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Biomimicry: Biologically Inspired Engineering

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Teleological
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« on: July 28, 2009, 13:35:19 PM »

Biomimicry: Biomimicry (from bios, meaning life, and mimesis, meaning to imitate) is a new discipline that studies nature's best ideas and then imitates these designs and processes to solve human problems.

The 15 Coolest Cases of Biomimicry

1. Velcro
2. Passive Cooling
3. Gecko Tape
4. Whalepower Wind Turbine
5. Lotus Effect Hydrophobia
6. Self-Healing Plastics
7. The Golden Streamlining Principle
8. Artificial Photosynthesis
9. Bionic Car
10. Morphing Aircraft Wings
11. Friction-Reducing Sharkskin
12. Diatomaceous Nanotech
13. Glo-Fish
14. Insect-Inspired Autonomous Robots
15. Butterfly-Inspired Displays

What to expect from the future?
In the case of solar fuel, we would do well to use design principles of the photosynthesis photosystem II mechanism to engineer our own solar fuel producing systems with similar efficiency.
E.g.:
Solar water-splitting into H2 and O2: design principles of photosystem II and hydrogenases
Taking design principles from nature is like taking a look at the future of our own designs.

And nanomotors?
Design principles in biomolecular motors are already inspiring future designs.
Clockwork That Drives Powerful Virus Nanomotor Discovered
Quote
Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines.


And what better place to manufacture these machines than the place where these machines are created in the first place. Intracellularly:
Using Living Cells As Nanotechnology Factories
Quote
ScienceDaily (Oct. 8, 2008) — In the tiny realm of nanotechnology, scientists have used a wide variety of materials to build atomic scale structures. But just as in the construction business, nanotechnology researchers can often be limited by the amount of raw materials. Now, Biodesign Institute at Arizona State University researcher Hao Yan has avoided these pitfalls by using cells as factories to make DNA based nanostructures inside a living cell.


Why not, with such optimal clockwork, error correction, efficient enzymes, structures folding other structures into place, nanotubes etc. mimicking designs in nature for our own future designs seems like a good idea.


Interesting TEDtalk about biomimicry:
Janine Benyus: 12 sustainable design ideas from nature


Feel free to post more interesting designs in nature that can be used for our own future designs.
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Teleological
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« Reply #1 on: September 18, 2009, 07:50:21 AM »

DNA is not only useful for storing information, it makes pretty pictures as well...on a nanoscale.

Nanoscale Origami From DNA
Quote
ScienceDaily (Aug. 7, 2009) — Scientists at the Technische Universitaet Muenchen (TUM) and Harvard University have thrown the lid off a new toolbox for building nanoscale structures out of DNA, with complex twisting and curving shapes. In the August 7 issue of the journal Science, they report a series of experiments in which they folded DNA, origami-like, into three dimensional objects including a beachball-shaped wireframe capsule just 50 nanometers in diameter.



[SIZE="1"]Scientists at the Technische Universitaet Muenchen and Harvard University have thrown the lid off a new toolbox for building nanoscale structures out of DNA, with complex twisting and curving shapes. They report a series of experiments in which they folded DNA, origami-like, into 3-D objects including a beach ball-shaped wireframe capsule just 50 nanometers in diameter. (Credit: Used by permission of H. Dietz, TUM Dept. of Physics, all rights reserved.)[/SIZE]

See the triangle? Look at what these guys are doing with it:

Building circuit boards using DNA scaffolding

High concentrations of triangular DNA origami binding to wide lines on a lithographically patterned surface; the inset shows individual origami structures at high resolution

Quote
There have been a few breakthroughs in recent years that hold the promise of sustaining Moore’s Law for some time to come. These include attaching molecules to silicon and replacing copper interconnects with graphene. Now IBM are proposing a new way to pack more power and speed into computer chips by using DNA molecules as scaffolding for transistors fabricated with carbon nanotubes and silicon wires.

The new approach developed by scientists at IBM and the California Institute of Technology uses DNA molecules as scaffolding or miniature circuit boards for the precise assembly of components such as millions of carbon nanotubes, nanowires and nanoparticles, that could be deposited and self-assembled into precise patterns by sticking to the DNA molecules.

The researchers say such a technique may provide a way to reach sub-22 nm lithography on surfaces compatible with today’s semiconductor manufacturing equipment. The technique allows for DNA nanostructures such as squares, triangles and stars to be prepared with dimensions of 100-150 nm on an edge and a thickness of the width of the DNA double helix.

“The cost involved in shrinking features to improve performance is a limiting factor in keeping pace with Moore’s Law and a concern across the semiconductor industry,” said IBM researcher, Spike Narayan. “The combination of this directed self-assembly with today’s fabrication technology eventually could lead to substantial savings in the most expensive and challenging part of the chip-making process.”

The research is detailed in the paper, “Placement and orientation of DNA nanostructures on lithographically patterned surfaces,” will be published in the September issue of Nature Nanotechnology.


More pics:



Directed self-assembly... Seems like a useful design tool to make use of nature and design to get to an optimal solution.
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« Reply #2 on: September 18, 2009, 07:58:43 AM »

How does this prove your god?
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« Reply #3 on: September 18, 2009, 08:11:45 AM »

Bio-inspired spam detection.... with the immune system as inspiration...

ALIFE Conference to reveal bio-inspired spam detection

Quote
An algorithm for spam recognition inspired by the immune system will be presented at the first European conference on Artificial Life (ALIFE XI) being held in Winchester this week.

Alaa Abi-Haidar and Luis Rocha from the Department of Informatics, Indiana University, Bloomington, USA and the Instituto Gulbenkian de Ciencia, Portugal, will present a paper entitled Adaptive Spam Detection Inspired by the Immune System on Thursday 7 August. They will describe how in the same way as the vertebrate adaptive immune system learns to distinguish harmless from harmful substances, these principles can be applied to spam detection.

In their presentation, the authors will claim that this bio-inspired spam detection algorithm based on the cross-regulation model of T-cell dynamics, is equally as competitive as state-of-the-art spam binary classifiers and provides a deeper understanding of the behaviour of T-cell cross-regulation systems.

The newly-formed Science and Engineering of Natural Systems (SENSe) group within the University of Southampton's School of Electronics and Computer Science (ECS) is to host this year’s conference, which will take place at the University of Winchester West Downs Campus, involving 250 participants and more paper presentations than ever before.

`This is a critical time for Artificial Life,' said Dr Seth Bullock at ECS, the conference chairman. `The field is on the verge of synthesising living cells, a feat that the Artificial Life community could only dream of when it started out in the late 80s.'

Keynote speakers include internationally leading experts such as Professor Stuart Kauffman, author of The Origins of Order, Professor Peter Schuster, editor-in-chief of the journal Complexity, Professor Eva Jablonka, author of Evolution in Four Dimensions (with Marion Lamb), and Professor Andrew Ellington, a leading pioneer in the new science of synthetic biology.

Professor Takashi Ikegami from the University of Tokyo will open the conference, speaking on work spanning self-organisation and autopoiesis in systems of birds, robots, children, flies, cells, and even oil droplets. The conference is unified by a focus on understanding the fundamental behavioural dynamics of embedded, embodied, evolving and adaptive systems.


No wonder scientists are increasingly taking on board computer science talk to describe biological systems.

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« Reply #4 on: September 18, 2009, 08:12:53 AM »

As evidenced here:
Bacteria as computers making computers
The immune system is no different.

Large-scale Study Probes How Cells Fight Pathogens
Quote
ScienceDaily (Sep. 6, 2009) — Scientists have deciphered a key molecular circuit that enables the body to distinguish viruses from bacteria and other microbes, providing a deep view of how immune cells in mammals fend off different pathogens.

Quote
The new research, which appears in the September 3 advance online edition of the journal Science, signifies one of the first large-scale reconstructions of a mammalian circuit and offers a practical approach for unraveling the circuits that underpin other important biological systems.

"Our findings address a fundamental question in human biology: how do immune cells recognize various pathogens and use that information to mount distinct responses," said senior author Nir Hacohen, of the Massachusetts General Hospital (MGH) Center for Immunology and Inflammatory Diseases, an assistant professor at Harvard Medical School and a senior associate member at the Broad Institute. "We now have a detailed view of the circuitry that controls this critical process, providing a deeper understanding of immune biology that could inspire novel ways to treat disease and design better vaccines."

"One of the remarkable things about this study is the approach," said senior author Aviv Regev, a core member of the Broad Institute, an assistant professor at MIT and an early career scientist at the Howard Hughes Medical Institute. "Our methods are not only general and applicable to almost any biological system, they are also practical for most laboratory settings. This is an important step that has broad implications for the scientific community."

Cells receive and process information much like computers. Information flows in, is read and processed through a complex set of circuits, and an appropriate response is delivered. But instead of tiny transistors, the internal circuitry of mammalian cells is made up of vast networks of genes and their corresponding proteins. A frontier of modern genomic research is to identify these molecular parts and their interconnections, which reflect the normal — and sometimes faulty — "wiring" that underlies human biology and disease. Until recently, research in this area focused on yeast and bacteria because it was nearly impossible to undertake in mammals.

With a deep-seated interest in specialized immune cells known as dendritic cells, a research team led by scientists at the Broad Institute of MIT and Harvard and Massachusetts General Hospital set out to reveal the full scope of their internal circuitry. Dendritic cells are among the first to detect pathogens and can differentiate one type of pathogen from another, allowing them to orchestrate a pathogen-specific immune response. These cells accomplish such tasks through two crucial functions: first, they present small pieces of an infecting pathogen to other immune cells so those cells can learn to recognize it; and second, they instruct other cells to respond in ways that will eliminate the culprit pathogen.

To begin, lead author Ido Amit, a postdoctoral fellow at the Broad Institute and Massachusetts General Hospital, worked with his colleagues to assemble a detailed picture of the circuit's output. The researchers did this by measuring the activities of thousands of genes after mixing parts of different pathogens, including RNA from viruses and pieces of the bacteria Escherichia coli, with primary mouse dendritic cells. ("Primary" cells are taken directly from the body, rather than propagated for long periods in the laboratory.)

Next, they scoured these data to identify genes whose activities change with varying conditions. These genes form the circuit's potential regulatory framework, responsible for controlling the flow of information.

To figure out how these potential regulators work and how they are wired together, the researchers systematically eliminated each of them, and recorded the changes in the circuit's output. This was made possible by the use of RNA interference (RNAi), which can reduce or "knock down" the activity of specific genes and can be applied to practically every gene in the mouse genome.

"Our use of RNAi was essential," said Hacohen. "We couldn't have done this work without the efforts of our collaborators in the Broad's RNAi Platform and the tools developed by The RNAi Consortium." The researchers also used a single-molecule technology that enabled them to generate sensitive readouts of gene activity.

Regev, Hacohen, Amit and their colleagues revealed a dendritic cell circuit with two major arms: an inflammatory arm, which is highly active during bacterial infections and can initiate a system-wide immune response; and an anti-viral arm, which is induced upon viral infections and coordinates a more focused response tailored to viruses. Together, these arms encompass about 100 regulators — roughly four times as many as were previously known to be involved — and include several proteins that were not suspected to direct immune responses. "These unexpected findings really underscore the power of an unbiased approach," said Regev.

Another remarkable finding is the way these regulators operate. The researchers identified a surprising number of connections between regulators and other circuit components, more than 2,300 connections in total. In addition, some regulators seem to control a relatively broad swath of the circuit, including 25 genes or more, while others influence just a handful of genes. "A good analogy is the tuning dials on an old radio," said Amit. "The big knobs provide coarse adjustments, while the little ones tend to be fine tuners."

One intriguing "coarse tuner" is a protein called Timeless. In fruit flies, it controls circadian rhythms, the internal clock that keeps biological processes operating on a 24-hour cycle. In mammalian dendritic cells, however, Amit and his colleagues discovered that Timeless is a chief regulator of anti-viral responses, controlling over 200 genes required to fight viruses.

Another interesting regulator is CBX4, a "fine tuner" that controls the levels of a key protein involved in viral infections. This protein, called IFNB1 (for Interferon beta 1) requires precise control: if a virus is present, it must be highly active, yet if bacteria are the offending agents, its activity should be minimized.
...


Circuits and circuitry, information processing, learning and instructing, fine tuning, control etc... simile and analogies and all, this is how things work on a subcellular scale with machines and codes regulating the processes.

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« Reply #5 on: September 18, 2009, 12:43:26 PM »

Mmm, looks like cut and paste is too easy these days. Let me try:
Please guys, this is not productive at all. Irreverend, you are quadruple posting and Mechanist you are mass cross posting without making any useful arguments. Please don't reply to this post - start a new thread or PM/email privately.
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« Reply #6 on: September 19, 2009, 13:27:14 PM »

Teleo-Phronetic-Mechano-Chap, are dropping the same posts into all the forums again, like a dog peeing on lampposts? Howzabout some bio-inspired crap detection? Or something bio-inspired to biodegrade your boring quote-mines?
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« Reply #7 on: May 12, 2010, 09:08:11 AM »

Ah, some more interesting news from the world of science for you science lovers:
DNA Could Be Backbone of Next-Generation Logic Chips
Quote
ScienceDaily (May 11, 2010) — In a single day, a solitary grad student at a lab bench can produce more simple logic circuits than the world's entire output of silicon chips in a month.



This is a closeup of a waffle. (Credit: Chris Dwyer)

Quote
So says a Duke University engineer, who believes that the next generation of these logic circuits at the heart of computers will be produced inexpensively in almost limitless quantities. The secret is that instead of silicon chips serving as the platform for electric circuits, computer engineers will take advantage of the unique properties of DNA, that double-helix carrier of all life's information.

In his latest set of experiments, Chris Dwyer, assistant professor of electrical and computer engineering at Duke's Pratt School of Engineering, demonstrated that by simply mixing customized snippets of DNA and other molecules, he could create literally billions of identical, tiny, waffle-looking structures.

Dwyer has shown that these nanostructures will efficiently self-assemble, and when different light-sensitive molecules are added to the mixture, the waffles exhibit unique and "programmable" properties that can be readily tapped. Using light to excite these molecules, known as chromophores, he can create simple logic gates, or switches.

These nanostructures can then be used as the building blocks for a variety of applications, ranging from the biomedical to the computational.

"When light is shined on the chromophores, they absorb it, exciting the electrons," Dwyer said. "The energy released passes to a different type of chromophore nearby that absorbs the energy and then emits light of a different wavelength. That difference means this output light can be easily differentiated from the input light, using a detector."

Instead of conventional circuits using electrical current to rapidly switch between zeros or ones, or to yes and no, light can be used to stimulate similar responses from the DNA-based switches -- and much faster.

"This is the first demonstration of such an active and rapid processing and sensing capacity at the molecular level," Dwyer said. The results of his experiments were published online in the journal Small. "Conventional technology has reached its physical limits. The ability to cheaply produce virtually unlimited supplies of these tiny circuits seems to me to be the next logical step."

DNA is a well-understood molecule made up of pairs of complimentary nucleotide bases that have an affinity for each other. Customized snippets of DNA can cheaply be synthesized by putting the pairs in any order. In their experiments, the researchers took advantage of DNA's natural ability to latch onto corresponding and specific areas of other DNA snippets.

Dwyer used a jigsaw puzzle analogy to describe the process of what happens when all the waffle ingredients are mixed together in a container.

"It's like taking pieces of a puzzle, throwing them in a box and as you shake the box, the pieces gradually find their neighbors to form the puzzle," he said. "What we did was to take billions of these puzzle pieces, throwing them together, to form billions of copies of the same puzzle."

In the current experiments, the waffle puzzle had 16 pieces, with the chromophores located atop the waffle's ridges. More complex circuits can be created by building structures composed of many of these small components, or by building larger waffles. The possibilities are limitless, Dwyer said.

In addition to their use in computing, Dwyer said that since these nanostructures are basically sensors, many biomedical applications are possible. Tiny nanostructures could be built that could respond to different proteins that are markers for disease in a single drop of blood.

Dwyer's research is supported by the National Science Foundation, the Air Force Research Laboratory, the Defense Advanced Research Projects Agency and the Army Research Office. Other members of the Duke team were Constantin Pistol, Vincent Mao, Viresh Thusu and Alvin Lebeck.


Hopefully they will do more than waffling Cheesy.
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« Reply #8 on: July 06, 2010, 13:22:43 PM »

More genetic inspiration for our own technologies.
Genetic Inspiration Could Show the Way to Revolutionize Information Technology

Quote
ScienceDaily (July 4, 2010) — Chemists at the University of Reading have created a synthetic form of DNA that could transform how digital information is processed and stored.


Quote
Just as the information in a book is made up of a linear sequence of letters, so the information needed for all living things to function and reproduce is embodied in a linear sequence of chemical units. These make up the chains of DNA and RNA, where an enormous amount of information (the 'genome') is stored in a very small space to direct the molecular processes of life.

A new paper, which appears in Nature Chemistry on June 27, shows for the first time that many of the features of biological information processing can be reproduced in synthetic polymer chains.

The Reading team, led by Howard Colquhoun, Professor of Materials Chemistry in the Department of Chemistry, has designed and synthesised short sequences of a synthetic, information-bearing polymer.

In the long term, researchers believe this could revolutionise the future of digital information. Synthetic polymer systems could allow information densities several million times higher than current systems.

Crucial to the work is the creation of tweezer-shaped molecules that pick out sequence-information along a polymer chain. The two arms of the tweezer 'feel' the different sequences available and then clamp on to the chain at the precise sequence where the chain structure and tweezer structure are most complementary.

Several tweezer molecules can bind next to one another on the polymer chain, allowing them to 'read' and translate extended, long-range polymer-sequence information. Most notable is that different types of tweezer molecules start reading at different positions on the chain. This selectivity means different types of information can be read from the same sequence which increases the amount of information available.

Professor Colquhoun said: "This type of process is paralleled in the processing of genetic information. In the future, we plan to develop methods for writing new information into the polymer chains with the long-term aim of developing wholly synthetic information technology, working at the molecular level.


And some more biomimicry:
Biologically Inspired Technology Produces Sugar from Photosynthetic Bacteria
Quote
ScienceDaily (June 29, 2010) — Researchers from the Wyss Institute for Biologically Inspired Engineering at Harvard and Harvard Medical School have engineered photosynthetic bacteria to produce simple sugars and lactic acid. This innovation could lead to new, environmentally friendly methods for producing commodity chemicals in bulk.

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