Talk:Systems biology/Archive 2

message: Hate to break it to you but a lot of biologists don't think much of systems biology or of Leroy Hood's activities therein (although his previous work on instrumentation is widely respected). He came to speak at our university before a large packed auditorium and his talk was extremely light on details. He also seemed to attribute to systems biology a lot of breakthroughs which were not achieved under the banner of systems biology (so why preferentially fund people who call themselves 'systems biologists'), whilst failing to point out any achievements, past, present or future, where systems biology as a field actively contributed. This was pretty much the unanimous opinion of my research group. Systems biology is nothing but a buzzphrase and it is difficult to believe that someone of Hood's stature does not know this. There are a lot of statements on this page that I find objectionable and I will try to restore a faithful representation of attitudes to systems biology, although as a declared non-believer I understand my contributions may not be welcome. Zargulon 14:32, 14 February 2006 (UTC)
thread_title:  Don't think much 

message: There has been a merger on Regulome for a long time.  Could someone who knows the subject please either make the merge, or offer an opinion on whether the merge should be done. I don't know the subject well enough. Kcordina  Talk  13:37, 22 March 2006 (UTC)
thread_title:  Merger 

message: I redirected a page that indicated it was a synonym of systems biology. Can someone with expertise confirm?  Thanks.--Chaser T 06:36, 11 July 2006 (UTC)
thread_title:  redirected page 

message: I think the POV tag was premature. The article is perfectly stable, there hasn't been any fighting and no-one has complained on the talk page for ages. Zargulon 14:33, 10 October 2006 (UTC)
thread_title: POV tag

message: *Westerhoff, H. V. and Alberghina, L. in their book "Systems Biology: definitions and perspectives" (Springer, 2005) begin with the following definition: "The science that discovers the principles underlying the emergence of the functional properties of living organisms from interactions between macromolecules." This is then refined by examples from a range of systems biology researchers and research groups.
*The Institute of Systems Biology, Seattle, on their website: "Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life" Systems Biology - the 21st Century Science
*Kitano, Japan, on his project site: "Systems biology is an emergent field that aims at system-level understanding of biological systems... Although systems are composed of matters, the essence of system lies in dynamics and it cannot be described merely by enumerating components of the system. At the same time, it is misleading to believe that only system structure, such as network topologies, is important without paying sufficient attention to diversities and functionalities of components. Both structure of the system and components plays indispensable role forming symbiotic state of the system as a whole." What is Systems Biology?
*The wikipedia article! "By studying the relationships and interactions between various parts of a biological system (e.g., gene and protein networks involved in cell signaling, metabolic pathways, organelles, cells, physiological systems, organisms, etc.) it is hoped that eventually explanatory or predictive models of whole systems can be developed."
Robnpov 15:15, 21 October 2006 (UTC)
replies: text: This article is becoming embarrassing.. systematic systems biology??? I couldn't have come up with that one if I had tried. Zargulon 19:27, 23 October 2006 (UTC)

text: I'm not sure who you are, Herbert Sauro.. is that your idea of a 'constructive criticism?' You have access to my entire corpus of comments on this page, which others have deemed constructive enough to respond to seriously.. I can only hope you will see them in the same light. Please stop using weasel terms 'some of..' and appeals to authority 'the leaders in the field..', it just wastes peoples time. The fact remains that, unlike serious scientific terms, the phrase "systematic systems biology" does not even come close to uniquely suggesting the (fuzzy) concept which, according to you, it represents. The word "system" must have at least 10 different meanings in science, so putting it together with itself makes 100. This is a term designed not to describe, but to impress. Zargulon 01:00, 25 October 2006 (UTC)

text: Herbert Sauro, I apologize. Zargulon 22:06, 26 October 2006 (UTC)

text: I agree, and there's been 5 days for objections to be raised to the changes proposed on the 26th of October. I understand this to be an appropriate amount of time, so I'll get right on it. Best Regards, Robnpov 19:57, 31 October 2006 (UTC)
thread_title:  Evidence of consensus on systems biology as a scientific concept - some definitions 

message: Moved from main article:
Several organizations have prepared extensive reviews of Systems Biology, the definition of the field and its potential socio-economic impact. These includes, example, The European Science Foundation and The Canadian Society for Systems Biology. These documents are free of diciplinary and personal bias, and are considered reliable sources of information on the topic.
The information is of interest, especially for sourcing. It appears to be a response to the discussion on neutrality/citations and as such belongs on the talk pages; in any case it is currently too discussional to be included in the article (e.g. includes  weasel term in the last phrase). Robnpov 01:54, 7 November 2006 (UTC)
thread_title: Reviews of Systems Biology

message: Most of the information currently in the introduction seems to me to be categorically false, or use ill-defined language, e.g. what is a mechanistic model in this context? Zargulon 10:46, 19 November 2006 (UTC)
replies: text: That is really just gibberish I'm afraid. Please sign your edits. Zargulon 08:08, 5 December 2006 (UTC)

text: Hi Nicolas, Welcome to Wikipedia. You should sign your edits with four tildes at the end, so that people know if two edits are by the same person. I'm delighted that you have had such a successful and interesting career. Please appreciate that on Wikipedia what counts is not who you are, but what you say. What exactly are you referring to, when you suggest that I am being dismissive of others' work? Zargulon 19:03, 5 December 2006 (UTC)

text: OK. In usual English, to say something is mechanistic means that is works automatically or robotically without any human thought or understanding. The definition you gave for "mechanistic" is the opposite. That is called "ill-defined language". I also do not accept your categorization of physiology of the 20th century.. in fact I find it dismissive. Zargulon 20:04, 5 December 2006 (UTC)

text: That is disingenuous. Mechanistic can mean "explained in terms of physical forces", but "explained" does not mean "explained, not described". It is equally accurate to say that mechanistic means "described in terms of physical forces". Mechanistic certainly does not refer to an enhanced level of understanding. Rather it refers to physical forces, as described by classical mechanics. Equally, the word phenomenological does not in normal English imply an absence of understanding. These words are being used carelessly and in a non-standard fashion, and they should be removed. Zargulon 23:08, 5 December 2006 (UTC)

text: A mechanistic model does not refer to the causes of a phenomenon either. It merely refers to mechanics in physics. Your note is irrelevant-Wolfram loves to invent his own meanings for words but that is not a definition. The word mechanistic is ill-defined outside of theoretical physics. So is the word "phenomenology", by the way, and I have changed the unsourced "phenomenology" page to reflect that. Hopefully this page will also change soon. Zargulon 10:38, 6 December 2006 (UTC)

text: I typed in "mechanistic models in biology" and got SIX hits. Is that what you mean by "most people"? Even out of those, some of them did not support your statetement. Some of them did. The disagreement is a sign that the term is ill-defined. On the other hand, there is near universal agreement that the sky  is blue, so I think you are making a false analogy. Zargulon 19:18, 6 December 2006 (UTC)

text: Ok, if it makes you happy.. in this case, even the first hit (Koonce and Pilla) doesn't support your statement. Zargulon 19:34, 6 December 2006 (UTC)

text: How does that quote support your statment that a "mechanistic model is one that aims to explain how a system works, not describe its function" or even your somewhat contradictory statement that a mechanistic model "refers to the underlying mechanisms, or causes"? Zargulon 23:52, 6 December 2006 (UTC)
thread_title: Introduction

message: I find it hard to believe that time and energy is being spent arguing the meaning of the term "mechanistic model". Everyone in the field of systems biology understands the meaning of this term. It simply means that the relationship between the inputs and outputs of the system are defined in terms of molecules and physical processes that can be quantified (and acted on). One of the primary drivers of  the field of systems biology is predictive medicine and to achieve that aim, you need mechanistic models. If you go into a doctor’s office and they do a blood test on you, they will get an answer in terms of specific molecules. With advances in molecular testing, we eventually will be able to measure almost any given molecule. However, to be able to broadly relate this kind of data to disease, we must understand them at a mechanistic level. We currently lack this information in many cases, instead only having correlative information. For example, the PSA blood test is correlated with prostate cancer, but has a high false positive rate because PSA is not part of the mechanism by which prostate cancer grows or spreads. HIV tests are very accurate because they evaluate specific molecules on the virus itself. Clearly, you do not need systems biology approaches to diagnose many diseases, but acurate diagnosis and treatment of many chronic diseases would be vastly improved by using it. Obvious examples are very complex diseases such as type 2 diabetes and cancer. Without a mechanistic model of how these diseases work, it will be extremely difficult to come up with adequate treatments. Phenomenological models are not adequate because they are inherently ambiguous.
I also do not understand why we let Zargulon bait us. The fact that he did not know of Herbert Sauro indicates how much he knows about the field of systems biology. Similarly, the debate about the meaning of “mechanistic modeling” is absurd. I know that Wikipedia is open to all contributors, but I would think that anyone who spends so much time arguing about the worthlessness of systems biology would at least try to become familiar with the field. On other discussion boards, we have a term for Zargulon. It is “troll”.FLeader 20:57, 25 December 2006 (UTC)
replies: text: Even if Fleader is right, that everybody in the field of Systems Biology knows the meaning of "mechanistic model", and even if systems biologists agree on its meaning (which is a stronger statement), it is still wrong to use "mechanistic model" in the introduction. People who read the introduction may not even know yet what systems biology is.. how can they be expected to know what a "mechanistic model" is? Zargulon 09:56, 26 December 2006 (UTC)
thread_title:  This is silly