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From page 25... ... is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. Read the entire page →
From page 26... ... SYSTEMS AND THEIR FUNCTIONS in this chapter we consider the functional information of both sym bolic systems (letter sequences and Avida artificial life genomes) and biopolymers (rnA aptamers) Read the entire page →
From page 27... ... What environ mental factors might influence these relationships? The function of some emergent systems is obvious: a sequence of let ters communicates a specific idea, a computer algorithm performs a spe cific computation, and an enzyme catalyzes at least one specific reaction. Read the entire page →
From page 28... ... introduced ‘‘functional information'' as a measure of complexity. They proposed that the complexity of an information-rich system, such as rnA aptamers (rnA structures that bind a target molecule) Read the entire page →
From page 29... ... Accordingly, we define functional information in terms of F(Ex) Read the entire page →
From page 30... ... Three examples (letter sequences, the artificial life platform Avida, and rnA aptamers) serve to illustrate the concept of functional information. Read the entire page →
From page 31... ... The functional information, I(Ex) , for a system that achieves a degree of function, ≥Ex, for sequences of exactly n letters is therefore I(Ex) Read the entire page →
From page 32... ... note that in this formulation of functional information the maximum possible value, I(Emax) , arises when a message is so specific that only a single letter sequence out of all possible letter sequences achieves a desired Read the entire page →
From page 33... ... THE FUNCTIONAL INFORMATION OF AVIDA POPULATIONS We have adapted the artificial life platform Avida (Adami, 1998; lenski et al., 2003) to explore the distribution of function in an emergent system. Read the entire page →
From page 34... ... This research focuses on the ability of a small fraction of all randomly generated Avida organisms to perform computational tasks that arise through the coordinated execution of multiple machine instructions (lenski et al., 2003) Read the entire page →
From page 35... ... Therefore, to explore fully the distribution of function within a sequence space, a large number of randomly generated sequences (i.e., equal probability) must be surveyed (see Methods) Read the entire page →
From page 36... ... The degree of function, E, is the number of times nAnD is executed by the genome, whereas functional information, I (in bits) , is −log2 of the fraction of all sequences that achieves at least that degree of function, F(E) Read the entire page →
From page 37... ... multiple distinct classes of solutions, perhaps with conserved sequences of machine instructions similar to those of words in letter sequences or active rnA motifs (Knight and yarus, 2003) Read the entire page →
From page 38... ... . each class may contain a normal distribution of degrees of function, but each has a different topology in sequence space and a different maximum degree of function, Ex. Read the entire page →
From page 39... ... We note, by contrast, that purely random statistical functions do not display steps. For example, if the degree of function is defined as the frequency of the appearance of the number ‘‘1'' in randomly generated sequences of 100 digits, then functional information follows a well behaved smooth curve (Fig. Read the entire page →
From page 40... ... and Ex is a general feature of functional information or an idiosyncratic characteristic of Avida genomes. FUNCTIONAL INFORMATION AND RNA POLYMERS The previous two examples, sequences of letters and Avida machine commands, illustrate the utility of the functional information formalism in characterizing the properties of symbolic systems that can occur in combinatorially large numbers of configurations. Read the entire page →
From page 41... ... and functional information (I) , a relationship analogous to that displayed by populations of Avida organisms (e.g., Fig. Read the entire page →
From page 42... ... Analysis of complex systems in terms of functional information reveals several characteristics that are important in understanding the behavior of systems composed of many interacting agents. 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) Read the entire page →
From page 43... ... METHODS Determination of the computational properties of a randomly generated instruction sequence is accomplished within Avida's analyze mode. The trace feature in analyze mode generates detailed information on the state of the virtual computer at each step in the processing of a genome, including a notation of when a recognized function has been executed. Read the entire page →

From page 25...

... is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree.