User talk:Chris Day

The account of this former contributor was not re-activated after the server upgrade of March 2022.	The account of this former contributor was not re-activated after the server upgrade of March 2022. Useful links on Citizendium Myths and Facts Biology Workgroup How to get started How to Edit The current policy outline Forums for discussion Biology forum News Community blog
User:Chris day/newmessage

I aim to restrict my replies to this talk page....

My hope is to preserve the context of each discussion rather than having them fragmented on mutliple talk pages. So please check back here for replies to messages you leave, thanks. Please sign comments with four tildes ~~~~ This makes it a lot easier to follow the ebb and flow of a discussion with multiple users. Indents are also useful to help track the sequence of replies and can be achieved using colons such as : or ::. Chris Day (Talk) 23:32, 13 November 2006 (CST)

For the benefit of newcomers, I mention that this can easily done by putting the page on one's watchlist, or setting the preferences to do so automatically.DavidGoodman

Lead in homeopathy

It's been suggested (not by me) that the new CZ style might incorprate a short and simple boxed message, and that for this article, that box might contain the text:

"Homeopathy is an Alternative Medicine system that tries to treat illnesses with tiny doses of the drugs that cause the same symptom as the illness. Homeopathy is based on the ideas of Samuel Hahnemann, a 19th century physician who observed that some contemporary medicines evoked symptoms similar to those of the illnesses for which they were prescribed. There is no clear evidence to support the efficacy of homeopathic remedies, and it is likely that the reported effects are placebo effects."

Keeping this here so we can see how it looks if and when style issues advanceGareth Leng 12:25, 9 November 2006 (CST)

That would make more sense. I have been trying to track down the CZ style guide/ideas with no luck. I have seen discussion here and there but nothing concrete. Am I missing something obvious? Chris Day (Talk) 12:31, 9 November 2006 (CST)

Hi Chris, No, you're missing nothing obvious, except that there is the intention to establish a new style on CZ but no firm proposals yet as to what that should be, just some suggestions as to what it might include. One of the initial functions of the pilot I think is to start discussions and experiments with style and layout.

Everything has been moving fast but unevenly; it's still very, very early days.Gareth Leng 06:55, 10 November 2006 (CST)

OK i'll kep my eye open for these discussions. Chris Day (Talk) 16:22, 10 November 2006 (CST)

Thank you Chris for your help. Nancy Sculerati MD 13:04, 24 November 2006 (CST)

Moving pages to avoid piping links

Rather than moving pages or piping links, I would put in redirects on the alternative spellings or capitalisations. The article should reside at the correct name with the correct capitalisation, not the common of most often used name. On the other spellings put in code like # REDIRECT [ [ SomePage ] ] to guide users automatically to the correct page without having to pipe anthing.

That is a good point. I had forgotten that redirects could be used for alternative forms. Chris Day (Talk) 08:30, 1 December 2006 (CST)

?? No idea??Gareth Leng 12:10, 4 December 2006 (CST)

We need to start building a Style manual with stuff like this, or maybe Help 2.0 David Tribe 15:02, 29 January 2007 (CST)

Bacteria

Here's an e.coli on a government site that we could grab, but it is B/W. I'll keep looking for a good color photo. --D. Matt Innis 16:35, 4 December 2006 (CST)

Chris, check out the salmonella picture on the NIH website. It's colorful [1] --D. Matt Innis 14:14, 10 December 2006 (CST)

Chris, could you take a look at these 2 articles?

In Barbara McClintock, I made some changes as per your suggestions and hope that accuracy has been improved. Would you please take a look? Secondly, if you look at my user page (talk) you'll see a reference that David Tribe put in for the first genetic map. I need to correct a mistake I made about that in biology, but I do think that we should try to work in the concept of a genetic map, can you help? thanks, Nancy Sculerati MD 08:19, 10 December 2006 (CST) Please take a look at the biology talk page.Nancy Sculerati MD 12:25, 12 December 2006 (CST)

Biology marathon

Chris, I'm writing a letter to Larry, and then putting it up in Forums- look for it. Meanwhile, I'm going through all the history of article and the discussion to see who contributed. I need that information for the text of the letter. In doing so, I came across a comment you made about a correction you did in the part about proteins (your comment was something like: the proteins were not sequenced, the DNA was). The correction is fine, it's just that your comment made me realize the age difference between us, and how that colors our point of view. When I was an undergraduate back in the 70's, the big news was sequencing proteins, forget about DNA. It was a big deal to figure out the exact amino acid sequence and then laboriously "hand calculate" how they folded and what the exposed sites were and do the experiments that confirmed the structure. Anyway, as much as we may have irritated each other along the way of the biology marathon, I want you to know that when I wrote it was a pleasure to work with people who are kind and bright in my user page- I was very much thinking of you. Nancy Sculerati MD 08:41, 13 December 2006 (CST)

Nancy, Thank you for your kind words, although you may be underestimating my age :) When I was an undergraduate Fred Sanger was still a hot topic, my lecturer believed he could have won three Nobel prizes for his work. And they did not let us forget how lucky we were to be able to use the new dideoxy sequencing, let alone not having to attempt Edman degradation. That said, i worked in a mitochondrial lab for quite a few years and there I did experience the importance and distinction of peptide sequencing. Firstly, to identify the cleaveage point of the mitochondrial import peptide it was critical to determine the peptide sequence of the amino terminal. Secondly, rarely we found discrepancies between the mtcDNA and mtDNA sequences. This was obviously a big deal since it could potentially lead to a different amino acid in the protein. Of course, we later realised that these were not our sequencing errors but rather an observation of the bizarre RNA editing that can occur in the mitochondia. In summary, we always need to be aware of where our sequence comes from, either DNA cDNA or peptide. I think you are correct to suspect that much of this is lost on the new generation of scientists. In fact, recently i had a graduate student who did not recognise the rRNA bands on their northern blot! I was blown away, but should not be surprised since we these topic are barely mentioned in lecture these days.

Anyway i think the team effort made the biology article come out pretty well. I look forward to future collaborations. Actually, I see McClintock is already on standby for number two! Chris Day (Talk) 11:06, 13 December 2006 (CST)

Talk link

Chris, what did you do to get the (talk) at the end of you signature? It's driving me crazy not to be able to just click on the talk link! --D. Matt Innis 10:30, 19 December 2006 (CST)

Hi Matt, first you need to set up your preferred signature in the my preferences above. Write into the signature box [[User:D. Matt Innis|Matt Innis]] [[User talk:D. Matt Innis|(Talk)]] (make sure you tick the raw signature box). If you paste that wikicode into the box, every time you type the four tildes your signature will look like this --> Matt Innis (Talk), with links to your user page and talk page. I hope this helps. Chris Day (Talk) 12:04, 19 December 2006 (CST)

This is my test... wish me luck --D. Matt Innis 12:25, 19 December 2006 (CST)

lol! I'll try it again.. --Matt Innis (Talk) 12:27, 19 December 2006 (CST)

YES! Thank you!!! --Matt Innis (Talk) 12:27, 19 December 2006 (CST)

Chris, re your proposal to remove certain external links in "Systems Biology" article

Chris, you say you're not sure we need the external links to labs and conferences in the 'Systems Biology' article. I feel strongly that they add to the quality of the article. For example, clicking on the link to the Institute for Systems Biology provides the reader with additional depth on the goals and approaches in the discipline not contained in the CZ article, examples of application, and webcasts. CZ gains that at little cost in space or distraction.

Moreover, those labs and conferences abound with experts in many fields, as systems biology operates as an interdisciplinary discipline. Whether those experts discover the CZ article linking to their sites, or we apprise them of the article (or related articles) as potentially benefitting from their expertise, CZ may have a chance of gaining their participation in the project.

I would suggest a compromise: Let's leave the links in, and I will go through each one, eliminating those sites that offer the reader little or no added-value to the main "Systems Biology' article.

Thanks for considering this.

Anthony.Sebastian 13:31, 19 December 2006 (CST)

Retrieved from "http://pilot.citizendium.org/wiki/Talk:Systems_biology"

Hi Anthony, certainly i can live with having some of the links. It just seemed a little strange having an exhautive list. One wouldn't consider such a list appropriate for a more mature science. Chris Day (Talk) 15:32, 19 December 2006 (CST)

THANKS!

No way! Real Life - what's that! Thanks so much, hopefully you can get back to help me clean up before we approve. Thanks Chris. --Matt Innis (Talk) 14:10, 20 December 2006 (CST)

Chris - can you make one more read through on the chiropractic article and make sure it satisfies your concerns. That way when we get Nancy and Gareth back, we'll be ready to approve quicker. I think the links look much better and the article is better for it. Thank you! --Matt Innis (Talk) 09:40, 21 December 2006 (CST)

metabolism

Chris, please look at metabolism, when you have a chance.Nancy Sculerati MD 09:45, 29 December 2006 (CST)

Cereals Template

Thanks The gif image is working well now in the cereals template. All the dopey glitecvhes in wheat are now fixed thanks Dave David Tribe 00:03, 3 January 2007 (CST)

Wheat

Chris, could you kindly look at wheat, when you have a chance? It is nearing approval. Thanks. Nancy Sculerati MD 09:03, 3 January 2007 (CST)

Main Template

I wrote the main template the way I did in order to get something up there, because red template links everywhere looked ugly. So if you want to improve on it, go for it! The primary purpose for pipelinks there is to make the names make more sense. "Please see our article on subtopic (topic) isn't as pretty, but that's not a crucial feature. Thanks for your help! --ZachPruckowski 13:51, 25 January 2007 (CST)

No problem, I'll play with it then, I just wanted to make sure I was not stepping on toes. I think you make a good point with respect to the subtopic (topic). i see another user has shown interest in the template too so we should be able to work it out together. Chris Day (Talk) 13:54, 25 January 2007 (CST)

Edits to Approved articles

YEs you're right about my abilities on editing. With Biology I took the initiative to clean up some minor glitches that were passing by uncorrected, and I was mindful of the surge in usage and pageviews that we are experiencing. My approach has been to leave overt electronic traces of my actions so that they are transparent. BTW A Google Image search of 'PLoS Biology' provides images galore, including better images of bacteria than we have been using.David Tribe 14:35, 25 January 2007 (CST)

yes I liked Biology 1.2 and found one redundant word in last sentance if i recall correctly David Tribe 01:10, 26 January 2007 (CST)

Recent Image Uploads

Can you try to provide more info when you upload pictures? It's not enough to say "from Wikimedia commons". We need to know the license of the picture and where it came from. If you could at least include a hyperlink to the appropriate commons page, that'd be appreciated. --ZachPruckowski 14:29, 26 January 2007 (CST)

Oops my bad, i was going to go back and do it at my leasure, as well as writing a more detailed descritpion. Thanks for doing the leg work for me!! Chris Day (Talk) 15:26, 26 January 2007 (CST)

No Problem! -- ZachPruckowski 15:56, 26 January 2007 (CST)

Pictures

	File:KildLaughing.jpg

Biology studies the variety of life

This is quite a tricky manoever ! David Tribe 16:20, 26 January 2007 (CST)

You think it is too complicated? i could just stitch them together as one jpg. Does it look a mess in your browser or do they all align tightly? The potential incompatability with different browsers might be a stumbling block unless there is some code tweeking that will work to fix it in firefox (at least). Looks good on my Safari browser though. Chris Day (Talk) 16:30, 26 January 2007 (CST)

Waatchout. Might be good to give file new file names as the images on the approved biology artivcle look shocking on my browser at the moment David Tribe 21:10, 26 January 2007 (CST)

Just hold 5 min Im fixing to approved copy David Tribe 21:16, 26 January 2007 (CST)

I don't think the file names are the problem but rather the coding of the table that makes up the montage. I can't trouble shoot on my MAC at present until i download a browser where i can recreate the problem. Good idea to comment out the table. I would be fine if you deleted it too., i have a copy here on my talk page to play with. Chris Day (Talk) 14:21, 27 January 2007 (CST)

The Biology image issue was a learning experience. My comments just above were made while I was nearly panicking in the middle of doing some approval stuff with things going wrong ALL over the place. Now that things have quietened down, and I'm moving along with welcoming new arrivals I noticed that you did the honours when I arrived, and I'm now really seeing the value in a helping hand to people who are a bit lost at the start. At that time I had very little idea of why people were usking about my userpage cos I didnt even knoe I had one (not having used one much at WP. Thanks. Maybe some thought can even be given to expanding the welcome template to be even more helpful ? Maybe not?

Possibly you didn't pick up on it (or have discussed it somewhere I missed), but the reloads you kindly and appropriatly made of images (typhoid) for Biology/Draft caused problems in the then approved Biology version. We need to highlight procedures for image re-upload - a warning to check if some uses of the existing figure lack thumbs perhaps on the upload page? Or a Advisory to give a different file name like Finch2.jpg when it replaces smaller Finch1.jpg? A rule of thumb (!) to always use thumbs? Do you see my point?

Do you have any good advice about primary image size. If we exceed the suggested 150 odd k and always use small thumbs are bandwidth problems solved?

cheers David Tribe 20:24, 28 January 2007 (CST)

Hi David,

• Welcome template: I just checked your talk page and sure enough I did help you a bit. Bit of a lame welcome though, all business no play ;) A simple template might not be a bad idea. I think it would be good to include links to how-to get started sort of pages. Certainly we need a page that explains how to use all the wikicode, as well as some general advice such as pointing out the useful tools such as the what links here and user contributions in the navigation bar to the left. I can remember being completely lost when i first used a wiki and it would have been good to learn those trick earlier than later.
• Changing image; size issues: Now I understand your comments above. I intially thought you were referring to the pictures in the montage. I now realise it was the knock on effect in the approved article with respect to the other figures you were refering too. I forgot that those figure changes would also be detrimental to the layout of the approved version, sorry to give you a panic attack. I'm still trying to get used to having two articles to consider (approved and draft). This type of conflict should not be a big issue in the future since the only reason those images in the biology article were coded that way was due to the fact that the imaging software (sizing) was not up and running in the early days here at CZ. Now it is fixed, the images should always have their sizes defined. With regard to size of the original picture.
• Changing image; bandwidth issues: I say upload the highest quality one available and obviously that is what i was doing. I don't believe there are any bandwidth issues, although, Zach might have a better idea or at least know who to ask. Chris Day (Talk) 02:28, 29 January 2007 (CST)

Re Image fixed quest

Ooo yes, it does look good now. I'm running Firefox 2.x in a Windows WP home environment now. I can check in in Windows explorer too. This is THE way to run browser checks! wiki checking. David Tribe 14:58, 29 January 2007 (CST)

OK in that case I'll extend the change into the draft version. Then at least you have the code for the next update. Chris Day (Talk) 15:04, 29 January 2007 (CST)

Good thinking Bullwinkle. (:0). On IE 7 on the same machine there is just a tiny white gap under the Big Earth picture tho. David Tribe 15:11, 29 January 2007 (CST)

On my IE7, montage in approved Biology appears without gaps, and otherwise looks good, too. Could extend image horizontally with additional lifeforms. --Anthony.Sebastian (Talk) 17:18, 29 January 2007 (CST)

Anthony, check out the other good picture here. http://commons.wikimedia.org/wiki/User_talk:Daycd Or make requests. I can easily add more or switch picture in and out. Chris Day (Talk) 17:50, 29 January 2007 (CST)

Personally, I'm not having issues with the image (Safari 2 and Konqueror), but I sort of feel like it might be worth looking into just linking a fixed montage image to a gallery if possible, or else using an ImageMap of some kind. I mean, I feel like this issue is solvable, but browsers change over time, and we also need a solution that's implementable in other articles. Both of those require some work on the backend, but then again, so does this. -- ZachPruckowski 18:14, 29 January 2007 (CST)

Hey Zach, this is an excellent idea. It will solve the compatability issues while still allowing the images to be accessible. I'll get started on it. First I'll have to figure out what image map is all about but the example they showed was very effective. In the short term, using an gallery will work very well. Chris Day (Talk) 12:21, 30 January 2007 (CST)

We would have to install an extension. It's doable. If you decide to go for it, email bugs@citizendium.org and I'll get it on the list of things to do. -- ZachPruckowski 12:33, 30 January 2007 (CST)

Another use that will be much more practical is for metabolic pathway diagrams. It will be excellent to be able to click on different metabolites and then be pointed to the CZ page about that molecule. Interactive figures could work really well for the project and we really should do it in the future. I'll e-mail them, although, I would not consider it a priority at this point. Chris Day (Talk) 12:38, 30 January 2007 (CST)

Chris: In Biology, the large blank space between the open image (montage) and the 'table of contents' could accommodate leftward additions, strengthening ilustration of the "variety of lifeforms" concept. I like most of the images in the 'commons' link you gave above. Especially the gaping feline. Beyond my techability to help, however. --Anthony.Sebastian (Talk) 21:28, 29 January 2007 (CST)

I can incorporate some more to the left if people don't think it looks cluttered. I'll put together some options and incorporate in Zach's idea of a gallery or image map functionality. Chris Day (Talk) 12:21, 30 January 2007 (CST)

Read your other notes Chris I understand in general whats going on and agree for the moment (weeks, months?) we should revert the montage to a fixed jpg. This has been a good learning experience, and the Imagemap extension for things like metabolic pathways seems a good idea. Have fun wth the images . Love the ?Yellowstone pool. Need it in orins of life or whereever David Tribe 14:01, 30 January 2007 (CST)

Just added a new version of the montage extending some pictures out to the left. I also added the gaping feline and replaced the running lion with a dolphin. Possibly a fish would be more appropriate since mammals are already well represented? I'm a bit worried that adding more begins to make it look more cluttered. If others agree which should go? If you like this new montage but don't like one of the pictures which would you like replaced and with what? We have many other photos at wikimedia commons that could be used to substitute these examples. Thanks for any feedback. Chris Day (Talk) 01:31, 31 January 2007 (CST)

Ooooooooh. A thing of beauty is a joy forever David Tribe 01:59, 31 January 2007 (CST) aka Milton. Bugs in space yo. I like that! David Tribe 02:00, 31 January 2007 (CST)

OK so it sounds like we can stick with this ;) Obviously this is a very small version. I'll make a bigger version for the actual biology article. Then I'll make a gallery for the pictures with a more detailed description of each photo. re: bugs in space, i really was thinking that when i placed it there. i thought the krills compound eye would make a nice moon too, or is that a death star? Chris Day (Talk) 02:04, 31 January 2007 (CST)

Other pictures

File:Chlamydomanas reinhardtii Flagella 3 - TEM.jpg

Re A N W in history logs

[2]

I discovered what W in the history log means. It seems to be done automatically when you call on special WP templates I used some code (including a command) specifying small references and 2 columns from WP RNA interference article and the W appeared. David Tribe 01:38, 31 January 2007 (CST) Ooo luverly pix BTW.

On second thoughts the W appeared when I un-commented your montage code in Biology/DraftDavid Tribe 01:56, 31 January 2007 (CST)

It appears if the "Content is from Wikipedia" box is checked. It seems to have starting defaulting to checked around the time you removed those comments. -- ZachPruckowski (Talk) 10:58, 31 January 2007 (CST)

montage

Hey, Anthony, is this the sort of thing you had in mind? Chris Day (Talk) 01:23, 31 January 2007 (CST)

• Chris, yes. Cool. Very nice. Do you make the montage's in PhotoShop?
• I know we can upload jpegs. Can we download uploaded ones for editing? Not that I want to edit your neat one, but for future reference.

--Anthony.Sebastian (Talk) 10:30, 31 January 2007 (CST)

That looks great! Have you seen this wikimedia help page on linking it to a gallery of some kind? That is the current plan, right? -- ZachPruckowski (Talk) 10:58, 31 January 2007 (CST)