Cybernetics!

Sunday, February 1, 2009

Synthetic biology

Synthetic biology is a new area of biological research that combines science and engineering in order to design and build ("synthesize") novel biological functions and systems.

A light programmable biofilm made by the UT Austin / UCSF team during the 2004 Synthetic Biology competition, displaying "Hello World"

History of the term

In 1974, the Polish geneticist Waclaw Szybalski introduced the term "synthetic biology", writing: Let me now comment on the question "what next". Up to now we are working on the descriptive phase of molecular biology. ... But the real challenge will start when we enter the synthetic biology phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes. This would be a field with the unlimited expansion potential and hardly any limitations to building "new better control circuits" and ..... finally other "synthetic" organisms, like a "new better mouse". ... I am not concerned that we will run out exciting and novel ideas, ... in the synthetic biology, in general. When in 1978 the Nobel Prize in Physiology or Medicine was awarded to Arber, Nathans and Smith for the discovery of restriction enzymes, Waclaw Szybalski wrote in an editorial comment in the journal Gene: The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes, but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated. Nevertheless, the term was largely unused or abandoned until the early 21st century (e.g., SB1.0, the First International Meeting on Synthetic Biology, was held in 2004).

Biology

Biologists are interested in learning more about how natural living systems work. One simple, direct way to test our current understanding of a natural living system is to build an instance (or version) of the system in accordance with our current understanding of the system. Michael Elowitz's early work on the Repressilator is one good example of such work. Elowitz had a model for how gene expression should work inside living cells. To test his model, he built a piece of DNA in accordance with his model, placed the DNA inside living cells, and watched what happened. Slight differences between observation and expectation highlight new science that may be well worth doing. Work of this sort often makes good use of mathematics to predict and study the dynamics of the biological system before experimentally constructing it. A wide variety of mathematical descriptions have been used with varying accuracy, including graph theory, Boolean networks, ordinary differential equations, stochastic differential equations, and Master equations (in order of increasing accuracy). Good examples include the work of Adam Arkin, Jim Collins and Alexander van Oudenaarden. See also the PBS Nova special on artificial life.

Chemistry

Biological systems are physical systems that are made up of chemicals. Around 100 years ago, the science of chemistry went through a transition from studying natural chemicals to trying to design and build new chemicals. This transition led to the field of synthetic chemistry. In the same tradition, some aspects of synthetic biology can be viewed as an extension and application of synthetic chemistry to biology, and include work ranging from the creation of useful new biochemicals to studying the origins of life. Eric Kool's group at Stanford, Steven Benner's group at Florida, Carlos Bustamante's group at Berkeley, and Jack Szostak's group at Harvard are good examples of this tradition.

Engineering

Engineers view biology as a technology. Synthetic Biology includes the broad redefinition and expansion of biotechnology, with the ultimate goals of being able to design and build engineered biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health and our environment . A good example of these technologies include the work of Chris Voigt, who redesigned the Type III secretion system used by Salmonella typhimurium to secrete spider silk proteins, a strong elastic biomaterial, instead of its own natural infectious proteins. One aspect of Synthetic Biology which distinguishes it from conventional genetic engineering is a heavy emphasis on developing foundational technologies that make the engineering of biology easier and more reliable. Good examples of engineering in Synthetic Biology include the pioneering work of Tim Gardner and Jim Collins on an engineered genetic toggle switch, the Registry of Standard Biological Parts, and the International Genetically Engineered Machine competition (iGEM).

Re-writing

Re-writers are Synthetic Biologists who are interested in testing the idea that since natural biological systems are so complicated, we would be better off re-building the natural systems that we care about, from the ground up, in order to provide engineered surrogates that are easier to understand and interact with. Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software. Drew Endy and his group have done some preliminary work on re-writing (e.g., Refactoring Bacteriophage T7). Oligonucleotides harvested from a photolithographic or inkjet manufactured DNA chip combined with DNA mismatch error-correction allows inexpensive large-scale changes of codons in genetic systems to improve gene expression or incorporate novel amino-acids (see George Church's and Anthony Forster's lab synthetic cell projects. As in the T7 example above, this favors a synthesis-from-scratch approach.

Human practices: Emerging social, ethical, legal challenges

In addition to numerous bioscientific challenges, the vast potential of synthetic biology to play a formative role in contemporary human life raises new questions for bioethics, biosecurity, biosafety, health, energy and intellectual property. To date considerable focus has been given to the so-called dual-use challenge. For example, while the study of synthetic biology can lead to more efficient ways to produce cures (e.g. against malaria), it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox). In addition, scientists, funders, policymakers, ethicists and others have recognized challenges presented by a post 9/11 political milieu. A new range of potentially malicious actors and actions (i.e., terrorists/terrorism) must now be taken into account by those seeking to govern scientific domains; and the internet and other new media provide global access to technological know-how and scientific knowledge. Such global access cannot be addressed using existing models of nation-specific regulation.(New Scientist, November 12, 2005). Some detailed suggestions for licensing and monitoring the various phases of gene and genome synthesis are beginning to appear. Other initiatives, such as OpenWetWare, diybio, biopunk, biohack, and possibly others, take a more proactive approach towards the proliferation of open source synbio projects.

There is also an ongoing, comprehensive, and open online discussion of so-called “societal issues” online at OpenWetWare, at the SYNBIOSAFE forum on issues regarding ethics, safety, security, IPR, governance, and public perception (background document).

Recently, efforts have been made to think beyond the “societal issues” model of ethics, politics, and science in relation to synthetic biology. This effort refuses the established convention of imagining society outside of and downstream of scientific practices, such that bioethics is assigned the task of limiting the negative impact of science on society. By contrast recent approaches focus on the integral and mutually formative relations among scientific and other human practices. These human practices approaches attempt to invent ongoing and regular forms of collaboration among synthetic biologists, ethicists, political analysts, funders, human scientists and civil society activists. To date collaborative work on “governance” or “society” or “ethics” in relation to synthetic biology has largely consisted either of intensive, short term meetings, aimed at producing guidelines or regulations, or standing committees whose purpose is limited to protocol review or rule enforcement. Such work has proven valuable in identifying the ways in which synthetic biology intensifies already-known challenges in rDNA technologies. However, these forms are not suited to identifying new challenges as they emerge. An example of efforts to develop ongoing collaboration is the Human Practices component of the Synthetic Biology Engineering Research Center (SynBERC), an NSF funded collaboration among a number of leading research universities. In Europe, the multi-partner project SYNBIOSAFE, coordinated by IDC, is investigating the biosafety, biosecurity and ethical aspects of synthetic biology. The International Consortium for Polynucleotide Synthesis was formed in 2006 to encourage sharing of ideas and resources for pro-actively monitoring synthetic gene orders and enforcing safe practices, (ICPS). The recently formed Industry Association Synthetic Biology (IASB) has also started to tackle open biosecurity problems for biotech companies doing gene synthesis.

Key enabling technologies

There are several key enabling technologies that are critical to the growth of synthetic biology. The key concepts include standardization of biological parts and hierarchical abstraction to permit using those parts in increasingly complex synthetic systems. Achieving this is greatly aided by basic technologies of reading and writing of DNA (sequencing and fabrication), which are improving in price/performance exponentially (Kurzweil 2001). Measurements under a variety of conditions are needed for accurate modeling and computer-aided-design (CAD).

Sequencing

Synthetic biologists make use of DNA sequencing in their work in several ways. First, large-scale genome sequencing efforts continue to provide a wealth of information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, synthetic biologists use sequencing to verify that they fabricated their engineered system as intended. Third, fast, cheap and reliable sequencing can also facilitate rapid detection and identification of synthetic systems and organisms.

Fabrication

A critical limitation in synthetic biology today is the time and effort expended during fabrication of engineered genetic sequences. To speed up the cycle of design, fabrication, testing and redesign, synthetic biology requires more rapid and reliable de novo DNA synthesis and assembly of fragments of DNA.

In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the first synthetic organism. This took about two years of painstaking work. In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks. In 2006, the same team, at the J. Craig Venter Institute, has constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and is working on getting it functioning in a living cell.

In 2007 it was reported that several companies were offering the synthesis of genetic sequences up to 2000 bp long, for a price of about $1 per base pair and a turnaround time of less than two weeks.

Modeling

Models inform the design of engineered biological systems by allowing synthetic biologists to better predict system behavior prior to fabrication. Synthetic biology will benefit from better models of how biological molecules bind substrates and catalyze reactions, how DNA encodes the information needed to specify the cell and how multi-component integrated systems behave. Recently, multiscale models of gene regulatory networks have been developed that focus on synthetic biology applications. Simulations have been used that model all biomolecular interactions in transcription, translation, regulation, and induction of gene regulatory networks, guiding the design of synthetic systems.

Measurement

Precise and accurate quantitative measurements of biological systems are crucial to improving understanding of biology. Such measurements often help to elucidate how biological systems work and provide the basis for model construction and validation. Differences between predicted and measured system behavior can identify gaps in understanding and explain why synthetic systems don't always behave as intended. Technologies which allow many parallel and time-dependent measurements will be especially useful in synthetic biology. Microscopy and flow cytometry are examples of useful measurement technologies.

Medical cybernetics

Medical Cybernetics is a field of applied cybernetics which utilizes the concepts of cybernetics to medical research and practice. It covers an emerging working program for the application of systems- and communications-theory, connectionism and decision theory on biomedical research and health related questions.

Overview

Medical Cybernetics searches for quantitative descriptions of biological dynamics primarily in the intact, but beyond also in the diseased organism in order to gain new insights into the principles of life and its perturbations and to gather evidence based foundations for clinical decision making. It investigates intercausal networks in human biology, medical decision making and information processing structures in the living organism.

Topics in Medical cybernetics:

Systems Theory in medical sciences: The scope of systems theory in the medical sciences is searching for and modelling of physiological dynamics in the intact and diseased organism to gain deeper insights into the organizational principles of life and its perturbations.

Medical information and Communication Theory: Motivated by the awareness of information as an essential principle of life the application of communication theory to biomedicine aims to mathematically describe signalling processes and information storage in different physiological layers.

Connectionism: Connectionistic models describe information processing in neural networks - thus forming a bridge between biological and technological research.

Medical Decision Theory (MDT): The Goal of MDT is to gather evidence based foundations for decision making in the clinical setting.

Homeostasis

Homeostasis (from Greek: ὅμος, hómos, "equal"; and ιστημι, histēmi, "to stand"; coined by Walter Bradford Cannon) is the property of a system, either open or closed, that regulates its internal environment so as to maintain a stable, constant condition. Typically used to refer to a living organism, the concept came from that of milieu interieur that was created by Claude Bernard and published in 1865. Multiple dynamic equilibrium adjustment and regulation mechanisms make homeostasis possible.

Biological

With regard to any given life system parameter, an organism may be a conformer or a regulator. Regulators try to maintain the parameter at a constant level over possibly wide ambient environmental variations. On the other hand, conformers allow the environment to determine the parameter. For instance, endothermic animals maintain a constant body temperature, while exothermic animals exhibit wide body temperature variation. Examples of endothermic animals include mammals and birds, examples of exothermic animals include reptiles and some sea animals.

Conformers may still have behavioral adaptations allowing them to exert some control over a given parameter. For instance, reptiles often rest on sun-heated rocks in the morning to raise their body temperature. Vice versa, regulators are usually responsive to external circumstances: if the same sun-baked boulder happens to host a ground squirrel, its metabolism will adjust to the lesser need for internal heat production.

Thermal image of a cold-blooded tarantula on a warm-blooded human hand

An advantage of homeostatic regulation is that it allows an organism to function effectively in a broad range of environmental conditions. For example, ectotherms tend to become sluggish at low temperatures, whereas a co-located endotherm may be fully active. That thermal stability comes at a price since an automatic regulation system requires additional energy. One reason snakes may eat only once a week is that they use much less energy to maintain homeostasis.

Most homeostatic regulation is controlled by the release of hormones into the bloodstream. However other regulatory processes rely on simple diffusion to maintain a balance.

Homeostatic regulation extends far beyond the control of temperature. All animals also regulate their blood glucose, as well as the concentration of their blood. Mammals regulate their blood glucose with insulin and glucagon. These hormones are released by the pancreas, the inadequate production of the two for any reason, would result in diabetes. The kidneys are used to remove excess water and ions from the blood. These are then expelled as urine. The kidneys perform a vital role in homeostatic regulation in mammals, removing excess water, salt, and urea from the blood. These are the body's main waste products.

Another homeostatic regulation occurs in the gut. Homeostasis of the gut is not fully understood but it is believed that Toll-like receptor (TLR) expression profiles contribute to it. Intestinal epithelial cells exhibit important factors that contribute to homeostasis: 1)They have different cellular distribution of TLR’s compared to the normal gut mucosa. An example of this is how TLR5 (activated by flagellin) can redistribute to the basolateral membrane which is the perfect place where flagellin can be detected. 2)The enterocytes express high levels of TLR inhibitor Toll-interacting protein (Tollip). Tollip is a human gene that is a part of innate immune system and is highest in a healthy gut, it correlates to luminal bacterial load. 3)Surface enterocytes also express high levels of Interleukin-1 receptor (IL-1R) -containing inhibitory molecule. IL-1R are also referred to as single immunoglobulin IL-1R (SIGIRR). Animals deficient of this are more susceptible to induced colitis, implying that SIGIRR might possibly play a role in tuning mucosal tolerance towards commensal flora. Nucleotide-binding Oligomerization Domain containing 2 (NOD2) is suggested to have an affect on suppressing inflammatory cascades based on recent evidence. It is believed to modulate signals transmitted through TLRs, TLR3, 4, and 9 specifically. Mutation of it has resulted in Crohn's disease. Excessive T-helper 1 responses to resident flora in the gut are controlled by inhibiting the controlling influence of regulatory T cells and tolerance-inducing dendritic cells.

Sleep timing depends upon a balance between homeostatic sleep propensity, the need for sleep as a function of the amount of time elapsed since the last adequate sleep episode, and circadian rhythms which determine the ideal timing of a correctly structured and restorative sleep episode.

Control Mechanisms

All homeostatic control mechanisms have at least three interdependent components for the variable being regulated: The receptor is the sensing component that monitors and responds to changes in the environment. When the receptor senses a stimulus, it sends information to a control center, the component that sets the range at which a variable is maintained. The control center determines an appropriate response to the stimulus. In most homeostatic mechanisms the control center is the brain. The control center then sends signals to an effector which can be muscles, organs or other structures that receive signals from the control center. After receiving the signal, a change occurs to correct the deviation by either enhancing it with positive feedback or depressing it with negative feedback.

Positive Feedback

Positive feedback is a mechanism by which an output is enhanced, such as protein levels. However, in order to avoid any fluctuation in the protein level, the mechanism is inhibited stochastically (I), therefore when the concentration of the activated protein (A) is past the threshold ([I]), the loop mechanism is activated and the concetration of A increases exponentially if d[A]=k [A]

Positive feedback mechanisms are designed to accelerate or enhance the output created by a stimulus that has already been activated.

Unlike negative feedback mechanisms that initiate to maintain or regulate physiological functions within a set and narrow range, the positive feedback mechanisms are designed to push levels out of normal ranges. To achieve this purpose, a series of events initiates a cascading process that builds to increase the effect of the stimulus. This process can be beneficial but is rarely used by the body due to risks of the acceleration becoming uncontrollable.

One positive feedback example event in the body is blood platelet accumulation, which, in turn, causes blood clotting in response to a break or tear in the lining of blood vessels. Another example is the release of oxytocin to intensify the contractions that take place during childbirth.

Positive feedback can also be harmful. One particular example is when a fever causes a positive feedback within homeostasis that pushes the temperature continually higher. Body temperature can reach extremes of 45°C (113°F), at which cellular proteins denature, causing the active site in proteins to change, thus causing metabolism to stop, resulting in death.

Negative Feedback

Negative feedback mechanism consists of reducing the output or activity of any organ or system back to its normal range of functioning. A good example of this is regulating blood pressure. Blood vessels can sense resistance of blood flow against the walls when blood pressure increases. The blood vessels act as the receptors and they relay this message to the brain. The brain then sends a message to the heart and blood vessels, both are the effectors. The heart rate would decrease as the blood vessels increase in diameter (or vasodilation). This change would result in the blood pressure to fall back to its normal range. The opposite would happen when blood pressure decreases, and would cause vasoconstriction.

Another important example is when the body is deprived of food. The body would then reset the metabolic set point to a lower than normal value. This would allow the body to continue to function, at a slower rate, even though the body is starving. Therefore people who deprive themselves of food while trying to lose weight, would find it easy to shed weight initially and much harder to lose more after. This is due to the body readjusting itself to a lower metabolic set point to allow the body to survive with its low supply of energy. Exercise can change this effect by increasing the metabolic demand.

Another good example of negative feedback mechanism is temperature control. The hypothalamus which monitors the body temperature, is capable of determining even the slightest of variation of normal body temperature (37 degrees Celsius). Response to such variation could be stimulation of glands that produces sweat to reduce the temperature or signaling various muscles to shiver to increase body temperature.

Both feedbacks are equally important for the healthy functioning of ones body. Complications can arise if any of the two feedbacks are affected or altered in any way.

Homeostatic Imbalance

Much disease results from disturbance of homeostasis, a condition known as homeostatic imbalance. As it ages, every organism will lose efficiency in its control systems. The inefficiencies gradually result in an unstable internal environment that increases the risk for illness. In addition, homeostatic imbalance is also responsible for the physical changes associated with aging. Even more serious than illness and other characteristics of aging, is death. Heart failure has been seen where nominal negative feedback mechanisms become overwhelmed, and destructive positive feedback mechanisms then take over.

Diseases that result from a homeostatic imbalance include diabetes, dehydration, hypoglycemia, hyperglycemia, gout, and any disease caused by a toxin present in the bloodstream. All of these conditions result from the presence of an increased amount of a particular substance. In ideal circumstances, homeostatic control mechanisms should prevent this imbalance from occurring, but, in some people, the mechanisms do not work efficiently enough or the quantity of the substance exceeds the levels at which it can be managed. In these cases, medical intervention is necessary to restore the balance, or permanent damage to the organs may result.

Varieties

The Dynamic Energy Budget theory for metabolic organisation delineates structure and (one or more) reserves in an organism. Its formulation is based on three forms of homeostasis:

Strong homeostasis, wherein structure and reserve do not change in composition. Since the amount of reserve and structure can vary, this allows a particular change in the composition of the whole body (as explained by the Dynamic Energy Budget theory).
Weak homeostasis, wherein the ratio of the amounts of reserve and structure becomes constant as long as food availability is constant, even when the organism grows. This means that the whole body composition is constant during growth in constant environments.
Structural homeostasis, wherein the sub-individual structures grow in harmony with the whole individual; the relative proportions of the individuals remain constant.

Ecological

Ecological homeostasis is found in a climax community of maximum permitted biodiversity, given the prevailing ecological conditions.

An example of a disturbed ecosystems or sub-climax biological communities was the island of Krakatoa after its major eruption in 1883: the established stable homeostasis of the previous forest climax ecosystem was destroyed and all life eliminated from the island. In the years after the eruption, Krakatoa went through a sequence of ecological changes in which successive groups of new plant or animal species followed one another, leading to increasing biodiversity and eventually culminating in a re-established climax community. This ecological succession on Krakatoa occurred in a number of stages; a sere is defined as "a stage in a sequence of events by which succession occurs". The complete chain of seres leading to a climax is called a prisere. In the case of Krakatoa, the island reached its climax community, with eight hundred different recorded species, in 1983, one hundred years after the eruption that cleared all life off the island. Evidence confirms that this number has been homeostatic for some time, with the introduction of new species rapidly leading to elimination of old ones.

The evidence of Krakatoa, and other disturbed or virgin ecosystems, shows that the initial colonization by pioneer or R strategy species occurs through positive feedback reproduction strategies, wherein species are weeds, producing huge numbers of possible offspring, but investing little in the success of any one. Rapid boom and bust plague or pest cycles are observed with such species. As an ecosystem starts to approach climax, these species get replaced by more sophisticated climax species, which, through negative feedback, adapt themselves to specific environmental conditions. These species, closely controlled by carrying capacity, follow K strategies, wherein species produce fewer numbers of potential offspring, but invest more heavily in securing the reproductive success of each one to the micro-environmental conditions of its specific ecological niche.

It begins with a pioneer community and ends with a climax community. This climax community occurs when the ultimate vegetation has achieved equilibrium with the local environment.

Such ecosystems form nested communities or heterarchies, in which homeostasis at one level contributes to homeostatic processes at another holonic level. For example, the loss of leaves on a mature rainforest tree creates space for new growth, and contributes to the plant litter and soil humus build-up upon which such growth depends. Of equal importance, a mature rainforest tree reduces the sunlight falling on the forest floor and helps prevent invasion by other species. But trees too fall to the forest floor, and a healthy forest glade is dependent upon a constant rate of forest regrowth, produced by the fall of logs, and the recycling of forest nutrients through the respiration of termites and other insect, fungal, and bacterial decomposers. In a similar manner, such forest glades contribute ecological services, such as the regulation of microclimates or of the hydrological cycle for an ecosystem, and a number of different ecosystems act together to maintain homeostasis, perhaps of a number of river catchments within a bioregion. A diversity of bioregions, in like manner, makes up a stable homeostatic biological region or biome.

In the Gaia hypothesis, James Lovelock stated that the entire mass of living matter on Earth (or any planet with life) functions as a vast homeostatic superorganism that actively modifies its planetary environment to produce the environmental conditions necessary for its own survival. In this view, the entire planet maintains homeostasis. Whether this sort of system is present on Earth is still open to debate. However, some relatively simple homeostatic mechanisms are generally accepted. For example, when atmospheric carbon dioxide levels rise, certain plants are able to grow better and thus act to remove more carbon dioxide from the atmosphere. When sunlight is plentiful and atmospheric temperature climbs, the phytoplankton of the ocean surface waters thrive and produce more dimethyl sulfide, DMS. The DMS molecules act as cloud condensation nuclei, which produce more clouds, and thus increase the atmospheric albedo and this feeds back to lower the temperature of the atmosphere. As scientists discover more about Gaia, vast numbers of positive and negative feedback loops are being discovered, that, together, maintain a metastable condition, sometimes within very broad range of environmental conditions.

Reactive

Example of use: "Reactive homeostasis is an immediate response to a homeostatic challenge such as predation."

However, any homeostasis is impossible without reaction - because homeostasis is and must be a "feedback" phenomenon.

The phrase "reactive homeostasis" is simply short for: "reactive compensation reestablishing homeostasis", that is to say, "reestablishing a point of homeostasis." - it should not be confused with a separate kind of homeostasis or a distinct phenomenon from homeostasis; it is simply the compensation (or compensatory) phase of homeostasis.

Other fields

The term has come to be used in other fields, as well.

Risk

An actuary may refer to risk homeostasis, where (for example) people that have anti-lock brakes have no better safety record than those without anti-lock brakes, because the former unconsciously compensate for the safer vehicle via less-safe driving habits. Previous to the innovation of anti-lock brakes, certain maneuvers involved minor skids, evoking fear and avoidance: now the anti-lock system moves the boundary for such feedback, and behavior patterns expand into the no-longer punitive area. It has also been suggested that ecological crises are an instance of risk homeostasis in which behavior known to be dangerous continues until dramatic consequences actually occur.

Stress

Sociologists and psychologists may refer to stress homeostasis, the tendency of a population or an individual to stay at a certain level of stress, often generating artificial stresses if the "natural" level of stress is not enough.

Jean Francois Lyotard, a postmodern theorist, has applied this term to societal 'power centers' that he describes as being 'governed by a principle of homeostasis,' for example, the scientific hierarchy, which will sometimes ignore a radical new discovery for years because it destabilizes previously-accepted norms.

Waste

Andrew Potter has used the term waste homeostasis in reference to the lack of net gain from energy-saving technologies.

Conversational

A 2007 study purported to find (and show clinically) conversational homeostasis in which overly-familiar people (such as spouses) condense their speech so much that they are actually worse at communicating novel information than strangers are, while not being conscious of this problem.

Metabolic

Some herbal medicines, known as adaptogens, have been defined to function as non-toxic metabolic regulators that can enhance metabolic homeostasis during stress.

Friday, January 30, 2009

Bionics

Bionics (also known as biomimetics, biognosis, biomimicry, or bionical creativity engineering) is the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology. The word "bionic" was coined by Jack E. Steele in 1958, possibly originating from the Greek word "βίον", pronounced "bion", meaning "unit of life" and the suffix -ic, meaning "like" or "in the manner of", hence "like life". Some dictionaries, however, explain the word as being formed from "biology" + "electronics".

The transfer of technology between lifeforms and synthetic constructs is, according to proponents of bionic technology, desirable because evolutionary pressure typically forces living organisms, including fauna and flora, to become highly optimized and efficient. A classical example is the development of dirt- and water-repellent paint (coating) from the observation that the surface of the lotus flower plant is practically unsticky for anything (the lotus effect).

Examples of bionics in engineering include the hulls of boats imitating the thick skin of dolphins; sonar, radar, and medical ultrasound imaging imitating the echolocation of bats.

In the field of computer science, the study of bionics has produced artificial neurons, artificial neural networks, and swarm intelligence. Evolutionary computation was also motivated by bionics ideas but it took the idea further by simulating evolution in silico and producing well-optimized solutions that had never appeared in nature.

It is estimated by Julian Vincent, professor of biomimetics at the University of Bath in the UK, that "at present there is only a 10% overlap between biology and technology in terms of the mechanisms used".

History

The name biomimetics was coined by Otto Schmitt in the 1950s. The term bionics was coined by Jack E. Steele in 1958 while working at the Aeronautics Division House at Wright-Patterson Air Force Base in Dayton. However, biomimicry or biomimetics is more preferred in technology world in efforts to avoid confusion between the medical term bionics. Coincidentally, Martin Caidin used the word for his 1972 novel Cyborg, which inspired the series The Six Million Dollar Man. Caidin was a long-time aviation industry writer before turning to fiction full time.

Methods

Often, the study of bionics emphasizes implementing a function found in nature rather than just imitating biological structures. For example, in computer science, cybernetics tries to model the feedback and control mechanisms that are inherent in intelligent behavior, while artificial intelligence tries to model the intelligent function regardless of the particular way it can be achieved.

The conscious copying of examples and mechanisms from natural organisms and ecologies is a form of applied case-based reasoning, treating nature itself as a database of solutions that already work. Proponents argue that the selective pressure placed on all natural life forms minimizes and removes failures.

Although almost all engineering could be said to be a form of biomimicry, the modern origins of this field are usually attributed to Buckminster Fuller and its later codification as a house or field of study to Janine Benyus.

Roughly, we can distinguish three biological levels in the fauna or flora, after which technology can be modeled:

Mimicking natural methods of manufacture
Imitating mechanisms found in nature (velcro)
Studying organizational principles from social behaviour of organisms, such as the flocking behaviour of birds, the foraging behaviour of bees and ants, and the Swarm Intelligence(SI)-based behaviour of a school of fish.

Examples of biomimetics

Velcro is the most famous example of biomimetics. In 1948, the Swiss engineer George de Mestral was cleaning his dog of burrs picked up on a walk when he realized how the hooks of the burrs clung to the fur.

Cat's eye reflectors were invented by Percy Shaw in 1935 after studying the mechanism of cat eyes. He had found that cats had a system of reflecting cells, known as tapetum lucidum, which was capable of reflecting the tiniest bit of light.

Leonardo da Vinci's flying machines and ships are early examples of drawing from nature in engineering.

Julian Vincent drew from the study of pinecones when he developed in 2004 "smart" clothing that adapts to changing temperatures. "I wanted a nonliving system which would respond to changes in moisture by changing shape", he said. "There are several such systems in plants, but most are very small — the pinecone is the largest and therefore the easiest to work on". Pinecones respond to higher humidity by opening their scales (to disperse their seeds). The "smart" fabric does the same thing, opening up when the wearer is warm and sweating, and shutting tight when cold.

"Morphing aircraft wings" that change shape according to the speed and duration of flight were designed in 2004 by biomimetic scientists from Penn State University. The morphing wings were inspired by different bird species that have differently shaped wings according to the speed at which they fly. In order to change the shape and underlying structure of the aircraft wings, the researchers needed to make the overlying skin also be able to change, which their design does by covering the wings with fish-inspired scales that could slide over each other. In some respects this is a refinement of the swing-wing design.

Lotus leaf surface, rendered: microscopic view

Some paints and roof tiles have been engineered to be self-cleaning by copying the mechanism from the Nelumbo lotus.

Nanostructures and physical mechanisms that produce the shining color of butterfly wings were reproduced in silico by Greg Parker, professor of Electronics and Computer Science at the University of Southampton and research student Luca Plattner in the field of photonics, which is electronics using photons as the information carrier instead of electrons.

The wing structure of the blue morpho butterfly was studied and the way it reflects light was mimicked to create an RFID tag that can be read through water and on metal.

Neuromorphic chips, silicon retinae or cochleae, has wiring that is modelled after real neural networks. S.a.: connectivity

Synthetic or "robotic" vegetation, which aids in conservation and restoration, are machines designed to mimic many of the functions of living vegetation.

Medical adhesives involving glue and tiny nano-hairs are being developed based on the physical structures found in the feet of geckos.

Specific uses of the term

In medicine

Bionics is a term which refers to the flow of concepts from biology to engineering and vice versa. Hence, there are two slightly different points of view regarding the meaning of the word.

In medicine, bionics means the replacement or enhancement of organs or other body parts by mechanical versions. Bionic implants differ from mere prostheses by mimicking the original function very closely, or even surpassing it.

Bionics' German equivalent, "Bionik", always adheres to the broader meaning, in that it tries to develop engineering solutions from biological models. This approach is motivated by the fact that biological solutions will usually be optimized by evolutionary forces.

While the technologies that make bionic implants possible are still in a very early stage, a few bionic items already exist, the best known being the cochlear implant, a device for deaf people. By 2004 fully functional artificial hearts were developed. Significant further progress is expected to take place with the advent of nanotechnologies. A well known example of a proposed nanodevice is a respirocyte, an artificial red cell, designed (though not built yet) by Robert Freitas.

Kwabena Boahen from Ghana was a professor in the Department of Bioengineering at the University of Pennsylvania. During his eight years at Penn, he developed a silicon retina that was able to process images in the same manner as a living retina. He confirmed the results by comparing the electrical signals from his silicon retina to the electrical signals produced by a salamander eye while the two retinas were looking at the same image.

Politics

A political form of biomimcry is bioregional democracy, wherein political borders conform to natural ecoregions rather than human cultures or the outcomes of prior conflicts.

Critics of these approaches often argue that ecological selection itself is a poor model of minimizing manufacturing complexity or conflict, and that the free market relies on conscious cooperation, agreement, and standards as much as on efficiency - more analogous to sexual selection. Charles Darwin himself contended that both were balanced in natural selection - although his contemporaries often avoided frank talk about sex, or any suggestion that free market success was based on persuasion, not value.

Advocates, especially in the anti-globalization movement, argue that the mating-like processes of standardization, financing and marketing, are already examples of runaway evolution - rendering a system that appeals to the consumer but which is inefficient at use of energy and raw materials. Biomimicry, they argue, is an effective strategy to restore basic efficiency.

Biomimicry is also the second principle of Natural Capitalism.

Other uses

In a more specific meaning, it is a creativity technique that tries to use biological prototypes to get ideas for engineering solutions. This approach is motivated by the fact that biological organisms and their organs have been well optimized by evolution. In chemistry, a biomimetic synthesis is a man-made chemical synthesis inspired by biochemical processes.

Another, more recent meaning of the term "bionics" refers to merging organism and machine. This approach results in a hybrid system combining biological and engineering parts, which can also be referred as a cybernetic organism (cyborg). Practical realization of this was demonstrated in Kevin Warwick's implant experiments bringing about ultrasound input via his own nervous system.

In 2006 Mercedes-Benz introduced its Bionic concept car.

Biocybernetics

Biocybernetics is the application of cybernetics to the biological science, comprised of biological disciplines that benefit from the application of cybernetics: neurology, multicellular systems and others. Biocybernetics plays a major role in systems biology, seeking to integrate different levels of information to understand how biological systems function.

Biocybernetics as an abstract science is a part of theoretical biology, and based upon the principles of systemics.

Terminology

Biocybernetics is a cojoined word from bio (Greek: βίο / life) and cybernetics (Greek: κυβερνητική / controlling-governing). It is sometimes written together or with a blank or written fully as biological cybernetics, whilst the same rules apply. Most write it together though, as Google statistics show. The same applies to neuro cybernetics which should also be looked up as neurological, when doing extensive research.

Same or familiar fields

As those disciplines are dealing on theoretical/abstract foundations and are in accordance with the popularity of computers. Thus papers and research is in greater numbers going on under different names: e.g. molecular cybernetics -> molecular computational systems OR molecular systems theory OR molecular systemics OR molecular information/informational systems

Please heed this when you engage in an extensive search for information to assure access to a broad range of papers.

What is Cybernetics?