Now it seems like not that easy to solve this issue. Some of you guys recommend me to resort all objects in a proper way, ...
Yep. Or else you try depth peeling as is suggested above by LS.
... but even if only a single organ displayed in the scene, the problem still remains. ...
Maybe this is because of the already mentioned concavity of the meshes? Question is, if you simplify the scene down to a single organ, do you have a chance to notice whether the problem occurs only if you look through a concavity. If so, then we are on the right track when suspecting the drawing order. A solution then will be to use sub-meshes.
But if concavity is not the cause, then we need to investigate further.
… And the thing is, in my case, each object is mapping to other stuff, resorting means changing everything. It does take time to solve this. ...
This isn't a problem solely related to yours. It is common in game engines and elsewhere. And hence there is a solution :)
It is possible to have more than a single order on objects. Notice that it is recommended to have several organizing structures, one for each task to do. It is absolutely fine to have a logical organization of the objects, a spatial organization (if collision or proximity is an issue), a render order, and perhaps more. Don't stuck with the über scene graph approach, or you will be lost sooner or later!
For example, you iterate the scene description and detect all objects that need to be rendered. You insert each object into a list (which is emptied before the scene is iterated). After finishing, you sort the list by some criterion, in your case using the distance from the current camera. Object rendering then is done in the order given by the list. So rendering has no influence on other aspects of object organization, and nevertheless is done in the required way.
I think Ohforf sake is right, Transparency is not as simple as enabling color blending, maybe this is the key point here!
Absolutely.