ADVENTURES IN MECHANICAL THINKING – Machines can learn, at least a little. With scientific advances they will continue to become smarter, and eventually may discover and perceive the world in their own way.
AFFINITY – The formation of structure in the universe — the coalescence of atoms into stars and planets and galaxies — is a type of self-organization or self-assembly. At the micro scale this self-assembly induces nuclear and chemical reactions that give rise to the molecules and materials that make our lives possible. The mathematical theories of self-assembly and chemical reaction networks help us understand the basis for such self-organization and how it can create complex and purposeful systems.
A FIRST TASTE – Exposure at a young age to the joy of discovery can cause serious imprinting and make a life-long impression upon one’s curiosity factor.
AGAINST ALL ODDS – Occasionally someone’s life story may seem scripted or contrived to the point of being impossible – a series of extraordinary events, coincidences, great hardships and crucial choices leading to that person’s unique work and expertise, as if by recipe.
ALMOST REAL – Mathematical abstractions never look exactly like the real thing, but they are often as powerful, and frequently more illuminating.
ANDY ELLINGTON – We can’t know how life started on Earth or how it starts elsewhere, but exploring how simple chemicals assemble, react, and evolve in the laboratory gives scientists an enriched and more grounded imagination for what the first organisms may have been like — and has already led to interesting biotechnologies.
A PREPARED MIND – Often the best scientific result is the simplest. A solution or discovery may, with hindsight, be so uncomplicated and obvious that it’s surprising, or elegant. Yet to approach that simple truth may have required sophisticated instruments and complex methods to explore thousands of possibilities.
A RIP IN THE FABRIC – Self-healing objects are capable of repairing damage to their structure. They range from simple (e.g. water) to complex (e.g. a salamander’s tail). In molecular biology, self-repairing fragments are good candidates for mutation, and therefore evolution. The process of mathematical discovery may itself be self-healing, as it balances the confusion caused by real-world paradoxes.
AUTODIDACT – Some of the most precious things in science – and in life – are an ability to learn for yourself, to tap into your own unique perspective and interests, and to do it with a sense of joy.
BUTTERFLY’S PATH – Eventually, one must leave the safety of home and set out to make their way in the world, where one’s eyes are opened by possibilities and dangers, by the edifices left behind by their predecessors, and by the wonders of life’s machinery.
CAPTURED – It’s hard to catch a molecule; they’re too fast and too small. So scientists get others to catch them by making molecules to catch molecules. Then they can be studied and programmed.
CEPHALOPOND – Computer programmers can be quite imaginative. The term “bug” itself is a fanciful metaphor. Some programmers have bugs in their programs; others have cuttlefish.
CITY OF LIFE – Entire organisms – be they trees, whales, frogs, or humans – develop from a single cell. When cells divide, each half innately ‘knows’ which part of the organism it should become next.
COME TOGETHER – Each of 100 trillion cells in your body has its own DNA, its own molecular factory for building proteins, and its own biochemical circuitry for making decisions. Though self-contained, these cells depend upon each other, and function together as a unified whole. Some species, such as slime molds, live as independent single-celled organisms in their early life, then unify with other slime mold cells into a multicellular organism for the latter part of their life. Roboticists may one day develop small robots that can similarly assemble themselves into a larger, unified meta-robot.
COMPRESSION – Squeezed light (photons whose vibrations are constrained relative to normal light) can be manufactured in the laboratory.
CONSONANCE AND DISSONANCE – Some ideas, like topology and knot theory, are so simple and pure, yet endlessly applicable, that they can entrance one into endless wondering, or even lead a scientific career to new lands.
CORE CONCEPTS – Organisms and their parts somehow ‘know’ when to stop growing. As computers count in an algorithmic, logarithmic or binary way, so does biology ‘count’ in its own biochemical way.
CYTOSKELETAL MOTOR – A cell’s cytoskeleton consists of a network of molecular-scale “I beams” that hold the cell in its shape. Some engineered cells can crawl by growing their cytoskeleton on one side while dissolving it on the other side.
DATA DANCER – DNA microarray chips allow doctors and scientists to read the internal workings of a cell. A single chip can have hundreds of thousands of pixels, each of which can detect the presence of RNA for a specific gene, or a certain genetic mutation. This information can lead to novel discoveries and insightful diagnoses.
DIGITAL HEALER – A microfluidic chip is a network of tubes, valves, reaction chambers and sensors packed into a small device capable of making sophisticated medical diagnoses.
DISCRETIZATION – The technological shift in electronics from analog to digital was paralleled by a paradigm shift in mathematics, with discrete and combinatorial maths replacing traditional continuous analytical maths. Continuous objects are now converted to discrete representations for processing on digital computers.
DRAGONFLIES – Objects exchange molecules upon contact. Residue left by each can start a new growth pattern, such as crystallization, on its new host.
DROPLET – Biochemical experiments often require tiny volumes of liquid – microliters, or less…a fraction of a raindrop.
ENTANGLED REALMS – After over a century of theories about quantum mechanics, and their experimental validation, scientists still grapple with the nature of reality. What is superposition, or probability, or entanglement? Where are we, within it? Perhaps they’re missing a shortcut which might give them easy access to wondrous and vibrational worlds.
500 YEAR PLAN – Interstellar travel could conceivably be managed by self-assembling spaceships, which would land on a convenient planet or meteor, assemble new parts from available raw materials, make repairs, and be on their way again.
FLOATING STILL LIFE – Those who have an instinct for assessing and doing what needs to be done, and for taking care of others’ needs, lift the spirits and improve the lives of those around them.
FLUORESCENCE – When light bombards a molecule, a photon may be absorbed, in which case the extra energy causes the molecule’s bonds to vibrate more vigorously. Some of that extra vibrational energy dissipates into the molecule’s surroundings as heat. If the energy is not completely dissipated, the vibrations may align to create and emit a new photon with lower energy and a (usually) longer wavelength; that is, they fluoresce.
FORCE OF IMPOSSIBILITY – In mathematics, one can define objects (such as sets or functions) that are impossible to compute. Yet these impossible objects can provide insight that clarifies what’s possible.
FOREST OF WIRES – Nature builds powerful computers, your brain being a prime example. Molecular self-assembly allows scientists to create electrical circuits by growing them.
FORGING AHEAD – Ideas and insights can appear as beautiful and fragile things.
FRAGMENTED VISION – In the brain, visual scenes are broken down into elementary pieces – edges, colors, corners, motion – from which more complex perceptions are derived – textures, shapes, actions – and eventually the important features of the scene are recognized. As with dreaming, a deeper look into the visual cortex reveals an even finer disintegration of each piece of a scene, pixelated and then reconstructed inside an observer’s head.
GOING BEYOND – Thrill seekers love to probe the unknown. For some, it’s the fresh powder on the slope of an uncharted mountain. For others, it’s the unexpected terrain of a new scientific field. For a few, it’s both.
GRÜN – The elegance of simplicity is a coveted end in scientific communities across time, place, and field of research. “What can be done with less is done in vain with more.” Willem of Occam
HANGING GARDENS – Molecular engineers can design and synthesize complex polymers that grow in almost lifelike ways. Like a spider, an engineered molecule can trigger insertion of polymer subunits behind it, thus effectively “excreting” a thread to which it remains attached. As engineering frontiers expand, even more lifelike behaviors will be attainable.
HATCHLING – With determination, and great patience, the seeker is often rewarded with the discovery of unique and surpassing results.
HEAT CAPACITY – To power nanomachines, a molecular fuel must store energy in a stable form – stable until it’s released.
HOMUNCULUS – As intelligent beings who learn from their environment, we contain within ourselves mirrors of the world, and even mirrors of ourselves. One remarkable example is that if you look at the brain’s sensory and motor cortex and ask what part of the body it pertains to, you get a (distorted) map of the body.
IF YOU DARE – Scientific investigation is never complete. From the vantage point of new experience and knowledge come new directions of pursuit.
INNER LIGHT – Intuition becomes stronger with use and nurture, and has a powerful way of breaking through the conventions and constrictions imposed by traditional approaches.
INNER SCAFFOLDING – Vestiges and fundamental qualities of our earliest ancestors remain encoded within us today. Whether plant or animal, fungus or virus, each living thing culminates out of a very long chain, bringing information from primordial times.
INSIDE OUTSIDE – Your brain hasn’t always known that your arm is your arm. It may have learned it the same way that someone with a prosthetic limb learns to experience the artificial limb as part of their own body. Extensive tool-use (imagine a racquetball racket, violin, or even a mechanized prosthetic) can also lead to the sense of the tool or machine being a part of your body.
INSTANTIATION – Computer programs must constantly create new data objects as they are needed. Often a standard template is used, and various numeric, textual, or algorithmic elements of the form are filled in to build the specific object of interest. To understand the world around us, the mind similarly creates new ideas by filling in general cached templates with information about the matter at hand.
INTERMINGLING – Intermingling matter on all levels, from neutrinos to the cosmos, necessarily exists in a container. The nestling importance of ’empty’ space is often overlooked simply because it ‘isn’t there.’
I WAS SO INVOLVED – Scientists and artists become absorbed in their work, forgetting to eat, or losing track of time, place and (when it’s really good) even self.
JOINING/SCISSION – Some scientists believe that free-range, pre-life organic molecules spontaneously joined together to make the first organisms. Joining and scission can be seen in the laboratory when scientists create self-assembling nanotubes known as `living polymers.’
KELP FOREST – On the surface of a DNA chip used to prototype an artificial cell, DNA strands are tethered to a ground, enzymes crawl up and down the strands, synthesizing new molecules that float away slowly. Some areas are active and crowded; later, the wave of activity will move along.
LET’S DO THIS – Throughout evolutionary history an astounding variety of life forms have been chanced upon, most of which would look alien and bizarre to us now. During the Cambrian era over 500 million years ago, many animals with very strange body plans and weird appendages (as strange and weird as ours might seem to them) evolved. Each of the life kingdoms that we know today — the protists (single-celled eukaryotes), monera (prokaryotes), archaea, fungi, plants, and animals — began with a unique distant ancestor.
MAPLE LEAF – In science, you can seldom directly see what you’re studying. Experimental results are colored by how a question is posed and what experimental apparatus is used. This issue is particularly prominent in quantum physics.
MIGRATORY PROCESSION – Distributed molecular robots are herds of simple machines communicating with each other to accomplish collective tasks. Like ants, these robots can attach to each other to form chains or walk on top of one another to create collective superstructures.
MOLECULAR FIELDS FOREVER – At the human scale, a flat surface is a simple thing. But closer in, its incredible complexity becomes apparent. Molecular engineering can control some of that complexity, using self-assembly to coat the surface and place complex molecules in specific locations.
MOLECULAR INTROSPECTION – When informational molecules such as DNA, RNA, and proteins fold from a floppy linear chain into a concrete shape, such as an enzyme or other nanomachine, the process is directed by subsequences along the chain that search for matching subsequences elsewhere in the chain, and then bind and lock up to stabilize the fold.
MYMOSH THE SELF BEGOTTEN – In a short story by Stanislaw Lem, Mymosh accidentally came into being when a jettisoned object from a passing spaceship rattled a post-nuclear garbage dump, causing various objects to tumble, collide, and attach, forming a thinking being.
NEUROTANGO – When listening to music, neurons in your ears encode the sounds into a sequence of electrical signals, called spike trains, that record the rhythm, tones, and texture of what you’re hearing. The spike trains are sent to your cortex, where the sounds are perceived, enjoyed, and interpreted.
NERVE CREATURE – Organisms envelope a self-contained informational unit awash in currents and forces, processing, deciphering, and responding to their environment. To create neural networks and analyze their behavior scientists must swim in the interconnected mathematical theories of information, computation, optimization, and adaptation.
959 – The nematode Caenorhabditis Elegans is mathematically unique in that wild-type individuals contain exactly 959 cells. The position of each cell is also precisely determined. C. Elegans is transparent, so cell function and lineage are easy to track.
NOTES TO SELF – A variety of communications, such as laughter, a wave, or a sigh, are readily understood by just about anyone, and even by some animals. Other signs and signals are more esoteric, perhaps only understood by just one or a few.
PHYSICS IN FORMATION – Upon entering the brain, visual information is separated into facets — depth, color, motion and so on — that is then processed and recombined into conscious awareness of a seamless reality. Similarly, the physical world comprises facets of heat, mass, motion, light, and vibrations that are seamlessly combined and entangled to form the world around us.
PORTRAIT OF PETER GACS – Ever since Pythagorus, and likely before, mathematicians have seen the world as being composed of numbers, and that has led to great insights.
PROCESS OF ELIMINATION – Advanced medical therapies involve molecular robots programmed to ‘crawl’ around the outside of targeted cells (such as cancer cells) after recognizing diagnostic cell-surface markers that identify them as malign. As the molecule interacts with the cell membrane it effectively cuts it open, destroying the cell.
QUANTUM BRIDGES – An essential part of working at the interfaces of science and technology is the ability to correlate phenomena at different length scales, where we are forced to think about matter and its properties in different ways.
RAINBOW FIBER – Interdisciplinary science requires an ability to synthesize many strands of knowledge, to bind them together and test their strength, then extract pertinent information.
RAIN OF ABSTRACTIONS – Technical problems are often solved by working out solutions to complex equations. In some areas of computer science, the most elegant solution to a problem is reached simply by defining the right abstract representations of data and processes, for a surprisingly simple solution.
REACTION – DIFFUSION – Chemical processes can create patterns similar to the spots on leopards, the patchwork on giraffes, the stripes on zebras. More complex patterns could be created if chemistry could be programmed.
REARRANGEMENTS – Self-assembly is a process that spontaneously creates order. At the molecular scale, self-assembling components don’t ‘know’ where to go – but they get there. Particles combine and settle in so many ways, randomly fitting together, that eventually, bit by bit, they become complex and can build even further.
RECURRENCE – Control theory studies how feedback loops between sensors and actuators can be used to make robust responsive systems, from a car’s cruise control to robots in a factory, or biochemical circuits within a cell.
ROCK NEST – Behind a seemingly impenetrable barrier is often a calm place of quiet sustenance; getting there may be easier, if more circuitous, than one thinks.
ROCK WHISPERER – Computer chip technology is basically artificial geology. Lithography, the technique used to carve wires and transistors into a silicon chip, can build many layers of structures on a slab of silicon, but to truly master the art of turning inanimate rock into a thinking machine requires understanding the nature of the material. It will tell you what it can do; listen to the silicon.
SEEKING THE SOURCE – A simple bacterium, only a micron in size, can find sustenance (say, sugar) by “smelling” its odor. It swims in a random direction and, if the smell gets stronger, it keeps going; if not, it tries a new direction, eventually reaching the source. Similarly, scientists may catch the glimpse of a higher truth from individual experiments, and blindly do the same.
SEIFERT’S WORLD – If you draw a random squiggly line on paper and, at the intersections clarify which part goes over and which goes under, there is, imaginably, a surface contained within your squiggle. A thin wire bent into a twisted but closed curve and dipped into soapy water reveals such a surface.
SELF ASSEMBLING TREE – Self-assembly is a ubiquitous process at the molecular scale (crystals, viruses, cytoskeletons) and macroscopic scale (dust bunnies, sand dunes, stars). Tree forms are also ubiquitous in nature, and are self-organizing at many scales (rivers, carbohydrates, traffic patterns). These universal forms can be found seemingly anywhere.
SHADOW OF PERFECTION – Mathematics studies perfect objects – the Platonic ideal – but often the proofs can be messy and confusing.
SIGHT – The retina is a complex network of neural cells that detect light and immediately begin signal processing to reduce noise, increase sensitivity, and identify regions of contrast and motion. While the insect eye consists of a regular hexagonal grid of nearly identical cells, each with its own lens and neurons, a mammal’s eye has a single lens and many somewhat irregularly spaced photoreceptor neurons.
SILENT NIGHT – Preparing a sample for atomic force microscopy, complex self-assembled molecules settle onto a mica surface, where they will soon be imaged. (Also see “Wings.”)
SKY AND EARTH – In our multifaceted lives, those things which anchor us to the earth, which ground us and provide a base, can allow our subtle minds to roam, to dream, and to visit faraway realms in our thoughts. Here thoughts and sensations travel faster than light.
S. S. S. – For all you see, there is more you don’t yet see. Science is driven by the perception of the invisible and the unknown.
STILL LIFE WITH ACTINOLITE – The naturalist feels an affinity to the myriad products of nature in all their peculiarity and beauty. Each of us being unique, we’re attracted to, or intrigued by a different set of textures, processes, functions, values, and colors of things. These things and combinations affect us in silent and invisible ways, shared across humanity.
STILL LIFE WITH PLUMS AND CHOCOLATE – When a new lab gets started, it’s important to keep it fueled with enthusiasm, energy, and especially midnight snacks.
SWARM AND FORM – An individual is a self-organized collection of smaller individuals. There are often two parts: global interactions of roving elements (such as bees or blood cells) and local arrays of geometrically arranged elements (such as nests or brain cells).
SYNCHRONIZATION – Groups of cells (neurons, heart muscle, slime molds, bacteria) and groups of organisms (a flock of birds, a school of fish, a colony of ants, or a tree of fireflies) can work together in concerted ways organized by spontaneous synchronization, following collective signals and patterns generated and perceived only by their group.
TENSEGRITY – Some structures are made from strings and struts, (like a suspension bridge, or the bones and tendons of living creatures) where every strut is separate, and every cable is pulled taut in such a manner that the structure doesn’t collapse. The tensional integrity of an object or system derived from the balance of tension members, as opposed to compression struts, is its tensegrity, aka: floating cohesion.
TERRESTRIAL MATRIX – A.G. Cairns Smith hypothesizes that clay crystals begat life. The crystalline latticework, as it grew and broke apart, provided scaffolding for new crystal growths. As these crystals incorporated more organic molecules into their structure, with reproductive advantage, the organic molecules eventually became sophisticated enough to co-opt their host’s matrix and float away, perhaps on the next tide, as autonomous life. (Also see ‘The Loss of Entropy’)
THE BEST OF ALL POSSIBLE WORLDS – The principle of least action states that, of all possible paths a particle, such as a photon, could take, it will take the one with minimal integrated energy. Analogous optimization principles are used in software that finds the best route from place A to place B, finds the best price for a concert ticket, or finds the most likely interpretation of data.
THE BREWERY – Many great and inspired ideas have occurred to thinkers while completely disconnected from their mental task. A long sought-after idea or solution may spontaneously surface during a moment of relaxation and distraction, an “Aha!” moment.
THE HURDLER – In the exploration of unknown frontiers, you never know what surprises will come up next. With persistent curiosity and careful thinking, clearly defined facts emerge from the chaos of multiple variables and experimental uncertainty.
THE LOSS OF ENTROPY – Life may have arisen from naturally occuring mineral crystals that replicated by spontaneous mineralogical processes, eventually providing the framework for, and stimulating the production of organic molecules which form the basis for modern organisms. (Also see ‘Terrestrial Matrix’)
THE FORCE OF IMPOSSIBILITY – In art and science, acheiving a given outcome is one small part of a long process. Desired outcomes are there to be realized, and with discipline and perseverance, they’ll eventually be attained. [would like to work this into the blurb:]The fastest and shortest algorithm for all well-defined problems.
THE MIRACLE OF SOOT – Nanotubes and Buckyballs (named after Buckminster Fuller) are atomic-scale, chicken-wire-like mesh cages, whose remarkable properties allow intriguing fundamental science and new technological applications. Found in the soot of burnt carbonaceous material they, like diamond, coal, and graphite, are formed by natural processes.
THE PATH THAT KNOWS – Crystals can grow in surprisingly complex ways. Synthetic bismuth crystals grow as square-angled spiral staircases. With the ability to design macromolecules, it’s now possible to create crystals with a programmed growth path, and which can “intelligently” respond to obstacles it encounters.
THETA BAY – During sleep, neural activity becomes quite different from when you’re awake. Isolated from the outside world, the brain slips into a progression of rhythmic modes, and waves of activity sweep across brain structures, changing through each sleep and dream stage. As you wake, these rhythms reorganize to encounter your waking reality.
THE WEAVER – With the right insight and careful touch, DNA can be programmed to assemble itself into incredibly complex nanoscale objects called ‘DNA origami’.
TINKER’S MOLECULAR WORKSHOP – Synthetic biology is the engineering and construction of molecular devices that work inside cells. The construction materials are restriction enzymes to cut DNA, polymerases to copy DNA and RNA, ribosomes to translate RNA into protein, and myriad chemical tricks for finishing touches.
TREASURE CHEST – All material objects are made of just one thing: atoms. If you could separate the atoms in one object, and put them back together again with extreme precision, you could make another object.
UNDECIPHERABLE – It’s a simple matter to tie a complex knot, or set a combination or code. It’s much harder to untie the knot or crack the code.
VASE MAKERS – People have long used biological materials — skin, hair, bone, wood — as the building material for crafting technological marvels — leather boots, wool sweaters, ivory knives, sail boats. Today we’re able to use biological polymers such as DNA, RNA, and protein to craft marvels at the molecular scale as well.
WATERFALL – Autonomous robotic vehicles process a bewildering cascade of information from cameras, sonars, gyroscopes, and many other sensors. Locally, the information is noisy; only when the whole scene is considered do the pattern and meaning emerge.
WHAT DREAMS ARE MADE OF – Molecules, molecular systems, and materials can be simulated and designed on computers, allowing visionary scientists to imagine and create environments from atoms on up.
WINGS – The Sierpinski gasket is a mathematical fractal constructed by repeatedly cutting the middle out of each triangle. Or, more akin to crystal growth, it may be generated by starting with a layer of 0′s with a single 1, then building new layers by placing a 0 above and between each pair of identical bits, while placing a 1 above and between each pair of differing bits.
ZOO OF PEARLS – In an emulsion, water droplets become surrounded and separated by oil. Each water droplet can be filled with a different set of (perhaps random) molecules, whose behaviors can then be observed. Scientists can use these droplets to run millions of tiny experiments in parallel.
ADVENTURES IN MECHANICAL THINKING – Machines can learn, at least a little. With scientific advances they will continue to become smarter, and eventually may discover and perceive the world in their own way.