong vision for an article that will be distinctive and interesting. Yes I agree fully that handling historical truth and scientific truth too can be very tricky, to simplify without loss of integrity, and this is where our combined expertise will be needed. I think some decisions need to be made to cut some things and develop others - there are a few hanging details that should either be developed or lost I think. There's still a bit of a logical gap in places and I'm wondering if Dreich's work might bridge a gap between the egg and DNA - his experiments (the motivation for vitalism for him) showed that early division of an embryo produces two perfect clones - so the information needed to build the whole is present in the component parts, and of course the explanation for what this vital spark was came with understanding of DNA?Gareth Leng 15:11, 28 November 2006 (CST)

New author from WP POV

Hey ya'll, I just had the opportunity to read your article. If all of CZ comes close to this, we will have something really valuable. I like the tone, narrative form and integration of history that allows the reader to be introduced to the biological sciences in a logical order that flows with the advancements in thought and technology. It also hints at the reductionist mindset that searched deeper and deeper into the origins of life with the microscope, EM, DNA, etc., while still being able to expose the lateral tangents of specialities such as marine biology, and emergent qualities of complex interconnectedness of ecological communities. All held together with a common theme of "where did we come from" that won't let the reader stop until they get to the end. Almost makes me want to be a biologist;) Good work! --D. Matt Innis 20:58, 29 November 2006 (CST)

Some comments on the first section

From a whole article perspective I wonder if the section titles are a bit too long. It might be better to be more concise and have a sub title to expand on the idea of each section. Specifically I read throught the 'scope of biology' section. i made a few copy edits but have saved major comments for here.

Whether scientific thinking about these issues is compatible with religious beliefs is itself contentious.

I find this sentence to be hanging. By saying "is itself contentious" seems to imply that the previous questions posed (When did life begin? What is life?), are also contentious. Is this the intent? Why not something along the lines of: "But whether scientific thinking about these issues is compatible with religious beliefs is contentious."

Some religious leaders have deplored the scientist's mechanistic view of nature that removes the requirement for active intervention by the divine.

Is this true? I don't think scientists remove the requirement for active intervention by the divine. The problem is that it can't be tested and therefore is not encompassed by science.

In this view, mathematical equations and the language of prophets are simply two different forms of human expression, each attempting to describe a higher dimension than ordinary humans experience.

It seems that others here like this type of big picture view, but i have to ask is this really topical for this article? I like the Crick reference but this is getting to be too far from biology. It seems to be more appropriate in the article on science.

Although science addresses fundamental issues about life, biology is also used to answer practical questions, which are posed to advance medical and dental care, agriculture and animal husbandry.

Again this sentence seems to be skipping between the umbrella of science and biology. Why "science addresses" rather than "biologists address"?

It is through applied biology that the health sciences became such effective healing arts and that the world's food supply has become both safer and more plentiful.

Here I don't understand the reference to healing arts. It seems to imply that medicine is a healing art, yet healing art does not appear to include modern medicine. Shouldn't this be more along the lines of "It is through applied biology that the health sciences transformed the healing arts into modern medicine" or something similar? Another related issue here is that the healing arts article should be titled Healing arts not Healing Arts otherwise healing arts will have to be piplinked every time it is mentioned in an article.

1. (see Albert Einstein for detailed discussion with references).
2. Many of the academic disciplines that make up biology are listed at the bottom of this article along with a brief description.
3. Further information about each is provided through links to other articles within Citizendium that can be accessed by clicking each discipline's name.

I have general question with regard to the three editorial comments that appear in the article. Can't we assume they know to click on links for more information? These types of comments seem unnecessary for articles. Chris Day (Talk) 02:24, 30 November 2006 (CST)

All good points, and I've tried to addresss them as I agree with them. Couple of minor things,

I'm quite anxious to avoid mixed metaphors, (sorry it's a wee bugbear of mine). Things like "roots" of biology, and can you spark a core? I'll do an edit for those sometime, don't mean to dull the language.

On where it goes - I think we need to mention the Human Genome project, the shock at the low number of genes, and then in the last para might go into systems biology as a post genomic way forward?Gareth Leng 09:03, 30 November 2006 (CST)

Medicine is a healing art. Biology is a science. Root has a well-recognized meaning that is not associated with plants, see Oxford Eng Dict. II. 6. a. The source or origin of some quality, condition, tendency, etc. I would argue that if a desire can be sparked, then the core of desire is also inflammable. Please smile, guys. Come on, there is a fine line between correction and nit-picking, language can only be changed to a point 'by commitee' without changing an essay into a list of words. Nancy Sculerati MD 09:37, 30 November 2006 (CST)

Nancy, please read our comments with a more jovial tone, you did ask for comments above. I think you are missing my smile and my effort to work with you on this article, I was the one that added the sparked mixed metaphor. Nevertheless, some of my comments above I do consider to be important issues, one I'll remention since no one has commented on this yet. The article writes: "scientist's mechanistic view of nature that removes the requirement for active intervention by the divine", but in what way does science remove the the requirement for active intervention? As far as I am aware the most we can say here is that the scientific method can not test for active invention by the divine. This might be viewed as nitpicking but the way it is currently written sounds like it's anti-religion. As we all know, science is not anti-religion, it just has nothing to say about religion.

I am not trying to force anything into or out of the article which is why I put the comments here on the talk page rather than making the edits myself. All my comments here are for you to take or leave. Above many good things have been said about this article, but what you really need to hear are your peers pointing out the weaker parts. This does not mean we are saying this article is bad. I, for one, am trying to be contructive and help you see areas that could be improved. Chris Day (Talk) 11:12, 30 November 2006 (CST)

Nancy Challenges You To Create An Approval Process

Nobody says this has to be the last article written on the subject, but it seems to me that it is complete and accurate enough to have a protected version generated and the approval process - which as you know is not at all worked out- to be started. This would be the very first article to start that process and the input for how it should proceed deserves the attention of you all. As we have already shown here, if we dwell on each editors preference for each word looking for unanimous consensus we are likely to simply continually unwrite and rewrite without notable progress.Yeah, the Human Genome Project is interesting and important, but it is a fool's task to encompass all that is interesting and important into a little essay on a major subject. Does the essay introduce the subject? Does it serve the goals outlined in the plan? There are illustrations to find and additional readings to pick. This article, once approved, is not cut in stone but refreshed on the web. Nobody says that it even has to be the ONLY article on biology, maybe it could be Biology (General) and there could be another version that is Biology (Professional Level). We have talked about having different levels. Nobody says that even if approved it could not be out on a wiki to be continually edited, and whatever it morphs into might eventually replace it as the approved article.

Perhaps we can have a category of approved articles that are off the wiki, meaning putting them in that category protects them, but there would also be an ongoing draft article of the same name. Like Category: Protected Current Approved Version for Biology (general) and Biology (general) in Category: Open Version Draft in Progress. I think it's important to distinguish between the two for reasons of liability, as well as keeping track of what we have approved and what's changing. Still, that leaves the approval process itself un-addressed.

Who has pragmatic ideas for an approval process? Nancy Sculerati MD 09:37, 30 November 2006 (CST)

This is an important article for CZ because it will be the first or one of the first to be approved - and obviously it's gtting there. I think it's important therefore that it really is exceptional - i.e. what would be Feature article standard for WP and better. We need images, and we need to feel happy not just that this article can be approved, but that this is one of our showcase products. We all want this to be great, and we all want to see it as something we feel as proud to have been part of as possible. We can take images from WP for now, but it would be nice to find new ones - unfortunately that's something I've not worked out how to do well myself. Matt I know is good at this though.. :) Gareth Leng 12:29, 30 November 2006 (CST)

Yes, Gareth, I did some on WP. I was looking earlier when Nancy was asking about it and noticed that the copyright process is different here on CZ. It does not seem to be as stringent. I am concerned that it will get us into trouble if we publish something that is not public domain, so I will look for those first. Give me some ideas of what you want. I noticed the animated DNA on the talk page, do you want it in the article? --D. Matt Innis 14:31, 30 November 2006 (CST)

Approval process here is complicated in that we shouldn't approve this ourselves as authors but need another party - and I guess for major showcase articles we need care. Gareth Leng 12:33, 30 November 2006 (CST)

Conceptually, the writer(s) need to think they're ready, it has to be copyedited (I don't think any of the copy-editors have yet been appointed, but a number of editors said they'd be willing to do this also) , and there needs to be an editor or editors, however volunteered/selected/drafted --and whether selected at the beginning or the end of the writing.

I think that this is at least 3 different people--no one can copy-edit their own writing all that well, and though in the RW editors often do it themselves, I think that given the method of composition, another check is required.

I think of the work you--and we-- have been doing here is collaborative writing, not editing in the CZ sense. (it would be "editing" in WPm but that's what we're trying to get away from.)

And the appinted editor was also I think going to have the editing discussed in the workgroup at least.

There's a discussion on this in the "approval standards" part of the "Editors" forum, and I think we probably should move the discussion there, as it's of general interest. DavidGoodman 12:44, 30 November 2006 (CST)

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 [2] Check out [3] especially [4] 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 [5] (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)

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?

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 concilatory 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)