Talk:Biology/Draft

Biology

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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)

Approval of Version 1.2.1.--Ruth Ifcher 00:53, 4 February 2007 (CST) 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 article re-approval. It is noted that person with sysop permissions other than User David Tribe will need to action this revision after the specified deadline has elapsed. David Tribe 14:31, 28 January 2007 (CST)

Version 1.3

http://pilot.citizendium.org/wiki?title=Biology/Draft&oldid=100033561 Issues being raised and assumed to be resolved But have your say

The Zebra finch.
The Einstein comment.
The Montage (a no brainer)
Minor links and amendments made already by David Tribe 20:26, 11 February 2007 (CST) (and otherS) after Ifcher action
Wot else?

FURTHER RESPONSES HERE:

As one editor only, I have thought carefully for a day or so, and consulted The Shorter Oxford Dictionary about the recent finely-balanced suggestion of changing 'Anatomy' to 'Morphology and see the argument for the change. I also realise there is a counter argument (Anatomy has its argument too, including being common usage.) I also am very pleased that (David Hume) is contributing vigorously to other articles connecting with this, and recognise the need to link to them. Thus I propose to accept this change after a wait of at least 24 hours from this time to allow counter opinion to be expression, if any . I personally feel there is no large harm either way, but its collegial to work contructively with give and take in tricky decisions. I may be off-line for 72 hours so another editor is welcome to do the honours David Tribe 15:46, 20 February 2007 (CST)

I'd say this debate has only just begun (see Talk:Biology). There appear to be three opinions with respect to the usage of morphology and anatomy; the relationship of the terms could be considered hierarchial, synonomous or distinct. Chris Day (Talk) 15:51, 20 February 2007 (CST)

interrupted mid-edit after reading other comments on Biology Talk. The Oxford dictionary defines morphology in terms of form or outward appearance, anatomy in terms of deeper dissect able structure. I'm now making a decision to action the changes prior to the morphology proposal, and its possible incorporation can wait (as previously did a significant number of substantial changes in version 1.3.)David Tribe 16:01, 20 February 2007 (CST)

David Tribe 20:26, 11 February 2007 (CST)

Version 1.4 approval

Anatomy/morphology still ongoing. Chris Day (Talk) 12:44, 5 March 2007 (CST)

I just made an editorial decision to equate structure with anatomy AND morphology. I have now requested that this article be reapproved to incorporate the new subpages structure. Other differences include decreasing the emphasis on Einstein and various copy edits. Differences between the version i am recommending and the current article can be seen here. Chris Day (talk) 17:07, 6 September 2007 (CDT)

Chris Day nominated the whole Biology Cluster for approval including the version dated 17:02, 6 September 2007 (CDT) of the article as well as all the subpages. The Biology Workgroup oversaw this approval and the cluster was approved on, or around, 20070910.

Approved September 10, 2007 using the individual editor method as the edits in question were not content related edits made by the nominating editor, Chris Day. --Matt Innis (Talk) 21:42, 10 September 2007 (CDT)

Formating conventions

The reference format style started in Horizontal gene transfer is being currently followed in an attempt at typographical consistency. Books 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, 'scientific method' for special emphasis.

Also possible is use of reference method: <ref name=Smith> giving names to citation when first used David Tribe 20:09, 26 January 2007 (CST)

A future style manual: citation from PloS Biology Slightly modified?

A section of discussion on development of CZ standards for citation has been copied to Help:citation style talk then deleted here

Taking raw PubMed text and PLos izing it, and shortening authors.

RAW starting Pubmed text:

1: Bernstein E, Caudy AA, Hammond SM, Hannon GJ.

Role for a bidentate ribonuclease in the initiation step of RNA interference.

Nature. 2001 Jan 18;409(6818):363-6. PMID: 11201747 [PubMed - indexed for MEDLINE]

The PubMed to PloS briefened conversion with only deletion and date typing and insertion of et al. Probably suited to a future automatic software algorithm for Pubmed conversion.

Exhibit A

1. Bernstein E et al. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409:363-6. PMID 11201747

WARNING

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

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)

Update: after a discussion with Zach on my talk page i think this montage should be one jpg. We can make it clickable in the future using ImageMap technology. For a cool example of ImageMap in action see here. http://www.chekmate.org/wiki/index.php/MW:_ImageMap_Extension#Samples This would also be a very powerful tool for metabolic diagrams and such. Or imagine a picture of a cell where you can click on the different organelles. The potential seems huge. For now, let's go with the jpg in combination with a link to a gallery. Then we don't have to worry about the compatability issues as browsers get updated in the future. Chris Day (Talk) 13:01, 30 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

Sorry to be slow getting back to this David. I guess my major concern here is to be able to compare the most recent draft with the last approved version, taking advantage of the comparison technology available here, i.e. the Compare selected versions option at the top of the draft history page. It would be great to be able to scroll down the page and select the radio button for the version that was copied over to the approved article page. If there was an A to distinguish that version it would make it a lot easier.

I see the A you are talking about in the biology article history, but aren't all these versions approved? I thought that was the point of the separating out the draft version. I understand that you made a few copy edits but nothing that would overide any approved version.

What I am trying to propose, and I'm not sure this has come across, it that what ever Larry did on that edit in the biology article history to make it an A instead of a N needs to be done each time a version from the draft page is approved. Does this make sense? I might start a seperate thread on this in the forum since it is a more general point than somethinjg specific to the biology or biology/draft articles. Chris Day (Talk) 17:28, 28 January 2007 (CST)

I dont know all the answers here Chris. Ill have to think and study about it but I need to go now. It would indeed be useful to air it on the forum. The appearance of the A seems to be by some high sysop permission and tool Larry and others have, possibley similar to standard disclaimer removal, but I'm guessing. We need to understand it better to be able to use it.David Tribe 18:24, 28 January 2007 (CST)

David, I'll take this to the forums and phrase it in the context of a more general issue. Chris Day (Talk) 02:46, 29 January 2007 (CST)

Forum thread can be found here: http://forum.citizendium.org/index.php/topic,499.0.html Chris Day (Talk) 12:41, 30 January 2007 (CST)

Stubs for red links

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)

Actually, you learned about Imam in Novemeber ;) , not sure how Iman got back in though. Chris Day (Talk) 01:16, 29 January 2007 (CST)

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For the future or for subpages

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

Anthony.Sebastian (Talk) 22:09, 29 January 2007 (CST):

David: Regarding the "mystery of consciousness": An interest of mine for decades, starting when I read: Jaynes J. (1976) The Origin of Consciousness in the Breakdown of the Bicameral Mind. Boston: Houghton Mifflin Co. I have in hand advanced drafts of three papers I plan to submit to the Journal of Consciousness Studies, someday, of course, Multiverse willing. I’ve had several posters accepted for the biennial Tucson conference "Toward a Science of Consciousness", the abstracts of two of which you can find at http://groups.msn.com/Anthony-Sebastian/. If interested, click there on 'documents' and look for files entitled:

Consciousness Made ‘Easy’ - The Perspective of a Lay Enthusiast.rtf
Defining 'Experience' As Prerequisite To Explaining 'Conscious Experience' [post conference revision].rtf

I’d love to start a draft on 'conscious experience' for CZ, but I’d have to give up my academic life first. I know the players in the (controversial) field fairly well, but I can’t think of anyone who would qualify as 'non-POV'. Will give further thought to whom we might try to recruit.

You have thoughts? --Anthony.Sebastian (Talk) 22:09, 29 January 2007 (CST)

microscope

according to my knowledge it was anthonie van leeuwenhoek who invented a microscope, or better was able to use a tiny lens to use AS a microscope. The first time thtat ever happened. That is why that fact made him to the Dutch (yes I am Dutch :) ) the inventor of the microscope. Others specifically in the UK and of the Royal Society invited him to show his invention. Like microsoft nowadays it was soon copied and improved. Robert Tito 23:42, 29 January 2007 (CST)

My memory for the details fails me (like so much I once counted on!) - and so I will have to look it up. No, he was not, as per established sources (which I will find -give me a moment!)[or two]) the "inventor", what was called a microscope was around and used in the textile trade to examine cloth. He made some kind of revolutionary improvement to it- and used it to look at, more or less, everything. In November (I think) I worked on his biography as a CZ Live article. It's in there-along with the references. By the way- he was much more impressive than simply an inventor of one thing, I think he's been "dwindled" by happenstance and history from the status he should have- meaning, I became a fan. Nancy Sculerati MD 05:59, 30 January 2007 (CST)

Agree with Nancy here, he did not invent the microscope but improved it to a point such that it had a huge impact on biology. Robert Hooke was using microscopes to look at cells, although dead, before Anthonie van Leeuwenhoek but his magnification was only about 30 times. Leeuwenhoek made microscopes that could magnify up to 300 times and was the first to see living cells. Chris Day (Talk) 12:33, 30 January 2007 (CST)

Leeuwenhoek did not invent the microscope as such yet he was the first to use it as a science instrument, to study living organisms. His lenses did magnify up to 500 times. It took until 1800 for multi lens microscope could match that magnification. So inventor of the scientific microscope heis. Lenses in general were present - but not perfect for scientific purposes. Robert Tito 13:13, 30 January 2007 (CST)

Certainly you could credit him with the discovery of the first effective scientific microscope. It all depends on how you define scientific; ~30X or ~300X. Maybe scientific is casually defined as the first instrument capable of seeing living organisms. But is that even true? Much of this comes down to what van Leeuwenhoek chose to look at as much as how good his intsrtument was. I'm not trying to take anything away from van Leeuwenhoek his work speaks for itself and he was a true giant in biology. The living organisms in combination with sublime optics is the key here. Chris Day (Talk) 13:26, 30 January 2007 (CST)

Two column refs

David , i like the two column refs. Interestingly i can't see it using MAC with mozilla or safari. Chris Day (Talk) 12:53, 30 January 2007 (CST)

Might be a CSS issue on the Mediawiki end. I have the same problem. -- ZachPruckowski 13:16, 30 January 2007 (CST)

This issue partly resolved with suggestion supplied by Zach? (memiory right?) elsewhere David Tribe 20:20, 11 February 2007 (CST)

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Zebra finch wrong?

Just a note the zebra finch is not an island specialist, as the text implies, but a continental generalist. Should be removed. --Michael Johnson 18:23, 4 February 2007 (CST)

It's really only there because it's a great picture of a bird with a specialized beak. Open call for submission a great photo (that is licensed such that we can use it) of one of the species of birds that Darwin actually observed in drawing his conclusions. I think we'd all agree that photo would be optimal. Nancy Sculerati MD 19:28, 10 February 2007 (CST)

The problem is that the Zebra Finch is an arid zone generalist, adapted to eat whatever is available. It's beak might be regarded as "typical". The point about Darwin's finches is that their beaks differed so much from a typical finch that Darwin did not identify them as such, and considered them to be members of different families. It was Gould who identified them as finches when mounting the birds back in England. If you wanted to include examples of birds from several different families to compare beaks, that might be useful. But it would not have anything to do with Darwin. As the photo and caption stands it is misleading. --Michael Johnson 15:38, 11 February 2007 (CST)

It is not the best illustration, agreed. Can you help us find a better one? We can be sure to review it before including the picture in another approved addition, and thanks. Nancy Sculerati MD 15:53, 11 February 2007 (CST) .

No unfortunately I do not have access to an image of Darwins finches, although there is one on Wikipedia, so they are around. I suppose it doesn't matter much in that this is not on public view, but it is something that anyone with any knowedge of the Estrildidae would have a giggle about. OTOH I guess the general public wouldn't know the difference. BTW shouldn't there be a policy that any image of an animal, at least in the context of a scientific article, identify the species? --Michael Johnson 17:38, 11 February 2007 (CST)

So, what are you suggesting? Just drop the photo altogther or change the caption to say something about a non-specialist beak? Can you devise a better caption?Nancy Sculerati MD 18:25, 11 February 2007 (CST)

I'd just delete it until you get a better image. To be frank, you could have used a picture of any bird at all instead of the zebra finch, they would have been just about as relevent (or rather, not). After all the whole point of the section is that it is talking about evolution, not finches. --Michael Johnson 19:12, 11 February 2007 (CST)

Einstein issue rears its 666 head again

David Tribe 20:20, 11 February 2007 (CST) thinks he can write a useful sentence to develop response to [an] issue [raised by] a PHILOSOPH on the forums. With various other issue raised David Tribe senses its time for another approval. Intends to pu a new approval tag up with a 7 day deadline to push through these revisions.

Please work on DNA. We have whole articles that are at least as important that are not in good shape. We have whole articles that are not even written. Nancy Sculerati MD 21:49, 11 February 2007 (CST)

Anatomy and Morphology discussion from the archive since it is still ongoing

anatomy

In reference to the following section:

"Some fields of biology focus on living organisms and their interactions within a certain realm of the earth, as in marine biology; others focus on particular aspects of living organisms, like their structure (anatomy) or function (physiology). Studies of animals form the field of zoology, whereas the study of plants is called botany. Medicine and the health sciences apply biology to understanding disease and to improving health."

I would like to replace the word anatomy with morphology, which refers particularly to structure as it applies to both plants and animals, while the term anatomy really applies more to animals and humans in particular; the term zootomy usually reserved for lower animals. I am working on the human skeletal system and believe a more natural order for the flow from biology to the human skeletal system would be: biology > morphology > anatomy > human anatomy > systems of the human body > human skeletal system.

I quote from the Encyclopaedia Britannica: morphology " in biology, the study of the size, shape, and structure of animals, plants, and microorganisms and of the relationships of the parts comprising them. The term refers to the general aspects of biological form and arrangement of the parts of a plant or an animal. The term anatomy also refers to the study of biological structure but usually suggests study of the details of either gross or microscopic structure. In practice, however, the two terms are used almost synonymously.

Typically, morphology is contrasted with physiology, which deals with studies of the functions of organisms and their parts; function and structure are so closely interrelated, however, that their separation is somewhat artificial. Morphologists were originally concerned with the bones, muscles, blood vessels, and nerves comprising the bodies of animals and the roots, stems, leaves, and flower parts comprising the bodies of higher plants. The development of the light microscope made possible the examination of some structural details of individual tissues and single cells; the development of the electron microscope and of methods for preparing ultrathin sections of tissues created an entirely new aspect of morphology—that involving the detailed structure of cells. Electron microscopy has gradually revealed the amazing complexity of the many structures comprising the cells of plants and animals. Other physical techniques have permitted biologists to investigate the morphology of complex molecules such as hemoglobin, the gas-carrying protein of blood, and deoxyribonucleic acid (DNA), of which most genes are composed. Thus, morphology encompasses the study of biological structures over a tremendous range of sizes, from the macroscopic to the molecular.

A thorough knowledge of structure (morphology) is of fundamental importance to the physician, to the veterinarian, and to the plant pathologist, all of whom are concerned with the kinds and causes of the structural changes that result from specific diseases. "

and

anatomy " a field in the biological sciences concerned with the identification and description of the body structures of living things. Gross anatomy involves the study of major body structures by dissection and observation and in its narrowest sense is concerned only with the human body. “Gross anatomy” customarily refers to the study of those body structures large enough to be examined without the help of magnifying devices, while microscopic anatomy is concerned with the study of structural units small enough to be seen only with a light microscope. Dissection is basic to all anatomical research. The earliest record of its use was made by the Greeks, and Theophrastus called dissection “anatomy,” from ana temnein, meaning “to cut up.” "

While I know the Encyclopaedia Britannica, dances around a bit on the distinction between morphology and anatomy, they do stress that morphology is often contrasted with physiology, which is what you are doing on the Biology page. From reading quite a few references it has become apparent to me that, while anatomy once had a broader sense, almost the same as morphology, over time it has come to refer more and more to the morphology of animals and mammals in particular, especially man. I can supply a large number of references, if you wish but I didn't want to overwhelm your discussion page.

I ask this because without the change morphology would be an orphan and, I hope you agree, it is the more general of the two terms, morphology and anatomy. I'm sure you agree that in setting up this online encyclopedia it is important to go always from the general to the particular so that viewers can burrow down in a branchlike structure as far as they wish. I'll admit that sometimes the choices are hard.

Even if you feel that "anatomy" is not a subset of "morphology" and that they are true equals, then you must say "anatomy or morphology" instead of just "anatomy".

You can let me know what you think by posting to the anatomy discussion page.

Thanks, David Hume.

I don't have time to write too much now but I will comment that anatomy of plants is a whole subject in its own right. Distinct from morphology too. So I would disagree that the term is more relevant to animal biology. Chris Day (Talk) 11:21, 17 February 2007 (CST)

Anatomy

I guess I'd hazard that it should be form (anatomy) or structure (morphology). I guess for the level that this article is written it would be appropriate to use "form (anatomy)" as these are more clearly understood by lay readers in their proper sense. I see the point though, it's a sound one - but let's think of the reader first. On balance I'd say that Anatomy should stay. Make any change on the draft but lets not revisit approval until substantial changes have accrued. In the meantime I think there are articles that are approaching approval that deserve closer attention than this one, for now.

Gareth Leng 03:31, 20 February 2007 (CST)

MORPHOLOGY vs. ANATOMY -- OED2

MORPHOLOGY I. Simple uses.

1. Biol. The branch of biology that deals with the form of living organisms and their parts, and the relationships between their structures. Formerly: spec. the comparison of the forms of organisms and their parts in order to identify homologous structures (cf. quots. 1853, 1859, 1872).

1828 R. KNOX tr. H. Cloquet Syst. Human Anat. 2 Descriptive Anatomy..is itself capable of being divided into the Particular Anatomy of Organs, or Morphology, and the Anatomy of Regions, or Topographical Anatomy, if we may use the expression.

1853 T. H. HUXLEY in Philos. Trans. Royal Soc. 143 29 The morphology of the Cephalous Mollusca is a subject which has been greatly neglected. No Savigny has determined the homologies of their different organs, and so furnished the only scientific basis for anatomical and zoological nomenclature.

1859 J. R. GREENE Man. Animal Kingdom: Protozoa Introd. 17 By some the word ‘morphology’ is employed in a restricted sense, to signify the study of homologous organs.

1872 R. G. LATHAM Dict. Eng. Lang., Morphology, doctrine of the fundamental identity of the parts constituting the flower..and fruit..with the leaf.

1904 W. L. H. DUCKWORTH Morphol. & Anthropol. ii. 14 This application of the principles of Morphology to the special case of Man constitutes the essence of Physical Anthropology.

1946 A. NELSON Princ. Agric. Bot. iii. 20 In both morphology and anatomy the relationships in space of the several parts..are important.

1992 P. J. BOWLER Fontana Hist. Environmental Sci. (BNC) 340 Morphology was a laboratory-based subject that did not encourage detailed study of how animals adapted to their local environment.

2. orig. and chiefly Science. Shape, form, external structure or arrangement, esp. as an object of study or classification. Also: a particular shape, form, or external structure, esp. of (a part of) an organism, landform, etc.

1844 Philos. Trans. Royal Soc. 134 303 The morphology of the thyroid gland.

1894 Jrnl. Physiol. 17 81 (heading) The morphology and distribution of the wandering cells of Mammalia.

1895 N. STORY-MASKELYNE (title) Crystallography: a treatise on the morphology of crystals.

1921 Geogr. Rev. 11 155 (heading) Morphology of the Altai Mountains.

1937 Rep. Brit. Assoc. Advancem. Sci. 373 (heading) A comparative study of the morphology of the North Downs and the Chiltern Hills. 1950 Jrnl. Gen. Physiol. 33 651 Two separate lines of approach..were required: a study of the functional behavior of the [nerve] fibers, and a study of their morphology.

1954 M. BERESFORD Lost Villages 23 In the study of village morphology..an opportunity of seeing a medieval village plan without any of the accretions of later building.

1964 R. C. EVANS Introd. Crystal Chem. (ed. 2) xi. 184 Before the discovery of X-ray diffraction, crystals could be classified only on the basis of morphology, and in terms of their symmetry were assigned to one or other of the thirty-two classes.

1965 E. GURR Rational Use of Dyes in Biol. I. 107 We can refer to the shape and/or size of a molecule as its morphology.

1971 W. A. PRYOR in R. E. Carver Procedures Sedimentary Petrol. vii. 142 Quantitative analysis of grain morphology requires measurement of particle radii, diameters, and lengths.

1990 Protein Engin. 4 23/1 Amphioxus, an invertebrate animal with the morphology of a fish.

ANATOMY

I. The process, subjects, and products of dissection of the body.

1. The artificial separation of the different parts of a human body or animal (or more generally of any organized body), in order to discover their position, structure, and economy; dissection.

1541 R. COPLAND Guydon's Quest. Cyrurg., Anathomy is called ryght dyuysyon of membres done for certayne knowleges.

1543 TRAHERON Vigo's Chirurg. (1586) 430 Anatomie..signifieth the cutting up of a mans bodie, or of some other thing.

1667 MARVELL Corr. 203 Wks. 1872 II. 403 As if a man should dissect his own body, and read the anatomy lecture.

1688 J. CLAYTON in Phil. Trans. XVII. 990 Dr. Moulin and my self..made our Anatomies together..we shew'd to the Royal Society, that all Flat-bill'd Birds..had three Pair of Nerves.

1712 ADDISON Spect. No. 275 1 Curious observations which he had lately made in an anatomy of an human body.

b. with quick, live: Vivisection. Obs.

1651 N. BIGGS New Dispens. Pref. 7 Where have we constant reading upon either quick or dead Anatomies?

1651 Life of Father Sarpi (1676) 16 He had formerly cut in pieces a number of living Creatures with his own hands to make Anatomies.

1668 CULPEPPER & COLE tr. Bartholinus' Anat. II. vi. 101 In Live Anatomies we can hardly perceive that the one is hotter then the other.

2. concr. a. A body (or part of one) anatomized or dissected, so as to show the position and structure of the organs. Hence b. A body or ‘subject’ for dissection. Obs.

1540 T. RAYNALDE Birth of Mankinde (1634) Prol. 3 As though yee were present at the cutting open of Anatomy of a dead woman.

1598 B. JONSON Every Man in his Humour IV. vi, They must ha' dissected, and made an Anatomie o' me. 1602 DEKKER Satirom. 197 Carving my poore labours, Like an Anotomy.

1611 TOURNEUR Ath. Trag. V. ii. 146 His body when 'tis dead For an Anatomie.

1611 DONNE in Coryat Crudities, Worst malefactors..Doe publique good cut in Anatomies.

1691 WOOD Ath. Oxon. II/610 He intended to have her made an Anatomy.

1751 CHAMBERS Cycl., Anatomy is sometimes used to denote the subject to be anatomized.

3. A model of the body, showing the parts discovered in dissection.

1727-51 CHAMBERS Cycl. s.v., An human anatomy in plaster of Paris, representing a man standing upright, with his skin flea'd off. 1753 Cycl. Supp., Who has not seen the waxwork Anatomy?

It seems 'morphology' more for form; 'anatomy' more for details of structure. But still iffy. Anthony.Sebastian (Talk) 14:59, 20 February 2007 (CST)

The problem, as I see it, is that anatomy and morphology are both different types of biological structure. The most accurate way to write the sentence is:

"others focus on particular aspects of living organisms, like their structure (anatomy and morphology) or function (physiology)."

Does this suit everyone? Chris Day (Talk) 15:17, 20 February 2007 (CST)

It's certainly inclusive! :-) But it does not suit me- the truth is that anatomy and morphology are broadly used as synonyms by biologists. Like crimson and scarlet, it is possible to find specific references that distinguish them, but that is rather misleading. All I can say is that I have taught college level biology courses in a university and given anatomy lectures in a medical school, and I do not agree that one is recognized as a subset of the other, or that both need to be mentioned. I do feel that the narrative writing should be crisp and engaging, and that to have to add in and morphology is not an improvement. Do we even have two different articles? David, I think your interest is great and I would be pleased to write some bone articles with you- but the Encyclopedia Brittanica just is not an authoratative source for this stuff. The hierarchy you propose here and in anatomy is not one that I agree with. Perhaps you could start an article on a favorite bone- how about: human skull- I can help you there! ;-) Nancy Nancy Sculerati MD 15:28, 20 February 2007 (CST)

addendum: I see that there is an anatomy and a distinct morphology article- basically both written by David Hume, and both written to support his view. Perhaps the other biology editors can look them over and comment/edit. I do not want to be confrontational, but I do believe that we cannot sacrifice truth to politeness. As we all know, I am often wrong-but never in doubt! Still, I do not believe that these articles are accurate as written. Nancy Sculerati MD 15:33, 20 February 2007 (CST)

Botanists do not use them as synonyms, I can't speak for zoologists or the medical profession. Certainly i would not regard one as a subset of the other. Chris Day (Talk) 15:43, 20 February 2007 (CST)

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Anatomy morpology continued

Anthony.Sebastian:

One can speak of the morphology of a protein molecule--its size and shape--without speaking of its amino acid sequence. In fact, knowing the amino acid sequence gives no clue to its shape, i.e., its morphology. If one spoke of the protein's anatomy, one would need to speak of its amino acid sequence. If it had definable components, like polyphenol and polysaccharide side-chains, one might anatomize it into its components and separately describe its morphology.
One can speak of the anatomy of a murder, but not of its morphology. If you did speak of its morphology, you might mean something like its modus operandi and compare that morphology with other murders with different anatomies.
The 1990 quote above from OED, "Amphioxus, an invertebrate animal with the morphology of a fish", suggests two biological entities could have the same morphology but different anatomies.

It does seem that each of the two words have certain domains of applicability all their own even if they share other domains. --Anthony.Sebastian (Talk) 18:48, 4 March 2007 (CST)

We seem to agree here Anthony. Chris Day (Talk) 12:47, 5 March 2007 (CST)

I cut my biology teeth on Darcy Wentworth-Thom(p)son's On Growth and Form. Form=morphology has a clear biological implications, but the point, I suppose, is how do we recognise this, or should we, and how to avoid confusion and clutter if we do ? David Tribe 14:41, 5 March 2007 (CST)