Information in Biology
Despite many controversies about the role of information in biology over the past several decades, we can now show that the creation and communication of information is not only necessary to understand biology, but that biology is a proper, if tiny, subset of information creation in the material universe, including the evolution of human minds and the abstract ideas created or discovered by our minds. Material information creation, in the form of planets, stars, and galaxies, went on for perhaps ten billion years before biological "agents" formed. At some time between three and four billion years ago, multicellular biological agents began to communicate with their component parts and with one another, processing and sharing information. With the appearance of life, agency, purpose, meaning, and values entered the universe.
This is not a teleological purpose that pre-existed life. It is what Colin Pittendrigh, Jacques Monod, and Ernst Mayr suggested we call teleonomy, a "built-in" purpose. Aristotle called it "entelechy," which means "having a purpose within." Mayr teaches us that biology is unlike physics and chemistry because it has a history. Our atoms and molecules do not contain information about where they have been in the past, nor do they have any control over where they will be in the future. Many mathematical physicists deny this. If determinism were the case, every particle path would contain that information. But a quantum analysis of statistical physics shows how microscopic path information is destroyed. Mayr's biology is a history that goes back nearly four billion years. In astronomy we can trace the history of cosmic evolution back 13.7 billion years. The goal for information philosophy is to write a new story of biological evolution as the growth of information processing, connecting it back into cosmological evolution as the creation of information structures, and illustrating the total dependence of biology on cosmological sources of negative entropy (potential information). Material information structures formed in the early universe - the elementary particles, atoms and molecules, galaxies, stars, and planets - all as the result of gravitation and quantum cooperative phenomena. But it is not until the emergence of life that information replication and information processing begins. In a deep sense, biology is information processing. Understanding the origin of life is to understand the concept of living information structures - biological agents that some call "interactors." Information processing is the signaling between interactors, using signs that have a syntax (linear sequences of symbols like words in a language) and a semantics (meaning), but most important, have pragmatic value. Interactors use meaningful information to control the use of matter and energy as they accomplish their purposes and goals. Interactors are powered by streams of matter and energy with low entropy. This flow of negative entropy (potential information) comes proximately from the Sun but ultimately from the expansion of the universe, which must be the starting point for explaining life. An interactor is a clearly definable agent who interacts with other agents by signaling, by coding the abstract information of a message into a material or energetic carrier that travels from the sender to the receiver. The receiver decodes the message and takes an action that depends on the meaning in the message. Interactors are information structures with internal functioning parts that make up an operational organic whole, so messages may be internal to an interactor or external between two interactors. The messages between interactors - cells, cell components like organelles, or cell combinations in multicellular organisms or communities of cells - are not (merely) "analogous" to human communication or "helpful metaphors." Biological communications have been present from the origin of life. Human communications are in every sense merely a very recent and very special example of (and homologous to) biological communication, despite the fact that most humans think communication is uniquely human. Without the communication and processing of meaningful information, there would be no life. To understand biology - and humanity - we must understand how the communication and processing of information allows living information structures to carry out their functions. And, thanks to biological evolution, we have the tool needed to understand biology and our selves, the extraordinary human mind. Human minds have created everything we know about how abstract immaterial information and concrete information structures (matter and energy with low entropy) have been created in the universe. Humans are co-creators of the universe, specifically the part known as "culture" as opposed to "nature," including all human artifacts and all human knowledge.
Beyond Reductionism? Even Beyond Darwinian Evolution?Is there something "holistic" happening in biology, something that cannot be explained by the material parts following the fundamental laws of chemistry and physics? The great quantum physicist Erwin Schrödinger thought life should be reducible to physics and chemistry, but that, he said, might require "new laws" of physics. This led some great scientists to turn from physics to biology to find those new laws. In the nineteenth century, "emergentists" and "vitalists" argued for new properties for complex organisms that are not present in their component parts, or for new "forces" that infuse mere matter with life. The most obvious evidence for something non-material was that life appears to violate the then recently discovered second law of thermodynamics. Many philosophers and scientists thought that life, and especially mind, could not be possible unless proto-life and proto-mind were already present in all physical particles. This is known as "pan-psychism." Panpsychism is still very popular among thinkers at the edges of science and religion. Where René Descartes considered mind (res cogitans) as something ontologically and substantially distinct from matter (res extensa), thus creating the mind-body problem, most of his contemporaries (e.g., Gottfried Wilhelm Leibniz and Baruch Spinoza) and philosophers down to the twentieth century thought mind an essential aspect of matter. The idea of emergence was implicit in the work of John Stuart Mill and explicit in
the work of "emergentists" like George Henry Lewes, Samuel Alexander, C. Lloyd Morgan, and C. D. Broad. Some wanted to explain the direct emergence of mind from matter, to solve the mind-body problem, but as Alexander put it, there are at least two distinct steps - first life emerges from the physical-chemical, then mind emerges from life. Charles Sanders Peirce thought the universe must have a property like mind. He thought the laws of nature were evolving "habits" of such a mind. He thought the chance element in Darwinism made it "greedy." Alfred North Whitehead's "Process Philosophy" is panpsychic, very popular today as "Process Theology." The French philosopher Henri Bergson argued that the creative aspect of evolution cannot be explained by random variation and selection. Vitalists like Bergson and Hans Driesch may not have used the term emergence, but they strongly supported the idea of teleological (purposeful), likely non-physical causes, without which they thought that life and mind could not have emerged from physical matter. Influenced by his countryman Bergson and the evolutionary philosopher Georg W. F. Hegel, the philosopher and Jesuit priest Pierre Teilhard de Chardin imagined an "Omega Point" toward which the universe and life are evolving, with the mind of man participating in the final evolutionary phase, a "noösphere" or mind sphere similar to what might be called an "infosphere," the locus of our Sum of human knowledge.. What these thinkers all have in common is that they believe that the material basis of living things cannot possibly have a creative power. In general, they are all looking for something more powerful than the neo-Darwinian, modern synthesis of biology, in which evolution is driven by variations that depend on ontological chance. A significant fraction of scientists, philosophers, and theologians today have what William James called "antipathy to chance." The new sciences of complexity and chaos theory are believed by many to provide a new explanation of the origin of life. Ilya Prigogine correctly described the reductions in local entropy of what he called "dissipative structures" as bringing "order out of chaos." Complexity and chaos are deterministic, dynamical theories that generate epistemological uncertainty, which is enough for some thinkers who dislike ontological chance. Complex phenomena very likely supported the formation of pre-biotic structures, "autocatalytic" combinations of elements that synthesized some of their own parts. But no classical dynamical phenomena can explain the origin of genuinely new information in the universe. That requires quantum chance.
A Benevolent, Providential UniverseBefore there was life, the galaxies, stars, and planets had a rich developmental and evolutionary history of their own. Astrophysics tells us that stars radiated energy into space as they dissipated the energy of gravitational collapse (the photons carrying away positive entropy to balance the new spherically symmetric order). The stars paused their collapsing when their interiors reached temperatures high enough to initiate thermonuclear reactions, which converted the lightest elements (hydrogen and helium) into heavier elements. When the fuel is exhausted, the stars resume collapsing, some exploding catastrophically and spreading their newly formed elements out into interstellar space. Geophysics tells us that the surfaces of planets also go through heating, then cooling, as they radiate away the energy of gravitation. Chemical processes produce ever more complex molecules in the dust and gas clouds of interstellar space and on planetary surfaces. They were produced in the stars as well, but usually they disassociate quickly in a hot star.
The Origin of Life
Molecular MachinesBiological communications, the information exchanged in messages between biological entities, is far more important than the particular physical and chemical entities themselves. These material entities are used up and replaced many times in the life cycle of a whole organism, while the messaging has remained constant, not just over the individual life cycle, but that of the whole species. In fact most messages, and the specific molecules that embody and encode those messages, have been only slowly varying for billions of years. As a result, the sentences (or statements or “propositions”) in biological languages may have a very limited vocabulary compared to human languages. Although the number of words added to human languages in a typical human lifetime is remarkably small. Biological information is far more important than matter and energy for another reason. Beyond biological information as “ways of talking” in a language, we will show that the messages do much more than send signals, they encode the architectural plans for biological machines that have exquisite control over individual molecules, atoms, and their constituent electrons and nuclei. Far from the materialist idea that fundamental physical elements have “causal control” over living things, we find that biological information processing systems are machines, intelligent robotic machines, that assemble themselves and build their own replacements when they fail, and that use the flow of free energy and material with negative entropy to manipulate their finest parts. Coming back to the great philosopher of logic and language Ludwig Wittgenstein, who briefly thought of “models” as explanatory tools that can “show” what is difficult or impossible to “say” in a language, we offer dynamic animated models below. The amazing operations of these machines are so far beyond man-made machines that it has called into question the ability of Darwinian evolution to create them by random trials and errors. But the most complex of these machines have been shown to be composed of dozens of smaller and simpler parts that did and still do much simpler tasks in the cell. The five biological machines that we choose are
• the ribosome, a massive factory that manufactures thousands of different possible proteins when messenger RNA carries a request for one of them from the nuclear DNA, • ATP synthase, which packages small amounts of energy into a nucleotide molecule that carries energy to any place in the organism that needs power to perform its function, • the flagellum, a high-speed motor that moves bacterial cells to sources of matter and energy in their environment, • the ion pump, which moves calcium and potassium ions to rapidly recharge the activation potential of a neuron so it is ready to fire again in a fraction of a second so the mind can make its decisions and take actions to move the body, • the chaperone, an error detection and correction system beyond the ability of our finest computers to protect memories from noise. Arthur Horwich Yale LectureBiology cannot prevent the occurrence of random errors. Indeterministic chance is the original source of variability in our genes that led to the incredible diversity of life forms, including us humans. But the nearly perfect operation of our biological machines and the phenomenal fidelity of copying our many genetic codes over billions of years shows the stability and “adequate determinism” of biology in the presence of ontological chance, a consequence of the noise-immune digital nature of biological information.
The New History of Cosmic and Biological EvolutionFrom an information philosophy perspective, the teleonomic purpose of all life has been to replicate itself and to improve its reproductive success, which is to say to replicate and expand its information. Richard Dawkins considered the possibility that genes are the driving force in reproduction - of their own information. Thus biological organisms are seen as the means by which the genes replicate. That may be contentious. But there is no question that over time, evolution has produced organisms that can both create and replicate more and more complex information processors, with humans the most complex. Through the admittedly narrow lens of information, the story of evolution begins with the cosmic creation of information structures (which do not communicate), followed by the evolution of biological information processors, our "interactors." These are products of the continuous stream of negative entropy coming from the cosmos, directly from the sun, but made possible by the expansion of the universe. Those of us living through the twentieth century were the first to see as close to the beginning of the universe as anyone will ever see. We also learned that the future of the universe is essentially infinite, relative to the lifespan of humans. In the middle of that century, around the time of one of the most destructive wars in world history, we transformed the meaning of "information" from informing one another to the analysis of language and all knowledge that breaks them into "bits." These "binary digits," "1 or 0" answers to "yes or no" questions, appeared first as the stuff of digital computers and digital communications. But at about the same time, biologists discovered that the hereditary material of all life is similarly encoded. Alan Turing, John von Neumann, and Claude Shannon created digital computers just a few decades after Albert Einstein's prediction about Brownian motion proved the existence of atoms. Matter consists of discrete discontinuous particles. Within a few years , James Watson and Francis Crick showed that life was based on a digital code. The coded sequence of nucleotides in the DNA molecule at the heart of the cell nucleus is transcribed, rewritten as messenger RNA that travels outside the nucleus with instructions to a ribosome to translate the genetic code into a matching linear chain of amino acids, a protein that folds itself to become a three-dimensional active enzyme. If digital computer codes had not already been invented, might the biological model have inspired them? Instead of computational models of the mind, we might have appreciated the mind as the ultimate extension of biological information processing!
The Origin and Future of KnowledgeJumping now to human evolution, we see humanity as a species of multi-molecular, multi-cellular organism that has found a way to not only create but also externalize information, storing it in the environment (culture), where it can be shared with new humans, who continue to add to this external store of knowledge. It is knowledge that has allowed humans to dominate the Earth, for better or for worse. The sharing of old and new information created with all other humans has enormous economic and moral implications. From a cosmologist's perspective, in the macrocosmos the human mind is the universe's means of reflection. In the microcosmos, it is one atom's way of knowing about other atoms. We call all of human knowledge the Sum, to go along with our free will model, the Cogito, and our basis for objective values, the Ergo. The Sum of human knowledge is vast of course, but we propose drafting suggestions for the most important things we know that should be known by everyone in the future.
ReferencesDefinitions of Life Information Processing IS Biology Information Theory in Biology (U. Illinois, 1952) Information Theory in Biology (Gatlinburg, Tennessee, 1956) Origin of Life Towards a Theoretical Biology (IUBS Symposia, 1966-67) The Major Transitions
Quotes"Life may be defined operationally as an information processing system—a structural hierarchy of functioning units—that has acquired through evolution the ability to store and process the information necessary for its own accurate reproduction. The key word in the definition is information. This definition, like all definitions of life, is relative to the environment. My reference system is the natural environment we find on this planet. However, I do not think that life has ever been defined even operationally in terms of information. This entire book constitutes a first step toward such a definition."
Evidently nature can no longer be seen as matter and energy alone. Nor can all her secrets be unlocked with the keys of chemistry and physics, brilliantly successful as these two branches of science have been in our century. A third component is needed for any explanation of the world that claims to be complete. To the powerful theories of chemistry and physics must be added a late arrival: a theory of information. Nature must be interpreted as matter, energy, and information.
"A central and fundamental concept of this theory is that of "biological information." since the material order and the purposiveness characteristic of living systems are governed completely by information, which in turn has its foundations at the level of biological macromolecules . The question of the origin of life is thus equivalent to the question of the origin of biological information."
"the evolutionary process is driven by an enormous flow ot thermodynamic information passing through the earth's biosphere."
"Information as the central concept in molecular biology
Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.."