Re: [Fis] Beijing FIS Group
Dear Xueshan, Is the creation of Systems Biology related to Genomics, Proteomics, Transcriptomics, Glycomics, and many many other "-mics"? If so, what is the relationship between the Systems Biology and information from the x-mics angle? It is a very good question. In my practical experience, the "omic" disciplines provide a lot of data, usually compiled into data-bases, so that one can obtain many "lists of parts" about most processes and cellular subsystems. But in many cases that info is insufficient. For instance I am working in the signaling system of Mycobacterium tuberculosis and, if I go to the "tuberculist" data base, I can obtain more than two hundred transcriptional factors presumably related to signaling functions (belonging either to the "one, two or three-component systems"), however the true signaling function of each component is very difficult to obtain (a painful task one-by-one, searching at the literature). Thus I have to spent a lot of time to get a systemic or general approach, and even more if I want to build some models... Systems Biology is like ecology, that has to deal with the integration of a lot of partial specialized information from many other disciplines. What is your opinion about Leroy E. Hood' words: "Biology Is an Informational Science". I think (it is a very personal opinion!, obviously influenced by Pedro) that the leaders of Bioinformatic and Systems Biology (Gilbert, Hood, Brenner, Kitano, etc.) are not very serious in that type of statements. What they mean is that biology and molecular biology are becoming not really information sciences but intensive "computer science users". Usually one doesnt find very deep theoretical reflexion in these guys although their works are very good from the technical point of view. Are there any difference between transmitter in Neuroscience and hormone in Endocrinology from the viewpoint of information transmission and communication ? Neurobiology is not my turf. Raquel will answer you very soon about that. By the way, do you know anyone working on Systems Biology in your University? Nice to talk to you! Jorge -- ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Beijing FIS Group
On Mon, Sep 20, 2010 at 9:26 AM, Stanley N Salthe ssal...@binghamton.eduwrote: Regarding the question: What is your opinion about Leroy E. Hood' words: Biology Is an Informational Science? In a general sense the meaning is that, although every locale in the world is mediated by history -- requiring information to be understand beyond knowledge of physical and material laws -- biological systems have internalized and replicate the results of historical accident as preserved in the information in the genetic system. In general, history passes away, but biological systems capture some of it in the form of species and variety differences. STAN On Mon, Sep 20, 2010 at 8:26 AM, Jorge Navarro López jnavarro.i...@aragon.es wrote: Dear Xueshan, Is the creation of Systems Biology related to Genomics, Proteomics, Transcriptomics, Glycomics, and many many other -mics? If so, what is the relationship between the Systems Biology and information from the x-mics angle? It is a very good question. In my practical experience, the omic disciplines provide a lot of data, usually compiled into data-bases, so that one can obtain many lists of parts about most processes and cellular subsystems. But in many cases that info is insufficient. For instance I am working in the signaling system of *Mycobacterium tuberculosis* and, if I go to the tuberculist data base, I can obtain more than two hundred transcriptional factors presumably related to signaling functions (belonging either to the one, two or three-component systems), however the true signaling function of each component is very difficult to obtain (a painful task one-by-one, searching at the literature). Thus I have to spent a lot of time to get a systemic or general approach, and even more if I want to build some models... Systems Biology is like ecology, that has to deal with the integration of a lot of partial specialized information from many other disciplines. What is your opinion about Leroy E. Hood' words: Biology Is an Informational Science. I think (it is a very personal opinion!, obviously influenced by Pedro) that the leaders of Bioinformatic and Systems Biology (Gilbert, Hood, Brenner, Kitano, etc.) are not very serious in that type of statements. What they mean is that biology and molecular biology are becoming not really information sciences but intensive computer science users. Usually one doesn´t find very deep theoretical reflexion in these guys although their works are very good from the technical point of view. Are there any difference between transmitter in Neuroscience and hormone in Endocrinology from the viewpoint of information transmission and communication ? Neurobiology is not my turf. Raquel will answer you very soon about that. By the way, do you know anyone working on Systems Biology in your University? Nice to talk to you! Jorge -- ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis FirmaJ.JPG___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Beijing FIS Group
At 03:26 PM 20/09/2010, Stanley N Salthe wrote: On Mon, Sep 20, 2010 at 9:26 AM, Stanley N Salthe ssal...@binghamton.edu wrote: Regarding the question: What is your opinion about Leroy E. Hood' words: Biology Is an Informational Science? In a general sense the meaning is that, although every locale in the world is mediated by history -- requiring information to be understand beyond knowledge of physical and material laws -- biological systems have internalized and replicate the results of historical accident as preserved in the information in the genetic system. In general, history passes away, but biological systems capture some of it in the form of species and variety differences. I would add to Stan's correct remarks that unlike physics, in which the laws tend to dominate, and boundary conditions are pretty irregular (but not always!), in biology the boundary conditions are very important, especially their regularities both in individual biological entities, within kinds of biological entities, and across kinds of biological entities. For example, most kinds of biological entities are cohesive levels or nestings in information hierarchies, which allows application of statistical mechanics to their information dynamics (Hierarchical dynamical information systems with a focus on biology Entropy 2003, 5, 100-124). Furthermore, inasmuch as biological systems are emergent, boundary conditions are not separable from their dynamical principles, so issues of form (which require information theory for full analysis, or as full as we can expect), are wound up with the system dynamics, or laws ( A dynamical account of emergence (Cybernetics and Human Knowing, 15, no 3-4 2008: 75-100)). The last point was made some time ago by Conrad and Matsuno, but has not been appreciated as much as it should (much lip service, perhaps, but not enough precise application). Cheers, John Professor John Collier colli...@ukzn.ac.za Philosophy and Ethics, University of KwaZulu-Natal, Durban 4041 South Africa T: +27 (31) 260 3248 / 260 2292 F: +27 (31) 260 3031 http://www.ukzn.ac.za/undphil/collier/index.html ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
