Talk:Systems biology/Archive 3

Hello everyone!
Yes, yes, yes, yes and yes. I agree with all of you. The term "mechanistic modelling" does exist, and among researchers in systems biology and physical sciences, the term is fairly well recognised. But Zargulon is right. The whole point of an introduction is that it should be comprehensible to non-experts.

Nicolas Le Novere's edits are so much of an improvement on the paragraph I originally wrote, it almost hurts. I say we keep the term "mechanistic modelling", and the changes, but we break it down further and explain more clearly what mechanistic modelling is. We just have to keep going at every sentence of the article.

Zargulon is a valuable devil's advocate, please don't let that put you off contributing to these pages.

It seem emotions are high and the mood is low, but we are stumbling along towards a good article here. Please everyone, stick with it and keep up the good work :) Robnpov 22:36, 5 January 2007 (UTC)

Daughter Project?
Greetings.

My name is Guido David Núñez-Mujica. Undergraduate student, working on my thesis in Systems Biology, no papers yet in this field, however, got some in totally unrelated fields (Future studies). I would like to suggest some terms we could add to the Wikipedia related to this entry, as they are quite a number and we are under the Molecular and Cellular Biology WikiProject, I would like to know if you think it would be a wise thing to create a Systems Biology WikiProject, to make it a Duagther Project or to remain under the Molecular and Cellular Biology WikiProject to avoid scattering our efforts.

I think these terms should be added or expanded:
 * Metabolic Flux
 * Stoichiometric Matrix
 * Metabolic Control Analysis
 * Control Coefficient
 * Elasticity Coefficient
 * Fundamental Subspaces of a Matrix
 * Elementary Modes Analysis

Also it would be worthy to detail to some extent the biological implications of topics like Null space or Graph Theory.

I apologize in advance for any mistakes in my English, which is not my first language.

Thanks in advance.

Guido

Link farm
The section listing research centers is looking like a link farm with no rhyme or reason to the list besides people wanting to promote their specific institutions (spam/self-advertising). The section should probably be removed and maybe recreated as a separate list page with any and all research centers instead of saying these select ones are "notable" (NPOV issue). The Bioinformatics article has adopted a similar scheme since everyone likes to list research centers for that too, by moving the list to List of Bioinformatics Research Groups. Since I don't edit this page frequently and I'm not in the Wikiproject that covers it, are there any objections? -Cquan 19:13, 19 March 2007 (UTC)


 * I think this is an excellent idea. Once one group is on, no-one wants to be left out. The only workable solution is to move them all. Zargulon 00:09, 20 March 2007 (UTC)


 * I've gone ahead and removed the list from the main page, created the list page and added a link to it under "See Also". I'm also adding a comment in the source of the main article for discussing proposed links so this page doesn't become a link farm again. -Cquan 01:00, 20 March 2007 (UTC)


 * I recommend using external listing service, DMOZ (Open Directory Project) instead. This was recommended in WP: (don't have the exact policiy right now, but I'm sure it's related to WP:NOT. Bioinformatics 'list' has been changed to use this and tagged for deletion. JetheroTalk 05:19, 12 April 2007 (UTC)

Scope
What's the relationship between systems biology and other life sciences (i.e. molecular biology, cell biology, physiology, ecology)? To me this is a question of scope. Please see the rheology page for a nice example of defining scope. The page relates rheology to the related fields of fluid mechanics, solid mechanics and their respective subfields. Perhaps something similar is appropriate here.
 * As of yet leading systems biologists are so diverse in their perspectives that the definitions of the scopes they have given are not mutually consistent. A flattering explanation is that systems biology is still a maturing field; no doubt you may come to form your own opinion. Zargulon 22:47, 8 April 2007 (UTC)


 * I think it might be useful to add a section on the applications of systems biology, e.g. to drug discovery and perhaps (in the future) to biological research as a whole. Without this the article doesn't communicate much about why this field is gaining so much pace. I could start something off but undoubtedly anything I write will be biased to my own perspective.... arhardy 16:38, 17 October 2007


 * A lot of similair articles (about a specific field of science) have a section "Applications of ...". So if you have some more information about this subject, please go ahead. It's eventually the intention, that all contributions are backed up (or refer to) independent sources. But it's always a good thing if someone makes a start. Good luck - Mdd 17:13, 17 October 2007 (UTC)

Systems biology organizations and communities link farm
I'll start by saying these are clearly some of the important communities in SysBio. However, this section is obvious external linkspam bait and a directory seed. It will continue to grow to the point that the few notable societies (in some people's opinions) will either have to continually be defended or will be diluted. It's all external links, it's an open-ended list/directory which are not referenced in this article. Specifically,
 * The International Society for Systems Biology; an international society aiming at advancing systems biology research world-wide by providing a forum of scientific discussions and various academic services. Organizer of the International Conference on Systems Biology (ICSB)
 * The Canadian Society for Systems Biology; the world's first national organization aiming to develop and facilitate systems biology research across scientific boundaries
 * ENFIN; a European network aimed at the integration of computational approaches in systems biology
 * The Yeast Systems Biology Network; an initiative aming to link various international research groups working on yeast
 * International E. Coli Alliance; an initiative linking to link various research groups working on bacteria
 * HepatoSys; a German initiavitve focusing on endocytosis, detoxification and regeneration in human hepatocytes
 * WP is not a directory WP:NOT, not a collection of info WP:NOT, not a repository of links WP:NOT
 * The list is open ended. Implied inclusion critera are highly subjective. To properly maintain WP:NPOV we'd have to eventually add virtually thousands of societies and communities in modern biology, and this is not feasible or desireable.
 * The links are all external, directly to organization's top pages that are in place for the point of marketing, rather than linking to information that would describe System's Biology to our readers, and assert notability of the topic and the communities. Simply linking to a society doesn't indicate why and how it's important to a topic. That must be done by an independant reliable source.
 * It's unencycopaedic. It does very little to add to the reader's understanding of what systems biology is.
 * Although designed for starting articles, WP:ORG describes what makes an organization notable. We could use these guidelines for considering the links above.
 * The information could perhaps be found by keyword searching the internet for organizations and communities with 'Systems Biology' in the title.
 * The information could be more easily managed in a DMOZ list. See Template:DMOZ.
 * Most of this applies to the other link farms on this page currently called 'books' and 'articles' (which are not used as inline references) and 'external links' JetheroTalk 03:43, 27 April 2007 (UTC)

Applications
Many predictions concerning the impact of genomics on health care have been proposed.
 * I moved this section here because it might be improved, and it added very little to my understanding of the applications of system's biology. However, an applications section might be a good addition. My intention is not to nit-pick the writing style -- I realize I should just improve it -- but I'm not an expert in this field so I'm only left with questions, not answers. Specifically:
 * what sort of predictions, by whom, how many, what impact. This tells me nothing.

For example, the development of novel therapeutics and the introduction of personalised treatments are conjectured and may become reality as a small number of biotechnology companies are using this cell-biology driven approach to the development of therapeutics.
 * Forward looking statements, unreferenced. What companies, what approach, what therapeutics? What's the connection between sysbio and pharmaco-genomics/-genetics or experimental or personalized medicine?

However, these predictions rely upon our ability to understand and quantify the roles that specific genes possess in the context of human and pathogen physiologies.
 * this sentence is not bad and gives me a glipse of what we mean by applying SysBio, or rather the challenges preventing us from applying sysbio, but doesn't stand on it's own.

The ultimate goal of systems biology is to derive the prerequisite knowledge and tools.
 * prerequisite to what? who's stated ultimate goal? (isn't tool development just the first, not ultimate step?) And this section is about application, not goals. The goals could be made clear in earlier paragraphs. JetheroTalk 04:03, 27 April 2007 (UTC)

Not four things, though not quite one thing either
Although S.B. isn't one thing it isn't 4 things either, these are 4 aspects of the field, and the wording I've reverted doesn't work I'm afraid. In particular the Science article is not talking "abstractly" but about a very specific paper in Science. And any actual work in S.B. tends to all all the aspects: approach, methodology, philosophy etc.. NBeale 15:59, 4 May 2007 (UTC)
 * I don't understand how any of those arguments is justification for a wholesale revert. You even reverted "operational protocol" back to "operational protocols" which is clearly wrong. I hope you eventually come to understand the nature of contributing constructively as well as you seem to believe you understand the nature of systems biology .. until then, well, I've done my best. Zargulon 19:44, 4 May 2007 (UTC)
 * Hi Zargulon. I thought quite hard about how to do this without a revert but I couldn't see any way of doing it. The problem with your wording was that it gave the impression that the 4 aspects being considered were quite distinct, whereas of course they can be combined to almost any degree. I agree of course that the problem with the existing text is that it could be read as giving the impression that S.B. was one definite and clearly defined field whereas of course there are nuances and shades of meaning, but I don't think that's a big problem because all such terms have such shades. However it may well be that you or another Editor can improve the wording further. I expect they will. NBeale 19:55, 4 May 2007 (UTC)
 * Ok.. IMHO you should have just said that here and then reverted after a day if I didn't respond. Reverts tend to be pretty blunt instruments as well having a mildly toxic effect on relations, although it is pretty clear to me now that you were acting in good faith. But I think the page either the page should go back to how I left it or you should share the effort of finding the right words.. you seem to be articulate and knowlegeable enough to help out. Zargulon 20:01, 4 May 2007 (UTC)
 * Hi Z. Point taken, though there is something to be said for being bold ;-). I've had a go at reflecting your point with "This variety of viewpoints is illustrative of the fact that systems biology refers to a cluster of concepts rather than a single well-delinieated field. However the term has widespread currency and popularity as of 2007, with chairs and institutes of systems biology proliferating worldwide." although a purist might place an OR tag on this if they were so minded. NBeale 13:43, 5 May 2007 (UTC)
 * Thanks - that's fine for now. Zargulon 21:33, 5 May 2007 (UTC)

External link additions
Discuss proposed additions (or deletions) of the external links here:
 * The First q-bio Conference on Cellular Information Processing - A conference in Santa Fe NM (Aug 8-11, 2007) focused on modeling of genetic regulatory and signal transduction systems and quantitatitve experimentation
 * Weak Oppose. This is their first conference, so I doubt that it is important enough to mention as of yet. It is on topic however. -Cquan (talk, AMA Desk) 18:03, 18 May 2007 (UTC)
 * Oppose non-notable. Zargulon 18:45, 18 May 2007 (UTC)

Systems theory
Amazing how it always he who knows nothing that is the severest critic. Suggest that some homework be done here on systems theory and those who have worked on it. As far as fluff is concerned, the value of systems theory is that properties of the whole cannot be found in the parts just like the meaning of these words cannot be found in an analysis of the black and white they are composed of. Unfortunately it is a waste of time trying to educate the smart one. This is one reason that alternative encyclopedias have cropped up. Bye
 * What are you suggesting, Mr. Bye? Zargulon 11:42, 30 June 2007 (UTC)