Smart Economy

Smart Bio Plastics from CO2 Flue Gas

Oakbio Makes Bioplastic at Cement Plant using

CO2 from Flue Gas and Electricity 

Milestone for cement industry
and renewable products

 

SUNNYVALE, CA (July 10,  2012) - Today Oakbio Inc.

announced the successful production of bioplastic

polymers in their bioreactor systems. Oakbio's

system creates bioplastic using inputs of cement

plant flue gas and electricity. The technology
uses bioreactors driven by non-toxic microbes

to capture CO2 and convert it to a variety of

sustainable products directly from the plant's

gas emissions.

 

This is the latest  development from an on-site

research collaboration at Lehigh Southwest Cement
Company's Permanente cement manufacturing

plant in Cupertino. Lehigh Southwest is part of

Lehigh Hanson, Inc., the North American operations

of the  Heidelberg Cement Group, a world leader

in construction materials with  approximately

52,000 employees in more than 40 countries.

 

Chief Scientist Brian
Sefton stated, "Our carbon conversion process

yields over 50% bioplastics in  microbe biomass

by dry weight from inputs of raw flue gas and

electricity. The type of plastic we make is not

only renewable, but biodegradable as
well.

 

"The effective conversion of captured CO2 into

a valuable bioplastic product represents an

important technical achievement for potential

large-scale bioplastics production. This result

also points the way to a new method for

greenhouse gas capture, making emissions

gas CO2 a feedstock for mass scale manufacturing."

 

CEO Russell Howard added:
"At Oakbio we see industrial CO2 as a carbon

resource. By converting virtually unlimited amounts

of low cost CO2 available from various industries

worldwide into sustainable products like biodegradable

plastics, Oakbio's technology can answer multiple

needs: full scale chemicals production without the

use of petroleum oil or agricultural feedstock;

replacement of petroleum oil-derived plastics

with bio-degradable renewable products; and

the capture of CO2 to prevent greenhouse gas

accumulation. The ability of our microbes to

perform their magic in cement flue gas is an

important step toward achieving this vision".

 

 

About Oakbio, Inc.

Oakbio is a private
technology-based company in Sunnyvale dedicated to sustainable production of
specialty chemicals using novel microbial production processes that combine GHG
reduction with manufacture of sustainable specialty chemicals (see www.oakbio.com).

Media
Contact:

Russell Howard, CEO,
Oakbio, (408) 930-7004; rhoward@oakbio.com

Smart Bio Plastics from CO2 Flue Gas

Oakbio Makes Bioplastic at
Cement Plant using CO2 from Flue Gas and Electricity 

Milestone for cement industry
and renewable products

 

SUNNYVALE, CA (July 10,  2012) - Today Oakbio Inc. announced the successful production of
bioplastic polymers in their bioreactor systems. Oakbio's system creates
bioplastic using inputs of cement plant flue gas and electricity. The technology
uses bioreactors driven by non-toxic microbes to capture CO2 and convert it to a
variety of sustainable products directly from the plant's gas
emissions.

 

This is the latest
development from an on-site research collaboration at Lehigh Southwest Cement
Company's Permanente cement manufacturing plant in Cupertino. Lehigh Southwest
is part of Lehigh Hanson, Inc., the North American operations of the
HeidelbergCement Group, a world leader in construction materials with
approximately 52,000 employees in more than 40 countries.

 

Chief Scientist Brian
Sefton stated, "Our carbon conversion process yields over 50% bioplastics in
microbe biomass by dry weight from inputs of raw flue gas and electricity. The
type of plastic we make is not only renewable, but biodegradable as
well.

 

"The effective conversion
of captured CO2 into a valuable bioplastic product represents an important
technical achievement for potential large-scale bioplastics production. This
result also points the way to a new method for greenhouse gas capture, making
emissions gas CO2 a feedstock for mass scale manufacturing."

 

CEO Russell Howard added:
"At Oakbio we see industrial CO2 as a carbon resource. By converting virtually
unlimited amounts of low cost CO2 available from various industries worldwide
into sustainable products like biodegradable plastics, Oakbio's technology can
answer multiple needs: full scale chemicals production without the use of
petroleum oil or agricultural feedstock; replacement of petroleum oil-derived
plastics with bio-degradable renewable products; and the capture of CO2 to
prevent greenhouse gas accumulation. The ability of our microbes to perform
their magic in cement flue gas is an important step toward achieving this
vision".

 

 

About Oakbio, Inc.

Oakbio is a private
technology-based company in Sunnyvale dedicated to sustainable production of
specialty chemicals using novel microbial production processes that combine GHG
reduction with manufacture of sustainable specialty chemicals (see www.oakbio.com).

Media
Contact:

Russell Howard, CEO,
Oakbio, (408) 930-7004; rhoward@oakbio.com

Frog feet could solve a sticky problem: design for self-cleaning sticky surfaces

Tree frogs have specially adapted self-cleaning feet which could have practical applications for the medical industry.

"Tree frog feet may provide a design for self-cleaning sticky surfaces, which could be useful for a wide range of products especially in contaminating environments - medical bandages, tyre performance, and even long lasting adhesives," says researcher, Niall Crawford at the University of Glasgow who will be presenting this work at the Society for Experimental Biology Annual Conference in Glasgow on 3rd of July, 2011.

Tree frogs have sticky pads on their toes that they use to cling on in difficult situations, but until now it was unclear how they prevent these pads from picking up dirt.

"Interestingly the same factors that allow tree frogs to cling on also provide a self cleaning service. To make their feet sticky tree frogs secrete mucus, they can then increase their adhesion by moving their feet against the surface to create friction. We have now shown that the mucus combined with this movement allows the frogs to clean their feet as they walk," says Mr. Crawford.

The researchers placed the White's tree frogs on a rotatable platform and measured the angles at which the frog lost its grip. When the experiment was repeated with frogs whose feet were contaminated with dust they initially lost grip but if they took a few steps their adhesive forces were recovered. "When the frogs did not move the adhesive forces recovered much more slowly," says Mr. Crawford. "This shows that just taking a step enables frogs to clean their feet and restore their adhesion ability."

White's tree frogs have tiny hexagonal patterns on their feet, which allow some parts of the pad to remain in contact with the surface and create friction, whilst the channels between allow the mucus to spread throughout the pad. This mucus at once allows the frog to stick and then, when they move, also carries away any dirt. If this can be translated into a man-made design it could provide a re-useable, effective adhesive.

Bio-inspired sensors hold promise-Turning to nature for inspiration

Bio-inspired sensors hold promise

To build the next generation of sensors – with applications ranging from medical devices to robotics to new consumer goods – Chang Liu looks to biology.

Liu, professor of mechanical engineering and electrical engineering and computer science at Northwestern University's McCormick School of Engineering and Applied Science, is using insights from nature as inspiration for both touch and flow sensors — areas that currently lack good sensors for recording and communicating the senses.

Liu will discuss his research in a symposium at the annual meeting of the American Association for the Advancement of Science (AAAS) in Washington, D.C., to be held from 1:30 to 4:30 p.m. Saturday, Feb. 19.

For the past 10 years, Liu has led a research group that develops artificial hair cell sensors. Hair cells provide a variety of sensing abilities for different animals: they help humans hear, they help insects detect vibration, and they form the lateral line system that allows fish to sense the flow of water around them.

"The hair cell is interesting because biology uses this same fundamental structure to serve a variety of purposes," Liu says. "This differs from how engineers typically design sensors, which are often used for a specific task."

By creating artificial hair cells using micro- and nanofabrication technology, Liu's group is increasing sensor performance while deepening the understanding of how different creatures use these sensors. For example, every fish in the world uses hair cells in the lateral line as sensors, but so far no manmade vehicle does. If a submarine had sensors similar to that of a fish, it could record much more information on water movement.

Liu's current focus is the medical application of these biologically inspired sensors. He hopes that artificial hair cells could be used to measure acoustics in an artificial cochlea or could be embedded as flow sensors in a wide variety of medical devices.

Liu is also developing new touch sensors to improve minimally invasive surgery techniques. Currently many minimally invasive procedures are conducted through a catheter that is inserted into the body and controlled by a doctor on the outside.

"During a heart treatment, the doctor controlling the catheter has no sense of touch and cannot tell if the catheter has touched the heart wall and successfully completed the therapeutic treatment," Liu explains. "We want to use microfabrication technology to put sensors on the end of the catheter to provide feedback."

In order to achieve his goals, Liu has assembled a multidisciplinary team that includes biologists, engineers, materials scientists and physicians. A mix of fundamental and applied research is necessary to make biologically inspired sensors a reality, he says.

"Using a bio-inspired approach is really important," Chang says. "Nature has a lot of wonderful examples that can challenge us. No matter how good some of our technology is, we still can't do some of the basic things that nature can. Nature holds the secret for the next technology breakthrough and disruptive innovation. We are on a mission to find it."

### 

Walter Derzko

 

Biomimicry: Next generation of algorithms inspired by problem-solving ants

The ants were able to find the shortest route from one end of the maze to the other in under an hour, then were able to adapt and find the second shortest route when obstacles were put in their path.

An ant colony is the last place you'd expect to find a math whiz, but University of Sydney researchers have shown that the humble ant is capable of solving difficult mathematical problems.

These findings, published in the Journal of Experimental Biology, deepen our understanding of how even simple animals can overcome complex and dynamic problems in nature, and will help computer scientists develop even better software to solve logistical problems and maximize efficiency in many human industries.

Using a novel technique, Chris Reid and Associate Professor Madeleine Beekman from the School of Biological Sciences, working with Professor David Sumpter of Uppsala University, Sweden, tested whether Argentine ants (Linepithema humile) could solve a dynamic optimization problem by converting the classic Towers of Hanoi math puzzle into a maze.

Finding the most efficient path through a busy network is a common challenge faced by delivery drivers, telephone routers and engineers. To solve these optimization problems using software, computer scientists have often sought inspiration from ant colonies in nature - creating algorithms that simulate the behavior of ants who find the most efficient routes from their nests to food sources by following each other's volatile pheromone trails. The most widely used of these ant-inspired algorithms is known as Ant Colony Optimization (ACO).

"Although inspired by nature, these computer algorithms often do not represent the real world because they are static and designed to solve a single, unchanging problem," says lead author Chris Reid, a doctoral student from the Behavior and Genetics of Social Insects Laboratory.

"But nature is full of unpredictability and one solution does not fit all. So we turned to ants to see how well their problem solving skills respond to change. Are they fixed to a single solution or can they adapt?"

The researchers tested the ants using the three-rod, three-disk version of the Towers of Hanoi problem - a toy puzzle that requires players to move disks between rods while obeying certain rules and using the fewest possible moves. But since ants cannot move disks, the researchers converted the puzzle into a maze where the shortest path corresponds to the solution with fewest moves in the toy puzzle. The ants at the entry point of the maze could chose between 32,768 possible paths to get to the food source on the other side, with only two of the paths being the shortest path and thus the optimal solution.  

The ants were given one hour to solve the maze by creating a high traffic path between their nest and the food source, after which time the researchers blocked off paths and opened up new areas of the maze to test the ants' dynamic problem solving ability.

After an hour, the ants solved the Towers of Hanoi by finding the shortest path around the edge of the maze. But when that path was blocked off, the ants responded first by curving their original path around the obstacle and establishing a longer, suboptimal, route. But after a further hour, the ants had successfully resolved the maze by abandoning their suboptimal route and establishing a path that traversed through the centre of the maze on the new optimal route.

But not all the colonies' problem solving skills were equal: ants that were allowed to explore the maze without food for an hour prior to the test made fewer mistakes and were faster at resolving the maze compared to the ants that were naive. This result suggests that the "exploratory pheromone" laid down by ants searching a new territory is key in helping them adapt to changing conditions.

"Even simple mass-recruiting ants have much more complex and labile problem solving skills than we ever thought. Contrary to previous belief, the pheromone system of ants does not mean they get stuck in a particular path and can't adapt. Having at least two separate pheromones gives them much more flexibility and helps them to find good solutions in a changing environment. Discovering how ants are able to solve dynamic problems can provide new inspiration for optimization algorithms, which in turn can lead to better problem-solving software and hence more efficiency for human industries."

Provided by University of Sydney

 Walter Derzko

Does quantum entanglement optimise photosynthesis?

Recently, academic debate has been swirling around the existence of unusual quantum mechanical effects in the most ubiquitous of phenomena, including photosynthesis, the process by which organisms convert light into chemical energy.  In particular, physicists have suggested that entanglement (the quantum interconnection of two or more objects like photons, electrons, or atoms that are separated in physical space) could be occurring in the photosynthetic complexes of plants, particularly in the pigment molecules, or chromophores.  The quantum effects may explain why the structures are so efficient at converting light into energy -- doing so at 95 percent or more.

In a paper in The Journal of Chemical Physics, which is published by the American Institute of Physics, these ideas are put to the test in a novel computer simulation of energy transport in a photosynthetic reaction center.  Using the simulation, professor Shaul Mukamel and senior research associate Darius Abramavicius at the University of California, Irvine show that long-lived quantum coherence is an "essential ingredient for quantum information storage and manipulation," according to Mukamel.  It is possible between chromophores even at room temperature, he says, and it "can strongly affect the light-harvesting efficiency."

If the existence of such effects can be substantiated experimentally, he says, this understanding of quantum energy transfer and charge separation pathways may help the design of solar cells that take their inspiration from nature.

###

The article, "Quantum oscillatory exciton migration in photosynthetic reaction centers" by Darius Abramavicius and Shaul Mukamel will appear in The Journal of Chemical Physics.  See: http://jcp.aip.org/

Semi-synthetic Life; Scientists swap entire natural bacterial genome for artificial man-made genome

Scientist Craig Ventner and his team have inserted an entire synthetic genome into  bacterial cells, that took over the operation of the cell from the natural genome. This follows previous successes in inserting snipets in DNA from species to species and transplanting the entire natural genome from one bacterial species into another.

Significance:

This could be rated as one of top 5 discoveries for 2010.

Proof of concept  that bacterila genomes can be swapped by synthetic versions of entire genomes. Leads to the next stage-interting unique bio-apps in to bacterial, viruses, fungi or algae-.like new apps (applications) for your smart i-phone. Creating semi artificail bacterial or algae that convert C02 in butyl alcohols or higher chain gasoline or gasohol. (ETA 2015-2020)

Will we be seeing basement biologists hacking and tinkering with life? Not very soon. A Science Commentary this week reports:

"The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It was achieved at great expense, an estimated $40 million, and effort, 20 people working for more than a decade. Despite this success, creating heavily customized genomes, such as ones that make fuels or pharmaceuticals, and getting them to "boot" up the same way in a cell is not yet a reality. "There are great challenges ahead before genetic engineers can mix, match, and fully design an organism's genome from scratch," notes Paul Keim, a molecular geneticist at Northern Arizona University in Flagstaff."

Background:

Negatively stained transmission electron micrographs of dividing M. mycoides JCVI-syn1. Electron micrographs were provided by Tom Deerinck and Mark Ellisman of the National Center for Microscopy and Imaging Research at the University of California at San Diego.

(PhysOrg.com) -- Scientists have developed the first cell controlled by a synthetic genome. They now hope to use this method to probe the basic machinery of life and to engineer bacteria specially designed to solve environmental or energy problems.

The study will be published online by the journal Science, at the Science Express website, on Thursday, 20 May.

The research team, led by Craig Venter of the J. Craig Venter Institute, has already chemically synthesized a bacterial genome and it has transplanted the genome of one bacterium to another. Now, the scientists have put both methods together, to create what they call a "synthetic cell," although only its genome is synthetic.

"This is the first synthetic cell that's been made, and we call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer," said Venter.

"This becomes a very powerful tool for trying to design what we want biology to do. We have a wide range of applications [in mind]," he said.

For example, the researchers are planning to design algae that can capture carbon dioxide and make new hydrocarbons that could go into refineries. They are also working on ways to speed up vaccine production. Making new chemicals or food ingredients and cleaning up water are other possible benefits, according to Venter.

In the Science study, the researchers synthesized the genome of the bacterium M. mycoides and added DNA sequences that "watermark" the genome to distinguish it from a natural one.

Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.
 

The scientists then transplanted the synthetic M. mycoides genome into another type of bacteria, Mycoplasm capricolum. The new genome "booted up" the recipient cells. Although fourteen genes were deleted or disrupted in the transplant bacteria, they still looked like normal M. mycoides bacteria and produced only M. mycoides proteins, the authors report.

Enlarge

The assembly of a synthetic M. mycoides genome in yeast. Figure from Gibson, D. G., J. I. Glass, et al. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, Published online May 20 2010.

"This is an important step we think, both scientifically and philosophically. It's certainly changed my views of the definitions of life and how life works," Venter said.

Acknowledging the ethical discussion about synthetic biology research, Venter explained that his team asked for a bioethical review in the late 1990s and has participated in variety of discussions on the topic.

"I think this is the first incidence in science where the extensive bioethical review took place before the experiments were done. It's part of an ongoing process that we've been driving, trying to make sure that the science proceeds in an ethical fashion, that we're being thoughtful about what we do and looking forward to the implications to the future," he said.

More information: 20 May 2010, Science, "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome."
J. Craig Venter Institute announcement: http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/

Provided by American Association for the Advancement of Science

Scope of Hydrated Fullerene (C60- HYFN) Research in Ukraine; Nanomedicine, nanomaterials on demand, sports medicine, cosmetics, pharmacology, agriculture, veterinary medicine etc

UPDATE  Nov 2010: HYFNs have been approved for manufacturing as Fullerene Water Solution (FWS)  drink in Ukraine by the  Ministry of Health  as of Nov 2010. It's the first nanotech based health drink in the world. For information about availability  contact me privately by email.

I received this updated list of research directions and activities surrounding hydrated fullerenes (C60) otherwise known as water soluble bucky balls, from my colleagues in Ukraine,who discovered and patented hydrated fullerenes (HyFn's) in the 1990's. They are looking for business and academic research collaborators around the world.

Scope of Hydrated Fullerene (C60- HYFN) Research in  Ukraine

  

Development of nanomaterials.

•  Synthesis of new nanosized composition on the bases of metal, dielectric and semiconducting materials.

•  Development and research of bio-nanocomposites.

  

Physical and chemical research of nanostructures.

•  Research of physical and chemical properties of nanostructural materials, and in the first place – fullerenes in hydrated state.

•  Research of structural organization of water and water solutions. Cluster nature of water.

•  Research of behaviour peculiarities of physical and chemical processes in heterogeneous media, structured by hydrated fullerenes.

•  Research of behaviour peculiarities in water solutions of substances at their small and super small concentrations.

•  Research of the heat-conduction process in media containing nanostructural materials.

•  Research of photocalytic processes in presence of nanomaterials in different media.

  

Biological research of nanostructures. 

•  Toxicological research of nanomaterials.

•  Development of biocompatible materials on the basis of nanostructural composites.

•  Research of biochemical reactions and biological processes in heterogeneous water media, structured by hydrated fullerenes.

•  Research of the biological role of cluster water structures.

•  Research of the influence of specific cluster organization of water on increasing of biological system stability against unfavourable environmental factors, including action of different electromagnetic fields and ionizing radiation.

•  Research of the use of nanoparticle solutions as components of nutrient medium for microorganisms growth, producers of specific antibiotics, vitamins, proteins, etc.; and as components of biological test-systems for biomedical analyses.

•  Research of the use perspectives of hydrated fullerenes for preservation, including cryoconservation, of different biological material (biomolecules, cells, blood and its components, organs and tissues).

•  Research of the influence of hydrated fullerenes on the processes of aging and their ability to slow down such kind of processes.

  

Nanostructures for pharmacology.

•  Development of medicinal forms of hydrated fullerenes for parenteral, oral, intranasal and other ways of administration.

•  Efficiency enhancement of existing pharmaceuticals due to incorporation of hydrated fullerenes into their composition.

•  Development and creation of new vaccines and serums with decreased allergenic and side effects.

  

Nanostructures for medicine.

•  Research and application of nanostructures as additional agents and components, enhancing efficiency of standard schemas of treatment of human diseases.

•  Research and application of hydrated fullerenes as antioxidative, immunoprotective, anti-inflammatory and antiallergic agents.

•  Research and application of hydrated fullerenes as highly effective radioprotective agents.

•  Research of the efficiency and application of hydrated fullerenes in clinic of cardio-vascular diseases.

•  Research of the efficiency and application of hydrated fullerenes for prevention and treatment of oncological diseases.

•  Research of the efficiency and application of hydrated fullerenes for diabetes and other endocrine and metabolic diseases.

•  Research of the efficiency and application of hydrated fullerenes in clinic of digestive organs’ diseases and kidney and urinary tract diseases.

•  Research of the efficiency and application of hydrated fullerenes in clinic of bronchopulmonary diseases.

•  Research of the efficiency and application of hydrated fullerenes for prevention and treatment of infectious diseases and diseases of ear, throat and nose.

•  Research of the efficiency and application of hydrated fullerenes for children’s diseases.

•  Research and application of hydrated fullerenes in clinic of surgical diseases.

•  Research and application of hydrated fullerenes in clinic of women's diseases.

•  Research and application of hydrated fullerenes for lesions of internal organs in case of alcoholism and toxicomania.

•  Research and application of hydrated fullerenes in geriatric practice.

•  Research and application of hydrated fullerenes in sports medicine.

•  Research and application hydrated fullerenes in balneology.

  

  

Nanostructures in sports.

•  Enhancement of exercise tolerance in sportsmen and their sport results without use of dopes, stimulators, anabolics, etc.

•  Improvement of adaptive abilities in sportsmen under stress conditions.

  

Nanostructures for cosmetics, perfumery and personal hygiene products.

•  Research and application of nanostructures with bioantioxidative and structure-organizing properties as components that significantly improve consumer properties of cosmetic and perfumery products.

•  Protection of “gentle” components of such products and prolongation of their shelf life.

•  Creation of brand new cosmetic and perfumery products and personal hygiene products with health-improving properties.

  

Nanostructures for food.

•  Research and application of nanostructures with bioantioxidative and structure-organizing properties as components that significantly improve consumer properties of food.

•  Protection of “gentle” components of such products and prolongation of their shelf life.

•  Substitution by hydrated fullerenes of hazardous conserving agents and stabilizers for food products.

  

Nanostructures for agriculture.

•  Research and application of hydrated fullerenes in agriculture for accelerated germination and growing of plants.

•  Research and application of hydrated fullerenes for enhanced plant resistance to disease-producing agents.

  

Nanostructures in veterinary medicine.

•  Research and application of hydrated fullerenes for prevention of animal diseases, including viral ones.

•  Research and application of hydrated fullerenes to enhance reproductive qualities, viability and quality of life of elite animals.

•  Research and application of hydrated fullerenes for animals in sports.

Anyone wishing to collaborate in joint academic research, outsource their research or start  contract research, please contact me directly. (from your business email)

Here is the Institute's new web page:  http://ipacom.com/index.php?lang=en.

Walter Derzko

Slime mould mimics Tokyo's rail system; Could be used to detect improvised explosive devices (IED's)

Who do think is better at creating an efficent, cost-effective and resilient network...1) communication network engineers designing the Tokyo railway system or 2) Nature i.e. the ordinary slime mould?

Well if you picked choice number 2).. Nature... you'd be right.

In an experiment comparing the growth of Physarum polycephalum (slime mould) against an existing man-made network, the slime mould performed admirably, as good as or better then human designed networks.

Researchers from Hokkaido University in Japan and Oxford University in England were able to demonstrate that slime mould can navigate its way to a number of food sources, using the most efficient route and minimal growth. Dr. Mark Fricker, in the Department of Plant Sciences at Oxford, and colleagues plotted this growth against the Tokyo rail network. The researchers believe that slime mould mimicry can be useful by inspiring greater efficiency in real life technology, including computer systems or communications networks

Scientists conclude:  

"Physarum is a large, single-celled amoeboid organism that forages for patchily distributed food sources... [It] can find the shortest path through a maze or connect different arrays of food sources in an efficient manner with low total length yet short average minimum distance between pairs of food sources, with a high degree of fault tolerance to accidental disconnection."

The researchers knew that capturing the essence of this biological system in simple rules could be useful to inform the construction of self-organizing and cost-efficient networks in the real world. They captured the core mechanisms needed by the slime mold to connect its food sources in an efficient manner and incorporated them into a mathematical model.

Since the slime mold has been subjected to countless rounds of evolutionary selection, this formula based on its feeding habits might provide a route to more efficient and adaptive network designs for transportation and communication.

Others offer similar opinions:

"The model captures the basic dynamics of network adaptability through interaction of local rules, and produces networks with properties comparable to or better than those of real-world infrastructure networks... This work  provides a fascinating and convincing example that biologically inspired pure mathematical models can lead to completely new, highly efficient algorithms able to provide technical systems with essential features of living systems, for applications in such areas as computer science."

The model provides a starting point for improving efficiency and decreasing costs for self-organized networks without centralized control, like remote sensor arrays (smart dust), mobile ad hoc networks, and wireless mesh networks.

A practical application of this can be used in war to save lives.

I always thought that our troops in Afghanistan should be using "smart dust" or wireless mesh networks sprinkled  along the roadside to identify suspicious movements along roads, as proxy indicator for terrorists, who regularly plant improvised explosive devices ( IED's) at night. Algorithms could be designed to distinguish between expected and unexpected incidents/ movements (humans vs animals). These sensors are inexpensive, now costing pennies each and have a range of 50 feet.

Full story here

Walter Derzko, Smart Economy, Toronto

 

Author of the soon-to-be published book- Opportunity 45 Scenarios to Drive Your Business in Challenging Times, published by J. Wiley and Sons

ISBN13: 978-0-470-73761-3

ISBN10: 0-470-73761-1

 

When are errors and mistakes good ? Cells defend themselves from viruses, bacteria with an army of protein errors

Our education system teaches us to avoid errors and mistakes, we are taught to aim to get the right answer…however in nature it’s not as clear cut as that...in some cases errors are helpfull.

 

A good rule of thumb in  science is "look under your nose."  and "challenge assumptions." The following story is a good example of how complex our body is and what we don't know about how our body works.

When cells are confronted with an invading virus or bacteria or exposed to an irritating chemical, they protect themselves by going off their DNA recipe and inserting the wrong amino acid into new proteins to defend them against damage, scientists have discovered.

 

These "regulated errors" comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed, said Tao Pan, Professor of Biochemistry and Molecular Biology at the University of Chicago. A team of 18 scientists from the University of Chicago and the National Institute of Allergy and Infectious Disease led by Pan and Jonathan Yewdell will publish the findings tomorrow, Thursday in the journal Nature.

 

"This mechanism allows every protein to get some protection," Pan said. "The genetic code is considered untouchable, but this is a non-genetic strategy used in cells to create a bodyguard for proteins."

Proteins are constructed through a process called translation where cellular elements use the genetic code to guide the assembly of building blocks called amino acids into the correct sequence. First, a copy of the DNA, called messenger RNA, is made and transferred to a cellular structure called a ribosome. Transfer RNAs (tRNA), one for each of the 20 amino acids used in building proteins, read the messenger RNA code and bring the proper amino acids to the ribosome, where they are bonded together to form a complete protein.

Each tRNA can be attached to only one of 20 amino acids, a specificity that prevents errors during the construction of proteins. In artificial laboratory preparations, scientists have observed that only one out of every 10,000 amino acids is placed into a protein incorrectly, and thus protein errors were thought to be exceptionally rare.

But Jeffrey Goodenbour, University of Chicago graduate student and co-lead author along with Nir Netzer of the NIAID, decided to look at how often tRNA errors, called misacylations, occurred in live cells.

 

After developing a novel technique for measuring these errors, published for the first time in this paper, the authors were surprised to find a much higher error rate in those cells for the amino acid methionine. As high as one out of every 100 methionines was incorrectly placed in proteins, they found.

 

When the cells were stressed by exposure to a virus, bacteria or a toxic chemical such as hydrogen peroxide, that error rate went even higher, as up to 10 percent of methionines placed into new proteins were different from what the gene specified.

"That was 1,000 times more than the textbook says should be there," Pan said.

 

Further experiments revealed that it was always the same amino acid, methionine, placed incorrectly into new proteins. Methionine is one of only two amino acids to carry sulfur atoms on its side chains, a feature that allows it to neutralize dangerous molecules called reactive oxygen species (ROS) that form inside an infected or stressed cell. ROS can damage proteins through a chemical process called oxidation, but methionine can be oxidized (and restored through a process called reduction) without being permanently damaged.

"The idea is that methionine can protect you from having oxidation of the active site of protein, which would ultimately completely block function of the protein," Goodenbour said. "You end up reducing the total reactive oxygen species load in the cell. It's a very interesting mechanism."

Cells normally put methionines near important parts of a protein to protect those segments from being damaged by reactive oxygen species. When the cell is under stress, and the amount of ROS increases, the number of methionine "errors" is ramped up tenfold, allowing new proteins to be even more resistant to attack.

"Think of a boxing match," Pan said. "If you put methionine close to active site, the reactive oxygen species has to get past it to get to the active site residues for oxidization. You've put something right in front of it so a protein can take a hit. If you have a lot of methionines, to knock this protein out will take many, many hits. So this is a strategy used in cells to create a bodyguard for a protein."

A remaining puzzle is to determine why extra protective methionines are not encoded as part of the DNA in the first place, instead of being left to the post-genetic random placement described in this paper. Pan suggests that random placement of the amino acids makes proteins even more resistant to attack, since no two are created alike. (Pay attention computer platform and anti-virus software designers !!)

 

"This sounds chaotic and doesn't make a lot of sense according to the textbook," Pan said. "But this way the cells can always ensure that a subset of these proteins is somewhat less sensitive to the extra hits. I think that's the most important part of this - to make every protein molecule different - and you cannot do this genetically."

Walter Derzko