Saturday, February 23, 2008

Published Method of Measuring Specificity (Function)

It looks like a PNAS article has finally caught up with and refined some of the work of Dr. Dembski. Here is the PNAS article that discusses measuring for functional information, and upon first read through seems to measure functional information in an extremely similar manner as Dr. Dembski measures for specificity as it relates to function in "Specification: the Pattern that Signifies Intelligence."

It seems that the main and only significant difference is that the PNAS article uses a measure of functionality (specificity) that doesn't rely on a human linguistic description of the pattern. Although the equation seems to be the same as far as I can tell (log2 [number of specified patterns related to the function * probability of the pattern in question]), the gauge for the number of specified patterns seems to be taken directly from the "independent" description as formulated by the system in question -- ie: the relation between biological function and its independent description in a specified RNA chain as opposed to an independent linguistic description of the biological function. IMO, this provides a more concrete and accurate measure of specificity and still does not detract from Dembski's work on CSI in any way as I had already basically incorporated that same method as used in the recently published paper when I discussed specifications here on this blog. As I have explained: "Now, let’s take a look at proteins. When it comes to measuring specificity, this is exactly like measuring specificity in a meaningful sentence, as I will soon show. Functional specificity merely separates functional pattern “islands” from the sea of random possible patterns. When specific proteins are brought together, you can have a pattern which creates function. That functional pattern itself is formulated by information contained in DNA which is encoded into RNA and decoded into the specific system of functional proteins. The functional pattern as the event in question is defined independently as a pattern of nucleic acids ... When measuring for a functional specification (within a set of functional "islands"), you apply the same equation, however, when measuring the specificity you take into account all other FUNCTIONAL patterns (able to be processed into function *by the system in question*) that have the same probability of appearance as the pattern in question."

As far as I can tell, the PNAS paper doesn't take into account any probabilistic resources, so it is not measuring for CSI; it only measures for SI, that is, specified or functional information (presented as a measure of complexity).

From the PNAS article:
"Functional information provides a measure of complexity by quantifying the probability that an arbitrary configuration of a system of numerous interacting agents (and hence a combinatorially large number of different configurations) will achieve a specified degree of function."


"Letter sequences, Avida genomes and biopolymers all display degrees of functions that are not attainable with individual agents (a single letter, machine instruction, or RNA nucleotide, respectively). In all three cases, highly functional configurations comprise only a small fraction of all possible sequences."

Of course, Dembski's definition of specificity does take specificity beyond merely function, however, in his discussion specificity most definitely includes function and the measurement seems to be in agreement with this recent PNAS article. According to Dembski's definition, specificity includes algorithmic compressibility, semantic meaning, and function. However, the other article uses specificity in a more strict functional sense which includes meaning and other "usable" function, and unlike Dembski has done, this PNAS article doesn't seem to even really attempt to provide a rigorous definition of a specified pattern. Dr. Dembski has defined a specified pattern as an event which can be formulated as a conditionally independent pattern. Of course, as I've already explained and shown, this includes algorithmically compressible patterns, as well as semantically meaningful events and functional events.

Compare the above PNAS article with Dembski's treatment of specificity and check it out for yourself.

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