Talk:Systems biology

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)

For example, in the article, "...complex assemblages of interrelated, dynamically interacting, coordinated and hierarchically organized naturally selected components[2]"

Shouldn't it read "...complex assemblages of interrelated, dynamically interacting, coordinated and hierarchically organized self-organized components[2]" Thomas Mandel 22:11, 11 July 2007 (CDT)

I understand your point about selection later. Natural selection does come after random mutation, as well as after natural experiments (e.g., symbiosis leading to mitochondria), but it still figures into systems biology because selection preserved the results of natural experiments and mutations that contributed to a fitter, better organized cell, say. Building hierarchies of self-organizing subsystems won't happen with just any collection of protein molecules, say. Self-organizing systems might have arisen 'spontaneously' but they also evolved in their functionality, which brings evolutionary forces into the act.

I would re-write: "...complex self-organized hierarchical assemblages of interrelated, dynamically interacting naturally produced and selected components..."

--Anthony.Sebastian (Talk) 22:17, 28 July 2007 (CDT)

Impressive

Lovely work here. Is it worth noting that the modern era of molecular biology began with an inspirational model - of the structure of DNA?Gareth Leng 11:44, 23 July 2007 (CDT)

Thanks. Yes, W-C's building a material structural model played a critical role in their discovery of the basic structure of DNA. Then the DNA molecule's structure became the model that molecular biology built on. I liked the way you expressed it. Will see where it might fit in the article. --Anthony.Sebastian (Talk) 22:24, 28 July 2007 (CDT)

When Isaac Asimov was a professor pf Biochemistry at the Boston School of Medicine, he attributed Avery's 1944 discovery of DNA as the birth of molecular biology. He writes" To the layman this discovery may not sound so important. Nevertheless, it competely reversed several concepts that biologists and chemists had been taking for granted for a century. It launched in a new direction the investigation into the nature of life and brought about new research methods. THe branch of science now known as molecular biology came into its own," Thomas Mandel 23:38, 27 July 2008 (CDT)

Undoing Mandel Ref #1

Tom:

I consider your reference citation (see below), inserted in the first sentence of the Introduction, after the first mention of the term 'systems biology', inadequate and inappropriatde for several reasons that led me to undo your edit:

The reference citation:

"Drack, Manfred., Apfalter, Wilfried., Pouvreau, David. (2007) On the Making of a System Theory of Life: Paul A. Weiss and Ludwig von Bertalanffy's Conceptual Connection. The Quarterly Review of Biology, Volume 82, No 4, The University of Chicago, Chicago Introduction IN TERMS OF publications, “systems biology” is currently an exploding field (see, e.g., Chong and Ray 2002; Grant 2003). Note, however, that system thinking is not at all new in biology. In the sciences of life, it can be traced back at least to the German “teleo-mechanicist” tradition inaugurated by Immanuel Kant’s Critics of Judgement, of which Johannes Mu¨ ller and Karl von Baer were the main proponents (Kant 1789; Lenoir 1982). More generally, integrative (or “holistic”) thinking is not a “discovery” of the 20th century. It has a rather long history going back to ancient Greek thinkers: Aristotle already claimed that “the whole is of necessity prior to the part” (Aristotle 1966:1253a20).. "

To the extent that it has instructive/explanatory value, I think it more appropriate in the 'history' section. And if included there, it must be done in such a way that contributes to the coherence of the 'history' section.

In the Introduction, we try to introduce the concept, and your edit does not, in my opinion, contribute to that goal.

As an aside, in inserting reference citations to an already developed article, one should try to observe the style the rest of the article uses -- unless you want to change that style throughout. You ignored that, which requires others to remedy. I would apply that point to the embedded references to Kant, to Lenoir, and to Aristotle — embedded in the single reference citation to Drack et al.

One important component in that regard: to make it as easy as possible for the reader to access the reference citation. If the article (or its abstract) can be accessed online, we should give the link to those. If not, sometimes, the reference citation can include a reproductioln of the abstract, if that make a genuine contribution to clarification. You did neither, which puts the onus of verification on the reader.

The point you editorially make as an addendum to the reference citation regarding 'systems biology' is an exploding field, you might note that that point is made explicitly later in the article, including an illustration showing the number of PubMed publications increasing exponentially over the past decade or so. If you could generate similar figures for the number of books treating systems biology during that period, that might contribute to the point.

The point that you make editorrially embedded in the Drack et al reference citation that systems biology can be traced to as far back as Aristotle: you may have missed the point in section 3.3 'Historical milestones in the development of systems biology': "Aristotle qualifies as a "systems biologist" as he viewed the behavior of a complex living system as finally explaining (final cause) why the system has the parts (material cause) interrelated (formal cause) and interacting coordinately (efficient cause) that it does;[citation given]. Neither you brief reference nor mine gives Aristotle his due, but that is remedied in part by further elaboration in the articles Life and Some modern views of the four Aristotelian causes of living things.

I do think you helped by pointing out some new reference material. I hope we can find a way to integrate them into the article.

--Anthony.Sebastian 22:08, 14 April 2008 (CDT)

Approval

I'm willing in principle to approve this article. I broke the intro up just to give it a concise lead. Usual minor copy edits, discard whatever. The empty section maybe delete for now?Gareth Leng 18:00, 14 January 2009 (UTC)

"behaviors — emergent in the sense of properties and behaviors unique to the system-as-a-whole" yes this is true, but only if unique is understood as meaning that the behaviours are expressed by the system-as-a-whole and not by its component parts. Not sure that this is as clear as you would like

"acquiring so-called '-omics' data" - needs some clarification, or at least links to proteomics, metabolomics and genomics

"However, the complete data complement of the system often greatly outstrips the sometimes enormous data-sets available, or technologically acquirable, such that the most refined models offer only a glimpse of the system’s complexity." Can this be put differently? (I think "refined" is vague) I think you're saying that however much data we may have acquired or can acquire about a biological system, this can only ever be a small part of all the data that would be needed to completely specify the system.

Gareth Leng 09:59, 12 January 2011 (UTC)

Gareth, all good points. I edited the article accordingly, though not yet completely satisfied with the first one. Thanks. —Anthony.Sebastian 04:07, 13 January 2011 (UTC)

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References

Many of the links provided in the References section of this article do not work. John R. Brews 17:01, 19 May 2011 (UTC)