Talk:Systems biology

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 14 January 2019 and 18 May 2019. Further details are available on the course page. Student editor(s): Jajc1128.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 10:37, 17 January 2022 (UTC)

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 28 August 2019 and 5 December 2019. Further details are available on the course page. Student editor(s): Mmmlg19.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 10:37, 17 January 2022 (UTC)

Reference to Bertalanffy

Could the author who introduced the reference to Bertalanffy's book check again. Such a book does not exist. —Preceding unsigned comment added by 139.30.6.52 (talk) 14:34, 17 August 2009 (UTC)

You are right. I modified the reference to the most widespread book of Von Bertalanffy. Nicolas Le Novere (talk) 21:39, 5 April 2010 (UTC)

Explaining vs. Describing

"In 1952, the British neurophysiologists and nobel prize winners Alan Lloyd Hodgkin and Andrew Fielding Huxley constructed a mathematical model explaining the action potential propagating along the axon of a neuronal cell"

The H-H model does not explain the phenomenon-explanandum of the AP. In fact, most biologists would agree that there are no explanatory laws in biology. Rather, biology explains mechanistically (cf. with systems biology); see the wikipedia entry "mechanisms (biology)". Consistent with this, neurophysiologists spent quite a bit of time and energy attempting to say why the H-H equations are they way they are. Thus, I changed "explaining" to "describing." 76.24.28.237 02:48, 12 November 2007 (UTC)

Well, this is not quite true. The difference between Hodgkin-Huxley's approach and classical physiology is that they based their model on an explanatory mechanism. This is not just curve-fitting, i.e. they do not describe. They predicted the existence of different ionic channels in the membrane conducting sodium and potassium. They explained how they worked, i.e. how their conductance evolved with the transmembrane voltage, and how that conductance, coupled with the electrochemical gradients explained the evolution of the currents, and the resulting depolarisation. And this is not the neurophysiologists who confirmed H-H mechanism but biochemist and molecular biologists. Not only H-H was the first predictive model, but it still holds firm more than 50 years afterward. There was actually a controversy in 2006 after the publication in Nature of a paper describing a possible different mechanism (based on lateral influence between channels), and after a bit of discussion, it seems that the observations could still be explained by a regular H-H. H-H is definitively not just a quantitative description, but an explanation Nicolas Le Novere (talk) 23:18, 15 December 2007 (UTC)

Whether it explains or describes, it is foolish to suggest that H-H's model was groundbreaking in a philosophical sense, or that it was the first predictive model in biology.. Haven't you ever heard of Mendelian genetics? Zargulon (talk) 22:39, 16 December 2007 (UTC)

This is a completely different subject. Mendelian genetics is a biological model. Many mathematical models were developed, to explain individual or population genetics. But the equivalent to H-H's work would be the first computer simulation of gene transmission in families or populations. There were a very large number of such simulations, but all designed after H-H. As far as I know, H-H's work is really the first simulation of a biological process. In fact, such a simulation was wished by Turing in his famous paper on morphogens, published the same year: "One would like to be able to follow this more general process mathematically also. The difficulties are, however, such that one cannot hope to have any very embracing theory of such processes, beyond the statement of the equations. It might be possible, however, to treat a few particular cases in detail with the aid of a digital computer. This method has the advantage that it is not so necessary to make simplifying assumptions as it is when doing a more theoretical type of analysis." Nicolas Le Novere (talk) 09:57, 19 December 2007 (UTC)

Your distinction is completely arbitrary.. Mendelian genetics is just as 'mathematical' as subsequent genetic models.. the mathematics is simpler and the accuracy lower due to unsophistication and systematic error.. but it is not categorically different either from more sophisticated genetic models or, indeed, from H-H. Zargulon (talk) 10:19, 19 December 2007 (UTC)

Mathematical biology

I stumbled across a well done page Mathematical biology going thorugh several useless "computational" pages, where authors forget that computer is just a tool to do the maths. More articles should be merged or linked to this. Plus mathematical models are actually what ppl call them, eg. Chen 2004 yeast cell cycle model. --Squidonius (talk) 19:02, 20 November 2007 (UTC)

Computer are not just tools to do the maths. One could actually argue that when it comes to simulation, they are prettey bad at doing math (symolic logic is different). Mathematical Biology is actually different than Computational Biology. The tools are different, the community are differents and the questions to address are sometimes different. And the same mathematical model can result in a wide diversity of computer simulations, according to the approach chosen (deterministic Vs stochastic, continuous Vs discrete etc). Chen 2004 is a good example. Table 1 gives the differential equations resulting from the chemical reactions, but the figures are all obtained, not by a mathematical treatment, but by a numerical simulation using a software called XPP. The results strongle depends on the solver used by the simulator. If you change the solver you may get different results (Often the case with complex models using reactions, rules and events). If you use a stochastic simulator (after unfolding the non-elementary reactions) you will definitiverly get different results. Nicolas Le Novere (talk) 23:28, 15 December 2007 (UTC)

One could of course come up with a definition of "doing math" that computers would be "pretty bad at". But can you really name any mathematical biologists who wouldn't try to evaluate the consequences of their models using any computational treatment, including stochastic methods, if it helps? Or any computational biologists who don't give any thought to the structure of the models that they simulate? If there is a distinction between these two pursuits I don't think you are doing justice to its subtlety. Zargulon (talk) 22:47, 16 December 2007 (UTC)

"an you really name any mathematical biologists who wouldn't try to evaluate the consequences of their models using any computational treatment". Yes, plenty. I am fighting them on a regular basis when it comes to decide government scientific policy. Extract from some conversations with mathematicians, now heads of "Systems Biology" institutes: "Who needs simulations and computers. I can model human metabolism with two conservation laws. DR" "Computer simulation tools are bad. They allow biologists to think they are doing relevant models, instead of letting the job to specialists. JS" Actually, in some countries like France and Belgium, the communities of biomathematics and computational biology are very different, the former being by far more powerful. And it is not foreign to the fact that those countries completely missed the bioinformatics revolution in the 80s and 90s. And we are witnessing exactly the same situation with systems biology, where all the efforts are going to qualitative modelling (boolean and logical modelling, petri-net, pi-calculus etc.) The inverse is not true. You are right saying that most of the simulation work is backed-up by mathematical description. "Most of", because this is not the case of agent-based methods, that have no mathematical counterparts. Nicolas Le Novere (talk) 10:08, 19 December 2007 (UTC)

I hope you win! JS wouldn't be a certain Jaroslav Stark by any chance ? .. Zargulon (talk) 10:21, 19 December 2007 (UTC)

List of Systems Biology Research Groups moved

The former "List of Systems Biology Research Groups" is moved to Wikipedia:WikiProject Systems/List of Systems Biology Research Groups. Anybody can still add there information over there. Thank you. -- Mdd (talk) 23:18, 8 April 2008 (UTC)

I'm a bit confused about the Bio systems AFD, so I've asked User:Neil for a comment - I don't know him very well, but I believe he's active on AFD a lot. I've also unlinked mainspace references to the wikiproject page - it's a valid resource for the wikiproject, but it kinda avoids the whole point of an AFD if its still linked as a mainspace article. I'll be cross-posting this on related pages touched by the discussion to see what kind of input comes up. WLU (talk) 00:15, 9 April 2008 (UTC)

diagrams

Diagrams shown are much too small to read on screen or printout. Unnecessary black background is wasteful of expensive printer ink.Jnbelcantu (talk) 19:25, 25 August 2009 (UTC)

The image allegedly illustrating systems biology does not contain a single feedback loop. It depicts a very conventional and problematic linear causality moving from the genes up to cells and on to applications. It has the words 'gene regulatory networks' but shows none of the circular causality one would expect as the basic architecture of such a network. The diagramme should be removed. — Preceding unsigned comment added by 146.199.139.38 (talk) 19:00, 7 November 2020 (UTC)

Please define "Paradigm"!!!!!!

"Other sources consider systems biology as a paradigm, usually defined in antithesis to the so-called reductionist paradigm (biological organisation)..."

I have read through the whole wiki article about the definition of "paradigm", but I still cannot found it meaning in the context of the sentence.

Paradigm can be simply defined as: "philosophical or theorectical framework of any kind"

If I put this equivalent into the sentence, it is:

"Other sources consider systems biology as a theoretical framework, usually defined in antithesis to the so-called reductionist theoretical framework(biological organisation)..."

The point is, system biology is considered as what theoretical framework?

As a holistic theoretical framework?

or a "(conceptual) protogramme for reducing the chaotic mass to some form of order)"

 —Preceding unsigned comment added by Snoopydoghk (talk • contribs) 15:04, 18 October 2009 (UTC) 

I am not sure if it is fortunate to talk about systems biology vs. reductionism as some antagonistic scientific views. The scientific approach must utilize both: first reducing the (purifying) system into elements you can study in detail(in dialmat it is called analysis) , then trying to put things together (called synthesis). —Preceding unsigned comment added by 78.139.7.218 (talk) 03:32, 17 September 2010 (UTC)

Most normal people agree with you. However systems biology was promoted, at least in its initial stages, by emphasizing the contrast between holism and reductionism. Zargulon (talk) 14:44, 9 December 2011 (UTC)

It might be useful to include an applications section at the end of the article so that readers may better understand what to do with the information presented. Also, it is important to define terms such as "reductionism" on this page so that it is accessible to a wide variety of readers. Lastly, including a section on the Human Genome Project may be of interest as it pertains to the systems biology of genetics. — Preceding unsigned comment added by Malloy.65 (talk • contribs) 04:05, 1 October 2014 (UTC)

Avoid repetions

in "Histoy": In 2002, the National Science Foundation (NSF) put forward a grand challenge for systems biology in the 21st century to build a mathematical model of the whole cell.[26] In 2003, work at the Massachusetts Institute of Technology was begun on CytoSolve, a method to model the whole cell by dynamically integrating multiple molecular pathway models.[27][28] Since then, various research institutes dedicated to systems biology have been developed. For example, the NIGMS of NIH established a project grant that is currently supporting over ten systems biology centers in the United States.[29] As of summer 2006, due to a shortage of people in systems biology[30] several doctoral training programs in systems biology have been established in many parts of the world. In that same year, the National Science Foundation (NSF) put forward a grand challenge for systems biology in the 21st century to build a mathematical model of the whole cell.[31] In 2012 the first.... — Preceding unsigned comment added by 2A02:810D:AF3F:EC88:516A:E67:44B8:6D37 (talk) 13:40, 7 January 2017 (UTC)

Systems Chemistry

Hi. I am interested in the topic 'Systems Chemistry'. Does anybody know if there is a related page (I think not, but want to verify)?

Entry created, Systems chemistry. omermar 06:38, 26 October 2017 (UTC)

A Commons file used on this page has been nominated for speedy deletion

The following Wikimedia Commons file used on this page has been nominated for speedy deletion:

• Tavassoly I et al, 2018.gif

You can see the reason for deletion at the file description page linked above. —Community Tech bot (talk) 02:21, 4 May 2019 (UTC)

My recent edits/deletions

Hi. I recently rewrote mostly the history part. I removed a large part of text associating famous people/works from before this concept was created, because it seemed misleading to associate them with this without any citations establishing the association of them with this. I could claim Einstein was the first in the field of "quantum ecology" (I just made that up) and cite it to his famous paper, that would be misleading, no?

I hid it instead of removing it, because I figured maybe someone would come up with a citation in the future. @CV9933: (thanks for solving the disambiguation thing), you've removed the references associated with that section. Shall I just get rid of the entire hidden text then? Leo Breman (talk) 17:58, 12 December 2020 (UTC)

This type of content is difficult to deal with and challenging or removing WP:OR/WP:SYNTH is fine but I don’t like the sea of red left behind in the ref section so I generally comment out, or delete unused refs as appropriate. CV9933 (talk) 11:53, 13 December 2020 (UTC)

Are you suggesting there was no systems biology before 2000? It depends of course on how one defines systems biology. For example, if systems biology is confined to the analysis of high throughput omic data then one could argue it started in the 1990s when the first microarrays emerged. Alternatively, if we consider systems biology as an approach that studies two or more interacting biological components, eg two enzymes, then systems biology has a long history, possibly starting in the 1930s Sewall Wright. Rhodydog (talk) 22:14, 19 June 2022 (UTC)

I have added part of this. It is widely accepted in this field that there were precursors to this, both Metabolic Control Analysis and Biochemical Systems Theory are clear precursors of Systems Biology. What they lacked in the 1970s is comprehensive molecular techniques to measure the system, but their theories (with some experimental papers) were clear systems biology.

This is not a matter of inventing a field, it is the case that this is recognized by the current practicioners in the field. For example see

Westerhoff & Palsson (2004) The evolution of molecular biology into systems biology. Nature Biotechnology 22:1249–1252 doi:10.1038/nbt1020 Gepasi (talk) 23:13, 24 October 2022 (UTC)

Glad to see someone readded the history of sys bio prior to 2000. There is a rich history of work in looking at cells as systems that goes back quite sometime. Rhodydog (talk) 23:59, 24 October 2022 (UTC)

This section is written like a personal reflection, personal essay, or argumentative essay

Whoever put this banner on the overview I disagree that the section reads like a personal reflection, personal essay, or argumentative essay especially given the ample citations to secondary sources. I don't know who wrote the overview but it seems reasonable to me. Could the person who added the banner be more specific, I think that would be helpful to understand the issue more fully. Rhodydog (talk) 20:42, 7 September 2023 (UTC)