The Demon in the Machine


What is Life?
  • The very nature of life seemed to defy one of physics’ fundamental laws – the so-called second law of thermodynamics – according to which there is a universal tendency towards degeneration and disorder.
  • Schrödinger said that for life to generate order out of disorder and buck the second law of thermodynamics, there had to be a molecular entity that somehow encoded the instructions for building an organism, at once complex enough to embed a vast quantity of information and stable enough to withstand the degrading effects of thermodynamics. We now know that this entity is DNA.
  • Threading through material complexity (the hardware of life) is an even more breathtaking informational complexity (the software of life), hidden from view but providing the guiding hand of both adaptation and novelty.
  • The information needed to build a given protein is stored in segments of DNA as a specific sequence of ‘letters’: A, C, G, T. These molecules adenosine, cytosine, guanine and thymine, collectively known as bases. Different combinations code for different proteins. Proteins are made from other types of molecules called amino acids; a typical protein will consist of hundreds of amino acids linked end to end to form a chain. The chemical properties of a protein will depend on the precise sequence of amino acids. To specify each amino acid, DNA uses groups of three in a row. There are sixty-four possible triplet combinations, or codons, of the four letters. The cell first transcribes the relevant codon sequence from DNA into a related molecule called mRNA (messenger RNA). Proteins are assembled by ribosomes, little machines that read off the sequence of codons from mRNA and synthesize the protein step by step by chemically linking together one amino acid to another.
  • DNA is a very ancient and deeply embedded feature of life on Earth, present in a common ancestor billions of years ago.
  • A living organism is out of equilibrium with its environment. To continue to function, an organism has to acquire energy from the environment and export something. There is thus a continuous exchange of energy and material with the surroundings.
  • In living things, most chemical activity is handled by proteins. Metabolism – the flow of energy and material through organisms – is necessary for life to achieve anything. The all-important organization of life requires a great deal of choreography, that is, some form of command-and-control arrangement. This is done by nucleic acids (DNA and RNA). Nucleic acids store the details about the ‘life plan’; proteins do the grunt work to run the organism. Both are needed.
  • The thing that separates life from non-life is information. The essence of biological reproduction, then, is the replication of heritable information.
Enter the Demon
  • There is a strict limit on the amount of heat that can be converted into useful mechanical activity. It is the flow of heat, not heat energy per se, that can perform work. To harness heat energy there has to be a temperature difference somewhere.
  • The law that says you can’t convert all the heat energy into work is the second law of thermodynamics.
  • At the micro-level, heat energy is none other than the energy of motion – the ceaseless agitation of molecules. The hotter the system, the faster the molecules move. When the faster-moving molecules collide with the slower-moving ones they will (again, on average) transfer a net amount of this kinetic energy to the cooler gas molecules. After a while the system will reach thermal equilibrium.
  • The second law of thermodynamics forbids the reverse process: the gas spontaneously rearranging its molecules so the fast-moving ones congregate at one end of the box and the slow-moving ones at the other.
  • Entropy is a measure of the disorder in a system. If the entropy of a system seems to decrease, just look at the bigger picture and you will find it going up somewhere else. On a cosmic scale, the second law implies that the entropy of the universe never goes down.
  • Maxwell’s Demons: Consider a box of gas that is divided into two chambers. A tiny demon observes the randomly moving molecules and operates the shutter to allow fast molecules to travel from the left-hand chamber to the right-hand one, and slow molecules to go the other way. A temperature difference has been established and useful work may then be performed. The demon thus converts disorganized molecular motion into controlled mechanical motion, creating order out of chaos and opening the way to a type of perpetual motion machine. But for this to work the demon must gather information about their speed and direction.
  • Information makes a difference in the world. We might say it has ‘causal power’. The challenge to science is to figure out how to couple abstract information to the concrete world of physical objects.
  • Shannon spotted that his mathematical formula quantifying information in bits is, identical to the physicist’s formula for entropy, which suggests that information is, in some sense, the opposite of entropy.
  • Whenever one takes an average some information is thrown away, that is, we accept some ignorance.
  • Information is about what you know, and entropy is about what you don’t know. One cannot say in any absolute way how much information there is in this or that physical system. Information is the reduction in the degree of ignorance or uncertainty about the system being measured. Even if the overall degree of ignorance is ambiguous, the reduction in uncertainty can still be perfectly well defined.
  • Electronic computers take input data, process it, output the answer, and irreversibly erase the stored information. Acts of erasure generate heat.
  • By demonstrating a link between logical operations and heat generation, Landauer found a deep connection between physics and information.
  • Information is physical: all information must be tied to physical objects: it doesn’t float free in the ether. Information shares some of the properties of energy. Like information, energy can be passed from one physical system to another and, under the right conditions, it is conserved. Information does have a type of independent existence and it does have causal power.
  • The three-way trade-off of information, heat energy and work. Maxwell’s and Szilárd’s demons process information to convert heat into work. Information engines do work by turning information into heat or by dumping entropy into an empty information register. Conventional engines use heat to do work and thereby destroy information (i.e. create entropy).
  • A blank or partially blank memory register acts as a thermodynamic resource that gets consumed when the demon acts as an engine. If erasing information increases entropy, then acquiring an empty memory amounts to an injection of fuel.
  • Researchers have built an information engine. They confirmed that ‘information known to a gate-operating demon’ serves as a fuel, while its erasure raises entropy ‘in agreement with Bennett’s resolution of the Maxwell demon paradox’.
  • Evolution has refined life’s information-management machinery to operate in a super-efficient manner. Organisms need to have perfected the art of storing and processing information or they would quite simply cook themselves to death with waste heat.
  • Organisms, being a good prediction machine means having the ability to learn from experience so as to better anticipate the future and make a smart move. To be efficient, however, a predictive system has to be choosy about what information it stores. All this requires some sort of internal representation of the world – a type of virtual reality – incorporating sophisticated statistical assessments.
  • Living organisms are not just bags of information: they are computers.
The Logic of Life
  • Kurt Gödel says no finite system of axioms can be used to prove its own consistency. That is, a god can never know everything.
  • Turing proved that a number was computable if and only if it could be the output of such a machine after a finite (but possibly huge) number of steps. The key idea is a universal computer: ‘a single machine which can be used to compute any computable sequence’. Turing’s paper is a proof that there isn’t, and can never be, an algorithm to solve the Entscheidungsproblem – the halting problem. There can be no way to know in advance, for general mathematical statements, whether or not Turing’s machine will halt and output an answer of true or of false. As a result, there will always be mathematical propositions that are quite simply undecidable.
  • No one can prove that a statement is undecidable. Undecidability guarantees that the mathematical universe will always be unbounded in its creative potential. If life represents something truly fundamental and extraordinary, then this quality of unconstrained possibility is surely key.
  • To be a truly universal constructor, the UC has to be able to build anything that is in principle constructible. A UC also has to be able to build a copy of itself. To replicate the instructions for how to make a UC and insert those instructions into the freshly minted replica. The crucial insight von Neumann had is that the information must be treated in two distinct ways. The first is as active instructions for the UC to build something. The second is as passive data simply to be copied as is replicated.
  • What makes biological replication non-trivial is its ability to evolve. If the copying process is subject to errors, and the errors are also copied, then the replication process is evolvable.
  • There is generally no simple connection between a gene, or a set of genes, and a biological trait at the level of the organism. Many traits emerge only when the system as a whole is taken into account.
  • Emergence: new qualities and principles may emerge at higher levels of complexity that can themselves be relatively simple and grasped without knowing much about the levels below.
  • We need to describe the molecular interactions and biochemical transformations that take place in living organisms, and then translate these descriptions into the logic circuits that reveal how information is managed.
  • Synthetic circuits are a rapidly expanding area of research in systems biology.
  • Biological circuitry can generate an exponentially large variety of form and function but, fortunately for science, there are some simple underlying principles at work.
  • Cells in your body have a circuit to control their cycles.
  • Transfer Entrophy:Tracking information flow in gene networks: if you look at, say, the three preceding steps of node A and note ‘on’ or ‘off’, does that three-step history improve the odds of you correctly guessing on or off for the next step? If it does, then we can say that some information has been stored in node A. One can then look at another node, say B, and ask, does knowing the current state of B improve the odds of correctly guessing what A will do next, over and above just knowing the history of A? If the answer is yes, it implies that some information has been transferred from B to A.
  • In the yeast gene network researchers zeroed in on a set of four nodes calling the shots. The special role of these four genes has earned them the name ‘the control kernel’. They seem to act like a choreographer for the rest of the network, so if one of the other nodes makes a mistake then the control kernel pulls it back into line. Control kernels seem to be a general feature of biological networks.
  • In spite of the great complexity of behaviour, a network’s dynamics can often be understood by looking at a relatively small subset of nodes.
  • Network theory confirms the view that information can take on ‘a life of its own’. In the yeast network my colleagues found that 40 per cent of node pairs that are correlated via information transfer are not in fact physically connected; there is no direct chemical interaction.
  • For some reason, ‘correlation without causation’ seems to be amplified in the biological case relative to random networks. There is no obvious relationship between the information pattern’s dynamics and the ‘circuit’ topology. Therefore, for many practical purposes, it pays to treat the information patterns as ‘the thing of interest’ and forget about the underlying network that supports it.
  • Of all the astonishing capabilities of life, Morphogenesis – the development of form – is one of the most striking. Somehow, information etched into the one-dimensional structure of DNA and compacted into a volume one-billionth that of a pea unleashes a choreography of exquisite precision and complexity manifested in three-dimensional space, up to and including the dimensions of an entire fully formed baby.
  • A ball of originally identical cells begins to differentiate into distinct cell types, partly under the influence of those elusive chemical morphogens that can evidently control gene switching.
  • All cells in your body have the same DNA. The information in DNA is referred to as the genotype and the actual physical cell is called the phenotype. So one genotype can generate many different phenotypes.
  • Some of the morphogens are responsible for causing undifferentiated cells to differentiate into the various tissue types – eyes, gut, nervous system, and so on – in designated locations. This establishes a feedback loop between cell differentiation and the release of other morphogens in different locations. It depends on the coupling between chemical networks and information-management networks. There are two causal webs tangled together and changing over time. All this is not just chemical gradients but physical forces – electric and mechanical – also contribute to morphogenesis.
Darwinism 2.0
  • Evolution operates on biological software just as it does on hardware.
  • Nobody can predict from a genomic sequence what the actual organism might look like, let alone how random changes in the genome sequence would translate into changes in phenotype.
  • Epigenetics is the study of all those factors which determine the forms of organisms that lie beyond their genes. Epigenetic factors drive the organization of biological information patterns and flows.
  • Physical mechanism significant in morphogenesis is known as Electro-transduction and deals with changes to an organism’s form arising from electrical effects. Most cells are slightly electrically charged. They maintain this state by pumping positively charged ions (mostly protons and sodium) from inside to outside through the membrane that encloses the cell, creating a net negative charge. Variations in voltage across large areas of the body serve as ‘pre-patterns’ – invisible geometrical scaffolds that drive downstream gene expression and thereby affect the path of development. Electrical pre-patterning appears to guide morphogenesis by somehow storing information about the three-dimensional final form and enabling distant regions of the embryo to communicate and make decisions about large-scale growth and morphology.
  • The centrepiece of Lamarckian evolution is that characteristics acquired by an organism during its lifetime can be inherited by its offspring. The most serious objection to the modern theory of evolution is that since mutations occur by “chance” and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs.
  • Stressed bacteria engineer their own high-speed evolution by generating genomic diversity on the fly. Clearly, evolution will work much better if the mechanisms involved are flexible and can themselves evolve – what is often called the evolution of evolvability.
  • Genomic Transpositions: Cells are able to monitor and actively edit their own genomes to a high degree of fidelity in an attempt to maintain the status quo. Segments of chromosomes can be transposed – switch places on the genome – a phenomenon popularly known as ‘jumping genes’. Cells are able to sense the presence in their nuclei of ruptured ends of chromosomes and then to activate a mechanism that will bring together and then unite these ends, one with another. When facing challenges, cells have many ways to ‘rewrite’ their genomes.
  • Adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.
  • The transition to multicellularity entailed a fundamental change in the logic of life. In the world of single cells, there is but one imperative: replicate, replicate, replicate! Multicelled creatures are made of cells that join the collective project. They die, and in return the organism takes on the responsibility to propagate the cells’ genes.
  • When individuals join a communal effort there is always vulnerability to cheating. There have to be layers of regulatory control, policed by the organism as a whole, to deter cheats. Cancer is a breakdown of the ancient contract between somatic cells and organisms, followed by a reversion to a more primitive, selfish agenda.
  • The Atavistic theory of cancer: it is not a product of damage but a systematic response to a damaging environment – a primitive cellular defence mechanism. It may be triggered by mutations, but its root cause is the self-activation of a very old and deeply embedded toolkit of emergency survival procedures. Cancer is a default state in which a cell under threat runs on its ancient core functionality, thereby preserving its vital functions, of which proliferation is the most ancient, most vital and most protected. Because cancer is deeply integrated into the logic of multicellular life, its ancient mechanisms highly conserved and fiercely protected, combating it proves a formidable challenge. Cells under stress turn cancerous by reawakening ancestral gene networks which, among other things, create a high rate of mutations.
  • Mutations in cancer cells are far from random: there are definite mutational ‘hotspots’ and ‘cold-spots’. Multicelled organisms work hard to protect key parts of their genomes, such as those responsible for running the core functions of the cell, and devote less resources to the ‘bells and whistles’ associated with more recently evolved and less critical traits.
  • Natural selection hasn’t eliminated the scourge of cancer. The ancient pathways and mechanisms that drive cancer fulfil the most basic functions of life.
Spooky Life and Quantum Demons
  • The secret of a quantum computer is something called superposition. A conventional (classical) computer a switch is definitely either on or off, representing 1 or 0. In a quantum computer it can be both a ‘superposition’ of 1 and 0. The superposition is not merely a fifty–fifty mix of the two numbers but all possible blends. This is a qubit (for ‘quantum bit’).
  • The phenomenon of electron tunnelling through organic molecules is actually quite widespread.
  • Enzymes connected with oxygenation, and the synthesis of the all-important energy molecule ATP, hinge on rapid electron transport. Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors.
  • Plant and photosynthetic bacterium use light to make biomass from carbon dioxide and water. The molecular complex that captures the photon and the reaction centre where the actual chemistry is done are not the same. Quantum interference effects seem to make a difference in the molecular complex responsible for photosynthesis.
  • Quantum-assisted energy transport: when the photon is absorbed it releases an electron from the antenna molecule (this is the familiar photoelectric effect), leaving behind a positively charged ‘hole’. Because the electron is embedded in a molecular matrix, it doesn’t fly off, free. Instead, it remains loosely bound to the hole in a very large orbit (delocalized). This arrangement is called an ‘exciton’. The exciton can itself behave in many respects like a quantum particle, with associated wavelike properties. It is this exciton, not an electron as such, that is passed. Constructive interference occurs across multiple molecules so that coherent excitons deliver the energy to the reaction centre before it can be dissipated into the molecular environment. A little bit of thermal noise can, paradoxically, boost the efficiency of energy transfer in the right circumstances.
  • All fundamental particles of matter possess a property called ‘spin’. Every electron has exactly the same amount of spin, as it does electric charge and mass. A moving electric charge creates a magnetic field. Even if an electron isn’t moving from place to place, it is still spinning, and this spin creates a magnetic field around it: they will respond to an external magnetic field. The electron will feel a force from the external field that will try to twist it so the poles oppose (north–south). When an external force acts on a spinning body, it doesn’t just swing round and line up, it gyrates – a process called ‘precession’. Most electrons are employed in atoms, and the internal electric and magnetic fields of the atom itself, arising from the nucleus and other electrons, swamp the Earth’s feeble field. An electron can displaced from the atom if the atom absorbs a photon. The atom’s magnetism weakens rapidly with distance from the nucleus, so the ejected electron will therefore gyrate differently when displaced.
  • Birds use a variety of methods to find their way around. A number of physicists claim that it is quantum physics that enables the bird to navigate, by allowing it to see the field. The bird’s eyes are being assailed by photons all the time. Somehow, the light-disrupted electrons have to engage in some chemistry to send a signal to the bird’s brain. Experiments suggest that the birds combine visual and magnetic data when making decisions on which way to go. Doubling the ambient magnetic field strength initially disrupts the bird’s directional sense, but somehow recalibrated their magnetic apparatus to compensate. Combining the results of many experiments with different frequencies and ambient light conditions shows the presence of a resonance – a familiar phenomenon in which the energy absorbed by a system spikes at a certain frequency.
  • The sense of smell: inside the nose are legions of molecular receptors – molecules sporting cavities of many different specific shapes. If a molecule in the air has a complementary shape, it will bind to the corresponding receptor. A signal is sent to the brain: this is the simple lock-and-key model. But in addition to a molecule’s size and shape, its vibrational signature might come into the story.
  • The electron that tunnels serves to communicate the docking molecule’s identity by absorbing a quantum of energy from the vibration. It’s all down to vibrational patterns rather than the shapes of molecules as such.
  • A quantum computer’s power rises exponentially with the number of entangled components.
  • Maxwell’s demon evades the degrading effects of entropy and the second law by turning random thermal activity into stored bits of information. The complexity of biological systems often precludes any simple way to untangle wavelike quantum effects from familiar classical vibrational motion, leaving most of the experiments done so far open to alternative interpretations.
Almost a Miracle
  • By coupling patterns of information to patterns of chemical reactions to achieve a very high degree of thermodynamic efficiency, life conjures coherence and organization from molecular chaos.
  • The evidence tells us that life was established on Earth by 3.5 billion years ago, but it gives little clue as to when life may have actually started.
  • There is no compelling evidence that terrestrial life started on Earth.
  • It has been estimated that some hardy radiation-resilient microbes could survive for millions of years inside space rocks.
  • Today, complex organisms require oxygen for their metabolism, but this was a late development. There was very little free oxygen in the atmosphere before about 2 billion years ago. Oxygen is a highly reactive substance that attacks and breaks down organic molecules. The truly essential element is carbon, the basis of all organic chemistry, and an ideal choice because of the limitless variety of complex molecules it can form.
  • A popular suggestion is that the first steps towards life happened in the vicinity of volcanic vents under the ocean. Genetic sequencing suggest that heat resilience is a very ancient feature of terrestrial biology.
  • The distinctive character of life is its ability to store and process information in an organized manner.
  • Nobody knows how life began! The pathway from non-life to life is not known. Once life gets going, natural selection can ratchet up the gains and DNA storage can lock them in. But chemistry without natural selection has no recourse to such mechanisms.
  • The backsliding problem afflicts almost all studies of the complexification pathway to life. Many clever experiments and theoretical analyses demonstrate the spontaneous formation of complexity in a chemical mixture, but they all hit the same issue: How does a chemical broth build on some spontaneously emerging complexity to then ramp up to something even more complex? And on and on.
  • Had life not started quickly, there wouldn’t have been time for it to evolve as far as intelligence before Earth became uninhabitable, fried to a crisp by the steadily increasing heat of the sun. (In about 800 million years the sun will be so hot it will boil the oceans.).
  • It’s entirely possible that the origin of terrestrial life was an extreme outlier, an immense fluke.
  • Life as we know it has three fundamental features: genes, metabolism and cells. One of the challenges in origin-of-life research is to decide what came first.
  • All the laws of physics and chemistry discovered so far are ‘life blind’ – they are universal laws that care nothing for biological states of matter.
  • If life does indeed get going easily, then surely it should have started many times on Earth. If it exists, an alien microbial population would be dubbed a ‘shadow biosphere’.
  • The history of evolution contains other major transitions such as Eukaryogenesis, sex and multicellularity. These are all reorganization of informational architecture.
The Ghost in the Machine
  • The phenomenon of consciousness is arguably the hardest problem facing science today and the only one that remains almost impenetrable even after two and a half millennia of deliberation.
  • It is tempting to suppose that some aspect of information will form a bridge between mind and matter, as it does between life and non-life. Somehow our mental world couples to the physical world through our brains.
  • The Turing test attributes consciousness purely by analogy. But isn’t that precisely what we do all the time in relation to other human beings?
  • An important feature of consciousness is awareness of surroundings and an ability to respond appropriately to changes.
  • Most of what the brain and associated nervous system does is performed unconsciously. Sensory signal processing and integration, searching memory, controlling motor activity, keeping the heart beating. Many regions of the brain tick over just fine when someone loses consciousness.
  • Distilling the problem: What sort of physical processes generate consciousness? Given that minds exist, how are they able to make a difference in the physical world? How do minds couple to matter to give them causal purchase over material things? This is the ancient mind–body problem.
  • If the informational basis of mind is right, then minds exist in the same sense that information exists. But we cannot disconnect mind from matter. Information is physical.
  • Time’s passage is an integral part of self-awareness. Everyday processes possess an inbuilt directionality in time.
  • It has been estimated that there could be as many as 1,000 trillion connections in the human brain. Neurons can ‘fire’ (send pulses down axons) at a frenetic rate – maybe fifty times a second. The brain does all that work with the same thermal output as a single low-wattage light bulb!
  • Whereas the electrical signals in a computer (or the power grid) consist of electrons flowing down wires, the analogue of the wires in the brain – the axons – operate very differently. Specialized proteins select different ions or "voltage gated ion channels". These open and close a gate to let the right ions through and shut out the wrong ones. This creates an electrical signal propagating down the axon. Neurons signal each other electrically via a travelling wave of polarity and not via a flow of electrical current.
  • The wiring architecture of the brain changes according to the individual’s experiences.
  • An attempt to define a type of Integrated Information as a measure of consciousness has been made by Giulio Tononi. The central idea is to capture in precise mathematical terms the intuitive notion that, when it comes to the brain, the whole is greater than the sum of its parts. Viewed from the outside, it will usually not be possible to deduce the circuit layout simply by examining the cause–effect relationship between inputs and outputs. Suppose you use a pair of cutters to sever some wires in the network. If a few snips dramatically alter the outputs, the circuit can be described as highly integrated.
  • Being a causally autonomous entity from the intrinsic perspective requires an integrated cause–effect structure; merely “processing” information does not suffice.
  • A fully deterministic, mechanistic universe has no room for free will; the future is completely determined by the state of the universe today. If the world is a closed mechanical system, then invoking a physical role for mind looks like a lost cause because it would imply Over-determinism (something being determined twice by two different things).
  • Maybe consciousness can indirectly affect atoms by loading the quantum dice? Unfortunately this would still amount to a violation of the laws of quantum mechanics in a statistical sense.
  • How does purpose, or, goal-oriented behaviour, emerge from atoms and molecules that care nothing about goals?
  • There is room for parallel narratives, one at the atomic level and another at the agent level, without contradiction, so long as the system is open. Tononi’s integrated information theory shows that not only is a higher-level description simpler, but higher-level systems can actually process more information than their components. There can be causal relationships that exist solely at the level of agents. The macroscopic states of a physical system (such as the psychological state of an agent) that ignore the small-scale internal specifics can actually have greater causal power than a more detailed, fine-grained description of the system, a result summed up by the dictum: ‘macro can beat micro’.
  • Quantum indeterminism can’t explain deterministic wills.
  • The Measurement Problem: at the atomic level, things get weird and fuzzy. When a quantum measurement is made, however, the results are sharp and well defined. A handful of physicists suggest that the ‘concretizing factor’ might be the mind. Integrated information, denoted Ф, provides a way to link quantum mechanics to consciousness. An atom has a very low Ф but, if the atom is coupled to a measuring device, then the Ф of the whole system might be large. Left alone, the atom would simply obey the normal rules of quantum physics, but for a sufficiently complex system with significant Ф would become important, eventually bringing about the wave function’s collapse.
  • It is impossible to derive the laws of information from the known laws of physics.
  • Laws that change as a function of the state are a generalisation of the concept of self-reference: what a system does depends on how a system is.

These notes were taken from Paul's book.
Find out more about Paul on Wikipedia

© 2020 Cedric Joyce