Biocomputers
Encyclopedia
Biocomputers use systems of biologically derived molecules, such as DNA
and proteins, to perform computational calculation
s involving storing, retrieving, and processing data
.
The development of biocomputers has been made possible by the expanding new science of nanobiotechnology
. The term nanobiotechnology can be defined in multiple ways; in a more general sense, nanobiotechnology can be defined as any type of technology that uses both nano-scale materials, i.e. materials having characteristic dimensions of 1-100 nanometers, as well as biologically based materials (34).4 A more restrictive definition views nanobiotechnology more specifically as the design and engineering of proteins that can then be assembled into larger, functional structures (116-117) (9).³,1
The implementation of nanobiotechnology, as defined in this narrower sense, provides scientists with the ability to engineer biomolecular systems specifically so that they interact in a fashion that can ultimately result in the computational functionality of a computer
.
shape of a specific molecule or set of molecules under a set of initial conditions serves as the output. Biomechanical computers rely on the nature of specific molecules to adopt certain physical configurations under certain chemical conditions. The mechanical, three-dimensional structure of the product of the biomechanical computer is detected and interpreted appropriately as a calculated output.
in highly specific manners based upon the initial conditions that serve as the input of the bioelectronic system.
sequences by biological molecules called ribosomes, which assemble individual amino acids into polypeptides that form functional proteins based on the nucleotide sequence that the ribosome interprets. What this ultimately means is that one can engineer a biocomputer, i.e. the chemical components necessary to serve as a biological system capable of performing computations, by engineering DNA nucleotide sequences to encode for the necessary protein components. Also, the synthetically designed DNA molecules themselves may function in a particular biocomputer system. Thus, implementing nanobiotechnology to design and produce synthetically designed proteins, as well as the design and synthesis of artificial DNA molecules, can allow the construction of functional biocomputers, e.g., Computational Genes
.
and mathematical calculations. Tom Knight of the MIT Artificial Intelligence Laboratory first suggested a biochemical computing scheme in which protein concentrations are used as binary
signals that ultimately serve to perform logical operations (349).² At or above a certain concentration of a particular biochemical product in a biocomputer chemical pathway indicates a signal that is either a 1 or a 0, and a concentration below this level indicates the other, remaining signal. Using this method as computational analysis, biochemical computers can perform logical operations in which the appropriate binary output will occur only under specific, logical constraints on the initial conditions. In other words, the appropriate binary output serves as a logically derived conclusion from a set of initial conditions that serve as premises from which the logical conclusion can be made. In addition to these types of logical operations, biocomputers have also been shown to demonstrate other functional capabilities, such as mathematical computations. One such example was provided by W.L. Ditto, who in 1999 created a biocomputer composed of leech neurons at Georgia Tech which was capable of performing simple addition (351).² These are just a few of the notable uses that biocomputers have already been engineered to perform, and the capabilities of biocomputers are becoming increasingly sophisticated. Because of the availability and potential economic efficiency associated with producing biomolecules and biocomputers, as noted above, the advancement of the technology of biocomputers is a popular, rapidly growing subject of research that is likely to see much progress in the future.
. Certainly, there is plenty of room to improve in the realm of biocomputer computational ability; one may reasonably expect the science of biocomputers to advance greatly in the years to come.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and proteins, to perform computational calculation
Calculation
A calculation is a deliberate process for transforming one or more inputs into one or more results, with variable change.The term is used in a variety of senses, from the very definite arithmetical calculation of using an algorithm to the vague heuristics of calculating a strategy in a competition...
s involving storing, retrieving, and processing data
Data
The term data refers to qualitative or quantitative attributes of a variable or set of variables. Data are typically the results of measurements and can be the basis of graphs, images, or observations of a set of variables. Data are often viewed as the lowest level of abstraction from which...
.
The development of biocomputers has been made possible by the expanding new science of nanobiotechnology
Nanobiotechnology
Bionanotechnology, nanobiotechnology, and nanobiology are terms that refer to the intersection of nanotechnology and biology. Given that the subject is one that has only emerged very recently, bionanotechnology and nanobiotechnology serve as blanket terms for various related technologies.This...
. The term nanobiotechnology can be defined in multiple ways; in a more general sense, nanobiotechnology can be defined as any type of technology that uses both nano-scale materials, i.e. materials having characteristic dimensions of 1-100 nanometers, as well as biologically based materials (34).4 A more restrictive definition views nanobiotechnology more specifically as the design and engineering of proteins that can then be assembled into larger, functional structures (116-117) (9).³,1
The implementation of nanobiotechnology, as defined in this narrower sense, provides scientists with the ability to engineer biomolecular systems specifically so that they interact in a fashion that can ultimately result in the computational functionality of a computer
Computer
A computer is a programmable machine designed to sequentially and automatically carry out a sequence of arithmetic or logical operations. The particular sequence of operations can be changed readily, allowing the computer to solve more than one kind of problem...
.
Scientific Background
Biocomputers use biologically derived materials to perform computational functions. A biocomputer consists of a pathway or series of metabolic pathways involving biological materials that are engineered to behave in a certain manner based upon the conditions (input) of the system. The resulting pathway of reactions that takes place constitutes an output, which is based on the engineering design of the biocomputer and can be interpreted as a form of computational analysis. Three distinguishable types of biocomputers include biochemical computers, biomechanical computers, and bioelectronic computers (349-351).²Biochemical Computers
Biochemical computers use the immense variety of feedback loops that are characteristic of biological chemical reactions in order to achieve computational functionality. Feedback loops in biological systems take many forms, and many different factors can provide both positive and negative feedback to a particular biochemical process, causing either an increase in chemical output or a decrease in chemical output, respectively. Such factors may include the quantity of catalytic enzymes present, the amount of reactants present, the amount of products present, and the presence of molecules that bind to and thus alter the chemical reactivity of any of the aforementioned factors. Given the nature of these biochemical systems to be regulated through many different mechanisms, one can engineer a chemical pathway comprising a set of molecular components that react to produce one particular product under one set of specific chemical conditions and another particular product under another set of conditions. The presence of the particular product that results from the pathway can serve as a signal, which can be interpreted, along with other chemical signals, as a computational output based upon the starting chemical conditions of the system, i.e. the input.Biomechanical Computers
Biomechanical computers are similar to biochemical computers in that they both perform a specific output that can be interpreted as a functional computation based upon specific initial conditions which serve as input. They differ, however, in what exactly serves as the output signal. In biochemical computers, the presence or concentration of certain chemicals serves as the output signal. In biomechanical computers, however, the mechanicalMechanics
Mechanics is the branch of physics concerned with the behavior of physical bodies when subjected to forces or displacements, and the subsequent effects of the bodies on their environment....
shape of a specific molecule or set of molecules under a set of initial conditions serves as the output. Biomechanical computers rely on the nature of specific molecules to adopt certain physical configurations under certain chemical conditions. The mechanical, three-dimensional structure of the product of the biomechanical computer is detected and interpreted appropriately as a calculated output.
Bioelectronic Computers
Biocomputers can also be constructed to perform electronic computing. Again, like both biomechanical and biochemical computers, computations are performed by interpreting a specific output that is based upon an initial set of conditions that serve as input. In bioelectronic computers, the measured output is the nature of the electrical conductivity that is observed in the bioelectronic computer, which comprises specifically designed biomolecules that conduct electricityElectricity
Electricity is a general term encompassing a variety of phenomena resulting from the presence and flow of electric charge. These include many easily recognizable phenomena, such as lightning, static electricity, and the flow of electrical current in an electrical wire...
in highly specific manners based upon the initial conditions that serve as the input of the bioelectronic system.
Engineering Biocomputers
The behavior of biologically derived computational systems such as these relies on the particular molecules that make up the system, which are primarily proteins but may also include DNA molecules. Nanobiotechnology provides the means to synthesize the multiple chemical components necessary to create such a system. The chemical nature of a protein is dictated by its sequence of amino acids—the chemical building blocks of proteins. This sequence is in turn dictated by a specific sequence of DNA nucleotides—the building blocks of DNA molecules. Proteins are manufactured in biological systems through the translation of nucleotideNucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
sequences by biological molecules called ribosomes, which assemble individual amino acids into polypeptides that form functional proteins based on the nucleotide sequence that the ribosome interprets. What this ultimately means is that one can engineer a biocomputer, i.e. the chemical components necessary to serve as a biological system capable of performing computations, by engineering DNA nucleotide sequences to encode for the necessary protein components. Also, the synthetically designed DNA molecules themselves may function in a particular biocomputer system. Thus, implementing nanobiotechnology to design and produce synthetically designed proteins, as well as the design and synthesis of artificial DNA molecules, can allow the construction of functional biocomputers, e.g., Computational Genes
Computational Genes
A computational gene is a molecular automaton consisting of a structural part anda functional part; and its design is such that it might work in a cellular environment.The structural part is a naturally occurring gene, which is used as a...
.
Economical Benefit of Biocomputers
A hallmark of all biological organisms and the chemical building blocks that comprise them is the ability to self-replicate and self-assemble into functional components; life could not be sustained if living organisms were not capable of replicating themselves. The economical benefit of biocomputers lies in this potential of all biologically derived systems to self-replicate and self-assemble given appropriate conditions (349).² For instance, all of the necessary proteins for a certain biochemical pathway, which can be modified to serve as a biocomputer, can be synthesized many times over inside a biological cell from a single DNA molecule, which can itself be replicated many times over. This characteristic of biological molecules makes their production highly efficient and relatively inexpensive. Whereas non-biological computer components require extensive production processes, the components of biocomputers can be produced in large quantities from tandem processes occurring in a single, easily attainable, convenient source—the replicating machinery present within most biological cells.Notable Advancements in Biocomputer Technology
Currently, biocomputers exist with various functional capabilities that include operations of logicLogic
In philosophy, Logic is the formal systematic study of the principles of valid inference and correct reasoning. Logic is used in most intellectual activities, but is studied primarily in the disciplines of philosophy, mathematics, semantics, and computer science...
and mathematical calculations. Tom Knight of the MIT Artificial Intelligence Laboratory first suggested a biochemical computing scheme in which protein concentrations are used as binary
Binary numeral system
The binary numeral system, or base-2 number system, represents numeric values using two symbols, 0 and 1. More specifically, the usual base-2 system is a positional notation with a radix of 2...
signals that ultimately serve to perform logical operations (349).² At or above a certain concentration of a particular biochemical product in a biocomputer chemical pathway indicates a signal that is either a 1 or a 0, and a concentration below this level indicates the other, remaining signal. Using this method as computational analysis, biochemical computers can perform logical operations in which the appropriate binary output will occur only under specific, logical constraints on the initial conditions. In other words, the appropriate binary output serves as a logically derived conclusion from a set of initial conditions that serve as premises from which the logical conclusion can be made. In addition to these types of logical operations, biocomputers have also been shown to demonstrate other functional capabilities, such as mathematical computations. One such example was provided by W.L. Ditto, who in 1999 created a biocomputer composed of leech neurons at Georgia Tech which was capable of performing simple addition (351).² These are just a few of the notable uses that biocomputers have already been engineered to perform, and the capabilities of biocomputers are becoming increasingly sophisticated. Because of the availability and potential economic efficiency associated with producing biomolecules and biocomputers, as noted above, the advancement of the technology of biocomputers is a popular, rapidly growing subject of research that is likely to see much progress in the future.
Future Potential of Biocomputers
Many examples of simple biocomputers have been designed, but the capabilities of these biocomputers are still largely premature in comparison to commercially available non-bio computers. However, there is definitely great potential in the capabilities that biocomputers may one day acquire. Evidence of the true potential of the computing capabilities of biocomputers exists in the most powerful, complex computational machine known to currently exist: the biocomputer that is the human brainBrain
The brain is the center of the nervous system in all vertebrate and most invertebrate animals—only a few primitive invertebrates such as sponges, jellyfish, sea squirts and starfishes do not have one. It is located in the head, usually close to primary sensory apparatus such as vision, hearing,...
. Certainly, there is plenty of room to improve in the realm of biocomputer computational ability; one may reasonably expect the science of biocomputers to advance greatly in the years to come.
See also
- BiotechnologyBiotechnologyBiotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...
- Computational GenesComputational GenesA computational gene is a molecular automaton consisting of a structural part anda functional part; and its design is such that it might work in a cellular environment.The structural part is a naturally occurring gene, which is used as a...
- Computers
- DNA computingDNA computingDNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area...
- Human BiocomputerHuman BiocomputerThe Human Biocomputer coined by John C. Lilly, refers literally to the "hardware" of the human anatomy. This would include the brain, internal organs, and other human organ systems such as cardiovascular, digestive, endocrine, immune, integumentary, lymphatic, muscular, nervous, reproductive,...
- Molecular electronicsMolecular electronicsMolecular electronics, sometimes called moletronics, involves the study and application of molecular building blocks for the fabrication of electronic components...
- NanotechnologyNanotechnologyNanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
- NanobiotechnologyNanobiotechnologyBionanotechnology, nanobiotechnology, and nanobiology are terms that refer to the intersection of nanotechnology and biology. Given that the subject is one that has only emerged very recently, bionanotechnology and nanobiotechnology serve as blanket terms for various related technologies.This...
- Peptide computingPeptide computingPeptide computing is a form of computing which uses peptides and molecular biology, instead of traditional silicon-based computer technologies. The basis of this computational model is the affinity of antibodies towards peptide sequences. Similar to DNA computing, the parallel interactions of...
- Wetware computerWetware computerA wetware computer is an organic computer built from living neurons. , at the Georgia Institute of Technology, is the primary researcher driving the creation of these artificially constructed, but still organic brains...