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DNA

[edit]
The general structure of a section of DNA

I'm not sure this is featured picture quality, but the topic is rather important and I think deserves an FP. If you don't support it, please try to give me hints on how to make a better one :-)

Comment regarding the "rainbow pattern": There have been some questions regarding coloring. The rainbow coloring of the two backbones is not arbitrary. In general usage, the 5' end of nucleic acids is colored blue, while the 3' end is colored red, and the intermediate sections vary in a rainbow-like fashion. I didn't make this up, folks ;-) mstroeck 20:20, 11 June 2006 (UTC)[reply]

Response regarding rainbow pattern I've consulted five different university-level molecular biology textbooks, and none use the rainbow pattern in representations of the DNA helix. Though I did not look very hard, I found no different colors for 5' ends vs. 3' ends either (in any case, 5' and 3' coloring could be used only to illustrate direction of strand and would not be suitable in a cyclic pattern like this). In the textbooks, the two strands are given different colors, so they are easily distinguished. Shading of the helix is used to represent twisting state, with same shades at every 360 degree turn of a strand. I agree that such shading makes much more sense than rainbow shading. (see my vote 'oppose' below) Jens Nielsen 09:40, 17 June 2006 (UTC)[reply]
  • Self-nominate. - Mstroeck 09:25, 10 June 2006 (UTC)[reply]
  • Support Superb and clear, my only gripe being the lack of info in the caption/image page. Currently, this image is used in an astounding 348 articles in the en wiki, not counting project & talk pages. Pretty useful by anyone's standards :-) ~ Veledan • Talk 11:23, 10 June 2006 (UTC) Bah, it's the genetics stub template of course ~ Veledan • Talk[reply]
  • Strong Support. Very clear and consise. This image at least meets every requirement, and excedes several. --Pharaoh Hound 13:21, 10 June 2006 (UTC)[reply]
  • Weak support. The colors of the nucleotide components seem to be keyed to type. That makes sense. However the helix frame has rainbow shading that looks nice but doesn't seem to correspond to anything. I'd suggest that the helix frame should be grey for better educational value. Also, maybe the nucleotides could be more clearly delineated by color, along with a legend showing which is adenine, guanine, cytocine and thymine. I would change my vote to "support" or "strong support" if that were done. Otherwise, this is useful for showing the double helix structure and scale, but not much beyond that. -- moondigger 14:00, 10 June 2006 (UTC)[reply]
Well, it's called "DNA Overview.jpg" for a reason ;-) I understand your concerns, though. I am planning a much more detailed second version of this, but I would like to keep this more or less as it is - as a general overview. Regarding coloring, see the note I added above. mstroeck 20:20, 11 June 2006 (UTC)[reply]
  • Oppose. I've compared the image with those in my molecular biology textbooks, and I tend to agree with moondigger. The rainbow shading is not very helpful. One backbone strand red and the other blue would be helpful, as it would aid keeping track on each strand. Shading would be ok, but then it should illustrate the 'twisting state' of the strand, and it would have to have same shading for every 360 degree turn. Present picture does the opposite, obscuring rather than clarifying the repeating pattern of the DNA helix. As for the color of the nucleotides, I'd prefer coloring purines in one color, pyrimidines in another. A legend would also be appreciated, as others have argued. Finally, I think this kind of 'stick' DNA representation is somewhat out of fashing in favour of the space filling DNA representations you see in most molecular biology books. In short, it's not a state of the art DNA representation, and not enough for FP. That being said, it is a nice piece of work and I applaud you for the efforts.Jens Nielsen 09:40, 17 June 2006 (UTC)[reply]
  • Support excellent illustration. What software did you use to make it, by the way? DVD+ R/W 17:28, 10 June 2006 (UTC)[reply]
Thanks! I used iMol for Mac OS X and (of course) PhotoShop. mstroeck 19:14, 12 June 2006 (UTC)[reply]
See above as to why the backbones are rainbow-colored. I am planning to add a very accurate description soon. mstroeck 20:20, 11 June 2006 (UTC)[reply]
Comment Just found the Peer review for this thing: Wikipedia:Featured_picture_candidates/DNA_Overview
Oops, even I had forgotten about that. I should have linked to that, thank you for including it. mstroeck 20:20, 11 June 2006 (UTC)[reply]
Sorry for going off-topic, but Mr. Lefty, that thing on your user-page must be one of the funniest things I've seen on Wikipedia :-) mstroeck 20:29, 11 June 2006 (UTC)[reply]
Hi Janke! Do you mean a legend in the picture, or on its page? I'm currently trying to track down the data file I used to make this image. When I have found it, I will add a complete description of the chemical structure to the page. mstroeck 07:06, 12 June 2006 (UTC)[reply]
The legend would hardly be visible in the thumbnail, so better to put it on the image page. Something like on this one: [1] --Janke | Talk 08:27, 12 June 2006 (UTC)[reply]
  1. As mentioned several times already, there’s no key/legend – it’s therefore really just a pretty-coloured picture. Perhaps a good start would be the elements, since you’ve gone to the effort of colour coding them (I think). As I see it, blue = nitrogen, green = hydrogen, red = oxygen, purple = phosphorous – am I correct? And, BTW, if that is correct, where’s carbon? I just can’t see that at all. Also not sure how you would then code the molecules, e.g., the bases, though perhaps they would need to be labelled individually.
  2. Why do those purple/red molecules penetrate the helix ‘backbones’? Are they the deoxyribose sugars, or the phosphate groups perhaps, which would give them some reason for being there? I don’t know, because there’s no key! I’m actually assuming they’re the phosphate groups, but if so, they should be bonding in some regular way with the sugars to the form the helices. These don’t all appear to be bonding, although looking very closely most do bond, so it could just be ‘our’ perspective that’s the problem. What is actually bonding with what is also an issue (especially with that missing carbon). Now if the molecules are what I think, the ‘backbone’ shouldn’t then IMO be shown as those solid bands, as it’s the phosphate/sugars that form the backbone – if you want the bands there perhaps they could be semitransparent, as they do help with visualising the thing.
  3. Why are there such huge gaps between some of the base pairs? Some appear to be touching, others you could drive a truck between. Again, is it just our perspective causing the variation? Regardless, I think the hydrogen bonds should be illustrated in some way to show that the base pairs are actually bonded (and how), even if there is a gap between the actual molecules.
    • You do know what a 3D representation is, right? There aren't different sizes in the gaps; you're just seeing different angles... — BRIAN0918 • 2006-06-13 22:52
  4. I’m not convinced that there’s always a purine and a pyrimidine base bonding. Again though, without the key or labelling, it’s hard to tell for sure.
  5. Again it may just be perspective problems, but I swear some of those nitrogenous bases, or at least the sugars, are looping around the outside of the shown helix bands.
  6. The horizontal and vertical scales are inconsistent. If you use the horizontal scale, the vertical height is only just over 3nm, not the 3.4nm it says it is. Is it legitimate to use two different scales in one diagram? IMO it’s not.
I really do like this, and think it has great potential, and apologise for being so harsh because it looks like it would have been a lot of work (and look, some of my assumptions and criticisms may be wrong). But the accuracy of something like this is pretty important. I’m sure I’ve seen it suggested before that maybe there should be a separate page for evaluation of this type of picture as opposed to the usual photos. That may be right, because too many people seem to support these diagrams just because they look pretty, with no regard for their accuracy (the cricket picture a couple of days ago was the same thing). Perhaps some of the criteria for judging these are different. I’ll wait with anticipation for your improved version. Maybe I’m being too picky given that you have said it’s just ‘an overview’, however I don’t think it’s a FP – not yet. --jjron 08:21, 13 June 2006 (UTC)[reply]
    • Thanks, jiron, for offering your comments. Since I am not a biochemist, I cannot know what is right or wrong. However, if everything can be sorted out, and mstoeck can fix any actual errors, I'll change my vote back to full support. --Janke | Talk 09:11, 13 June 2006 (UTC)[reply]
  • Strong Oppose Not the best illustration of DNA I have ever seen, and where the heck is the legend? I'd support placing the legend within the picture, rather than outside as a user suggested above (changing the color of a few boxes isn't difficult at all). Whether anyone likes it or not, people will use Wikipedia's pictures and anyone who sees this outside of Wikipedia is going to feel just as lost as I do right now. For example, a while back I created a map showing the global distribution of snakebite morbidity, (just noticed how bad the colors are). If I had not included the legend within the image anyone who saw this outside of Wikipedia would have no idea what was being shown. Not to mention most diagrams have the legend within the picture anyway; its the standard on these things. Anyway, I ultimately agree Janke on this one. --Mad Max 21:14, 13 June 2006 (UTC)[reply]
When the legend is within the picture, it is (a) either unreadable without enlarging the picture, or entirely too large when the picture is enlarged, and (b) very hard to edit and translate (i.e. change the text, not just the colour). Zocky | picture popups 15:27, 14 June 2006 (UTC)[reply]
  • Oppose. This diagram has a few problems imo.
  1. I notice colors of atoms are different from, for instance, the other drawing in DNA. Is there a standard for atom colors? Probably there can be variations, but it seems to me that green carbons are very unusual. You can also have a look at the Commons category for molecules for more drawings. How can we feature a drawing that detracts so much from conventions?
  2. As Jiron said, it is strange that sometimes the atom bindings cross the helix bands and sometimes not. Also, the whole molecule seems to be leaning on the right toward the top, why? It would be good to have the original molecular data to help understand (a PDB file perhaps?).
  3. I am going to be a bit picky, but the colors in the helix bands are not continuous and the bindings between sections are not clean.
  4. For information, what exactly has been done in Photoshop and what in iMol? Looking at iMol's web page, it seems it can make similar images by itself.

Apart from that, I can see strengths in this drawing: atoms are of a good size, and the black borders help distinguish them. --Bernard 19:49, 16 June 2006 (UTC)[reply]

  • Oppose I would * love* to see this go through, but there are too many problems at this point and still no legend. Lets have another go at this pic when it has been cleaned up and the controvercy cleared up. I would suggest the discussion page on this would be a good place to discuss after it is closed. -Ravedave 05:44, 18 June 2006 (UTC)[reply]
  • oppose i don't like the way the ribbon back bone obscures the ball and stick model. It seems to be a bad compromise between a cartoon and a technical drawing. David D. (Talk) 05:46, 18 June 2006 (UTC)[reply]

Not promoted There are some questions about the accuracy/design philosophy of this diagram. A modified version that addresses at least some of the concerns expressed above would likely be promoted, judging by the comments. The utility of such a diagram is obvious. -- moondigger 16:31, 18 June 2006 (UTC)[reply]

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