I just can give my personal opinion about the "organic theory". I would prefer to call it the "organic model", because theories usually require more formalism. But models, are just that... models. Our limited intelligence doesn't permit us to understand how the nature works. We just know a bit about it. So, we need models to explain how we think that the things work. And models are just approximations to the reality and can be totally ficticious but they can tell us something and make us to feel comfortable about some explanation. For instance, the atomic model of Böhr is still useful for teaching kids about the nature of an atom. Nowadays, we know that it's not a real picture but it would be less wise trying to teach the principles of quantum mechanics to a child.
Beyond the validity and applicability that this "organic model" could have, the valuable thing is that somebody is trying to see the things from a different point of view. We have to remember that for many years the planet was flat and supported by elephants.
I think that the relevance of this discussion for molecular biology is that in my personal opinion, it is needed a new change in the paradigm. Just think on the cellular pathways. At the begining, a picture with a few number of boxes with protein or gene names and arrows describing a pathway in the cell was ok. But nowadays, we know that the picture is rather much more complicated and the problem to describe a signalling pathway is becoming intractable. Then, we have to think about what is the usufulness to have a chart full of boxes and arrows connecting one each other without any parameter describing the relationship? How we can predict the behavior of a system described like a web? So, I think it is time to think in something else...
Inscara, If you have a minute you may want to check out
[Only registered users see links. ]
which is an essay to formalize the principle.
Hi, I took some time to read that PDF file. Trying to convince scientists that simplicity is more difficult to achieve than complexity is a daunting task. For many scientists, complexity produces that kind of feeling of robustness and trust in the same way that a high-price product produces that kind of high-quality feeling in a housewife. In many cases it is a resource used to create an intellectual ghetto or convince funding institutions to invest more money in a project. Whatever the case is, and whatever this organic principle will be, I could identify a niche where it could be succesfully applied even when it has been reinveted many times. I've found in that PDF file a sentence that could be significant for the success of the principle if it reach maturity someday: "...And the very first thing they will overlook is the inherent advantage of such a plain, simple, informal theory, that it easily translates into other sciences or that other sicences easily translate into theirs. So the problem here is simplicity of form rather than absence of formality." The niche that I'm seeing there is in the frontier of disciplines that need interaction. For example, Bioinformatics, Biocomputing and Computational Biology. The dilema nowadays is that Computer Science and Molecular Biology are so huge fields by itself that for one person to be specialist in both is almost impossible. Then, arise the question if a Bioinformatician or a Computational Biologist should be a person with a degree in Computer Science and a post-graduate specialization in Molecular Biology or vice-versa. It would be very helpful to have a theoretical framework to translate concepts from one field to another in such a way that whatever the background of a person is, that person can specialize in another discipline and work in the frontier. There are already succesful examples of this kind of transferable way-of-thinking from one discipline to another in order to simplify the domain of study. For example, object oriented programming was a mathematical concept that once implemented as an standard in the software industry became a revolution. Systems Biology is another promising field where its success depends on the translation and application of concepts from other disciplines such as electronic engineering to explain biological systems. By the way, probably you would like to check out the following webpage about the KISS concept: [Only registered users see links. ]. Probably you already know about it, but it's possible other people is unaware of it.
entity: computer science
main two parts: hardware - software
entity: molecular biology
main two parts: I'm not a molecular biologist, any suggestions?
There are practical reasons why a person could be interested to specialize in two different fields and work in the frontier. Nowadays, biosciences and computing sciences are just an example and I thougth that it could be a good starting point to test the concept because if it works there you will be helping a lot of people like Charly. For example, see the post: [Only registered users see links. ]
Following your suggestion to use the principle applied to Computer Science, I would attempt a first approach for Molecular Biology:
entity: molecular biology
core: the cell
main two parts: molecules and biology
So, it would be interesting to have opinions from other members of the forum with different points of view about this classification.
The "main two parts" could be explained by correlation with the computer model, saying for example, that proteins are the physical components (the hardware) that constitutes "the cell" (the core) and "biology" is the set of rules (the software) that explains the relationships between the physical components in such a way that "the cell" can perform its functions.
I have to say in pro of the principle, that I've spent a couple of days thinking on what could be the correlations between the elements describing both fields. At the begining, the complexity was obscuring a classification such that one I'm proposing for Molecular Biology. But now, I think that for Charly it should be clear and simple provided that it's valid under the rules of the principle.
It remains to define the 3 levels in which each part could be divided. That could left as an exercise for another reader, what do you think? .
By the way, just for the sake of curiosity, can I ask what's your background?.
I was also wondering how to include the genes as part of the classification. However, I think that still the core should be "the cell" since Molecular Biology is interested not in study any kind of molecule but just those molecules associated with the functions of the cell. Then, the normal and pathological states of the cell can be associated to different phenotypes. Otherwise, there would not be differences with the Chemistry field which is interested in study the properties of any kind of molecule. So, what do you think if we reformulate the concept with "the cell" at the core level and "the molecules" and "the genes" as the parts of the core. Then, only those molecules somehow related to the genes will be important for the study of Molecular Biology. So, in this case, "the genes" could be considered "the program" with instructions on how to build molecules with functional roles in the cell.
I haven't had time this week to check the posts. Now I was reading and I think that the concept applied to Cellular Biology is taking shape. I'm not a biologist neither, so I cannot help you with the precisions of the terminology. However, I come from the organic chemistry and computer programming fields but I'm now working in the bioinformatics field. So, that's the reason I have a personal interest on topics that help to transfer concepts from one field to another. But, as you said, it would be nice to have feedback from other people in the forum about how the discussion is going on.
I think that the concept is working quite well in this particular case. I think that people without any knowledge about Cellular Biology could easily catch the idea about it and identify the elements in which the discipline is focused before to get confused trying to find out just by themselves, for example searching the web. But now I was wondering if it is possible that this process will result in an ontology classification of disciplines. I was imagine a centralized database of disciplines and its concepts classified by the OP and curated by specialists in each field around the world. Then imagine that you can browse the database at different levels (zooms) to get general or more specialized definition of concepts. But, because the organization of the database would be ruled by the OP, then it would be easier to compare different fields and the correspondence of elements. Then, there would be much easier to adapt models from one discipline to another. For instance, you can find what would be the correspondence between computer network elements and social networks. What do you think?
probably a good reference starting point could be [Only registered users see links. ]. Maybe there are already some software tools that could be used or adapted at least for experimental purposes. The only experience I have with ontology databases is with the "gene ontology" database that is very useful when you analyze gene expression data. However, the key point (as in any other database project) is to have a good architecture of the database to ensure the scalability.
Sorry, probably I didn't explain myself. I was not talking specifically about OWL as the implementation platform. What I mean is just that there are some software tools that can be used at the experimental level. These tools could in principle let you to test different ways to organize the information in a computer. For example, OBO-Edit is quite simple application that let you organize ontologies as a tree. But there are others. Then how you represent the underlying data to the end-user that is just a matter of user interface that can be any that you consider appropiate, but what it is important first is to have a solid foundation on how the data is organized and stored in the computer. For example, you were asking what to use as the root of the classification. With some simple editor you can just try different roots, organize them in different ways and see what is the more appropiate way of representation. Once you can define a simple way to organize the data to guarantee that the software can efficiently work with it, then which programming language to use, which kind of graphical user interface you want to implement and so on is just a matter of personal taste. For example, a simple user doesn't need to know anything about HTML language to surf the net. Every webpage you open is described in HTML language, but your browser parses that information in a way that the end-user can easily deal with it.