Talk:Biology/Draft

Version record area

Version 1.1 approval

(Earlier details of V 1.1 commented out for clarity)

Version 1.2 approval

Updated termplate url pointer reflecting Chris Day's/ D Tribe's minor edits David Tribe 01:08, 26 January 2007 (CST) Further updated approval url pointer David Tribe 00:53, 27 January 2007 (CST)

Biology version 1.2 created here in Biology log. David Tribe 01:05, 27 January 2007 (CST)

Version 1.2.1 approval

David Tribe has nominated this version of this article for approval. Other editors may also sign to support approval. The Biology Workgroup is overseeing this approval. Unless this notice is removed, the article will be approved on January 30, 2007.

Further updated url pointer and reinstated "To approve" template to incorporate two minor edits (full stops and blank spaces plus emergency changes to several figures caused by changes in primary file sizes of figures that lack thumbnails).

This update involves no change to the substance of approved version 1.2 and is occurring to ensure a due process is followed for artice re-approval. It is noted that person with sysop privilages other than User David Tribe will need to action this revison after the specified deadline has elapsed David Tribe 14:31, 28 January 2007 (CST)

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Formating conventions

• The reference format style started in Horizontal gene transfer is being currently followed in an attempt at typographical consistency. Boooks are being cited here by the authors' full name and ISBN numbers are being used to minimize needed detail.

• At some later stage we may well use non abbreviated jounal titles for clarity but currently this would expand the size of some articles with many references

• "Quotes", for direct quotes, 'scientic method' for special emphasis.

• Also possible is use of reference takes giving names to citation when first used David Tribe 20:09, 26 January 2007 (CST)

WARNING

Warnings: alterations to any figures and templates used in the draft page may affect the appearance of Biology approved page

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General commentary, edit context discussions

I'm happy with it but I have to tell you my spelling is an issue and I'm not in a position to bless it from that angle. David Goodman raised an objection in the Forums over having the sperm picture captioned "magnified" without an exact magnification as being a terrible blunder, wrote that he would not have approved the article previously had he noticed it. I myself, do not see it that way as I think it is being used in the context of the homunculus and van Leeuwenhook, and illustrates an important point in the article very nicely - I think the exact magnification is a trivial point. I would certainly agree with him if the article was about sperm cells, however and used the same picture with the same caption as it does here.. I bring this up though for explicit discussion, because I do not wish to ignore his opinion-which I generally respect. Anyway, I approve the new draft. Nancy Sculerati MD 10:38, 24 January 2007 (CST)

I measured and estimated the magnif as close to 150x. Fixed legend. I see differences between you and DG on this as due to different conceptions of what CZ should do. I think your concept actually works well for the lead article in a general area, but DGs conception is important for mmany subsidiary articles and that there is a role for both concepts. David Tribe 15:17, 24 January 2007 (CST)

Pixel counts suggest 125x is more precise David Tribe 22:23, 26 January 2007 (CST)

Thanks for fixing it.Please look down at the next section, read the letter and comment.Nancy Sculerati MD 15:21, 24 January 2007 (CST)

Looks good too me, if you still need a vote. Chris Day (Talk) 01:22, 25 January 2007 (CST)

Article Criticisms from outsider 1/23/07

I recently received an email from someone who had read and reviewed the copy of the Biology article that we posted publically. Could you all please take a look at it here, ideally before re-approving. (note that I didn't write it, he just emailed it to me). --ZachPruckowski 11:51, 24 January 2007 (CST)

Do you have any idea of what the yellow marks mean? I don't.Nancy Sculerati MD 12:24, 24 January 2007 (CST)

They are comments - hover over them with your mouse and they show up. Ian Ramjohn 13:02, 24 January 2007 (CST)

Now that I have read the comments, I must say I liked them better as yellow marks. They are written in the tone of the All-knowing, which is particularly amusing coming from an anonymous commentor. The comments seem to assume that the article has no hyperlinks, and that "being encyclopedic" is something that any of us hold as a positive absolute value. If the person is actually interested in making constructive comments, let them sign up and join in. Nancy Sculerati MD 13:46, 24 January 2007 (CST)

The reader has at least noticed that Nancy has injected emotional engagement and subjective judgement into it. (irony warning). Having been trained to write flat but lucid scientific journal articles I noticed too!. But I value a LOT what Nancy has brought to the table. On the other hand, maybe I can retrieve some valid small revision from the yellow taking care not to obliterate Nancy. Exactly why emphasis is verboten I cannot fathom though. May need to extend Approval deadline a day or too. We may as well do it well. David Tribe 15:35, 24 January 2007 (CST)

PS Just to be sure, what I ment by emotion is esthetic appeal and reader engagement with a sympathetic style. Ive happily accepted from NS several improvments to my unengaging prose. I also take to point that anonymous jusgement are of very low priority, and by devaluing those we elevate those who put their real names on the line. Im thinking to see if buried in that yellow there snippets of value. Ill also do a WORD auto spell check David Tribe 17:53, 24 January 2007 (CST)

Hey, don't kill me over it, I'm just passing along what I was sent by that guy (because he happened to catch me in the IRC channel). I don't care how you take it, I'm just passing it up the line. I don't know if he has any sort of relevant training at all, or how seriously you should take it. That's up to you guys. I didn't even read it through all the way. --ZachPruckowski 15:43, 24 January 2007 (CST)

P.S. no angst felt towards anyone by David Tribe.

I was trying to be funny with "kill me over it". I don't feel angsted upon or whatever :-) --ZachPruckowski 18:10, 24 January 2007 (CST)

Prize Quote from the yellow anonymous commentator

"The start of this paragraph is more appropriate for an essay. An encyclopedic article should not try to communicate with the reader." [sic]

Well well, thats exactly what Nancy's done: an essay on biology as a hyperlinked lead into the huge resources we want to develop, a hypertext preface if you like, and surely that's one of the reasons we liked it? It succeeds in communicating with the reader. Its a good thing that we haven't called Citizendium an encyclopedia, and isnt this comment an encouragement for us to do something other than what this reader suggests? David Tribe 00:16, 25 January 2007 (CST)

To finish with the yellow critique: I have gone through the yellow points and considered every issue. There is little of substance, I tried hard and found one redundant word.

Mostly, the writer has a serious lack of comprehension of the role of good communication, and poor judgement about what Citizendium should hope for. The 17th century biologists who mapped veins can wait for The History of biology. I put in a link to Kary Mullis, and to Cell (biology). Nancy - you can sleep well tonight, feeling thoroughly vindicated. Lets move on David Tribe 01:00, 25 January 2007 (CST)

Sounds good. Again, I didn't really even look at it. I just passed on what had been emailed to me. I certainly hope no one lost sleep over it. --ZachPruckowski 19:56, 25 January 2007 (CST)

Zach, just passing something from an anonymous person without checking it is not nothing. It's a mistake. If an anonymous person contacts you by e-mail in the future please reply with the CZ address and let them register and make their own criticisms directly. That's the whole point of the no anonymous contributions policy: there are no anonymous contributions. And, as this example (which was no big deal, but was somewhat hurtful and was a waste of everybody's time-including yours) nicely illustrates: anonymous contributions are more likely to be of trivial value than attributed statements and criticisms. They are more likely to be mean spirited, and the fact that the knowledge and background of the person making them cannot be evaluated in any way makes them difficult to assess appropriately. Nancy Sculerati MD 20:19, 25 January 2007 (CST)

I would normally not have done it, but we specifically put this article up as a model and to seek commentary. I certainly am fully in favor of the anti-anonymity rule, but we did put this up as outside Citizendium. I apologize if it hurt anyone and I apologize for wasting people's time. -- ZachPruckowski 21:22, 25 January 2007 (CST)

Nancy, are you taking his criticisms personally? I don't think many of the editors comments were that off the wall and he had some interesting ideas as well. I have a hard time thinking that it was a waste of anyone's time. It's always nice to see where others think writing can be improved. -Tom Kelly (Talk) 21:34, 25 January 2007 (CST)

I just read the anons comments and non seemed to be out of order. In fact, they all seemed pretty trivial which in its own right is a complement. Chris Day (Talk) 22:48, 25 January 2007 (CST)

Please update approved article after vetting this change. 1/22/2007

Added link to 'orphan' article "Systems Biology", per Larry's request

Anthony.Sebastian (Talk) 14:07, 23 January 2007 (CST)

Edits since first approval

http://pilot.citizendium.org/wiki?title=Biology/Draft&diff=prev&oldid=100013668

I request to get this edit edited by editors and considered for approval. -Tom Kelly (Talk) 18:43, 4 January 2007 (CST)

Personally, I think people should be able to add little links like this and get them in to the approved article faster. I think this could seriously be a negative to CZ if this small issue isn't addressed. However, CZ does a great job getting scientific 'experts' involved in editing. However, ease of addition is an important concept in wikis. -Tom Kelly (Talk) 18:47, 4 January 2007 (CST)

I concur. I also made a request to fix spelling errors in the approved version (a couple of the errors being rather glaring), but the talk page does not seem to be active, so I am also making this request here as well. --Ted Zellers 22:37, 12 January 2007 (CST)

Suggestions

Talk about Biology, the major, as part of the definition of biology (?) or would that be another article. -Tom Kelly (Talk) 18:43, 4 January 2007 (CST)

Perhaps a redirect to Education in biology? DavidGoodman 02:21, 13 January 2007 (CST)

Minor Edits

Thomas, I don't want to turn you off, but at this point in the CZ pilot, we are not so much into minor edits, and this is why: we have an idea to work on a large number of articles and get them into an "approved" status. It seems that the idea of an approved article in CZ is not the same as a WP feature article. Instead, it's a coherent article that is true and useful. The idea being that a user can access CZ and, reading approved article, feel confident that this is the real deal, so to speak. On a wiki where changes are constant, or at least very frequent, it's a dynamic state where improvements happen quickly, but so do mistakes or language that might not be an outright mistake, but something that confuses the explanation. There are only a few of us working now, and the system for approval is cumbersome. There are so many important topics that need to be totally rewritten that the task of tweaking an article that is in good enough shape to have been approved is not a current priority. Hopefully, when there are more people and a new server, this is not an issue. Biology was the first approved article and its far from perfect, but its basically ok. As far as Biology the major, that would be another article. We will get back to incorporating your, and other, suggestions from the draft into the next edition of the approved biology, but realistically, revised editions of approved articles are not going to be daily or weekly or, at this early stage, even monthly. The draft, on the other hand, is open to continual updates. That's how I see it, anyway. Nancy Sculerati MD 21:53, 12 January 2007 (CST)

P.S. I acually don't agree with the definitions of microbiology that seem to be the edits in question. Sorry. Nancy Sculerati MD 22:09, 12 January 2007 (CST)

am I understanding this correctly? You disagree that medical microbiology includes the study of bacteria, viruses, fungi, and the immune response to them?? -Tom Kelly (Talk) 22:15, 12 January 2007 (CST)

forgot parasites. -Tom Kelly (Talk) 19:50, 13 January 2007 (CST)

I have replied to this in the biology forum as follows:

'I think this is exactly wrong. We are trying to produce a well-edited version, one that will be obviously well-edited. This means accuracy, bt it also means copyediting. There is nothing that gives the appearance of amateurism faster than inconsistence and error in style, punctuation, and detail. (well, spelling mistakes are even worse, but I think the article has been checked for this.)' To say, 'let's do a haphazard job, and hope people will make corrections,' is one of the factors that has done in the reputation of Wkipedia DavidGoodman 02:42, 13 January 2007 (CST) (heading interruption to comment)

micrographs

The micrograph of sperm cells does not have a scale or a magnification factor. I apologize for not having noticed it before. This one I consider a major error. DavidGoodman 02:42, 13 January 2007 (CST)

Ive calculated magnif as 150x and added the texct to the legend David Tribe 21:57, 23 January 2007 (CST) Better 125x David Tribe 22:25, 26 January 2007 (CST)

Microbiology

Microbiology is not listed in Biology today a survey of the science of life section of this article http://pilot.citizendium.org/wiki/Biology/Draft#Biology_today.2C_a_survey_of_the_science_of_life

I listed it in the draft page because I think microbiology is a major subfield of biology. In studying microbiology, one usually studies bacteriology, virology, parasitology, mycology, and then in doing so you learn about virulence factors, host response, immunology, inflammation, pathology, etc.

I knew immunology would probably be controversial to have listed in such a short segment, although I think hematology and immunology and clinical immunology are fascinating aspects of Life, and the science of life and they deserve recognition somewhere.

I did not foresee virology being controversial but not understand the argument is "are viruses alive?" I'd rather not get in to that argument and just list them as "a major part of life," but that is just me. I do not foresee anyone solving the question if virology should be listed as a biological science in the near future and would vote on just removing it from the list, but then linking it somewhere else in the article (!!!!).

I don't like the format of my edit and was looking for advice - that's why I've been trying to get editors attention.

I don't like the wording exactly either - I think subgroup sounds funny - but again, I was just putting this out there as a criticism to the incompleteness of the list and trying to add some things to maybe improve it. It's just a minor edit but I think mainly, getting microbiology on the list is essential and getting some more sub-specialties in biology listed is also essential. -Tom Kelly (Talk) 00:17, 15 January 2007 (CST)

Forum post on minor edits to approved articles

http://forum.citizendium.org/index.php/topic,421.msg3264.html#msg3264

haematology , hematology

I'd like to see hematology added to the list. thoughts?? -Tom Kelly (Talk) 22:01, 16 January 2007 (CST)

How do I edit the box at the bottom of the article? -Tom Kelly (Talk) 21:48, 17 January 2007 (CST)

It's a template. Apparently, it's Template:Biology-footer. Go to that page, click edit, and go to town. Note that you may need to re-edit this draft page to make the display on the page change. --ZachPruckowski 21:57, 17 January 2007 (CST)

I'm tending towards Hematology being a Health Science topic and maybe its covered by the Links at the top? David Tribe 19:13, 24 January 2007 (CST)

ok -Tom Kelly (Talk) 19:21, 24 January 2007 (CST)

I guess, does it take away from the article being there? -Tom Kelly (Talk) 19:22, 24 January 2007 (CST)

David, I don't disagree (aka agree) with the removal of heme from this general topic article and understand it fits in a different niche, however, I would argue (as a fun way of joking :)) that pathogy is not a word - i believe you meant pathology, and if so, Heme is a lot more than just a specialty of pathology-Tom Kelly (Talk) 22:09, 24 January 2007 (CST)

lol, i mis-spelled the description of my joke!! pathogeny, haha -Tom Kelly (Talk) 22:12, 24 January 2007 (CST)

Gee. I was interupted by students for an hour mid edit and now my typing clumsyness is there for all to see Grrrr.Have to go hom,e now and continue work there.David Tribe 22:30, 24 January 2007 (CST)

Just suggest minimising redlinks - especially overt links to articles that don't exist...Gareth Leng 04:26, 25 January 2007 (CST)

I think red links are fine. Larry thinks blank pages will encourage people to write more anyway - he might be right. -Tom Kelly (Talk) 21:36, 25 January 2007 (CST)

Consider for approval added paragraph at end of section "The Continuing Story"

I added paragraph at end of section "The Continuing Story" designed to expand the thoughts in the preceding paragraph.

I think that it is not an improvement, too technical, writing needs a lot of work. Nancy Sculerati MD 16:06, 25 January 2007 (CST)

I tried to merge it into to what was already there. See what you think. Chris Day (Talk) 16:14, 25 January 2007 (CST)

I played with it some, and I think it has potential. It needs polishing, and a great last line.Nancy Sculerati MD 16:52, 25 January 2007 (CST)

Version 1.2possibly near?

Also narrowing the red link categories in History of biology, as Gareth proposes, has the added advantage of focussing effort by others on the more general History of biology, field first,ahead of any History subfields, and I propose that's good strategy.

I support the more polished mention of systems biology and an editor such as Nancy slapping another Approval Template to generate version V1.2. I can efficiently handle the final approval of an existing approved article mechanics. I've had practice now 17:15, David Tribe 17:17, 25 January 2007 (CST)

David, I've done the best I can. Could you take over now, please? Thank you, Nancy Sculerati MD 18:15, 25 January 2007 (CST)

I just made some more edits to help the flow. See what you think. Chris Day (Talk) 23:08, 25 January 2007 (CST)

seem good to me, Ill scoop them into V 1.2 David Tribe 01:04, 26 January 2007 (CST)

Looking at the comments of the anonymous reviewer, I think they deserve consideration. I've adjusted the Einstein mention. The sentence below caught my eye as needing redrafting as it's a bit clumsy but my brain's not working fast enough to redraft it... "The development of biology has drawn on many more topics, and a much larger geographical area than referred to here, but the science of biology has had a continuous thread through the centuries that began with the ancient Greek philosophers, and has generally followed the winding pattern of advancement presented here."Gareth Leng 08:26, 26 January 2007 (CST)

Just how did we let that through? Ill look at when my brain is alive too David Tribe 09:03, 26 January 2007 (CST)

Had a go, perhaps not good, and made some adjustments in note of the comments of Zachs reiewer. This sentence I've also cut: "That amorphous material that Harvey could not fathom as the progenitor of organs might have seemed to him to be of a wholly different nature had he the advantage of magnification." I thought it was hard to digest and did not really add anything. Please revert anything I've done without hesitation if you disagree.Gareth Leng 09:08, 26 January 2007 (CST)

I'd like to sign off as an editor/author here. I have read and changed this article so many times I think I have developed an allergy to it! Please continue without me. Nancy Sculerati MD 09:14, 26 January 2007 (CST)

I havnt been exposed to the heavy dose that Nancy's taken on so heroically, and can tolerate more.

"Greek philosophers, and since then has advanced over the centuries in a winding pattern to embrace a multitude of topics."

? through different avenues, maybe. Hmmm.

I think youve captured some extra value in several places Gareth. David Tribe 09:34, 26 January 2007 (CST)

Montage updated to individual pictures

I just discovered that the sizing option for pictures is now functional. i changed the montage to make it individual pictures that are now clickable. I will write a blurb for each picture in the future. This montage is different to the other one. It is very easy to switch pictures in and out, so other, better, pictures can be used. We can have fewer pictures too. See here for more options. Chris Day (Talk) 11:04, 26 January 2007 (CST)

I just checked the montage on a different computer (sun with firefox browser). In that environment there are inconsitent white gaps between some of the individual pictures, whereas on my MAC running safari they are all tightly aligned. What do other people see? It might be impossible to do this montage in a way that is good for all browsers. although I hope not since I think the clickable picture feature is useful. Chris Day (Talk) 13:34, 26 January 2007 (CST)

YES with Firefox on Windows XP I see gaps. Well have to revert to premontage. But worse, They are fixed now on approved, but changing primary images ruins the approved version (of the other figures ). I used my Sysop status to do emergency repairs so DO NOT please change them back Chris David Tribe 22:31, 26 January 2007 (CST)

Revision status

I just noted something in the history of theis draft that may have been there for a long time. There is a classification for revision status written as follows; Revision status: N=normal A=approved. To the left of each saved version is a N. This will be a great feature for quickly identifying the last approved version for comaprsion with the most recent draft. However, scrolling through all the version I do not see any with an A, and by my calculation there should be at least two. What is the procedure for getting a version tagged with the A when the sysop finally cut and pastes a draft version to the main article? Chris Day (Talk) 12:55, 26 January 2007 (CST)

Yes indeed, I noticed that too. See the non draft version Biology though - *its history log*. I suggest that we keep links to the souce files in the talk section there. The history log there automatically accumulated A notation so it is natural to exploit that. Also is used space effectively. i.e.use the TOP page (non draft extension) for logging identity of approved A files and the draft for editing progress of revision. What do you think Chris D? David Tribe 20:13, 26 January 2007 (CST

I've been looking at this article as a sort of map for the Biology workgroup, I would like to generate some reasonable stub forms of articles for major subfields in biology that are "red". I hope these can be seeds for us to all make grow. I know that Health science is a CZ Live article, and I keep failing at piping the link. Could you please fix it? Thanks, Nancy Nancy Sculerati MD 21:14, 26 January 2007 (CST)

I have reverted the edit by Gareth referred to. Please let me know is I have done it badly. It enabled me to see the AntoniE that need fixing too David Tribe 22:22, 26 January 2007 (CST)

Ive had that trouble before . I eventually found that the software is kind about the initiasl cap but cant understand internal caps eg Health Sciences vs Health sciences. Gosh itsa stuupid. Doesnt like singular either. We need to create a few redirect pages too. David Tribe 21:36, 26 January 2007 (CST) All authors and editors who take initiatives on figs and tables READ WARNING at top! David Tribe 21:37, 26 January 2007 (CST)

Another minor point: The point about Harvey and the microscope was that his failure to grasp that the early contents of the fertile womb were continuous with the macroscopic contents was the technology- the lack of a microscope. That's why that line you took out was there. I think you should re-write it and put it back. It was a link in the theme. Nancy Sculerati MD 21:52, 26 January 2007 (CST)

deletion reverted David Tribe 22:27, 26 January 2007 (CST)

Restoring NS text, Gareth, with sentance break in bold:

This article explores just a few selected themes; those themes center on the origin of life (both 'life on earth' and the creation of a new infant) and are followed through the centuries from ancient Greece to the present day. It is apparent that a philosophy of critical thinking, investigative methods that rely on empirical evidence, and the availability of technological tools have, together, accounted for how these ideas have changed. The development of biology has drawn on many more topics, and a much larger geographical area than referred to here. But the science of biology has a continuous thread through the centuries that began with the ancient Greek philosophers, and has generally followed the winding pattern of advancement presented here.

Im starting to know how you feel Nancy. David Tribe 23:01, 26 January 2007 (CST) Still need to revert early montage David Tribe 23:03, 26 January 2007 (CST)

That whole bit about the "This article explores just a few selected themes..." was a reply to several criticisms bemoaning the fact that ALL of biology was not covered through ALL time and the entire world. I finally decided to sort of define my domain explicitly, in a sort of mathematics sense, to shut them up (I do mean that with affection, believe it or not) as it was getting ridiculous. Do with it what you want.Nancy Sculerati MD 23:07, 26 January 2007 (CST) But it might be better: This article explores just a few selected themes; those themes center on the origin of life (both 'life on earth' and the creation of a new infant) and are followed through the centuries from ancient Greece to the present day. It is apparent that a philosophy of critical thinking, investigative methods that rely on empirical evidence, and the availability of technological tools have, together, accounted for how these ideas have changed. The development of biology has drawn on many more topics, and a much larger geographical area than referred to in this article. However, the science of biology has had a continuous thread through the centuries that began with the ancient Greek philosophers, and has generally followed the winding pattern of advancement presented here. OH NO_I'm breaking out in a rash....gotta go! Nancy Sculerati MD 23:39, 26 January 2007 (CST)

Version 1.2 actioned

Now I'm breaking out in a rash.;0)

I've just actioned creation of version 1.2, before coming here to discover more commentary to address. I believe I have reversed two changes made by Gareth if I recall correctly to very close to the previous original, but with some smal genuflection to the point of the criicism.

I think we've gotta all call a halt to Biology revision for a while, with the possible exception of a better montage, which I regard as a non-contentious minor change where Chris' valiant efforts have been already vetted but still are a risk due to browser variation generating ugliness.

Let's get on with other stuff. I learn't one new fact: Imam is the standard spelling of the Islamic leader. Plus I learn't a lot about how ethical processes and having an editorial 'leader' working constructively with real name colleagues is very important David Tribe 01:19, 27 January 2007 (CST)

For the future or for subpages

• The mystery of consiousness S Pinker David Tribe 21:58, 27 January 2007 (CST)