a. By "theory," the Foundation means a thorough explanation and mechanism explaining how natural events might have given rise to a phenomenon like the genetic sign system, algorithmic programming, and code bijection. The Prize is not being offered for creating life in vitro, but for a plausible, empirically supported theory of mechanism within nature.
b. By "mechanism," the Foundation means a scenario of sequential, cause-and-effect (or at least "functionally dependent"), empirically correlated events explaining how genetic prescriptive information (instruction) arose naturally within Nature sufficient to give rise to current life.
c. By "prescriptive information," the Foundation means the instructions necessary for biochemical function, the end-product-oriented specification of monomeric sequence, the "recipe" and "biomessage" of messenger molecules which are so manifest in all known forms of phenomenological life. As pointed out by Hubert Yockey, all known genetic information is observed in a physical matrix sequence that is linear, segregatable, and digital. These linear sequences must be translated via code to other linear sequences for prescriptive information (instruction) to be received at the receiver end of any Shannon channel. They are in effect algorithmic sequences of decision-node configurable switch settings. Algorithms alone produce sophisticated biofunction. A phase space of stochastic ensembles has never been observed to produce even the simplest of biochemical pathways. See "algorithms" under the "Discussion" section.
By "prescriptive information (instruction)," the Foundation does not mean mere order or structure, as in a snowflake. By "prescriptive information (instruction)," the Foundation does not mean mere pattern or periodicity, as in a sine wave, kaleidoscopic image, or redundant inanimate crystal. By "prescriptive information (instruction)," the Foundation does not mean mere physical "complexity," as many complex conglomerates contain no instructional information. By "prescriptive information (instruction)," the Foundation is not merely referring to the probabilistic uncertainty concepts of Shannon, nor to Maxwell-Boltzmann-Gibbs entropy, nor to Kolmogorov-Solomonoff-Chaitin compression theory of mere sequence "complexity" alone. Internal algorithmic compression of alphanumberic symbol sequences defines "complexity." But such comlexity has nothing to do with external algorithmic meaning or function. Sequence complexity is no measure of algorithmic utility. "Function" extends into additional dimensions altogether from mere sequence "complexity." External algorithmic function changes its environment and accomplishes some task external to itself.
d. By "genetic code," the Foundation means "the linguistic-like, symbolic representation of commands from one alphabet and syntactic language (e.g., codon sequence) to another (e.g., AA sequence), conveying seemingly conceptual biological instructions to cell systems." Code is a one-to-one correspondence or "bijection" from one alphabetical system/language to another. See "The source of genetic code in nature" in the "Discussion" section.
Genetic instructions represent a form of "prescriptive information (instruction)" rather than just "Shannon combinatorial/probabilistic information." Genetic "recipe" has been called "aperiodic specified complexity." See "Aperiodic specified complexity" under "Discussion."
e. By sustained, free-living "life," the Foundation means any system which from its own inherent set of biological instructions can perform all nine of the following functions:
1. Delineate itself from its environment through the production and maintenance of a membrane equivalent, most probably a rudimentary or quasi-active-transport membrane necessary for selective absorption of nutrients, excretion of wastes, and overcoming osmotic and toxic gradients,
2. Write, store, and pass along into progeny prescriptive information (instruction) needed for organization; provide instructions for energy derivation and for needed metabolite production and function; symbolically encode and communicate functional message through a transmission channel to a receiver/decoder/destination/effector mechanism; integrate past, present and future time into its biological prescriptive information (instruction) content,
3. Bring to pass the above recipe instructions into the production or acquisition of actual catalysts, coenzymes, cofactors, etc.; physically orchestrate the biochemical processes/pathways of metabolic reality; manufacture and maintain physical cellular architecture; establish and operate a semiotic system using "signal molecules"
4. Capture, transduce, store, and call up energy for utilization (work),
5. Actively self-replicate and eventually reproduce, not just passively polymerize or crystallize; pass along the apparatus and "know-how" for homeostatic metabolism and reproduction into progeny,
6. Self-monitor and repair its constantly deteriorating physical matrix of bioinstruction retention/transmission, and of architecture,
7. Develop and grow from immaturity to reproductive maturity,
8. Productively react to environmental stimuli. Respond in an efficacious manner that is supportive of survival, development, growth, and reproduction, and
9. Possess relative genetic stability, yet sufficient diversity to allow for adaptation and potential evolution.
All classes of archaea, bacteria, and every other known free-living organism, meet all nine of the above criteria. Eliminate any one of the above nine requirements, and it remains to be demonstrated whether that system could remain "alive."
RNA strands, DNA strands, prions, viroids, and viruses shall not be considered free-living organisms, since they fail to meet many of the above well-recognized characteristics of independent "life."
Even in historical science, there must be some degree of empirical accountability to our theories. Proposing a mechanism that explains the origin of life must not consist of "defining down" the meaning and essence of the observable phenomenon of "life" to include "nonlife" in order to make our theories "work." Any scientific life-origins theory must connect with "life" as we observe it (the "continuity principle"). Science will never be able to abandon its empirical roots in favor of purely theoretical conjecture. On the other hand, science must constantly guard itself against Kuhnian paradigm ruts. We must be open-minded to the possibility that life has not always taken the form that we currently observe. We must take into consideration the problems inherent in any historical science where the observation of past realities is impossible.
Biophysicist Hubert P. Yockey makes the unique observation that "there is nothing in the physico-chemical world [apart from life] that remotely resembles reactions being determined by a sequence and codes between sequences. The existence of a genome and the genetic code divides living organisms from non-living matter." (Computers and Chemistry, 24 (2000) 105-123). This may well constitute the most concise and parsimonious dichotomization of animacy from inanimacy available in the literature. We must remember, however, that the full compliment of nucleic acid code, ribozymes, and protein enzymes are still present immediately after cell death. Life, therefore, would appear not to be reducible to coded prescriptive information (instruction) alone. Life is also not "a bag of enzymes." "Life" is characterized by ongoing homeostatic metabolic process and algorithmic function, including development, growth, and reproductive potential. The inability of mules to reproduce has no relevance to discussions of protocellular viability.