Talk:Theoretical biology

Article start

Starting independent article on 'theoretical biology'. Original page had no content, only a redirect to Mathematical biology. Methinks Theoretical biology encompasses more than Mathematical biology and warrants an independent article. --Anthony.Sebastian 23:15, 1 October 2008 (CDT)

Formatting

Please remove the spaces that precede footnotes. In proper style, there should be no such spaces. --Larry Sanger 14:46, 12 October 2008 (UTC)

I removed all the spaces preceding footnotes. --Anthony.Sebastian 22:00, 12 October 2008 (UTC)

Larry, regarding your remark that the inventor of <blockquote></blockquote> needs to brush up re whether to italicize indented blockquotes: In the Intro, I show an alternate form of blockquote, sans italics, font-size slightly larger than the miniscule one used by standard blockquote, and bolded. Any objections using that format throughout? --Anthony.Sebastian 22:00, 12 October 2008 (UTC)

Tom Morris might object. --Anthony.Sebastian 22:00, 12 October 2008 (UTC)

I most certainly will, and in the strongest possible terms. I removed all that formatting crapola from the article - it looks silly. If the Citizendium doesn't look right, it shouldn't be fixed by adding custom HTML to specific articles, but by getting the tech people to change the stylesheet globally. On the Web, it is good practice to follow the separation of presentation and content. This applies here. Blockquotes (marked with a blockquote element or not) should look consistent across the whole article. We just write the material for the pages - the style is site-wide. There's aboslutely no reason why the block quotes should be dark blue and larger on Theoretical biology and nowhere else. Consistency and content/style separation are important. --Tom Morris 22:33, 12 October 2008 (UTC)

Tom, I respect you for your interest, and for your strong feelings about consistency. I regret our disagreement on this 'blockquote' issue. I, too, have a great interest in the quality of CZ, in respect of both content and presentation. I support the idea of consistency of presentation within articles and certainly a foundation of consistency among articles. In the case of Theoretical biology, Larry has already asked for consistency in eliminating spaces preceding footnote designators, and clearly he intends that to apply 'among articles'. In addition, he has commented to the effect that the <blockquote></blockquote> function lacks quality, specifically that it italicizes an indented blockquote whereas it should not. I agree. But I submit that the <blockquote></blockquote> function also lacks quality in virtue of its reduced font-size, which deemphasizes the quote when we put it in to emphasize a point. I agree the font-size of the blockquote needn't equal that of the font-size of the main text, and think a 10-15% reduction sufficient to help set it off from the main text, which the right-and-left indentations also help do. Bolding seems appropriate, and a little color can only help the emphasis. For long blockquotes, I like Gareth Leng's idea of putting them in text boxes.

I do not advocate that every CZ article utilize my attempt in Theoretical biology at improving the presentation of blockquotes, though I do advocate consistency within the article. CZ still calls itself 'beta', so honest attempts to make changes do not seem inappropriate.

Thank you again for your earnest thoughts. I hope others will weigh in. --Anthony.Sebastian 01:05, 13 October 2008 (UTC)

I am puzzled. Why aren't we simply using : for indented quotations? If there are very, very long quotations, using special box format might make sense. But standard style as explained e.g. in the Chicago Manual of Style (if I am remembering correctly) is to indent them, use the same font size, no italics, no bold.

And, Tom--typography is never worth "the strongest possible terms." :-) --Larry Sanger 10:43, 13 October 2008 (UTC)

The strongest possible terms that the context allows, then. --Tom Morris 12:51, 13 October 2008 (UTC)

Larry, if we use : for indented quotations, we get left indent only. Personally, I prefer left-and-right indent as the <blockquote></blockquote> function gives. I use a slightly smaller font-size than main text, because bolding makes font-size appear larger; I prefer bold to emphasize the quote. I have used a similar format in numerous articles that I initiated and developed — planning to go back to them and remove italics — with no comments except Gareth Leng's idea of putting long quotes and excerpts in text boxes, to which I agree.

Larry, I suggest we allow some blockquote flexibility 'among articles', but ask for consistency 'within articles'. (We do that for citation styles.) Standards for blockquotes: left-and-right indent; no italics; font-fize equal to or only slightly smaller than main text. Bolding for emphasis optional, with consistency within articles. My HTML code is trivial and could be posted in CZ:Blockquotes. --Anthony.Sebastian 19:46, 13 October 2008 (UTC)

If you think that left-and-right indent is preferable, we should change that at the stylesheet level. We spend years advocating for CSS, so that if, say, we decide that we don't like how blockquotes look, we can change one file on the server and the whole site changes. 'Within article' consistency is no consistency at all. It's a recipe for anarchy, and is completely insane. --Tom Morris 19:51, 13 October 2008 (UTC)

Regarding blockquotes

All: Please review the format of the blockquote in the Introduction. I propose to render all the blockquotes in this article with the same format. Please weigh in, and offer any suggestions you might have. I outlined my thoughts on this in the Talk item preceding this. --Anthony.Sebastian 01:04, 13 October 2008 (UTC)

That's not how it works. There is absolutely no reason why quotes should be dark blue and bold on Theoretical biology and on no other article. If you want to change how quotes look, you need to argue for it on a general basis, and get the agreement of the community, and have it changed at the stylesheet level. If you want to show different ways that you think quotes should look, mock them up in your User space, not on a public article then ask the community for feedback. Also, if you look at the markup, the way you've done it is very much not how it should be done. –Tom Morris 19:28, 13 October 2008 (UTC)

I agree with you, Tom, but could you please calm down a little?  :-) It seems you're upset. Please don't be. Anthony is an extremely reasonable guy, maybe reasonable to a fault if that's possible! --Larry Sanger 20:18, 13 October 2008 (UTC)

I'd like to hear from other Citizens here. I'm inclined to think we should have a uniform standard about block quotations. --Larry Sanger 20:25, 13 October 2008 (UTC)

Some comments

I assume Derek Harkness coded how the current Quotes look, i.e. italicised and smaller font. I kind of like how they currently look, although the size might be a little on the small side.

I don't recall how Gareth used the boxes exactly, possibly on the Life* article with respect to the Origin of Species section in yellow? Some quotes are mentioned tangentially in the text and in those instances a box, expecially for long quotes, might be useful. *Tom, don't look at that page and blow a gasket :)

For consistency I do agree we need to decide what we are going to do and code them in a CSS stylesheet. Chris Day 20:30, 13 October 2008 (UTC)

Let's have consistency in the quality of the writing and content. Let's have a consensual foundation of consistency among articles. Let's have limited flexibility in presentation. --Anthony.Sebastian 01:20, 14 October 2008 (UTC)

The approach you are taking is inflexible and totally unacceptable. If you look at the markup given by these silly blue things, they are far less accessible for people with disabilities. Quotes should be in a 'q' or 'blockquote' tag in the HTML. This is why we have a distinction between wiki syntax and the underlying markup it generates. If you wish to change the way blockquotes are rendered, you need to argue for it on a site-wide level. –Tom Morris 09:08, 14 October 2008 (UTC)

Tom, there is no need to get aggressive over this issue. Just explain your rationale. This discussion has barely started I don't understand why you can't lead with calm reasoning? Chris Day 15:31, 14 October 2008 (UTC)

Tom, regarding the markup given by “these silly things”, presumably referring to my blockquotes, as far less accessible to people with disability, I feel certain we can teach or render the markup so as to make it quite accessible, as we have many CZers with the talent to do that. You surely recognize that many MediaWiki markups qualify as quite difficult even for people without disabilities.

By the way, I myself work as a productive author, editor and innovator on CZ despite my condition as a quadriplegic requiring mouthstick keyboarding, voice recognition software, 24/7 mechanical ventilation, though you may have had in mind other kinds of disabilities. Anyway, the “silly blue things”, presumably referring to my blockquotes, no longer appear in Theoretical biology, though the quotes do not stand out in any way except for the indents — not a partuclarly desirable state of affairs, in my opinion. A little color can remedy that, and I will continue to explore font-colors to seek an optimal one, perhaps one even you might find acceptable and not meritorious of invective. After all, we use blue for wiki-links, dark blue for disclaimers, and other colors for special things (e.g., maroon for wiki-links to empty pages).

I will continue to explore blockquote formats in the hope of coming up with one that seems generally acceptable. Thank you for your continuing interest. --Anthony.Sebastian 17:40, 14 October 2008 (UTC)

I don't think I'm being particularly aggressive. I'm stating my opinion in the same way that I would in a technical mailing list or at a conference or whatever. The font colours are not the issue. The issue is that quotes should be the same markup and the same style across the whole wiki. It shouldn't be that they are rendered as blockquotes on all articles except this one, where they are rendered as indented paragraphs with an inline style attribute. One of the premises of good markup practice is that of the semantic meaning of attributes - the markup should describe the meaning of the page, while the stylesheet makes it look a particular way.

Again, I'm not opposed to innovative proposals - in fact, I'm all for us creating a distinctive style for the site. Look at the discussion we had over the colour of links to non-existent articles on the forum - the discussion happened in the forum, with people putting up pages in their user space to show different possible colours. We didn't just decide: I know, I don't like the colour of these links, so I'll go and change them on this article - the red faction going and changing this article and the green faction going off to change another article. As I said, unless you have a consistent side-wide style, you end up with anarchy. And you can't do proper cross-browser testing, because each article messes around with the site style.

The accessibility concerns I was referring to were specifically screen readers which use the blockquote and q elements in HTML to 'off-set' the voice, so that blind users can distinguish between quotations and body text. Having something which is a quote and not putting it in the relevant element for that means that people cannot make such distinctions. --Tom Morris 17:52, 14 October 2008 (UTC)

Actually, on further reading, I'd like to apologise for my rude tone. I do get irritated by these types of matters quite quickly. Again, I apologise for being overbearing and aggressive in tone. --Tom Morris 18:09, 14 October 2008 (UTC)

Thanks, Tom, though no apologies needed. Will start a forum topic, as Matt suggests. --Anthony.Sebastian 16:46, 15 October 2008 (UTC)

Constable comment

Tom, thanks for offering the fig leaf. May I suggest, as you have already, that this become a discussion on the forums. While it is certainly a "style" issue that falls within the realm of editorial decision-making, my concern is that it is worked on professionally. As our EIC has already checked in and asked for more input, how about moving the discussion to the forums and perhaps even using this article as the "trial and error" page. Otherwise, do remember that these articles are works in progress, so expect things to change daily. Feel free to contact me if necessary. D. Matt Innis 01:59, 15 October 2008 (UTC)

Thanks, Matt. I started a forum topic on the subject in 'Content issues > Article policy > Blockquote format'. --Anthony.Sebastian 17:47, 15 October 2008 (UTC)

new blockquote format for Theoretical biology

From the forum, I changed the blockquote format in Theoretical biology to one that received some approbation. It seems neat, has no italics, indents distinctly left-and-right, same font-size as main text (1.0em), though 'appearing' slightly smaller, and sets off from the main text with a font that appears slightly but not obstrusively different.

Codes as follows:

<blockquote> <p style="margin-left: 2%; margin-right: 5%; font-size: 1.0em; font-family: Trebuchet MS;">BlockquoteText<ref>xx</ref></p> </blockquote>

Looks good to me. Though I wouldn't mind a little color. --Anthony.Sebastian 00:18, 22 October 2008 (UTC)

Towards approval

I would very much like to see an article on this topic approved but I feel this current version does not quite reach the target yet, as it does not go much beyond a list of "things related to theoretical biology".

What I am missing here is a bigger picture, the kind of well-phrased overview that people supposedly seek in an encyclopedia. For example, what are the biological subfields or subtypes of research questions for which theoretical approaches are generally or currently more common, more promising or otherwise distinct from experimental or other empirical approaches, and how can the different approaches be integrated to extend biological knowledge as a whole.

So in my eyes, the article would be "developing" rather than "ready for approval" but given that four editors have already signaled their approval, I have not removed the notice but extended the deadline instead, hoping for some productive collaborative editing here. Perhaps we can make this the BIG collaboration of the biology workgroup for the upcoming write-a-thon? I will get back to this later with some notions on developments in theoretical biology in the 1980s and adjacent decades. --Daniel Mietchen 09:07, 1 December 2008 (UTC)

Incidentally, why do we just have Theoretical biology and not Experimental biology? --Daniel Mietchen 09:09, 1 December 2008 (UTC)

——

Daniel, I feel fine about the extension of deadline for the purposes of collaborative work on the article, and hope you and others will begin editing. I had no intention of instigating a ploy to encourage collaboration, but great if it happens.

I like your questions:

1. what are the biological subfields or subtypes of research questions for which theoretical approaches are generally or currently more common?
2. what are the biological subfields or subtypes of research questions for which theoretical approaches are generally or currently more promising?
3. what are the biological subfields or subtypes of research questions for which theoretical approaches are distinct from experimental or other empirical approaches?
4. how can the different theoretical approaches integrate to extend biological knowledge?

correction: I meant "how can the different theoretical and non-theoretical approaches be integrated to extend biological knowledge?" Here, I basically think of a cycle with phases more inclined towards theory and others more towards experiment. --Daniel Mietchen 07:44, 2 December 2008 (UTC)

Daniel, sounds like you have something specific in mind. Perhaps you could elaborate. --Anthony.Sebastian 03:21, 3 December 2008 (UTC)

1. what are the historical trends in theoretical biology in the last 100 years?

I will think about how to create separate sections within which to articulate answers.

A truly quality result might take longer than the extended period, however, so I would not be surprised if producing that might require work in a draft version after approval of a worked-on version of the current introduction to the topic. --Anthony.Sebastian 23:11, 1 December 2008 (UTC)

I know that it will probably take longer but I'd rather extend the deadline again or remove the notice altogether if the article has not improved substantially by Dec 19. I do hope, though, that a collaborative effort will do some good here, and the topic seems to be an ideal showcase for that, since (at least theoretically), every life scientist at CZ should be able to contribute. --Daniel Mietchen 07:44, 2 December 2008 (UTC)

If my request for approval brings about a collaborative effort, great. --Anthony.Sebastian 03:21, 3 December 2008 (UTC)

Fundamental Problem with the article

I agree with Daniel that the current version is not acceptable. An article on this subject should provide an introduction to the subject, not a variety of definitions and several different lists of subtopics. Tp follow the definition (which I think is broadly correct) by saying that "all biologists are to some extent theoretical biologists" makes manifest the meaninglessness of the definition. To me, as i think to the author of the quotation, "theoretical" anything is less of a subject matter distinction than an approach. For the sciences, it contrasts with "experimental" and "descriptive" and in practice typically means "mathematical" (there are other approaches: philosophical , historical, biographical, but they don';t form the same contrast. (There's another, older, meaning of "theoretical" which I assume is not being used here--theoretical as distinct from "applied" By this rubric, all of biology that is not medicine and agriculture is theoretical.) The approach is so general, that I am not all that sure how an article on it can be written. I know i would not attempt it, though i would describe particular broad classes of theories.

Based on the literature in theoretical biology, 'theoretical' definitely does not contrast predominantly with 'mathematical'. --Anthony.Sebastian 03:38, 3 December 2008 (UTC)

The presentation of the nature of the field as the most cited articles from a particular journal, followed by the tables of contents from a report, does not explain the subject. The fact that a journal should happen to be called "Journal of Theoretical Biology" does not mean that it is accepted as defining the subject. Almost every one of the most downloaded articles would fit at least equally well or perhaps better into other journals and other specialties. As the article points out, not all are mathematical (but a proper article would analyze this, not simply state it)--the question then arises what the others are; some seem to fall into the domain of molecular modeling.

No math in Darwin's Origin or Watson and Crick's DNA structure paper. Many theories of aging, mostly argumentative.

The report seems improperly used here. The list of chapter headings do not represent what the journal considers theoretical biology, but rather what many would call a list of "Major unsolved problem areas in biology" -- worded in such general terms as to be meaningless --though I know the report itself does explain a good deal further. The article lists the conclusions of the report as "specific" -- to me they seem about as non-specific as possible, a statement that biologists need to pay more attention to theory, and, as inevitable in a NAS report, a statement that the field should receive more attention in funding. DavidGoodman 05:46, 2 December 2008 (UTC)

I agree and think one could improve the situation with more annotation of items listed. --Anthony.Sebastian 03:38, 3 December 2008 (UTC)

Some suggestions for the re-write phase

I have seen numerous popular scientific elaborations on questions like "Why is the sky blue?" or "Why do elephants have big ears?" and I think such an approach would also be beneficial to the present article. So I would suggest to take a set of "why questions" of interest to every child, and illustrate how to approach such issues (even in the absence of definite answers) from an experimental or theoretical perspective. Thus, we would have to select a set of such questions suitable for brief encyclopedic elaboration (probably wouldn't hurt understanding if they would touch upon the most basic concepts in biology), and during the collaborative writing phase, everyone could pick their favourite and write a paragraph about it. I'll make some suggestions below. Please add yours to the list. --Daniel Mietchen 10:10, 2 December 2008 (UTC)

PS: The reason I used "why" is that it paves the way for explanations in terms of Nikolaas Tinbergen's four approaches to "why" questions:

• Ontogeny: Add brief definition or description
• Phylogeny: Add brief definition or description
• Mechanism: Add brief definition or description
• Function: Add brief definition or description

Daniel Mietchen 11:05, 2 December 2008 (UTC)

Daniel, what you suggest seems more like doing theoretical biology rather than explaining to readers what theoretical biologists do. It seems to me your "why paragraphs" belong in the articles to which they pertain, your first one belonging in Whale, for example. Theoretical biology involves so many "why" questions we could not possibly do justice to the subject of theoretical biology. I could come up with hundreds of of biological "why" questions. Any finite set of "why" questions arbitrary. --Anthony.Sebastian 04:02, 3 December 2008 (UTC)

Learning by doing or by observing others do is not necessarily a bad way of learning. Of course, any example has drawbacks, and a larger collection of examples does not necessarily overcome this point. But if we had a number of such "why paragraphs" (possibly imported from or exported into other articles), this could serve as a scaffold for the synthesis that this article needs (I would expect few of--Daniel Mietchen 21:32, 3 December 2008 (UTC) the words but much of the spirit of these why paragraphs to survive into the first approved version). Otherwise, it would probably take much longer to arrive at a broader view. And on your question above: Yes, I do have a relatively detailed outline of the topic in my mind but I currently do not have the time to write it up in one coherent piece, and I would also like to see whether the potential of a wiki for collaborative editing could be harvested for such broad topics like this one. So, for the time being, I will concentrate, as time permits, on stimulating the discussion and providing input for a collaborative overhaul. --Daniel Mietchen 09:39, 3 December 2008 (UTC)

Daniel, re "Learning by doing or by observing others do is not necessarily a bad way of learning.": What I plan to do in that regard, annotate apropriately published theoretical biology papers, so the reader can see the questions asked, the aproaches taken, and the conclusions reached, however tentative or qualified, and however stimulating of new questions. Hoping that will help the reader understand what theoretical biologists find important and how they approach it. --Anthony.Sebastian 19:02, 3 December 2008 (UTC)

I plan instead to extend and structure the related articles as an additional scaffold on which to develop the article. Perhaps we will meet somewhere on the way. --Daniel Mietchen 21:32, 3 December 2008 (UTC)

Suggestions for "why paragraphs"

Voting mechanics are as for the CZ:Article of the Week.

Nominated question	Score	Supporters	Specialist supporters	Related biological concept	Another related biological concept
Why is a whale not a fish?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Taxonomy	Convergent evolution
Why do children grow, while their parents don't?	3		Daniel Mietchen 11:10, 2 December 2008 (UTC)	Growth	Allometry
Why are mammals the biggest animals on land and in the oceans but not in fresh water?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Poikilothermy	Natural selection
Why can most birds fly but no pigs?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Biomechanics	Homology
Why are flowers so colourful but their leaves almost always green?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Coevolution	Photosynthesis
If bacteria can grow so quickly, why isn't the whole planet overgrown by them?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Nutrition	Steady state
Why can some organisms survive freezing, others not?	3		Daniel Mietchen 10:10, 2 December 2008 (UTC)	Cryobiology	Life
Why can a comparison of short-lived molecules like DNA or proteins tell us when the human and chimp lineages split off?	3		Daniel Mietchen 11:08, 2 December 2008 (UTC)	DNA	Molecular clock
Why do brains fold?	3		Daniel Mietchen 11:43, 2 December 2008 (UTC)	Brain development	Gyrification
Why do suspended cells rotate in rotating electric fields?	3		Daniel Mietchen 11:43, 2 December 2008 (UTC)	Cell membrane	Electrorotation
Why are nerve fibers wrapped in a fatty sheath?	3		Daniel Mietchen 11:47, 2 December 2008 (UTC)	Nerve signaling	Myelinzation
Why do we like chocolate?	3		Daniel Mietchen 11:47, 2 December 2008 (UTC)	Reward system	Dopamine

I am going to remove approval

Because 3 biology editors deem this article unready for approval, I am going to remove the To Approve tag. I think I have the power, but if not someone please speak up. David E. Volk 14:46, 2 December 2008 (UTC)