Re: [Fis] Beijing FIS Group
Hi! thank you Xueshan for the question: Are there any difference between transmitter in Neuroscience and hormone in Endocrinology from the viewpoint of information transmission and communication ? I can only give a few hints, as otherwise the message would be awfully long: In the reception aspect there are clear differences: neurotransmitters information enters into the cell by means of the activation of ligand-gated channels (also throughout G proteins pathways) and it is a very fast process, often in miliseconds; while hormones (e.g. steroids) affect very slow pathways usually of intracellular receptors with only one-component. But this difference is often blurred as hormones may occupy G proteins pathways too. As for the emission aspect, hormones are often endocrine (holistic impact via circulatory system) and paracrine (regionally secreted) while neurotransmitter are terribly localized at the level of the synapse. Again things get complicated, as neuropeptides for instance may be working in both ways; endocrine-paracrine as neuromodulators, and locally as neurotransmitters (even mixed also at the level of their reception pathways!!). Better if we dont speak about transportation ;-) !! Was it useful at all? A good reference can be found in Kandel et al. Mc Graw-Hill 2000 (a very tough book!) Best regards, Raquel -- ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
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
Re: [Fis] Beijing FIS Group
Hi! We are Jorge Navarro and Raquel del Moral, we both work with Pedro in Systems Biology and Neuroscience (we are experimentalist and theoretical too, very close to some of you). Congratulations for your great group it looks very impressive-- and welcome to the FIS. We expect we will exchange ideas and cooperate with you in not so long time.:) Its always nice to share knowledge about science! -- ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Beijing FIS Group
Dear Xueshan and Beijing colleagues, After the salutation, given that the main business of the FIS list is discussion, let me make a few comments on your methodological point. 3. OUR COMMON VISION ON INFORMATION SCIENCE: Within the diversity of opinions of the group, a common position is that the advancement of Information Science should be fueled by theoretical and empirical work inside the major disciplines, both in the natural sciences and the humanities. There is a little difference from our colleagues in Europe, as they are adopting a top-down process while we do like a down-top (bottom-up) process in methodology to unify the different informational realms. We advocate the gradual convergence among Natural Information Sciences, Technical Information Sciences, and Social Information Sciences. I completely agree with the common position of the Group in the first paragraph. However (that wonderful term for disagreeing!) there is a lot to say about the second paragraph. My personal opinion is close to what you mean, but I want to emphasize a couple of aspects. First, that the construction of new disciplines is not a clean theoretical act after a great new, central theory as we usually assume; rather it becomes a haphazard process with lots of historical accidents and non-formal components. In the conference I made some references to the historical origins of major disciplines along the Founding fathers and Great Books scheme. But presumably this is not going to work for Info Science. Rather than around a central theory, the new discipline may revolve about the establishment of a new way of thinking (the case of Biology, with the hegemony of the evolutionary thinking two generations in advance of the modern NeoDarwinian Theory is a clear case). Thus, I think that the gradual convergence you mention (and which I agree) will be possible in the extent to which a common way of thinking is advanced. Thus, in contra-position to the hegemonic view in natural sciences (things in parts, atomism, reductionism, specialism, etc.) an informational way of thinking would contain maybe --entities in the making, constructivism communication, integrationism, perspectivism... Well, and this leads to the second aspect, about the model systems on which a Science of Information can more easily fit (and say original things or solve some entrenched problems). Cells, Brains, Societies (and the quantum) are my bet. Information Science becomes sort of the scientific study of informational entities, those entities that self-construct in continuous communication with their environment... and a workable notion of information seems achievable for living cells and beyond: information as distinction on the adjacent. It was very pleasant realizing in the conference that there are new ideas on Artificial Natural Intelligence, information physics, logics, etc. where these info ideas can be confronted and recombined. The whole field seems to be in a metastable state that can easily conduce to a reordenation/ crystallization of the new science ---a fast and intense episode in the social evolution of knowledge. Thanks for the opportunity to discuss! Pedro -- - Pedro C. Marijuán Grupo de Bioinformación / Bioinformation Group Instituto Aragonés de Ciencias de la Salud Avda. Gómez Laguna, 25, Pl. 11ª 50009 Zaragoza, Spain Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554 pcmarijuan.i...@aragon.es http://sites.google.com/site/pedrocmarijuan/ - ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
[Fis] Beijing FIS Group
Dear FIS colleagues, By this posting we would like to publicly announce to the FIS community, and to all information scientists in general, the creation of the Beijing FIS Group. 1. CONSTITUTION OF THE BEIJING FIS GROUP: During the last 10 years, one dozen professors from different Schools and Departments of Peking University have been gathering regularly to discuss the fundamental information problems that emerged from different scientific fields related to information, we have finally decided to appear publicly as a thought collective. 2. ACTIVITIES OF THE GROUP: Apart from continuing with our internal debates, we are going to organize educational sessions as well as public seminars, conferences, meetings, conventional ones and in the web and email discussions formats, etc. Most contemplation results will be published for next year; particularly we are going to participate in the FIS discussion list as such collective of thought. 3. OUR COMMON VISION ON INFORMATION SCIENCE: Within the diversity of opinions of the group, a common position is that the advancement of Information Science should be fueled by theoretical and empirical work inside the major disciplines, both in the natural sciences and the humanities. There is a little difference from our colleagues in Europe, as they are adopting a top-down process while we do like a down-top (bottom-up) process in methodology to unify the different informational realms. We advocate the gradual convergence among Natural Information Sciences, Technical Information Sciences, and Social Information Sciences. 4. SCHOLARLY CONTRIBUTIONS: We think that at the time being FIS is the most mature site to promote the regular and focused scholarly exchanges needed to advance in the convergence among information fields. We hope that our initiative will be a very modest step in such convergence / advancement. We will be happy to cooperate with other similar groups and thought collectives inspired in the same goals, either in China, other Asian countries and in the whole international sphere. We send our best greetings to all the Information Scientists from Beijing. Yan Xue-Shan Department of Information Management, Peking University Ma Ai-Nai School of Earth and Space Science, Peking University Feng Guo-RuiDepartment of Philosophy, Peking University. Zhu Zhao-Xuan Department of Mechanics and Aerospace Engineering, Peking University Luo Xian-HanSchool of Earth and Space Science, Peking University Xu Guang-Xian College of Chemistry and Molecular Engineering, Peking University Lin Jian-Xiang Graduate School of Education, Peking University Yu Dao-Heng School of Information Science and Technology, Peking University Jiang LuDepartment of System Science, Beijing Normal University Miao Dong-Sheng Department of Philosophy, Renmin University of China Zou Xiao-HuiVisiting Scholar at Peking University, Higher Education Research Institute of CUG (Beijing) - Yan Xue-Shan Department of Information Management, Peking University Sept.14, 2010 ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
