1. what is life?

By Luis M. Rocha

Lecture notes for I400/I590 - : Biologically Inspired Computing. School of Informatics, Indiana University. Also available in adobe acrobat pdf format

“What was life? No one knew. It was undoubtedly aware of itself, so soon as it was life; but it did not know what it was”. Thomas Mann [1924]

threshold of complexity

“Seeking a connecting link, they had condescended to the preposterous assumption of structureless living matter, unorganized organisms, which darted together of themselves in the albumen solution, like crystals in their mother-liquor; yet organic differentiation still remained at once condition and expression of all life. One could point to no form of life that did not owe its existence to procreation by parents”. Thomas Mann [1924]

“Nothing in biology makes sense without evolution”. Theodosuis Dobzhansky [1973]

Biologically-inspired computing is a new interdisciplinary field that formalizes particular processes observed in living systems to design computational methods for solving complex problems, or simply to endow artificial systems with more natural traits. But to draw more than superficial inspiration from Biology we need to understand and discuss the concept of life. It should be noted that for the most part of the history of humanity, the question of what life is was not an important issue. Before the study of mechanics became important, everything was thought to be alive: the stars, the skies, the rivers and mountains, etc. There was no non-life, so the concept was of no importance. It is only when people start seeing the World as determined by the laws of mechanics that the question arises. If all matter follows simple physical laws, then what is indeed the difference between life and non-life, between biology and physics? Let us then start with a current dictionary definition:

“life adj.— n.1. the general condition that distinguishes organisms from inorganic objects and dead organisms, being manifested by growth through metabolism, a means of reproduction, and internal regulation in response to the environment. 2. the animate existence or period of animate existence of an individual. 3. a corresponding state, existence, or principle of existence conceived of as belonging to the soul. 4. the general or universal condition of human existence. 5. any specified period of animate existence. 6. the period of existence, activity, or effectiveness of something inanimate, as a machine, lease, or play. 7. animation; liveliness; spirit: The party was full of life. 8. the force that makes or keeps something alive; the vivifying or quickening principle.” [Random House Webster’s Dictionary]

The definitions above fall into three main categories: (1) life as an organization distinct from inorganic matter (with an associated list of properties), (2) life as a certain kind of animated behavior, and (3) life as a special, incommensurable, quality---vitalism. Throughout this course we will see that all principles, and indeed all controversies, associated with the study of life fall into one of these categories or the differences between them. The third category has been discarded as a viable scientific explanation, because for science nothing is in principle incommensurable. The question of whether life is organized according to a special design, intelligent or mysterious, pertains to metaphysics. If the agent of design of the special quality cannot be observed with physical means, then it is by definition beyond the scope of science as it cannot be tested.

While metaphysical dispositions do not pertain to science, many scientists have observed that a naive mechanistic decomposition of life may also fail to explain life. The traditional scientific approach has lead the study of living systems into a reductionist search for answers in the nitty-gritty of the biochemistry of living organisms. This alternative sees life as nothing more than the complicated physics of a collection of moving bodies. However, the question remains unanswered since there are many ways to obtain some complicated dynamics, but of all of these, which ones can be classified as alive? What kind of complexity are we looking for? No one disputes that life is some sort of complex material arrangement, but when do we reach a necessary threshold of complexity after which matter is said to be living? Is it a discrete step, or is life a fuzzy concept? To understand it without meaningless reduction, must we synthesize organizations with the same threshold of complexity (first category above), or is it enough to simulate its animated behavior (second category above)?

information organizes and breeds life

“Life is a dynamic state of matter organized by information”. Manfred Eigen [1992]

“Life is a complex system for information storage and processing”. Minoru Kanehisa [2000]

Traditionally life has been identified with material organizations which observe certain lists of properties, e.g. metabolism, adaptability, self-maintenance (autonomy), self-repair, growth, replicability, evolution, etc. Most living organisms follow these lists, however, there are other material systems which obey only a subset of these rules, e.g. viruses, candle flames, the Earth, certain robots, etc. This often leads to the view that life is at best a fuzzy concept and at worst something we are, subjectively, trained to recognize — life is what we can eat — and is thus not an objective distinction. Objectively or subjectively, we do recognize some material organizations as being alive. It is perhaps in this ability to recognize and categorize events in our environments that an important difference between living and non-living systems lies.

Life requires the ability to both categorize and control events in its environment in order to survive. In other words, organisms pursue (or even decide upon) different actions according to information they perceive in an environment. Furthermore, living organisms reproduce and develop from genetic information. More specifically, genetic information is transmitted “vertically” (inherited) in phylogeny and cell reproduction, and expressed “horizontally” within a cell in ontogeny and plain functioning of living organisms. Indeed, the difference between living and non-living organizations seems to stand on the ability of the former to use relevant information for their own functioning. It is this “relevant” which gives life an extra attribute to simple mechanistic interactions. When an organization is able to recognize and act on aspects of its environment which are important to its own survival, we say that the mechanisms by which the organization recognizes and acts are functional in reference to the organization itself (self-reference). Physics is not concerned with function. A physical or chemical description of DNA is certainly possible, but will tell us nothing as to the function of a DNA molecule as a gene containing relevant information for a particular organism. Only in reference to an organism does a piece of DNA function as a gene (e.g. an enzyme with some effect in an environment).

emergence and explanation

“First, nothing in biology contradicts the laws of physics and chemistry; any adequate biology must be consonant with the ‘basic' sciences. Second, the principles of physics and chemistry are not sufficient to explain complex biological objects because new properties emerge as a result of organization and interaction. These properties can only be understood by the direct study of the whole, living systems in their normal state. Third, the insufficiency of physics and chemistry to encompass life records no mystical addition, no contradiction to the basic sciences, but only reflects the hierarchy of natural objects and the principle of emergent properties at higher levels of organization”. Stephen Jay Gould [1984]

This issue could be rephrased in terms of the notion of emergence. Whatever organization exists after the complexity threshold for life is passed, we may say that it is emergent to the physical level because its attributes cannot be completely explained by the previous level. In particular, function, control, and categorization cannot be explained by the mechanics and dynamics of the components of life alone. Notice, however, that emergence does not imply vitalism or dualism. When we say that certain characteristics of life cannot be explained by physics alone, we mean that they must be explained by different, additional models---namely, informational, historical and functional descriptions. In other words, though biological function, control, and categorization cannot be explained by physics alone, organisms, like anything else, must nonetheless follow physical laws. But information is contextual, and therefore requires more than universal models to be described: it requires contingent, context-specific descriptions. In particular, the origin of life, is a problem of emergence of information from a physical milieu under specific constraints [Eigen, 1992].

The definition of emergence as an epistemological, explanatory requirement, is related to the notion of emergence-relative-to-a-model [Rosen, 1985; Cariani, 1989] or intensional emergence [Salthe 1991]. It refers to the impossibility of epistemological reduction of the properties of a system to its components [Clark, 1996]. As an example, we can think of phase transitions such as that of water in its transition from liquid to gas. Water and its properties cannot be rephrased it terms of the properties of hydrogen and oxygen, it needs a qualitatively different model. Another example of complementary models of the same material systems is the wave-particle duality of light.

Artificial life concerns both the simulation and realization of life in some artificial environment, usually the computer. At least regarding the second of its goals, artificial life cannot escape the main issues raised above for biological life. Conversely, bio-inspired computing, as a more pragmatic endeavor, does not need to concern itself with synthesizing actual life, but only with drawing analogies from life (real and artificial). Nonetheless, if the main motivation of bio-inspired computing is that life with its designs has already solved versions of many complex engineering problems we are interested in, then a thorough and accurate understanding of the essential characteristics of life is inescapable

for the next lectures read

Forbes, N. [2004]. Imitation of Life: How Biology is Inspiring Computing. MIT Press. Preface, pp. ix - xv

Kanehisa, M. [2000]. Post-genome Informatics. Oxford University Press. Chapter 1, Blueprint of life, pp. 1-23.

Langton, C. [1989], “Artificial Life” In Artificial Life. C. Langton (Ed.). Addison-Wesley. pp. 1-47.

Pattee, H. [1989], "Simulations, Realizations, and Theories of Life". In Artificial Life. C. Langton (Ed.). Addison-Wesley. pp. 63-77.