Modules
by MikeGeneLet's consider more from the Hartwell et al. paper:
We argue here for the recognition of functional "˜modules' as a critical level of biological organization. Modules are composed of many types of molecule. They have discrete functions that arise from interactions among their components (proteins, DNA, RNA and small molecules), but these functions cannot easily be predicted by studying the properties of the isolated components.
Okay, a module is a) composed of many different parts such that b) the function stems from the interaction of those parts and c) a study of the isolated parts would not lead us to expect the function of the module. Would a module thus have an IC core?
April 25th, 2008 at 11:43 pm
Hi, Mike,
Strictly in engineering, if a component of a module fails, then that module will fail to perform its function, and because of complexity and interaction with other modules, the failure could be minor or catastrophic, immediately noticeable or invidiously hidden, depending on the frequency with which the module is utilized. To the extent that a module must have all of its components working properly, then the module is an example of IC, with one exception. Some modules have redundancy built into them. For example, for cost effectiveness it is common to have generic modules which perform very limited and well defined tasks, which can be wired into more than one type of circuit. A module whose sole function is to provide, let's say, the service of an AND gate, may have 8 such gates available for use. In one type of circuit, maybe only 5 of the gates will be actually wired into the system. The other three gates in the module would be unused. In that particular circuit, those 3 gates could fail with no effect on the system. However, that same particular module, if put into a circuit in which all the gates are used, could cause extensive system failures.
In the analogy mentioned in the article, I take it that the authors would refer to the cell as representing the system, and the components of the cell are the modules. In an attempt to make the components of the cell resemble an engineering-like paradigm, I would probably want my cellular modules to exhibit persistence. In other words, organelles, DNA, the Endoplasmic Membrane, the Golgi apparatus, etc., would be modules. Short-lived proteins that travel from one part of the cytoplasm to another seem less analogous to modules, and more like the cellular equivalent of signal flow between the cell's modules, i.e. act as the triggers that cause the persistent parts of the cell to do their specific functions.
There is also the question of redudancy. There are thousands upon thousands of ribosomes in the cell. What would happen to the cell if one failed? Two? A hundred? In fact, is redundancy built into the cellular system on purpose? If one Mitochondrian organelle fails, will the others in the cell be sufficient to carry the load? In fact, redundancy seems to be a vital part of the cell's makeup. And going up a level, there is the very practical situation of redundancy in the makup of the organ system, composed of millions of (redundant?) cells. However, back inside the cell, there is only one nucleus, one Endoplasmic membrane, and one Golgi apparatus. There is probably a reason for this.
Comment by AnaxagorasRules — April 25, 2008 @ 11:43 pm
April 25th, 2008 at 11:59 pm
Hi AnaxagorasRules,
Nice post.
You note:
True. But this is why I asked about an IC core. If a module is defined as being composed of multiple parts, and the function of the module depends on the interaction of mutliple parts, it would seem to me that a module must have an IC core. In other words, although all parts might not be necessary for function, function is dependent, at some level, on the interaction of multiple parts.
Comment by MikeGene — April 25, 2008 @ 11:59 pm
April 26th, 2008 at 1:26 am
Hi, Mike,
I'll go along with that. The exception case I mentioned, in which the unused parts of a generic module, if they failed, would have no effect on the module's function (in relation to the overall system), is peculiar probably only to engineering systems. With biological modules, such as organelles, Golgi Apparatus, etc, I would specify that their parts should include the entirety of the parts. In other words, if a Mitochondrian organelle had a dozen or so ribosomes fail, the organelle would probably still function. But if the organelle had NO ribosomes, then it would fail, and that would be because of the ICness principle.
Comment by AnaxagorasRules — April 26, 2008 @ 1:26 am
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