Talk:Mathematical biology/Signed Articles/Biology's next microscope: Mathematics

See: "About this article:" at beginning of article

A test case for wiki-style scholarly interaction

On the occasion of this article appearing at CZ, I wish to raise a few issues related to it in a wider context, and I simply post them here, as I do not know of a better place (I do not find the forum suitable):

• I think this article could make for a good test case in terms of assessing the potential of wikis for scholarly interaction, as advocated by initiatives like OpenWetWare and especially at a time when the Original Research Policy at CZ is being discussed, while others have started to collect arguments why traditional journal-style publications should be abandoned altogether. We're not there yet, though, and I certainly view PLoS Biology amongst the most progressive journals currently around (that's why I plan to present CZ and Biology Week there, see here - readers of these lines are welcome to join in).
• Back to the article, I wonder how to treat such a large-scale citation. One way would be to put it onto a subpage (e.g. Mathematical biology) and leave it as it is, perhaps allowing for reformatting to CZ style. Another option could be to colour-code the original phrasing differently than subsequent edits here at CZ, at least as an option to the page viewer. With time, the article could then evolve from a representation of the state of the art into one of the history of the state of the art in the subject it covers. In principle, this could be done to many other articles, licensing permitting.

• Given that PLoS Biology's open-access policy allows article reuse without restriction in respect of modification, except for attribution to the original source, I believe that in the case of certain PLoS Biology articles — e.g., reviews, primers — CZ's knowledge-base improves better if CZ reuses such articles in the form of main articles rather than as subpages. The former invites group editing to a greater extent than subpages do, which should enrich the original author's hard work in knowledge organization, and also eliminate any segments with point-of-view character. Liberal use of internal links can substitute for subpages in cases such as this. Open-access articles not of strictly 'original research' character, such as reviews and primers, could provide a rich source of material for main articles in CZ. --Anthony.Sebastian 10:18, 6 June 2008 (CDT)

• Even though "Group editing encouraged" should be considered the default of wiki type environments like this one, I welcome Tony explicitly stating it again on this month's Write-a-thon page in relation to this article, since many of the articles here are edited by very few people (at least before suggested approval), much similar to scholarly traditions. Yet a wiki like this has a wider potential! I am thus glad to see initiatives like Workgroup Weeks or London Research Day which encourage collaborative editing, and I would like to see it more often in Eduzendium, too (e.g. by means of {{EZarticle-open-auto}}, which I will try in a summer school course later this year).

Daniel Mietchen 04:50, 5 June 2008 (CDT)

• I hope we can also find ways to truly encourage group editing of minimally collaborated-upon-articles within and between Workgroups. --Anthony.Sebastian 10:18, 6 June 2008 (CDT)

Title

I'll be interested to see how the experiment goes, and as usual I greatly appreciate Tony's initiative. The one problem I can immediately identify is that the title does not seem to be the title of an encyclopedia article. Hence, it seems to me the article must be either retitled or moved.

Like some journal articles, it uses a metaphor, whereas we want our encyclopedia article titles to be literal, straightforward, and identify a general topic of interest. For example, a more appropriate title for us (entirely off the top of my head, and having only lightly skimmed the article) might be: the intersection of mathematics and biology.

If the source article was the first time in a published article that someone compared mathematics to a microscope in this way, I'm not sure that we should be buying into the metaphor lock, stock, and barrel the way the article does. But that is a question I would leave to the biologists. For all I know, the metaphor is obviously apt and innocuous.

Of course, if the article were made a signed article, this particular problem would be finessed. --Larry Sanger 14:16, 5 June 2008 (CDT)

I agree with Larry here. The title sticks out like a sore thumb. I suggest changing it to something like Role of mathematics in biology. Great work, but not encyclopedic. –Tom Morris 19:29, 7 February 2010 (UTC)

For the record, as I see it, science cannot proceed without metaphor: transcription; translation; lock and key; entanglement; pumps. So neither can writing about science subjects. Try writing about the mind in cognitive science without metaphor: mind as a machine; representation; firing. Mathematics as microscope teaches something key about the role of mathematics in extending the vision of biologists, the ability to apprehend the otherwise invisible.

I speak of conceptual metaphor. Science needs concepts and poetry to unweave the rainbow. Encyclopedias that treat science subjects need both conceptual and poetic metaphor to promote public understanding of science topics. I hope CZ does not mandate explication writ dry. How about this title: Mathematics as microscope (biology). Might inspire "Mathematics as Virtual reality (physics)." Anthony.Sebastian 23:07, 11 November 2010 (UTC)

Sure, but that doesn't mean that the metaphors need to be article titles. The metaphor can be used in the article itself. –Tom Morris 18:05, 16 November 2010 (UTC)

Templates to keep different sets of references separate?

After starting to wikify the original references, I am wondering about ways to keep the original references separate from ones (and footnotes) added here at CZ. Of course one could think of copying ref to ref2 and reflist to reflist2 and then calling the two sets separately but I suspect the issue has come up earlier and has a known solution other than that. -- Daniel Mietchen 03:37, 6 June 2008 (CDT)

Also, would it be possible to display in the text the author names instead of the numbers that point to the references? -- Daniel Mietchen 05:32, 6 June 2008 (CDT)

Those aren't templates, but build into MediaWiki. As such, they would be very hard to change. However, before ref came in, Wikipedia uses other, template-based, systems for references, and you could certainly use one of them in parallel to refs. You can find some links to them here. J. Noel Chiappa 23:02, 6 June 2008 (CDT)

Daniel: A simple way to keep the original references separate from those added by Citizendium: For the latter, use bold font for the author names, and insert an explanatory note re that in the "References cited" section. I added a reference (Waller 2002) with Waller bolded. I put a second superscripted citation (=note) after "About this article' at the beginning of the intro to explain the procedure. Seems unambiguous. See what you think.

However, I do not feel as strongly as you seem to that we must keep the original article distinct, given its open-access permission and given that the reader can always click on the link to the original in PLoS Biology if they want to view the original. --Anthony.Sebastian 14:53, 7 June 2008 (CDT)

Your Waller approach seems workable and so is fine with me. The reason I would like to highlight the original text somehow is the potential historical function mentioned above - that's something no medium other than a wiki can easily provide, and it would fit in here. -- Daniel Mietchen 02:41, 9 June 2008 (CDT)

Am I dreaming...?

...or is this, like, completely unencyclopedic? This is an encyclopedia, not a place to provide original commentary on published scientific articles. Perhaps someone's slipped something into my orange juice, but this seems like a very funny thing to have on an encyclopedia. --Tom Morris 18:07, 7 June 2008 (CDT)

Tom, if CZ qualified strictly as an encyclopedia, I'd agree with you. But the search box asks, "What do you want to know?" And the article originated from a talk given by an unquestionable expert as the keynote address at the National Science Foundation (NSF)–National Institutes of Health (NIH) Joint Symposium on Accelerating Mathematical–Biological Linkages, Bethesda, Maryland; on June 12, 2003, as the first presentation in the 21st Century Biology Lecture Series, National Science Foundation, Arlington, Virginia; and on July 10, 2003, at a Congressional Lunch Briefing, co-sponsored by the American Mathematical Society and Congressman Vernon J. Ehlers, Washington, D.C. It appears that many scientists and congresspersons wanted to know what Dr. Cohen had to say about biology's role in the evolution of mathematics.

To characterize the article as "original commentary on published scientific articles" seems to me, with all due respect, to underestimate its quality as a creative synthesis of knowledge and prospects at the intersection of biology and mathematics. By annotating Dr. Cohen's citations and providing as many links to them as we can, CZ it seems to me does a service to those who want to know where mathematic biology and biological mathematics stand at this moment.

But consensus burgeons, and the article may need moving out of the main space. I do not think the 'Signed article' subpage appropriate if CZ editors/authors develop the article further, as the original author may not appreciate 'signing' an article that goes beyond his original. Perhap we need a new subpage, e.g., Citizendium-developed open-access articles.

But perhaps I'm doing the dreaming. --Anthony.Sebastian 18:38, 7 June 2008 (CDT)

I don't doubt that it is a valuable resource, and should be on the Web - probably on the wiki Web. But that does not mean it is suitable for "an open wiki project aimed at creating an enormous, free, and reliable encyclopedia" (CZ:About). I think that some kind of wiki for annotating scholarly papers is a great idea. But I do not think Citizendium is the place for that. --Tom Morris 18:59, 7 June 2008 (CDT)

Thanks Tom, for a thoughtful and reasonable response. I'll definitely try to make this right for CZ and its community. --Anthony.Sebastian 22:43, 7 June 2008 (CDT)

Hi Tom, thanks for your thoughts on the article. I concur with Tony that this page is meant as an in-depth add-on to CZ articles on the interface between mathematics and biology, and so I expect it to be of use to CZ readers. As for the dreaming part, I may be in there, too: I mentioned in the Talk:Biology's next microscope: Mathematics#A test case for wiki-style scholarly interaction section above, the Original Research Policy at CZ is currently being discussed. I personally see CZ (or a special namespace therein) as one of several good candidates to try such a thing (others would include OpenWetWare, also mentioned above, and upscaled versions of existing wiki-based peer-reviewed journals like Ancilla Iuris). I had placed that section here for lack of appropriate alternative venues, but perhaps it should rather go to CZ:Dreaming? -- Daniel Mietchen 02:57, 9 June 2008 (CDT)

Put in new subpage?

All,

What would you think about a subpage: Citizendium-developed open-access articles?

We could take an open-access article, like this one, give ample attrbution to article's originator, open it to group editing, monitored by the main Workgroup (or a select group of its editors).

For the article Biology's next microscope: Mathematics, we could subpage it to Mathematical biology, or subpage it to more than one main article (e.g., Biology, Systems biology, etc.).

Thoughts? --Anthony.Sebastian 23:07, 7 June 2008 (CDT)

That would be fine with me, but new subpage types require the CZ:Editorial Council's approval. -- Daniel Mietchen 02:58, 9 June 2008 (CDT)

I've been thinking idly about this. I have a question. What relationship would this article bear to the CZ encyclopedia articles about the same topic? Is this article aimed at explaining the intersection of biology and mathematics, or mathematical biology (whatever that is)? If so, doesn't it simply replicate the function we want our encyclopedia article(s) on the same topic(s) to perform? That's fine for signed articles, because people tend to write them off-wiki. But in this case, I'm frankly a little concerned that the effort going into this article is directly competing, both for reader attention and for contributor effort, with our main encyclopedia article offerings. If I could understand the use of these sorts of articles vis-a-vis our encyclopedia articles, I would not be quite so worried.

Of course, my worry would be resolved entirely if this article were simply converted into one or more collaborative encyclopedia articles, suitable for use in our main article space. --Larry Sanger 09:39, 12 June 2008 (CDT)

I think such articles can at least serve as a temporary scaffold for encyclopedic entries (e.g. Mathematical biology) and as a quarry for related articles (which should then of course be labeled with a disclaimer analog to WP-derived content – something like "Part of the material contained in this article has previously appeared in an article by Joel E. Cohen at PLoS Biology"). There might be further uses of such articles, e.g. in Eduzendium or in cross-talk with scientific journals but to find this out, we will have to experiment a bit. -- Daniel Mietchen 11:41, 12 June 2008 (CDT)

Clearly, this experiment brings up many questions and opportunities. I would like to see certain types of open-access articles (reviews, syntheses, essays) brought into CZ and open to group editing and consequent further development, with appropriate attribution to original source and statement that our edited version does not mean the original source endorses it.

Right now I think the best way to achieve that is through a new subpage: "Citizendium-developed open-access articles". For Biology's next microscope: Mathematics, we could subpage it to Mathematical biology, an article we would want for CZ, but for now we could just generate a stub to create a place for the new subpage.

There's an excellent open-access review/instructional article "Epigenetics of the mammalian cell" in PLoS Biology. Our Epigenetics article is a stub. The new subpage could accommodate the PLoS article, as a start in providing epigenetic information to readers, and perhaps motivate work on the main article. --Anthony.Sebastian 15:34, 12 June 2008 (CDT)

My question is, what's the reason that this, and all similar review articles, could not be transformed into our own (top-level, non-subpage) encyclopedia articles? I'd appreciate an answer to this. Is there, for example, a purpose you think this article serves that an excellent encyclopedia article can't or typically doesn't? --Larry Sanger 22:36, 14 June 2008 (CDT)

Yes, this article does serve a purpose -- to review the roles of biology and mathematics in influencing each other's development, and the prospects for future mutual developmental influence. The original full title was: "Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better". Hard to do better with a separate article covering those interrelated themes. But I'm happy with putting it as a subpage of Mathematical biology. I just think it's a great expert-written article, and CZ should use it, somehow. --Anthony.Sebastian 23:11, 14 June 2008 (CDT)

Lay explanation of mathematical space concepts with biological examples

An inspiring video on Euklidean space, spherical space and hyperbolic space, coral reefs and crochet that may be of relevance here. --Daniel Mietchen 01:19, 25 July 2009 (UTC)

Nice work, editing, Daniel

Should we ask for approval consideration? Anthony.Sebastian 16:44, 23 January 2010 (UTC)

Not yet — wikification is far from complete, but I'd really like to see this one approved. Anyway, I had sent you an email on the matter yesterday. --Daniel Mietchen 00:38, 24 January 2010 (UTC)