- From: Oliver Ruebenacker <curoli@gmail.com>
- Date: Mon, 23 Mar 2009 13:41:19 -0400
- To: Peter Ansell <ansell.peter@gmail.com>
- Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Hello Peter, All, On Sun, Mar 22, 2009 at 5:06 PM, Peter Ansell <ansell.peter@gmail.com> wrote: > 2009/3/22 Oliver Ruebenacker <curoli@gmail.com>: >> There is an infinite number of possibilities. What is the criteria >> for being relevant? > > The possibility I was referring to was the option for going through > and defining the properties of the class of molecules as distinct from > a random instance with instance specific variables. I would define the > relevance of that method to be relative to the usefulness of the extra > complexity involved in making sure that in each case the properties > assigned to the random instance of the class were specific/precise > enough to be more useful to scientists than the case where everything > is placed as a property on the class of molecules. As you can't likely > define all the configurations for a given instance of a complex > molecular structure with respect to its environment, this would be > difficult, but if you found an application that was grounded in a > given environment it would be a possibility. I must have misunderstood you. I thought you were talking about not making a commitment whether the world should be viewed through the lens of a typical Systems Biologists (ensembles) or a Nano-Physicist (single particles). My reply would have been that (a) Systems Biologists already have such a hard time developing an ontology that serves there own needs that serving other people's needs seems like a luxury we can not afford and (b) should we consider other people's needs, it is not clear which other people should have priority. >> Can you give an example? > > For example... How do you define a gene? Tough question I know, but do > you define everything that can be transcribed as being a gene? How do > you really associate genes across organisms considering mutations? If > a gene acts as a promoter for its transcription in one gene but > doesn't in another due to a mutation in the relevant upstream region > can you really say the same sequence is the same gene? Even though its > position in the intracellular space could still be the same, and its > protein 3D conformation is still the same, there would be a duality > where you would then have to redefine the gene as being a regulator > for itself if you wanted to include its molecular functions inside the > cell as part of its property set. It sounds counterintuitive to have > to refer to the gene in two different ways just because in one > organism its function didn't bind to its environment. > > One non-biological example I was referring to was the wave-particle > duality for light, where if you wanted to be really in depth and > define the light "thing", then you would either contradict yourself > per current theory or you would create a dual distinct model that > violated someones previous god-like decision that ":wave > owl:distinctWith :particle" Sorry if I was not clear. I meant an example of how decisions you consider "god-like" can be avoided. What is the alternative? Take care Oliver -- Oliver Ruebenacker, Computational Cell Biologist BioPAX Integration at Virtual Cell (http://vcell.org/biopax) Center for Cell Analysis and Modeling http://www.oliver.curiousworld.org
Received on Monday, 23 March 2009 17:41:55 UTC