Sunday, May 30, 2010

Setting up and getting the ball rolling in R language

You can download and install R for Linux, windows or Mac from here. Select the platform that best describes your system and install R.

In Linux, R can be started from the command line or terminal by just typing "R" and pressing enter.Once the R language is started, we are free to use the R language commands to perform various functions. You can come out of R by typing "q()" and pressing enter.

Most R installs come with a html help manual which opens in the default browser and can be started by typing "help.start()" and pressing enter.You can even look here if your httpd server is running.

Saturday, May 29, 2010

Sheep grazing in the field

Sheep eating grass in a field surrounded by electric fencing. Eco-friendly grass cutting?

Friday, May 28, 2010

Flowers after a rain

Yellow and red hues in the flower sprinkled with water droplets after a light drizzle.The Green background adds to the contrast.

Thursday, May 27, 2010

Animal eyes in the dark

See the glow in the eyes of all the three goats. I always wondered about the glow in the eyes of animals after seeing them in cartoons. Now saw it live through the camera. Rather than the eyes glowing, it seems to be the reflection from the camera flash.

Wednesday, May 26, 2010


The fossil fuels where formed over millions of years from plant biomass. Rapid use of the fossil fuels is releasing carbon from these fuels in the form of carbon dioxide. Hence, there is a increase in the carbon dioxide concentration in the earths atmosphere. With the growing energy demands and the depleting fossil fuel reserves, we are in need of alternative renewable sources of energy.

A large-scale transition to renewable energy is not possible in the short term due to the current technology for harnessing the alternative sources not being cost effective. Use of biomass for meeting the needs of the energy has been explored with significant success. Gaseous forms of fuel products from biomass such as biohydrogen and biomethane are considered as good sources due to their portability and efficiency.

Hydrogen can be produced by the electrolysis or from fossil fuels in either a small or a large scale.Large scale production from fossil fuels has the advantage of being able to capture the carbon dioxide to be utilized for stimulating plant growth or for storage in chemical form such as carbonates or in underground reservoirs.

Methane production through anaerobic process of digestion of wastewater and residues involves hydrogen as an intermediate product which is rapidly taken up and converted to methane by methane producing micro-organisms. The degradation of organic matter to methane and carbon dioxide in the absence of oxygen by microorganisms is called as Anaerobic microbial digestion. This digestion occurs in several phases involving many microbes. The complex organic compounds are first degraded to simple molecules. In the second phase the molecules are degraded into organic acids and hydrogen. The last step involves organic acids and hydrogen being converted into methane.

Biophotolysis involves many microalgae and cyanobacteria which are able to split water into hydrogen and oxygen with the aid of absorbed light energy. However, this process is limited by the efficiency of the enzyme involved in the conversion process. The enzyme is inhibited by the oxygen produced in the process of splitting water. Several variants of this process are being developed to separate the hydrogen and oxygen production steps.

Organic compounds like acetic acid are converted into hydrogen and carbon dioxide with sunlight by bacteria in what is known as photofermentations. However, this process is difficult to scale up as it requires a large surface area to capture the light needed for the driving the process.

Photosynthesis, CO2, Biomass from Plants & Algae, Biohydrogen

The changing energy need dynamics is going to affect not only the way energy is produced but also how its going to be used. The winning entry for the city of the future competition of History channel predicts a future for San Francisco that has hydrogen fueled hover car networks. The city will have specific structures to collect, store and distribute water and power from various sources. Harvesting the solar energy would be a very effective contributor. Currently energy is produced by processing the biomass into ethanol and biodiesel. However, energy is lost in producing all the other complex compounds that form the part of the complex biomass. Photosynthetic organisms that produce biofuels directly will be more energy efficient than processing the biomass thats produced by plants. This concept of producing a fermentation product called photanol with the input of carbon dioxide, water and solar energy into a synthetically designed organism.

Being able to produce hydrogen for use as a fuel by splitting water using solar energy is a long term goal to overcome the energy crisis. Various options are being explored to perform the task of splitting. However, using cyano bacteria for photo biological production of hydrogen has been found to be a very promising option. Many micro-organisms can produce hydrogen using enzymes called hydrogenases. This hydrogen production will produce the Biohydrogen which can be used a fuel for various purposes due to its portability.

Two different approaches are being pursued to produce biohydrogen. The first approach is the nitrogenase based approach and it involves knocking out the uptake hydrogenase. The second approach is to introduce a foreign hydrogenase. Both the approaches are being tried out by various companies. Different growth conditions and mechanisms are being observed to get the optimal system.

Interesting developments in using LED technologies as an additional, low-energy artificial supply of light with optimal properties for photosynthesis is being explored. Growing understanding of genetic engineering, regulation of transcription and translation will improve the design of the organism used to produce the fuel. Other areas such as mass culturing of the microorganism can also lead to significant cost reduction and stability.

Due to the complex nature of the biological systems, various problems such as auto inhibition of growth in the model organism while producing the new compound. The resistance mechanisms to such inhibition has to be studied and expressed in the organism to get a higher yield.

Tuesday, May 11, 2010

Energy forests, Salix program & breeding

The increasing demand for energy and decreasing oil production has made it imperative to find and exploit new forms of energy. Various forms of energy such as hydro power, nuclear power, wind and biomass are being used as alternative sources of energy. Biomass has emerged as a very important form of alternative energy due to its renewable nature, low impact on the environment and cost benefits. Growing energy in the form of forest trees has been found to be a sustainable model for the production of energy. However, strict regulatory policies on the felling and growth rates are required to ensure the balance in the forest cover.

Deciduous trees of the genus salix are found to grow mostly in moist soils in cold and temperate regions of the Northern hemisphere. Being a perennial crop with a life span of 20 to 25 years, its ideally suited for cultivation with the aim of harvesting for biomass. It requires low input of fertilizers and pesticides for its growth making it easy to cultivate.

The advantage of growing these energy forests can be further increased by using these tree for phytoremediation. The short rotation crops such as willows offer the double advantage of high biomass yields and removal of hazardous compounds through frequent harvests.The cleaning of polluted sites which contain heavy metals such as cadmium can be helpful in cleaning up various wastes.

Breeding programs to improve the biomass production, drought and heat tolerance and resistance towards pests are underway. With the aim of growing the plants in southern Europe which has higher temperatures, the heat tolerant strains are being sought. Leaf beetles are the major pests of willows and reduce the biomass by up to 40%. Leaf rust caused by fungi also cause loss of biomass in excess of 40%. As a result of the breeding programs, new strains which increase the biomass production by 60% have been selected for use.

Genomics based approaches which use the sequences genomes of the trees have been used to find genes associated with specific traits. Molecular markers identified by crossing have been associated with the concerned genes.It has been predicted that successful use of knowledge from genome sequencing projects will require the successful identification of polymorphisms associated with traits of interest, the frequency of superior alleles in the base breeding population and their phenotypic effect. Hence, just the sequencing of the genomes without proper understanding of the mechanisms involved in the various traits will not be of much use. Efforts to sequence EST's and studies of the expression patterns associated with different environmental conditions are being undertaken to bridge this gap.

Tuesday, May 4, 2010

Artificial photosynthesis and Synthetic biology

Future global energy needs cannot be met by any single source of energy known to us today. Contributions from different energy sources might make it possible to meet the energy needs. Solar energy is converted into biomass which can be used as energy source. However, the production of biomass is a inefficient process. Hence, different approaches to mimic the efficient parts of the system is being attempted.

Hydrogenase enzyme which catalyzes the formation of hydrogen is coupled to photosystem II to use water for utilizing the solar energy more effectively. Among the different steps involved in photosynthesis, the following are considered to be worth mimicking.

1.Absorb light and funnel energy
2.Convert energy to charge separated state
3.Couple charge separation to catalysis
4.Higher level of organization

Different molecules and molecular complexes are being perfected for each of the steps in the hope of increasing the efficiency.

Synthetic biology is the design and construction of new biological parts, devices and systems for useful purposes. The purpose of making parts and devices is to be able to have standardized components which could be used to build devices. The registry of standard parts is one such collection of parts such as promoters, ribosome binding sites, protein domains, protein coding sequences, translational units, terminators etc.

The standardized parts known as bricks are characterized and ready to use for that specific function. Computer aided design and simulations will play a significant role in this process. Simulating the model of the system can give results which can be used for designing the system. Unpredictable results may occur while using these design principles due to cross talk between the different components. These have to be taken care of and modularized.

Application areas for synthetic biology are widespread. It could help in fields such as bioenergy, drugs and chemicals, biomaterials, medicine etc. Coordinating the bacteria or yeast involved in fermentation by engineering the microbes could eliminate the need for monitoring the culture as it will be self regulated. With an increased knowledge of the various cellular processes, it should be possible to engineer entire new cellular systems as per requirement. Such a use of synthetic biology to design a cell from ground up might be made possible by integrative synthetic biology.

Sunday, May 2, 2010

The last statue

His hand stopped short of the lever. After having demolished more than a million statues, it seemed weird that he should feel guilt at having to destroy this small statue.

May be it was the burden of the knowledge that this was the only statue made by man still standing. If he just pushed the lever, mankind would probably never make another statue ever. All knowledge about the arts had been destroyed in the revolution. It seemed these stones where the only proof of a saner time.

"Whats taking you so long", the supervisor was shouting at him from the ground. If he dint do it somebody else would. At least they could not erase the statue from his mind.

He touched the lever with a sinking feeling in his heart and aimed the crushing ball at the statue.