Talk:Systems biology

Article Checklist for "Systems biology"

Workgroup category or categories	Biology Workgroup [Editors asked to check categories]
Article status	Developed article: complete or nearly so
Underlinked article?	No
Basic cleanup done?	Yes
Checklist last edited by	Ben Gardiner 21:56, 17 April 2007 (CDT)

To learn how to fill out this checklist, please see CZ:The Article Checklist.

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Beginning Edit

I plan to update/edit this article in stages as time permits. Anthony.Sebastian 14:57, 17 December 2006 (CST)

Regarding Chris Day's Removal of Externals Links

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 comprise: 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 13:18, 19 December 2006 (CST)

I am fine with such a compromise, especially if you feel strongly. I would suggest that an exhaustive list is not appropriate. I suppose the original reason for those lists were the novelty factor of systems biology. Such a list would not be considered for a more mature branch of biology so we should keep that in mind too. Chris Day (Talk) 15:36, 19 December 2006 (CST)

Chris, wil keep your suggestions in mind as I edit lists.Anthony.Sebastian (Talk) 13:21, 20 December 2006 (CST)

Added section: On the Nature of Biological "Systems"

It seemed me to make the article on 'Systems Biology' more intelligible to the general reader to say something about what systems biologists mean when they speak of 'systems'. I tried to cover just the main points, and to exemplify them. Comments, sggestions, etc., welcomed.

Anthony.Sebastian (Talk) 14:19, 19 December 2006 (CST)

Work Done and Needed

So far I have re-written the Introduction--though still not completly happy with it--including incorporating one in-text citation, and have written a new section, following the Introduction, to elucidate the meaning of biological systems, giving examples.

I think the "History" section important to an ultimate grasp of systems biology as a major discipline of biology. It needs fleshing out with a description of the several historical roots converging to modern systems biology. I have begun the re-write offline, and plan to make that my next contibution to the article. Anthony.Sebastian (Talk) 14:25, 23 December 2006 (CST)

Hi Anthony. I've dropped a section into this that I wrote for the Vitalism article; it is more appropriate here - I thought the references would be helpful for you to retain even if you want to dismantle the section, if you do that's fine with me. The new vitalism idea has been picked up in a few more recent articles, but is tangential. There's a great quote from Sydney Brenner around that would be perfect - I'll try to find it again Gareth Leng 14:40, 23 December 2006 (CST)

P.S. Hodgkin and Huxley's model was of action potential propagation - not really a nerve cell model (they modelled propagation not initiation of action potentials).Gareth Leng 14:52, 23 December 2006 (CST)

• Gareth: Very nicely done piece on 'emergence'. The concept definitely needs cogent/lucid explication with examples if we want to reach the reader, and it seems apposite for this article. I will check out your references. I will have to convince myself of the wisdom of introducing the term 'vitalism', but I have an open mind. Glad to have someone with your level of expertise and experience working on the article, and to have someone to get feedback from. Anthony.Sebastian (Talk) 21:32, 23 December 2006 (CST)

• Gareth: Re the Sydney Brenner quote: Vitalism is dead [see http://www.asa3.org/ASA/BookReviews1949-1989/12-81.html]? I need to check the original source in Nature.
  • Gareth: Perhaps you meant this quote: “Much has been written about the philosophical consequences of molecular biology. I think it is now quite clear what the enterprise is about. We are looking at a rather special part of the physical universe which contains special mechanisms none of which conflict at all with the laws of physics. That there would be new laws of Nature to be found in biological systems was a misjudged view and that hope or fear has just vanished. Our job is simply to find out how these interesting pieces of machinery work, how they get built and how they came to be the way they are. In one sense, the answers already exist and all we have to do is to find out how to look them up in Nature. That is why molecular biology seems to me to be the art of the inevitable.” New directions in molecular biology, Sydney Brenner, 26 April 1974 Vol 248 No 5451 pp785-787.

Added new section: "History of Systems Biology"

I have drafted the beginning of a new section on the history of systems biology. I will further develop the section as time permits. I will incorporate some of the existing "History" section, then delete "History".

Comments welcomed.

Anthony.Sebastian (Talk) 22:53, 25 December 2006 (CST)

Brenner quote (Gareth Leng & Anthony Sebastian)

This is what I was recalling: The editorial in Nature Biotechnology begins with a quote from Sydney Brenner "In one way, you could say all the genetic and molecular biological work of the last 60 years could be considered a long interlude...We have come full circle—back to the problems left behind unsolved. How does a wounded organism regenerate exactly the same structure it had before? How does the egg form the organism? In the next 25 years, we are going to have to teach biologists another language...I don't know what it's called yet; nobody knows..."

and goes on to say

"Delivered over 30 years ago, Brenner's cautionary words resound even more forcefully today. Although we may now have a term, 'systems biology,' for his 'language' ..., the central problem remains: how to transform molecular knowledge into an understanding of complex phenomena in cells, tissues, organs and organisms? In the intervening decades, we have become spectacularly successful at creating inventories of genes, proteins and metabolites, but remained spectacularly average at pinpointing key points for medical intervention in disease pathways or determining which recombinant gene(s) to add to generate a complex trait. There is no clear connection between molecular description and such 'systems' phenomena."

Thought it might be worth incorporating?Gareth Leng 13:14, 14 January 2007 (CST)

• Thanks Gareth: I will track down the reference for source-citation, and then try to incorporate Brenner's remarks, in the 'History' section probably. I consider this whole article a 'work in progress', and a slow one for me, as other projects make their demand. --Anthony.Sebastian (Talk) 18:14, 14 January 2007 (CST)

Started new section: "Modeling in Systems Biology" - Work in Progress

See article for initial work.

Ilya Prigogine?

Interesting and challenging topic. Also timely and modern. Does Ilya Prigogine fit in here somewhere?

Brenner's comments remind me a bit of the Eric Landers Journey to the Centre of Biology idea (about molecular genomics) I've mentioned in connection with Genetics in the Biology forum.

After you done a genome, that's the end of reductionism in one sense. The rest is largely integration.

Post genomics has forced us towards systems biology.

It may be good to add in a few more figures soon. They liven up the task of writing, as well as the reading. David Tribe cheers D

David:

I have read, in the sense of having ingested but not necessarily absorbed or metabolized every sentence, of the follow Prigognine books, gathering dust on my study ("The Darwin Room") shelves:

• Prigogine I. From Being to Becoming: Time and Complexity in the Physical Sciences.Renz, Peter San Francisco: W.H. Freeman and Company, 1980. [Ref ID: 24075]

• Prigogine I, Stengers I, Toffler AF. Order Out Of Chaos: Man's New Dialogue with Nature. Toronto: Bantam Books, 1984. [Ref ID: 23757]

• Prigogine I. The End of Certainty: Time, Chaos, and the New Laws of Nature. New York: The Free Press, 1997. [Ref ID: 24415]

You have, as you have in the past, diverted me from the mundane to the sublime--so I have no choice but to re-read (at least in part) those texts in the present context to test your intuition. I have percolating in my near-subconcious the implications of far-from-equilibrium states and how to bring their implications coherently into a didactic exposition on systems biology without overwhelming the non-expert reader who hardly needs to read a CZ article on the subject. I made brief mention in the "History Section" under construction.

Regarding illustrations, I resonate harmoniously. I plan to keep myself focused on a coherent text, then add illustrations later--which necessarily will entail textual revision. Such befits the beginner's efforts.

Any illustrations you think might have didactic value, I would welcome--or edit in yourself.

--Anthony.Sebastian (Talk) 21:11, 19 January 2007 (CST)

Prigogine I. The End of Certainty: Time, Chaos, and the New Laws of Nature, is one of the best books on natural philosophy ever. Suplime, indeed. Kauffman, I find , could benefit from an aggressive editor David Tribe 15:02, 24 January 2007 (CST)

HGT and Systems Biology

This just came out in Nature: Havnt read it but I will. Nature Essays: Connections

QUOTE From cell biologists to quantum physicists, researchers are struggling to work out how systems involving large numbers of interacting entities work as a whole. In this collection of Essays, scientists explain how a systems approach, in parallel with the reductionism that dominated twentieth-century science, promises to yield fresh insight, and in some cases, to challenge the most widely held concepts of their field.

Essays: Connections Biology's next revolution The emerging picture of microbes as gene–swapping collectives demands a revision of such concepts as organism, species and evolution itself. Nigel Goldenfeld and Carl Woese (FREE ACCESS BUT DONT HAVE NON PROXY LINK YET Go via Nature webstite to latest issue) Nature 445, 369 (25 January 2007) doi:10.1038/445369a UNQUOTE

Gene swapping collectives indeed! It just made me realise that HGT the origins of cells, and the origins of life relate to YOUR topic here. If we can make that connection well this page could shine brighter. There's hard work involved too, tho David Tribe 15:02, 24 January 2007 (CST)

David: Thanks for directing me to the Nature Connections Essay emphasizing the importance of the systems view of bacteria as cooperative collectives of gene-swapping (aka HGT) subsystems, which continually receive information from the environment in the form of energy and information-dense organic molecules, altering themselves and each other, and responding collectively as a unit of selection. As you say, that view alone relates directly to the topic of "systems biology". To make a strong case for such a systems view of microorganisms as essential to understanding the evolution of complexity and emergence in biological systems: a bright light indeed. Eagerly await the follow-up essays and your evolving thoughts.

For your convenience, I emailed you a PDF of the Goldenfeld and Woese essay.

Anthony.Sebastian (Talk) 19:57, 24 January 2007 (CST)

Sources

Hi Anthony, I noticed that you deleted out a lot of the old wikipedia stuff. I'm not sure if you also meant to remove the sources and categorys. I have replaced the sources here since it might be useful to migrate some of these back to the article?

Books

• EXPANDED AND MOVED TO ARTICLE Anthony.Sebastian (Talk) 17:27, 23 February 2007 (CST)

Articles

• Vidal M, Furlong EEM (2004) Nature Reviews Genetics From OMICS to systems biology

• Werner E (2005) The future and limits of systems biology, Science STKE pe16 (2005).

• ScienceMag.org - Special Issue: Systems Biology, Science, Vol 295, No 5560, March 1, 2002
• Nature - Molecular Systems Biology
• Systems Biology: An Overview - a review from the Science Creative Quarterly
• Guardian.co.uk - 'The unselfish gene: The new biology is reasserting the primacy of the whole organism - the individual - over the behaviour of isolated genes', Johnjoe McFadden, The Guardian (May 6, 2005)
• Trewavas AJ (2006) A brief history of systems biology: "Every object that biology studies is a system of systems." Francois Jacob (1974). Plant Cell 18:2420-30 Fulltext or PDF need access rights

External links

• BioChemWeb.org - The Virtual Library of Biochemistry and Cell Biology: A Guide to Biochemistry, Molecular Biology & Cell Biology on the Web
• Systems Biology Portal - administered by the Systems Biology Institute
• Community for Interactomics - Systems Biology Wiki
• Systems Biology Medicine Symposium 2006 - View webcasts (in Real Player or Windows Media Player) of a symposium on research and applications of systems approaches in Medicine

Isn't selection after the fact?

I am questioning the use of natural selection in a systems article. As you know selection occurs after the fact and has nothing whatsoever to do with the preceding evolutionary step. As far as I can tell, that evoutionary step is accorded to random mutations, in other words it just happens. In systems science the notion of "self-organization" accounts for matter and life to organize itself into new wholes. That is to say, by definition a system is an evolutionary (emergent) system. See ↑ Jantsch E (1980) The Self-Organizing-Universe. Pergamon Press Thomas Mandel 22:25, 2 July 2007 (CDT)