Talk:Apoptosis

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To-do list for Apoptosis:	edit · history · watch · refresh
Make outline of apoptotic pathways clearer Convert bullet points to prose when necessary Images of pathways? FAC-worthy article - organise it! Integrate references into text using <ref></ref> tags

Contents 1 About the apoptosis signalling pathway 2 Why mention of Sonic hedgehog (Shh) was restored 3 Whole sections of this article (Programmed cell death in plant tissue, Evolutionary origin...) have been moved 4 Statistics on cells developing into cancerous cells 5 Cleanup 5.1 On the size of the page 6 Philosophical implications 7 intercellular signals for apoptosis 8 Section merger 9 Apoptosis Pronunciation 10 Role of NO

[edit] About the apoptosis signalling pathway

The VDAC interacts with Bak to inhibit its own mitochondrial outermembrane permeablisation (MOMP) activity? I thought Bak or Bax can interact with VDAC to directly induce permeablisation (when they multimerise), and it's the binding of these pro-apoptotic proteins to the anti-apoptotic Bcl-2/Bcl-Xl that inhibits MOMP?

Can someone clarify?

[edit] Why mention of Sonic hedgehog (Shh) was restored

On 12 Aug. 2004, an unregistered user with address 24.226.57.247 deleted mention of Sonic hedgehog in the Development section of the apoptosis article. The edit summary states that Sonic the Hedgehog stuff was taken out because it was irrelevant. I know that the name sounds funny, but that is how molecular biologist called this particular gene and its corresponding protein molecule. This is how it appears in scientific literature. I am adding a link to the abstract of Thibert and colleagues Science article in Medline /PubMed (a free access web search system) for anyone who would like to verify this: [1].

[edit] Whole sections of this article (Programmed cell death in plant tissue, Evolutionary origin...) have been moved

See the article on Programmed cell death. Other sections, especially concerning history of PCD research, will be moved there as well (see discussion in the PCD article). -- jaimeglz

[edit] Statistics on cells developing into cancerous cells

I know I read somewhere that (statistically) each day, every human has two cells developing into cancer cells, but are stopped by the immune system via apoptosis. If someone can back this up, it should be included in the article. --Magnus Manske

The statistics mentioned by Magnus are quite relevant: I will add mention to this as soon as I find corroboration in a trusted publication. Of course, if someone corroborates this before I do, please add it. -- jaimeglz

[edit] Cleanup

(copied from User talk:Steinsky)

At the end of October you began to do some work in the article on Apoptosis. You began to change the way references and citations were handled en that article (since they took up a lot of text), and used one of the accepted and respected styles; namely, to create a References section and refer to the citation by (Author, year). After giving it a thought, it occurs to me that the best way to handle this in Wikipedia is not by (Author, year), but to proceed as follows: 1) Make a direct hyperlink to the summary of the article in the on-line journal or a hyperlink to the on-line book, as long as they are free and require no registration (examples: a hyperlink to an article summary in PNAS, or to The Molecular Biology of the Cell); 2) If the direct link to the article is not possible, the hyperlink should be directed to solid and reputable public sites like PubMed or arXiv.org (example: when citing Nature or Science, which require subcription); 3) Use (Author, year) as the last resourt, because it is quite bothersome to Wikipedia users to search the publication and go back-and-forward to the References section. Thanks in advance for your attention to this note, and please use the discussion section in the Apoptosis article to tell me if you agree with this, so I can proceed to make the changes throughout the article. JaimeGlz

That sounds like a good idea. At the moment I'm concerned with the way references are included in the text, which IMO makes it difficult to read, and I think simple links would clear that up at least as well as my system. I'm also concerned with the size of the page (IIRC it's larger than the recomended limit of 32kb), and this would help sort that problem.

Nowadays the typical way to deal with the references section is with the PMID autorecognition (e.g. PMID 12345) and with Template:DOI. Should we work on converting this? --User:Chinasaur, Sep-2005

I implemented this change after seeing that no objection had been raised to your suggestion after a couple of months sitting here. Courtland 05:06, 18 December 2005 (UTC)

Now, as for the problem of size of the page. Does anyone have any ideas for how we could split sections into separate pages and reduce bits of this page to short summaries? I was thinking we could have Functions of apoptosis, Apoptotic process and Apoptosis and disease pages, allowing us to reduce those sections to summaries on the main page? Joe D (t) 01:58, 15 Nov 2004 (UTC)

[edit] On the size of the page

Thanks for your comments, Joe. Although I'm not of the opinion that "rules are made to be broken", I suggest not to divide the artcle on Apoptosis (with the exceptions that I will explain in what follows). This is one of the hottest topics in molecular and cellular biology, as well as in medicine. For instance, back in 2001, Lockshin and Zakeri estimated the ammount of publications on this topic at 80,000. So we have to be very even-handed on keeping a representative article on results by both young and old researchers, women and men, top-scientific journals and not-so-well known ones, and so forth (hopefully, add contributions by so-called "Third-World" scientist), as long as we are dealing with significant contributions.

Programmed Cell Death in general, and Apoptosis in particular, are now implicated in an almost incredible variety of biological processes and deseases.

I would agree that it is quite a challenge to make the article ammenable to the casual Wikipedia reader and to the high-school student, and at the same time to make it interesting and worth while to college students, post grads and whoever... So we will have to continue to work on it, so as to make it readable, to keep it up to date and worth-while to people knowledgeable on the subject, and at the same time to make it as precise and solid as possible.

However, nothing will be gained by splitting it into a special article on "biochemichal execution of apoptosis", for instance, because who on Earth would search for such as topic?. If the concerns are readability and physical disk space, the result would be counterproductive: non-intuitive topics such as "Morphology of the apoptotic cell" will not only be unlikely to serve as search criteria, but will certainly produce overhead use of disk and Wikipedia space. So I suggest the following:

1. The article is not su much above the recommended limit so as to make it imperative to break it up. 2. Move appropriate sections to closely related articles such as programmed cell death and Autophagy, and make the corresponding links. 3. Be carefull when adding new sections, so as to keep article size in check (I do have a long back-log of stuff I have dug up and that is quite significant, but I am holding it back until I am satisfied that it is sensible to add it). 4. Do add new sections on topics that naturally correspond to other other articles (specific proteins, subprocesses, new therapeutic agents, and so forth...), as has been done with Gefitinib and peptidomimetics. 5. Keep on scrubbing, like you (Joe) have done with the references...

Cheers, and thanks for your ideas and concerns.

JaimeGlz

I'm not sure you understood what was being suggested. What I'm proposing is splitting those sections and then linking to them from each subsection of this page, so that they are, effectively still part of the same article, but on other pages. For an example, see Evolution where the main article has a number of subpages, like Timeline of Evolution, Evolutionary biology and History of evolutionary thought. These pages are still effectively part of the Evolution article, but the bulk of the text has been moved to its own page, and the section on the main Evolution article reduced to a concise summary and a link to the sub-page. This isn't a case of breaking style rules, btw, browsers start having problems editing pages over 32kb. Joe D (t) 14:15, 15 Nov 2004 (UTC)

[edit] Philosophical implications

What the article doesn't seem to discuss much is the philosophical implication of having a cell programmed to kill itself on purpose. Which is all fine and well, since its mostly a scientific article, but I have read many many articles in magazines that discuss apoptosis and cite it as the fact that being a kamikaze or a suicide bomber, or suicide itself isn't as "unnatural" as everyone makes it out to be, whether this is true/NPOV or not. But would there be a place for this in the article?

And on a different note, I think this article can make it for WP:FAC if there were some neat diagrams and images - I have already emailed a webmaster for permission to use one (which happens to be 300 KB large), but of course to be an FA you have to have more images. -- Natalinasmpf 06:33, 30 Apr 2005 (UTC)

Response: Sorry for taking so long to answer. There is no doubt on the importance of the implications of this topic for the philosophy of science. As Lowe et al. mention in their 18 Nov. 2004 Nature article, "Intrinsic tumour suppression": "Cell proliferation and cell death are such diametrically opposed cellular fates that the discovery that the two are linked and interdependent processes was a great surprise." However, the only way I foresee to legitimately introduce wider philosophical questions into a Wikipedia article like "apoptosis" would be to quote or paraphrase highly recognized authors' opinions. And there is an additional difficulty involved, because it has already been suggested that the article is too long (see discussion above). Suggestions are welcome, but probably the best solution will be to place material on the wider implications (when found) into articles dealing with the philosophy of science.

jaimeglz, 5 Mar. 2006.

[edit] intercellular signals for apoptosis

This article doesn't appear to elaborate on this too much, especially, how do immune cells recognise cells that have been infected by viruses? Do their cell membranes change, or something? Do they withdraw signals? And of other things, for example, a lack of a cell stimuli as much as presence of stimuli can also cause apoptosis (I have read) - ie. if there's a cell without an "anchor" tying it to other cells at a cer Would the article explain more on this programming? Can more be elaborated on this? If we don't know (we probably don't know a lot), can the article clarify? -- Natalinasmpf 19:22, 24 Jun 2005 (UTC)

Response: There is abundant reference material on cell signalling at the end of the article. Follow the links and take a look: many of the papers are quite readable for the non-specialist. Would you really like to dig into the subject? Alberts et al. monumental Molecular Biology of the Cell (with its step-by-step explanation) can be read for free on the web. jaimeglz 5 Mar. 2006

[edit] Section merger

Should not the sections "#Etymology" and "#Coining of the term apoptosis" be merged? Courtland 05:09, 18 December 2005 (UTC)

Response: Thanks for the suggestion. Please check the way the sections were merged.

jaimeglz, 5 Mar. 2006

[edit] Apoptosis Pronunciation

The article only mentions one pronunciation, and the reference link provided says that it's controversial. I've heard the word said by professionals in any of 4 different ways, and don't like the idea that the article only mentions one. While I pronounce it with a silent second-p, I don't accept that as standard because I also don't pronounce "helicopter" as "helicotter," nor do I use Greek and Latin plurals when an English one is acceptable. To me, the pronunciation as indicated is derived from pretentiousness rather than accuracy, because if accuracy was the issue, ptosis wouldn't be the most accurate Greek suffix.--Trypsin 15:31, 2 May 2006 (UTC)

I have always pronounced it as A-POP-TOW-SIS, I have only ever heard this pronounciation. I would like to see some mention in the article that the pronounciation is disputed (just like the linked to article). Adenosine | Talk 17:56, 27 June 2006 (UTC)

[edit] Role of NO

Hi, I am a little puzzled that the role of nitric oxide in regulating apoptosis has not been given due importance in this article. I would be enlightened if someone could include the significance of NO given that this topic of research is being pursued greatly in scientific circles. Thanks. Sriram sh 07:39, 6 December 2006 (UTC)