Biomimicry: Biologically Inspired Engineering

[Phronesis]

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

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

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.

Feel free to post more interesting designs in nature that can be used for our own future designs.

 

[Phronesis]

Hair Structures Of Blind Cavefish Inspire New Generation Of Sensors

ScienceDaily (Mar. 24, 2009) — A blind fish that has evolved a unique technique for sensing motion may inspire a new generation of sensors that perform better than current active sonar.

Although members of the fish species Astyanax fasciatus cannot see, they sense their environment and the movement of water around them with gel-covered hairs that extend from their bodies. Their ability to detect underwater objects and navigate through their lightless environment inspired a group of researchers to mimic the hairs of these blind cavefish in the laboratory.

While the fish use these hairs to detect obstacles, avoid predators and localize prey, researchers believe the engineered sensors they are developing could have a variety of underwater applications, such as port security, surveillance, early tsunami detection, autonomous oil rig inspection, autonomous underwater vehicle navigation, and marine research.

"These hair cells are like well-engineered mechanical sensors, similar to those that we use for balance and hearing in the human ear, where the deflection of the jelly-encapsulated hair cell measures important flow information," said Vladimir Tsukruk, a professor in the Georgia Tech School of Materials Science and Engineering. "The hairs are better than active sonar, which requires a lot of space, sends out strong acoustic signals that can have a detrimental effect on the environment, and is inappropriate for stealth applications."

In a presentation on March 20 at the American Physical Society meeting, researchers from Georgia Tech described their engineered motion detector that mimics the underwater flow measurements made by the blind cavefish. This research was sponsored by the Defense Advanced Research Projects Agency (DARPA).

Tsukruk and graduate students Michael McConney and Kyle Anderson conducted preliminary experiments with a simple artificial hair cell microsensor made of SU-8, a common epoxy-based polymer capable of solidifying, and built with conventional CMOS microfabrication technology. They found that the cell by itself could not achieve the high sensitivity or long-range detection of hydrodynamic disturbances created by moving or stationary bodies in a flow field. The hair cell needed the gel-like capsule – called the cupula – to overcome these challenges.

"After covering the hair cell with synthetic cupula, our bio-inspired microsensor had the ability to detect flow better than the blind fish. The fish can detect flow slower than 100 micrometers per second, but our system demonstrated flow detection of several micrometers per second," said Tsukruk, who also holds an appointment in Georgia Tech's School of Polymer, Textile and Fiber Engineering. "Adding the cupula allowed us to detect a much smaller amount of flow and expand the dynamic range because it suppressed the background noise."

In addition, the hydrogel encapsulation protects the sensors and increases their ability to withstand deformation due to impact. It also helps the hairs better withstand the marine environment by resisting corrosion and microorganism growth.

Before the research team began synthesizing the gel-like material in the laboratory, they used optical microscopy and confocal fluorescence microscopy to determine the size, shape and properties of real cavefish cupula. One type of cupula they found was cylindrical-shaped, with a height approximately five times larger than its diameter. The tallest part of the cupula was far enough away from the surface that it was exposed to free-flowing water and could bend with the hair to detect changes in flow.

To create the synthetic cupula in the laboratory, McConney dropped a solution of poly(ethylene glycol) tetraacrylate dissolved in methanol directly on the hair flow sensor. Once the droplet dried, he lowered another droplet until it made contact with the last drop and continued adding droplets until he constructed a tall hydrogel structure. Once the entire cupula structure dried, McConney exposed it to ultraviolet light to crosslink it, forming a three-dimensional network.

"This method of adding one droplet at a time allowed us to control the width and height of the cupula and the distance from the bottom of the cupula to the base of the hair," said McConney.

While the researchers found that placing the synthetic cupula closest to the sensor platform enhanced the durability and lifetime of the capsule, they captured the best flow measurements when the cupula structure started halfway up the hair and extended past the hair by 50 percent.

They achieved the best flow results with fabricated hairs that were 550 millimeters long with dried cupula that started 275 millimeters above the base of the hair and extended 275 millimeters above the hair, giving the total hair-cupula structure a height of 825 millimeters.

To date, the researchers have fabricated an array of eight microsensors and shown that the array is able to detect an oscillating object underwater. They are currently looking for industrial partners to efficiently scale-up the research by fabricating arrays of thousands of these sensors and testing them in real marine environments.

Cheryl Coombs from Bowling Green State University and Chang Liu from the University of Illinois also contributed to this research.

After covering the hair cell with synthetic cupula, our bio-inspired microsensor had the ability to detect flow better than the blind fish. The fish can detect flow slower than 100 micrometers per second, but our system demonstrated flow detection of several micrometers per second,"

Natural selection or artificial selection?

 

[Phronesis]

Chemists Create Bipedal, Autonomous DNA Walker

ScienceDaily (Apr. 2, 2009) — Chemists at New York University and Harvard University have created a bipedal, autonomous DNA "walker" that can mimic a cell's transportation system. The device, which marks a step toward more complex synthetic molecular motor systems, is described in the most recent issue of the journal Science.

Two fundamental components of life's building blocks are DNA, which encodes instructions for making proteins, and motor proteins, such as kinesin, which are part of a cell's transportation system. In nature, single strands of DNA—each containing four molecules, or bases, attached to backbone—self-assemble to form a double helix when their bases match up. Kinesin is a molecular motor that carries various cargoes from one place in the cell to another. Scientists have sought to re-create this capability by building DNA walkers.

Earlier versions of walkers, which move along a track of DNA, did not function autonomously, thereby requiring intervention at each step. A challenge these previous devices faced was coordinating the movement of the walker's legs so they could move in a synchronized fashion without falling off the track.

To create a walker that could move on its own, the NYU and Harvard researchers employed two DNA "fuel strands" (purple and green in the above video). These fuel strands push the walker (blue) along a track of DNA, thereby allowing the walker and the fuel strands to function as a catalytic unit.

The forward progress of the system is driven by the fact that more base pairs are formed every step—a process that creates the energy necessary for movement. As the walker moves along the DNA track, it forms base pairs. Simultaneously, the fuel strands move the walker along by binding to the track and then releasing the walker's legs, thereby allowing the walker to take "steps".

The track's length is 49 nanometers—if the track was one meter long, an actual meter, enlarged proportionally, would be the approximate diameter of the earth.

For a video demonstration of the walker, go to http://www.nyu.edu/public.affairs/videos/qtime/biped_movie.mov.

The walker was created in the laboratory of NYU Chemistry Professor Nadrian Seeman, one of the article's co-authors. The paper's other authors were Tosan Omabegho, a doctoral candidate at Harvard's School of Engineering and Applied Sciences, and Ruojie Sha, a senior research associate in the NYU Chemistry Department.

 

[Phronesis]

Scientists Control Complex Nucleation Processes Using DNA Origami Seeds

ScienceDaily (Apr. 8, 2009) — The construction of complex man-made objects--a car, for example, or even a pizza--almost invariably entails what are known as "top-down" processes, in which the structure and order of the thing being built is imposed from the outside (say, by an automobile assembly line, or the hands of the pizza maker).

"Top-down approaches have been extremely successful," says Erik Winfree of the California Institute of Technology (Caltech). "But as the object being manufactured requires higher and higher precision--such as silicon chips with smaller and smaller transistors--they require enormously expensive factories to be built."

The alternative to top-down manufacturing is a "bottom-up" approach, in which the order is imposed from within the object being made, so that it "grows" according to some built-in design. (Me: Front loading comes to mind here, see below)

"Flowers, dogs, and just about all biological objects are created from the bottom up," says Winfree, an associate professor of computer science, computation and neural systems, and bioengineering at Caltech. Along with his coworkers, Winfree is seeking to integrate bottom-up construction approaches with molecular fabrication processes to construct objects from parts that are just a few billionths of a meter in size that essentially assemble themselves.

In a recent paper in the Proceedings of the National Academy of Sciences (PNAS), Winfree and his colleagues describe the development of an information-containing DNA "seed" that can direct the self-assembled bottom-up growth of tiles of DNA in a precisely controlled fashion. In some ways, the process is similar to how the fertilized seeds of plants or animals contain information that directs the growth and development of those organisms.

"The big potential advantage of bottom-up construction is that it can be cheap"--just as the mold that grows in your kitchen does so for free--"and can be massively parallel, because the objects construct themselves," says Winfree.

But, he adds, while bottom-up approaches have been extremely useful in biology, they haven't played as significant a role in technology, "because we don't have a great grasp on how to design systems that build themselves. (Me: Well, life can do it just fine: machines that make machines.) Most examples of bottom-up technologies are specific chemical processes that work great for a particular task, but don't easily generalize for constructing more complex structures."

To understand how complexity can be programmed into bottom-up molecular fabrication processes, Winfree and his colleagues study and understand the processes--or algorithms--that generate organization not just in computers but also in the natural world. (Me: Yep, these guys are front loading future designs by understanding the basic processes and algorithms of the laws of nature.)

"Tasks can be solved by carrying out well-defined rules, and these rules can be carried out by a mindless mechanism such as a computer," he says. "The same set of rules can perform different tasks when given different inputs, and there exist 'universal programs' that can perform any task required of it, as specified in its input. Your laptop is such a universal computer; it can run any software that you download, and in principle, any feasible task could be programmed."

These principles also have been exploited by natural evolution, Winfree says: "Every cell, it appears, is a kind of universal computer that can be instructed in seemingly limitless ways by a DNA genome that specifies what chemical processes to execute, thus building an active organism. The aim of my lab has been to understand algorithms and information within molecular systems."

Winfree's investigations into algorithmic self-assembly earned him a MacArthur "genius" prize in 2000; his collaborator, Paul W. K. Rothemund, a senior research associate at Caltech and a coauthor of the PNAS paper, was awarded the same no-strings-attached grant in 2007 for his work designing scaffolded "DNA origami" structures that self-assemble into nearly arbitrary shapes (such as a smiley face and a map of the Western Hemisphere).

The structures designed by Rothemund, which could eventually be used in smaller, faster computers, were used as the seeds for the programmed self-assembly of DNA tiles described in the current paper.

In the work, the researchers designed several different versions of a DNA origami rectangle, 95 by 75 nanometers, which served as the seeds for the growth of different types of ribbon-like crystals of DNA. The seeds were combined in a test tube with other bits of DNA, called "tiles," heated, and then cooled slowly.

"As it cools, the first origami seed and the individual tiles form, as their component DNA molecules begin sticking to each other and folding into shape--but the tiles and origami don't stick to each other yet," Winfree explains.

"Then, at a lower temperature, the tiles start to stick to each other and to the origami. The critical concept here is that the DNA tiles will only form crystals if the process gets started by a seed, upon which they can grow," he says.

In this way, the DNA ribbons self-assemble themselves, but only into forms such as ribbons with particular widths and ribbons with stripe patterns prescribed by the original seed.

The work, Winfree says, "exhibits a degree of control over information-directed molecular self-assembly that is unprecedented in accuracy and complexity, which makes me feel that we are finally beginning to understand how to program information into molecules and have that information direct algorithmic processes." (Me: yeah well, unprecedented for human designs I guess. These type of processes are carried out thousands of times per second in even simple bacterial cells.

The other authors of the paper are undergraduate Robert D. Barish and visiting scholar Rebecca Schulman. The work was supported by grants from the National Aeronautics and Space Administration's astrobiology program, the National Science Foundation, and the Focus Center Research Program, and a gift from Microsoft Research.

Fascinating work.

 

[Phronesis]

The future of our own designs....

'Gecko Vision': Key To Future Multifocal Contact Lens?

ScienceDaily (May 8, 2009) — Nocturnal geckos are among the very few living creatures able to see colors at night, and scientists' discovery of series of distinct concentric zones may lead to insight into better cameras and contact lenses.

The key to the exceptional night vision of the nocturnal helmet gecko is a series of distinct concentric zones of different refractive powers, according to a new study.

This multifocal optical system is comprised of large cones, which the researchers calculated to be more than 350 times more sensitive than human cone vision at the human color vision threshold.

"We were interested in the geckos because they – and other lizards – differ from most other vertebrates in having only cones in their retina," said project leader Lina Roth, PhD, from the Department of Cell and Organism Biology at Lund University in Sweden. "With the knowledge from the gecko eyes we might be able to develop more effective cameras and maybe even useful multifocal contact lenses."

The nocturnal geckos' multifocal optical system gives them an advantage because light of different ranges of wavelengths can focus simultaneously on the retina. Another possible advantage of their optical structure is that their eyes allow them to focus on objects at different distances. Therefore the multifocal eye would generate a sharp image for at least two different depths. Geckos that are active during the day do not possess the distinct concentric zones and are considered monofocal, Roth said.

The scientists also developed a new method to gather optical data from live animals without harm with their modifications to the Hartmann-Shack wavefront sensor.

"Studies of animals with relatively large eyes, such as owls and cats, have included surgery and fixation of the head," the article states. "In this study, we demonstrate that it is possible to obtain high-resolution wavefront measurements of small, unharmed gecko eyes without completely controlling the gaze or the accommodation of the animal eyes."

Copying the machines of life:
First Fully Automated Pipeline For Multiprotein Complex Production

ScienceDaily (May 7, 2009) — Most cellular processes are carried out by molecular machines that consist of many interacting proteins. These protein complexes lie at the heart of life science research, but they are notoriously hard to study. Their abundance is often too low to extract them directly from cells and generating them with recombinant methods has been a daunting task.

A new technology to produce multiprotein complexes, developed by researchers at the European Molecular Biology Laboratory [EMBL] in Grenoble, France, and the Paul Scherrer Institute [PSI] in Villigen, Switzerland, now makes the biologist's life easier.

In a paper published in the current issue of Nature Methods, researchers of the groups of Imre Berger at EMBL and Michel Steinmetz at the PSI describe ACEMBL, the first fully automated pipeline for the production of multiprotein complexes. Requiring much less effort and materials, the new pipeline will speed up structural studies of protein complexes and will allow to decipher as yet elusive molecular mechanisms of health and disease.

ACEMBL can produce complexes consisting of different types of components, including protein, RNA and other biomolecules. Currently designed to express proteins in the standard system Escherichium coli, the automated pipeline will in future be adapted for complex production in eukaryotic cells. This will allow the study of even larger, more complicated complexes of human origin, including many promising drug targets. The system has already attracted commercial interest.

 

[Phronesis]

Stirred, Not Shaken: Bio-inspired Cilia Mix Medical Reagents At Small Scales

ScienceDaily (June 30, 2009) — The equipment used for biomedical research is shrinking, but the physical properties of the fluids under investigation are not changing. This creates a problem: the reservoirs that hold the liquid are now so small that forces between molecules on the liquid's surface dominate, and one can no longer shake the container to mix two fluids. Instead, researchers must bide their time and wait for diffusion to occur.

Scientists at the University of Washington hope to speed up biomedical reactions by filling each well with tiny beating rods that mimic cilia, the hairlike appendages that line organs such as the human windpipe, where they sweep out dirt and mucus from the lungs. The researchers created a prototype that mixes tiny volumes of fluid or creates a current to move a particle, according to research published in the journal Lab on a Chip. They used a novel underwater manufacturing technique to overcome obstacles faced by other teams that have attempted to build a similar device.

Diffusion, or random mixing of molecules, is slow but often the only option for mixing the small volumes that are increasingly common in modern biomedical research. A plate that once held 96 wells now can have 384 or 1,536 wells, each of which tests reactions on different combinations of liquids. The volume of liquid in each well of the 384-well plate is just 50 microliters, about the volume of a single drop of water.

"In order to mix water with juice, you can shake it, because the mass is very big," said Jae-Hyun Chung, a UW assistant professor of mechanical engineering and corresponding author of the paper. "(For the wells used in biomedical assays) you can't shake the well to mix two fluids because the mass of liquid in each well is very small, and the viscosity is very high."

The problem of mixing at small scales has confronted biomedical researchers for about 40 years, Chung said. Other strategies for mixing -- shakers, magnetic sticks, ultrasonic systems, vortex machines -- have not worked in biomedical research for various reasons, including the shear stress, the need to have a clear view of each well, and damage to the enzymes and biological molecules.

In the past decade, various research groups have tried to develop structures that mimic cilia, which do the small-scale moving and shaking inside the human body. The problem is that each cilium finger must be very flexible in order to vibrate -- so delicate, in fact, that manufactured cilia of this size collapse as they are placed in water.

The UW team solved the problem by manufacturing the cilia underwater, Chung said. The resulting prototype is a flexible rubber structure with fingers 400 micrometers long (about 1/100 of an inch) that can move liquids or biological components such as cells at the microscopic scale.

The team varied the length and spacing of the fingers to get different vibration frequencies. When they now apply a small vibration to the surrounding water, the fingers on the UW prototype move back and forth at 10 to 100 beats per second, roughly the vibration frequency of biological cilia.

The results show the device can mix two fluids many times faster than diffusion alone and can generate a current to move small particles in a desired direction. A current could be used, for example, to move cells through a small-scale diagnostic test.

Co-authors are UW mechanical engineering doctoral student Kieseok Oh and mechanical engineering professors Santosh Devasia and James Riley. The research is funded by the National Science Foundation.

The team has obtained a provisional patent on the technology, and has funding from the UW's Royalty Research Fund to build a prototype 384-well plate lined with cilia.

"We are currently trying to develop the technology for high-throughput biochemical applications," Chung said. "But we can also do micro-mixing and micro-pumps, which have many potential applications."

Nice videos about cilia and flagella:
[ame]http://www.youtube.com/watch?v=E1L27sUzwQ0[/ame]
[ame]http://www.youtube.com/watch?v=Ey7Emmddf7Y[/ame]
[ame]http://www.youtube.com/watch?v=hLTFiekwFy8[/ame]

Hard work to mimic these engineering feats....

 

[Phronesis]

Human Eye Inspires Advance In Computer Vision

ScienceDaily (June 22, 2009) — Inspired by the behavior of the human eye, Boston College computer scientists have developed a technique that lets computers see objects as fleeting as a butterfly or tropical fish with nearly double the accuracy and 10 times the speed of earlier methods.

The linear solution to one of the most vexing challenges to advancing computer vision has direct applications in the fields of action and object recognition, surveillance, wide-base stereo microscopy and three-dimensional shape reconstruction, according to the researchers, who will report on their advance at the upcoming annual IEEE meeting on computer vision.

BC computer scientists Hao Jiang and Stella X. Yu developed a novel solution of linear algorithms to streamline the computer's work. Previously, computer visualization relied on software that captured the live image then hunted through millions of possible object configurations to find a match. Further compounding the challenge, even more images needed to be searched as objects moved, altering scale and orientation.

Rather than combing through the image bank – a time- and memory-consuming computing task – Jiang and Yu turned to the mechanics of the human eye to give computers better vision.

"When the human eye searches for an object it looks globally for the rough location, size and orientation of the object. Then it zeros in on the details," said Jiang, an assistant professor of computer science. "Our method behaves in a similar fashion, using a linear approximation to explore the search space globally and quickly; then it works to identify the moving object by frequently updating trust search regions."

Trust search regions act as visual touchstones the computer returns to again and again. Jiang and Yu's solution focuses on the mathematically-generated template of an image, which looks like a constellation when lines are drawn to connect the stars. Using the researchers' new algorithms, computer software identifies an object using the template of a trust search region. The program then adjusts the trust search regions as the object moves and finds its mathematical matches, relaying that shifting image to a memory bank or a computer screen to record or display the object.

Jiang says using linear approximation in a sequence of trust regions enables the new program to maintain spatial consistency as an object moves and reduces the number of variables that need to be optimized from several million to just a few hundred. That increased the speed of image matching 10 times over compared with previous methods, he said.

The researchers tested the software on a variety of images and videos – from a butterfly to a stuffed Teddy Bear – and report achieving a 95 percent detection rate at a fraction of the complexity. Previous so-called "greedy" methods of search and match achieved a detection rate of approximately 50 percent, Jiang said.

 

[Nerhzelok]

*rubs eyes*

 

[Phronesis]

The Virus That Binds: A Novel Idea Marries Biology And Mining

ScienceDaily (July 22, 2009) — Researchers often make progress by applying a proven scientific method from one realm to another, connecting seemingly disparate disciplines. Such interdisciplinary approaches are powerful tools in the drive for scientific innovation.

But who would ever dream of applying viruses to mining?

Professor Scott Dunbar of UBC’s Norman B. Keevil Institute of Mining Engineering would.

“I read an article about bacteriophage – viruses that infect bacteria – being used to create nanodevices in which proteins on the phage surface are engineered to bind to gold and zinc sulfide,” says Dunbar. “And it struck me: if zinc sulfide, why not copper sulfide? And if so, then it might be possible to use these bio-engineered proteins to separate common economic sulfide minerals from waste during mineral extraction.”

Bacteriophage, commonly called phage, refers to viruses that infect bacteria. Typically phage consists of an outer protein coating that enclose genetic material—DNA. They are the most abundant life form on Earth, numbering as many as 1031. Phage replicate by infecting bacteria but are harmless to humans, animals and plants. Only a few nanometers in diameter, hundreds could fill the diameter of a single human hair.

Current methods of sulfide mineral separation add detergent-like chemicals called collectors to a tank containing a slurry of finely ground ore particles. Collectors render specific sulfide particles in the ore hydrophobic (“afraid” of water) so that they attach to bubbles in the tank and float to the surface forming a sulfide concentrate. However, in some cases, particularly with ores that contain several sulfide minerals, the recovery of specific sulfide minerals can be poor.

Dunbar has partnered with UBC colleagues Sue Curtis and Ross MacGillivray from the Centre for Blood Research and the Department of Biochemistry & Molecular Biology to bring the idea from concept to laboratory. Together they recently published a paper entitled Biomining with bacteriophage: Selectivity of displayed peptides for naturally occurring sphalerite and chalcopyrite in the journal Biotechnology and Bioengineering.

The researchers found that it is possible to identify proteins on bacteriophage that bind to minerals of economic interest such as sphalerite (zinc sulfide), the chief ore mineral of zinc, and chalcopyrite (copper iron sulfide), the chief ore mineral of copper. The procedure is called “bio-panning,” a type of genetic engineering.

“You begin with a phage library which may contain one billion phage particles, each with different protein sequences. A few of these have the binding protein of interest. When the entire library is exposed to the mineral of interest, these few will bind to the mineral,” explains Dunbar. “You wash away the non-binding phage, then expose the binding phage to E. coli, which they infect and reproduce. The resulting phage would have DNA that contains the ‘codes’ for the binding proteins of interest. The procedure is repeated four or five times to amplify the number of binders. It’s somewhat like breeding animals for particular features.

“I knew we had phage that could bind specifically to sphalerite and to chalcopyrite,” says Dunbar. “But then, so what? The phage had to do something to the mineral surfaces to be useful.”

It turns out that the phage that bind to a mineral do affect the mineral surfaces, causing them to have a different electrical charge than other minerals. The proteins on the phage also form links to each other leading to aggregation of the specific sulfide particles. “The physical and chemical changes caused by phage may be the basis for a highly selective method of mineral separation with better recovery. Another possible application is bioremediation, where metals are removed from contaminated water” says Dunbar.

Dunbar and his colleagues are the first to apply phage to mineral processing. Their work is supported in part by the Applied Research and Technology group of Teck Corporation and the Michael Smith Foundation for Health Research. Prof. Valery Petrenko of Auburn University supplied a phage library.

 

[DJ...]

RAS...

 

[Phronesis]

ROFL, what's next? Are you going to moan sciencedaily.com is a creationist site? Get a grip won't you?

 

[DJ...]

I've got enough of a grip to know the difference between a thread intended to initiate debate, and spamming. The latter being what you are doing...

 

[Phronesis]

You want to DEBATE? You know.... there is this section called the Philosophical DEBATES section.
Also, please differentiate between spamming and posting scientifically relevant information. Read the posts above and see who is spamming and who is posting scientifically relevant information. :erm: Wake up

 

[DJ...]

Chap, it is pure and utter spam. If the point is merely to post links and videos, then you've completely missed the point of a forum. Go blog about it if you feel so compelled. You're proving to be both a troll and a spammer now...

 

[Phronesis]

Chap, it is pure and utter spam. If the point is merely to post links and videos, then you've completely missed the point of a forum. Go blog about it if you feel so compelled. You're proving to be both a troll and a spammer now...

Chap... go troll another thread and bait some other chap mmk.

 

[DJ...]

Kewl - we'll leave this one to die of natural causes then. Intentionally...

 

[Phronesis]

Don't worry about that, as long as the baiting and trolling are stopped, this thread will do juuuust fine. Since there are so many designs in nature we can use to make our own future designs... perhaps on a bigger scale. Here ya go:

[ame="http://www.youtube.com/watch?v=n77BfxnVlyc"]http://www.youtube.com/watch?v=n77BfxnVlyc[/ame]​

 

[Phronesis]

Mimicking and retooling evolution to design medicinally relevant compounds...
Researchers Rapidly Turn Bacteria Into Biotech Factories

ScienceDaily (July 26, 2009) — High-throughput sequencing has turned biologists into voracious genome readers, enabling them to scan millions of DNA letters, or bases, per hour. When revising a genome, however, they struggle, suffering from serious writer's block, exacerbated by outdated cell programming technology. Labs get bogged down with particular DNA sentences, tinkering at times with subsections of a single gene ad nauseam before moving along to the next one.

A team has finally overcome this obstacle by developing a new cell programming method called Multiplex Automated Genome Engineering (MAGE). Published online in Nature on July 26, the platform promises to give biotechnology, in particular synthetic biology, a powerful boost.

Led by a pair of researchers in the lab of Harvard Medical School Professor of Genetics George Church, the team rapidly refined the design of a bacterium by editing multiple genes in parallel instead of targeting one gene at a time. They transformed self-serving E. coli cells into efficient factories that produce a desired compound, accomplishing in just three days a feat that would take most biotech companies months or years.

"We initiated the project to close the gap between DNA sequencing technology and cell programming technology," explains graduate student Harris Wang, the paper's co-first author.

"The goal was to use information gleaned from genetics and genomics to rapidly engineer new functions and improve existing functions in cells," adds postdoctoral researcher Farren Isaacs, the other first author. "We wanted to develop a new tool and demonstrate how to apply it; we were determined to hand labs a hammer and a nail."

The key was to break free of linear genetic engineering techniques and move beyond the serial manipulation of single genes.

The researchers selected a harmless strain of the intestinal nemesis E. coli and added a few genes to its solitary circular chromosome, coaxing the organism to produce lycopene, a powerful antioxidant that occurs naturally in tomatoes and other vegetables. Now they could focus on tweaking the cells to increase the yield of this compound.

Traditionally, labs would accomplish this type of transformation by using recombinant DNA technology, also known as gene cloning, a complicated technique that involves isolating, breaking up, reassembling, and then reinserting genes.

The Church lab researchers took a different approach, blending an engineer's logic with a biologist's appreciation for complexity. "Genes function in teams, not in isolation," says Wang. "Cloning often encourages us to ignore the interdependence of genes and oversimplify the cellular system. We might forget, for example, that one mutation can strengthen or weaken the effects of another mutation."

"It's nearly impossible to predict which combinations of mutations will confer the desired behavior," explains Isaacs. "Biology is so complex that we don't know the optimal solution."

So the team retooled evolution to generate genetic diversity at an unprecedented rate, increasing the odds of finding cells with desirable properties.

The E. coli bacterium contains approximately 4,500 genes. The team focused on 24 of these—honing a pathway with tremendous potential—to increase production of the antioxidant, optimizing the sequences simultaneously. They took the 24 DNA sequences, divided them up into manageable 90-letter segments, and modified each, generating a suite of genetic variants. Next, armed with specific sequences, the team enlisted a company to manufacture thousands of unique constructs. The team was then able to insert these new genetic constructs back into the cells, allowing the natural cellular machinery to absorb this revised genetic material.

Some bacteria ended up with one construct, some ended up with multiple constructs. The resulting pool contained an assortment of cells, some better at producing lycopene than others. The team extracted the best producers from the pool and repeated the process over and over to further hone the manufacturing machinery. To make things easier, the researchers automated all of these steps.

"We accelerated evolution, generating as many as 15 billion genetic variants in three days and increasing the yield of lycopene by 500 percent," Harris says. "Can you imagine how long it would take to generate 15 billion genetic variants with traditional cloning techniques? It would take years."

The pathway the team refined plays a role in the synthesis of many valuable compounds, ranging from hormones to antibiotics, so the reprogrammed bacteria can be used for a variety of purposes. In addition, the MAGE platform itself unlocks new possibilities.

"We decided to engineer in the context of biology, embracing evolution rather than trying to fit a square peg in a round hole," says Church. "This automated, multiplex technology will allow labs to engineer entire pathways and genomes and take cell programming to a whole new level."

This research is funded by NSF, DOE, DARPA, the Wyss Institute for Biologically Inspired Engineering, NIH and NDSEG.

What a brilliant evolutionary design as a result of some intelligent minds.... scientists .

 

[Phronesis]

World's Smallest Computers Made of DNA and Other Biological Molecules Made to 'Think' Logically

ScienceDaily (Aug. 3, 2009) — Biomolecular computers, made of DNA and other biological molecules, only exist today in a few specialized labs, remote from the regular computer user. Nonetheless, Tom Ran and Shai Kaplan, research students in the lab of Prof. Ehud Shapiro of the Weizmann Institute’s Biological Chemistry, and Computer Science and Applied Mathematics Departments have found a way to make these microscopic computing devices ‘user friendly,’ even while performing complex computations and answering complicated queries.

Shapiro and his team at Weizmann introduced the first autonomous programmable DNA computing device in 2001. So small that a trillion fit in a drop of water, that device was able to perform such simple calculations as checking a list of 0s and 1s to determine if there was an even number of 1s. A newer version of the device, created in 2004, detected cancer in a test tube and released a molecule to destroy it. Besides the tantalizing possibility that such biology-based devices could one day be injected into the body – a sort of ‘doctor in a cell’ locating disease and preventing its spread – biomolecular computers could conceivably perform millions of calculations in parallel.

Now, Shapiro and his team, in a paper published online August 3 in Nature Nanotechnology, have devised an advanced program for biomolecular computers that enables them to ‘think’ logically.

The train of deduction used by this futuristic device is remarkably familiar. It was first proposed by Aristotle over 2000 years ago as a simple if…then proposition: ‘All men are mortal. Socrates is a man. Therefore, Socrates is mortal.’ When fed a rule (All men are mortal) and a fact (Socrates is a man), the computer answered the question ‘Is Socrates Mortal?’ correctly. The team went on to set up more complicated queries involving multiple rules and facts, and the DNA computing devices were able to deduce the correct answers every time. At the same time, the team created a compiler – a program for bridging between a high-level computer programming language and DNA computing code. Upon compiling, the query could be typed in something like this: Mortal(Socrates)?. To compute the answer, various strands of DNA representing the rules, facts and queries were assembled by a robotic system and searched for a fit in a hierarchical process. The answer was encoded in a flash of green light: Some of the strands had a biological version of a flashlight signal – they were equipped with a naturally glowing fluorescent molecule bound to a second protein which keeps the light covered. A specialized enzyme, attracted to the site of the correct answer, removed the ‘cover’ and let the light shine. The tiny water drops containing the biomolecular data-bases were able to answer very intricate queries, and they lit up in a combination of colors representing the complex answers.

Prof. Ehud Shapiro’s research is supported by the Clore Center for Biological Physics; the Arie and Ida Crown Memorial Charitable Fund; the Phyllis and Joseph Gurwin Fund for Scientific Advancement; Sally Leafman Appelbaum, Scottsdale, AZ; the Carolito Stiftung, Switzerland; the Louis Chor Memorial Trust Fund; and Miel de Botton Aynsley, UK. Prof. Shapiro is the incumbent of the Harry Weinrebe Chair of Computer Science and Biology.

 

[DJ...]

More RAS...