Life, Information, Entropy, and Time: Vehicles for Semantic Inheritance

Abstract

Attempts to understand how information content can be included in an accounting of the energy flux of the biosphere have led to the conclusion that, in information transmission, one component, the semantic content, or "the meaning of the message," adds no thermodynamic burden over and above costs arising from coding, transmission and translation. In biology, semantic content has two major roles. For all life forms, the message of the genotype encoded in DNA specifies the phenotype, and hence the organism that is tested against the real world through the mechanisms of Darwinian evolution. For human beings, communication through language and similar abstractions provides an additional supra-phenotypic vehicle for semantic inheritance, which supports the cultural heritages around which civilizations revolve. The following three postulates provide the basis for discussion of a number of themes that demonstrate some important consequences. (i) Information transmission through either pathway has thermodynamic components associated with data storage and transmission. (ii) The semantic content adds no additional thermodynamic cost. (iii) For all semantic exchange, meaning is accessible only through translation and interpretation, and has a value only in context. (1) For both pathways of semantic inheritance, translational and copying machineries are imperfect. As a consequence both pathways are subject to mutation and to evolutionary pressure by selection. Recognition of semantic content as a common component allows an understanding of the relationship between genes and memes, and a reformulation of Universal Darwinism. (2) The emergent properties of life are dependent on a processing of semantic content. The translational steps allow amplification in complexity through combinatorial possibilities in space and time. Amplification depends on the increased potential for complexity opened by 3D interaction specificity of proteins, and on the selection of useful variants by evolution. The initial interpretational steps include protein synthesis, molecular recognition, and catalytic potential that facilitate structural and functional roles. Combinatorial possibilities are extended through interactions of increasing complexity in the temporal dimension. (3) All living things show a behavior that indicates awareness of time, or chronognosis. The ∼4 billion years of biological evolution have given rise to forms with increasing sophistication in sensory adaptation. This has been linked to the development of an increasing chronognostic range, and an associated increase in combinatorial complexity. (4) Development of a modern human phenotype and the ability to communicate through language, led to the development of archival storage, and invention of the basic skills, institutions and mechanisms that allowed the evolution of modern civilizations. Combinatorial amplification at the supra-phenotypical level arose from the invention of syntax, grammar, numbers, and the subsequent developments of abstraction in writing, algorithms, etc. The translational machineries of the human mind, the "mutation" of ideas therein, and the "conversations" of our social intercourse, have allowed a limited set of symbolic descriptors to evolve into an exponentially expanding semantic heritage. (5) The three postulates above open interesting epistemological questions. An understanding of topics such dualism, the élan vital, the status of hypothesis in science, memetics, the nature of consciousness, the role of semantic processing in the survival of societies, and Popper's three worlds, require recognition of an insubstantial component. By recognizing a necessary linkage between semantic content and a physical machinery, we can bring these perennial problems into the framework of a realistic philosophy. It is suggested, following Popper, that the ∼4 billion years of evolution of the biosphere represents an exploration of the nature of reality at the physicochemical level, which, together with the conscious extension of this exploration through science and culture, provides a firm epistemological underpinning for such a philosophy.

FIGURE 1

Scheme to show how the solar energy intercepted by the earth is redistributed. The photosynthetic yield of ∼0.5% is available for consumption by animals, fungi, and bacteria, and sustains the biosphere, but is eventually lost to space as IR radiation (Adapted from http://asd-www.larc.nasa.gov/erbe/components2.gif). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 2

The mind, its external interfaces, and the thermodynamic carriers for sensory and semantic input. Penfield's sensory homunculus, projected on the cortex of the brain (left), or as a model distorted in proportion to the area of the cortex concerned with touch (middle), and the physical or chemical vehicles that impinge on different sensory interfaces (right). (The model is in the Natural History Museum, London, and has been released to the public domain. Models for other senses could be constructed along similar lines). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 3

Dissecting the biochemical machinery underlying bacterial chronognosis. The apparatus through which the bacterium detects changes in gradients includes the following elements. Detection of attractant or repellant molecules through a chemoreceptor (MCP), which transmits a signal across the cell membrane; the subsequent triggering of a signal transmission cascade through a two-component histidine kinase (CheA) and response regulator (CheY) system; and modulation of flagella response (insert, lower left). This involves phosphorylation of CheY (catalyzed by CheA) or dephosphorylation (CheC, CheZ) to change the direction of rotation. An essential component of the mechanism is adaptation, a biochemical process with variable time constants involving methylation (catalyzed by CheR), and demethylation (catalyzed by CheB) by reversible esterification of acidic side chains in the receptor, which modulate the degree of aggregation, likely by neutralizing the coulombic repulsion from like charges. This leads to deactivation or activation of the signal transmission pathway. The precise role varies between species, but the system can be regarded as involving competing decay and refresh pathways, in which the time constants for some functions are under control by the state of activation of the receptor. This allows recognition of gradients— changes in local concentration—with a time scale on the seconds-to-minutes range. Details of mechanism vary in different bacterial families; the scheme here is appropriate for Bacillus subtilis, in which an additional mechanism for amidation and deamidation (CheD) of the acidic residues also contributes. An interesting variant recently reported [99, 100] is a activation of a similar CheA kinase through binding of sensory rhodopsin II to its membrane partner HtrII on photoactivation in haloarchaea. Art work adapted from Ref. 85 by addition of a serine receptor dimer model from Ref. 84.

FIGURE 4

Pierre Simon Laplace (1749–1827) and the deterministic view: “We ought to regard the present state of the universe as the effect of the antecedent state and as the cause of the state to follow. An intelligence knowing all the forces acting in nature at a given instance, as well as the momentary positions of all things in the universe, would be able to comprehend the motions of the largest bodies as well as the lightest atoms in the world, provided that its intellect were sufficiently powerful to subject all data to analysis; to it nothing would be uncertain, the future as well as the past would be present to its eyes …”. Laplace, 1820, A philosophical essay on probabilities. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com]

FIGURE 5

Top: Combinatorial complexity on going from one to four dimensions. Left, the double helix contains two complementary copies of the genome with identical information content. In bacteria, this single genome restricts dimensionality to 1D, but in sexual reproduction additional combinatorial levels are opened, effectively in 2D, by chromosomal crossover. The 3D level (middle) is represented by the bc₁ complex catalytic core (PDB ID 2bcc, 3bcc) [101], with the cytochrome b subunit surface colored to show its physicochemical surface (as electrostatic potential: red, negative; blue, positive). This complex has two catalytic sites for oxidation or reduction of ubiquinone species (or binding of inhibitory mimics), internal pockets for binding of four metal centers (3 hemes and an iron-sulfur cluster), two external catalytic interface for interaction with a mobile domain of the iron-sulfur protein, a hydrophobic membrane interface, several interfaces for interaction with other subunits, and a dimeric interface. Bottom: The adenine nucleotide translocator (PBD ID 1okc). The surface is colored to show electrostatic potential. This stereo view (for crossed-eye viewing) allows a glimpse into the pocket where adenine nucleotide binds, which is occupied here by the inhibitor carboxyatractyloside. This protein is thought to act in dimeric form to exchange ADP for ATP⁻ across the mitochondrial membrane through large conformational changes; the surface is quite complex and shows not only the internal binding pocket, but also two aqueous polar interfaces, a hydrophobic collar that interfaces with the membrane lipid, and a dimeric interface.

FIGURE 6

The arrow of time. The arrow is shown as a spiral (represented by an α-helix) passing from the past through the “plane of present” to the future. The “plane of present” is represented by a spiral galaxy (with a period long compared to human timescales). Start- and end-points are the big bang, and “entropic death” (represented metaphorically by a detail from “Hell” by Hieronymus Bosch. There would of course be none of those discernable gradients in a universe at equilibrium). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 7

The exodus from Africa. The origins of all modern human populations can be traced back to ancestors from Africa, through comparison of sequences of mitochondrial DNA (female lines, or “Eve”, beige), and DNA from the “Y” chromosome (male lines, or “Adam”, cyan). Migrations from Africa date back ∼70,000 years, providing an anthropocentric start to our history. The blue lettering indicates major mitochondrial lineages, the dark red italic lettering shows Y-chromosomal lineages, and the dark green numbers followed by kya show that arrival time in thousands of years ago. Only lineages dating back to the period 35–40 kya are shown), and the land masses and glaciation (white) reflect this time period. This Figure was constructed using data made available through the National Geographic Society's Genographic Project web pages (https://www3.nationalgeographic.com/genographic/index.html), and this informative and interesting site is gratefully acknowledge.

FIGURE 8

Lascaux cave drawings, and similar cave art and figurines from the pre-historic era, represent early examples of the representation in physical form of semantic content abstracted from the mind (image from Wikipedia, http://en.wikipedia.org/wiki/Image:Lascaux2.jpg) [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com]

FIGURE 9

Scheme to illustrate the levels of combinatorial complexity arising from increased dimensionality following semantic translation at the somatic level (top). The residual information content refers to that originating from the genome at conception; in metazoans, the mature phenotype obviously contains many diploid copies, but most of these are not involved in reproduction, and only half the original is passed on in each haploid gamete. The estimated number of protein coding genes (∼24,000) represents <2.5% of the genome. A smaller fraction encodes RNA directly involved in the translational machinery. A much larger fraction (probably >80%) is transcribed, and from its characteristics is likely involved in determination of tissue specificity, ontogenic sequencing, etc. For a recent review, see . The combinatorial possibilities expand with dimensionality more dramatically than shown; the vertical axis of the schematic should be thought of as on a log scale. Complexity inherent in language (bottom). The representation of complex thought in literature, conversation, etc. depends on the combinatorial exploitation of a relatively small number of symbols in sentences whose structure encodes meaning. The ideas (memes) are the units of semantic transmission, and the complexity of our culture depends on the translational processing and mutation in individual minds (not shown). Similar schemes could be shown for mathematics, logic, music, etc. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 10

Cuneiform tablet from Ancient Babylon (∼1700 BC) showing Pythagorean triplets. Plimpton 322 from the Plimpton collection (Columbia University) (image from Wikipedia, http://en.wikipedia.org/wiki/Image:Plimpton_322.jpg). For much of the information about the development of mathematics, I am indebted to the MacTutor Web site (see Supplementary Sources for URL).

FIGURE 11

The Council of Nicaea. Bishop Nicholas forcefully argues for the homoousian cause (Sistine Chapel fresco). The transformation of St. Nicholas into Santa Claus is a nice example of memetic mutation (see text). Image courtesy of St. Nicholas Center (www.stnicholascenter.org), which has a nice account. The forcefulness of Bishop Nicholas was not just verbal! [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 12

Popper's Worlds 1, 2, and 3, expanded into three dimensions. We see ourselves as individual minds (World 2). Our perception of the physical World 1 might be unique (arrows from left showing sensory input), but we all experience the same world, tied by physical laws. Our “conversations” (central column) involve exchanges in which translational processing, access to associative memory, mutation of ideas, etc. are so rapid as to appear automatic. The semantic heritage of World 3 (right) appears dynamic, but is static except for the horizontal exchanges with individual minds. The Internet traffic is a relatively new feature, but we depend on a copying function that is error-free, so the vertical exchanges indicated do not change the heritage. However, the speed of exchanges via the Internet is contributing to an acceleration in exploration of combinatorial possibilities made possible by the horizontal exchanges with minds. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 13

Scheme to show the role of semantic transmission in Darwinian evolution. All evolving systems follow the same pattern in which the meaning of a thermodynamically encoded message is transmitted via a translational machinery to allow reproduction. The overall process is subject to error, so that the translational product may include “mutations.” The translational product is tested in an “ecosystem” against competitors. Products that survive reproduce, thus propagating the more successful traits, leading to improvement. In reproduction (enclosed by dashed line), the step for semantic transmission is shown as separate from that for the copying of the replicator to accommodate obvious difference in the degree of linkage for different forms. The tightness of linkage decreases in the order: bacteria reproduction by cell division; asexual reproduction in the protista; sexual reproduction in the metazoan; and supra-phenotypical inheritance. In all cases, the transmitted message needs to find itself in a competent translational environment. However, the linkage between transfer of the message and the translational apparatus also depends on the case considered, in a similar order (see text for explanation). The mature phenotype is reproduced after whatever mutation changes it, so that what looks like a cycle in this 2D representation would project to a 3D version (see Figure 12) and a spiral through time in 4D (see Figure 6). All processes that we perceive as cyclical are spirals through time, with pitches and lengths spanning many orders of magnitude. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 14

Detail from “The Fall of the Rebel Angels” by Pieter Brueghel the Elder, from the Webmuseum, Paris (http://www.ibiblio.org/wm/paint/auth/bruegel/). Dennett's treatment of the states underlying consciousness [56] involves demons, homunculi, memes, and other agents, a metaphor nicely illustrated by Brueghel's painting. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 15

EROS maps showing cortical neuronal activity measured noninvasively through changes in near infrared transmission. The optical apparatus measures IR transmission through the brain cortex from outside the skull. Here, the stimulus was a thumb-twitch, elicited by electrical stimulation of the wrist, and maps are similar for different repetition frequency (top). The responses occur at 16–32 ms after stimulation. Events on this time scale are obviously registered (since they induce the response seen), but are probably not yet consciously perceived. The Z score represents differences from baseline. The darker gray shows the area monitored. The brain image was from structural MRI, used to determine the brain area corresponding to the response. Similar maps can be measured following sensory stimulation by sight or sound, but these elicit responses with greater latency, and in areas dependent on sensory and semantic context. The time scale of measurement here is fast enough for exploration of the mechanisms underlying consciousness (from Maclin et al. [102]; reprinted with permission from Elsevier).

FIGURE 16

The relation between chronognostic range and evolution of the biosphere. The plot of chronognostic range (CR, in years) against years before the present (YBP) is shown on a log vs. log scale to accommodate the many orders of magnitude involved. The slope in the early part of the graph reflects the contribution from advances in behavioral complexity. A few “markers” will illustrate the approach. The bacterial world was constrained by the biochemical processes discussed in the text (CR in the seconds range; see also Figure 3). As evolution led to more advanced forms, the temporal perception lengthened, perhaps to the lifetime for an advanced vertebrate. But even in the case of early human societies, the range was constrained to a few 100 years and was limited by oral transmission. With the development of archival information storage, this was extended into the thousands of years range. The change in slope reflects an acceleration arising from the development of a supra-phenotypical semantic heritage. The choice of points is biased, since the latter part of the plot is based on developments in the civilization of Europe and the West. However, in Western thought, it was not until the Copernican revolution, Bruno, and Galileo that our perception of the universe was stretched further than the Greco-Roman-Arabic Ptolemaic tradition, and not until Darwin that our temporal range was stretched beyond the “biblical limit.” In modern times, this range is determined by cosmological time scales, accessible to interpretation though advances in our understanding of astronomy and its relativistic scales of time and distance. The graph reveals a dramatic change in slope in the mid-13th century. A strong case is made by Jack Weatherford in Genghis Khan and the Making of the Modern World [103] that the flowering of intellectual life in the 14th century owed much to the spread of ideas after the establishment of the Mongol Empire. This opened trade routes that facilitated an exchange of ideas and culture between Europe, the Islamic Empires, and East Asia. Subsequent developments leading to the astonishing slope must include the dawn of humanism, the reformation, the development of literature in the vernacular, the renaissance, the age of exploration, the spread of printing in the West, and the emergence of a rational science from the constraints of dogma. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

FIGURE 17

Paradoxes of time: meme selection at the machine level? A small sample of the images delivered by Google in response to arrow of time; the recall of associative images from the Web represents a second-hand dipping into a pool of images deposited by human agency. Left: “Time flies like an arrow”, and middle: “Fruit flies like a banana”, both from Harvey Galleries (www.harveygallery.com/, reproduced with kind permission of Henry Harvey); right: the CPLear experiment (www.cern.ch/cplear/) to test charge, parity, time (CPT) invariance, reproduced with kind permission from CERN. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com]