Let's Fight from the Inside, Lad!

Immune System (picture taken from Medicues)

In every organism, there is a system that play important role in protecting the body from all kind of intruders such as viruses, worms and pathogens. In simpler organisms, especially unicellular organisms like bacteria, the protection is performed by enzymatic systems that shielding them against viral infections. In eukaryotes, such as insects, a basic immune mechanism is found which include antimicrobial peptides that works pretty well to keep the organisms safe from unfamiliar components of the systems. More complex organisms including human, on the other hand, posses more complicated mechanisms to protect them against these intruders. In general, this system, called immune system, releases a group of machinery cells, antibody, that tackles infections from the intruders by fusing themselves with these unnecessary components as they mobilize in the bloodstream. By doing this, the intruders may not affecting or harming any process in the body.

In recent study, a group of researchers, lead by Dr. Leo James at the Laboratory for Molecular Biology in Cambridge, found that there is a possibility for the antibodies in immune system can work within the cells, instead of produced and take action in the bloodstream. This study showed that antibodies are not only preventing viruses from harming cells, but also can move after the viruses in the cells and perform an immunity attack from the inside. This may contradict to what has been long believed by most scientists that there is low chance for the immune components to take action when the viruses had already entering the cells.

Dr. James and co-workers showed that once the virus has entered to a cell, antibodies may suddenly attract a protein, TRIM21, to call a large cluster of proteins called proteasome. The proteasome works similar to a disposal machine where, upon called, this group of proteins will docked to TRIM21 and disassemble the virus. This process is very quick, usually before the virus has a chance to take any harmful action in the cell (for more information, go to Guardian website and this work has been published in Proceeding of the National Academic of Sciences). Therefore, this may open a new insight in drug discovery and most importantly, it is very crucial to always keep the body health in good condition as the strength of immune system is always depends on it.

The World is Not Enough - coz we can built one or more!

Google Liquid Galaxy Platform (figure from Google Open Source)

Let's imagine that we can discover the world with a touch of our finger.... Of course, we're have already experienced this with a help of Google Earth. But, imagine if we can built a platform with several large monitors (or maybe HD!) that simulate our world in more realistic way, with only $80,000! How is it possible?

Recently, Google has launched it's new project called Liquid Galaxy, which permits ordinary users like us to develop our own "star trek" platform to explore the world. This project, initiated as a Google 20% Project, is basically built on a cluster of computers that run Google Earth engine. For software part, we have to simply download and install Google Earth in different computers, choose one as the master and directly synchronize them through internet protocol (IP). On the other hand, for hardware part, the frame (place where we put the monitors, input devise and cockpit) is built based on the custom design and materials, as shown in figure below.

Frame Design from Google Open Source

Currently, Google has promoting this project by installing this impressive platform in their offices around the world and also displaying them in most outrageous conferences and exhibitions such as recent Technology Entertainment and Design (TED) conference held in San Francisco. According to Engadget, using 8 Linux-based machines, users may able to even flying through the digital skies by voice command and sheer mental strength!

Watch the video for more awesome experience!

Embryonic Stem Cell for Eye Treatment

Stem cell plays a very important role in all multi-cellular organisms. This cell is known by its ability to regenerate itself through mitotic division and differentiate into a diverse range of specific cell types. In other words, the stem cell can be exploited to produce new tissue, or even organ, for replacing or repairing damaged one. The most popular stem cell (or technically, most commonly used) is embryonic stem cell, that are isolated from the inner cell mass of early stage of embryo called blastocysts. This is due to the fact that, stem cells can differentiate into all of the particular embryonic tissues, usually when the embryo is developing, through cell culture. Recently, a group of researchers from UC Irvine reported that they have successfully utilized human stem cells to differentiate into retinal cell, represented as the first 3D tissue structures (published in Science Direct). Instead of using telescopic devices surgery to overcome vision loss on human (report and illustration from Singularity Hub), this breakthrough is seems to be more natural because it uses biological cells itself without involving any mechanical hardware. Moreover, since retinal cells are directly produced, it is possible that this discovery may revolutionizes traditional retinal transplant therapies, in the near future. In addition, culturing new retinal cells may also overcome s' retinal supply' scarcity problem. The only potential challenge of this visionary finding is the differentiation procedure is highly complicated since retina involves a complex set of cell types to allow it to work. Thus, embryonic stem cells have to be placed onto a patch of retinal pigment epithelium in order to make sure that the cultured cells may growth correctly (see the report here). However, despite of this challenge, this finding can be see as an innovative achievement to medical research and since it still in preliminary work, it may bring remarkable improvement along with hope to society all over the world.

Figure courtesy from Wiki

Can I charge my car here?

It's has been more than 20 years, we have been exposed with a lot of science fiction movies. One of the most popular is Back to The Future. The movie (and its sequels) told us a time-traveling adventure of a high school student portrayed by Michael J. Fox, who befriend with an eccentric, Enstein-like scientist played by Christopher Lloyd, who invented a time machine from a DeLorean car. In the first movie, the car is powered with plutonium but its second movie showed that the car is improved which only used garbage as its main fuel. This movie is very inspiring, especially for the futuristic time-traveling car, even though many of its fans did not satisfied with its ending, where the car is totally crashed by a mere train. Today, the long memory of futuristic cars, such in the movie, has brought back to life in reality. It's not about cars that can bring us to the past, but cars that not need petroleum as their fuel. Yes, we're going to have cars that powered by electricity and this technology may be widely used by us. Electric cars are commonly run by on-board battery packs and already known by their good performance in speed. Despite of this advantage, the main problem of this technology, the low energy capacity of these batteries making them to have relatively poor range between charge and also need a significantly long time to be recharge. However, a group of Japan Electric Vehicle Club managed to shed a light of new opportunity of this technology using their modified Daihatsu Mira, in an attempt to create a new world record of longest distance electric car traveling without recharging. The car, equipped with a Sanyo lithium ion power system containing more than 8,320 batteries, recorded a distance of 1,003.184 kilometers on a single charge (see the full news here). Therefore, this proves that the challenge of power capacity in electric car can be possibly overcome. On the other hand, many vehicle manufacturers have announced a number of projects in order to commercialize the electric cars. People around the world are now seeking for new alternatives for fossil fuel due to the environment sustainability issues. In fact, U.S. government recently planned to implement and encouraging its citizen to use electric and plug-in hybrid vehicles by 2015 (read the report here). A leading car manufacturing project, Megacity Project, announced that the company is planned to launch a new sub-brand, a sub-specification for all future electric BMW car (read the report here).

Dude, I've Got Transistor in my Body!

Transistor has play a major role in our life, especially in modern electronic applications. This tiny (mostly) semiconductor device is used to amplify and switch electronic signal by changing the current or voltage flowing of a terminal to another terminals. Today, this unit is implemented beyond of our thought - embedded in our body for screening diseases. Scientists from University of California has discovered a new way to extend the use of everyday transistor for observing human health. According to Aleksandr Noy, one of the scientists, this new finding exploits the real biological machinery, protein, by working as a part of microelectronic circuit. In this technology, silicon, which the common material used in ordinary transistors, is replaced with new rod-shape material known as carbon nanotube. This material is basically constructed from a single curved layer of arranged carbon atoms. This material is covered with a mixture of lipid and protein, forming a lipid bilayer similarly to the outer membrane of actual cells. Then, the scientists supplied a solution of potassium ions, sodium ions and adenosine triphosphate (ATP) over the constructed transistor in order to power up the device with voltage. Since ATP is crucial element to energize the biological cells, the actual process in ordinary transistors is applied by powering the embedded proteins in the bilayer. Consequently, the ion pump charged the electric charge within the cell, which the charge that going through the transistor. Therefore, scientists can measure and observe the electrical changes. Currently, the scientists believe that this technology can be implemented to monitor and even treat specific diseases; assisted to study poisons and toxins; and even started the development of more futuristic applications such as controlling electronic devices through brain wave. source: Discovery News and MSNBC. Thank you to my friend, Muhammad Faiz Misman, for alerting me with this news.

Look! It's birds... It's planes... No.. It's Supercomputers

Recently, the TOP500 Project, a prestigious project that aims to provide a reliable basis for tracking and identifying tendencies in high-performance computing (HPC), has released its latest 35th list of world's top supercomputers performance, on May 31, 2010 during International Supercomputing Conference 2010 (ISC10) in Hamburg, Germany (for full list, please visit TOP500 website). Guess what, the Cray Jaguar has currently won the crown as the world's faster supercomputer. The machine, which powered by 22,4162 cores of Cray XT5-HE Opteron Six Core 2.6 GHz and run in Cray Linux Environment (CLE), has scored a top speed of 1.75 petaflops per second. Notably, the system has provide supports for scientists to simulate the star explosions and, worth to mention, the uranium flow in Columbia river as a result of old underground storage infrastructure.

So, there goes the tag line of recent update for this technology. For those who are working on this related field, surely it is not so much difficult to understand. In contrast, it is almost impossible for those who are not, to really see the sacred beauty behind this technology. Well, a supercomputer is actually a computer that is at the front-line of current processing capacity, especially in term of computational speed. So, what is a big deal about that? Actually, the most wonderful thing about this technology is how these monsters manage to organize their speed for solving a number of computational tasks simultaneously in parallel through innovative frameworks. Therefore, memory hierarchy of these systems' architecture has to be very well designed in order make sure the processors are kept fed with data and instructions at all times. More recently, chip maker giant, Intel, has planned to introduce a new architecture consists of multicore 64-bit processors configured as co-processors. The architecture, called Many Integrated Core (MIC), tend to focus on replacing lots of standard Xeon processors used in massively parallel supercomputers with many-cored system-on-chip (SoC) processors.

Another important part for supercomputers is the software. As we are already belief, hardware and software must get along together for any system to operate efficiently. Most supercomputers currently are usually run in diverse Linux distributions. This is due to fact that this operating system permits customization and good lower-level monitoring features, which important to observe hardware operational processes, including memory allocation and parallel compatibility. On the other hand, special programming techniques have to be considered particularly to penetrate the speed performance. Fortran or C programming languages are usually used as the base language, using special libraries such as Message Passing Interface (MPI) to share data between nodes. In further extend, an intelligent solution provider company, Adaptive Computing, has launched innovative web portal for deploying HPC as a service and workload-driven HPC cloud architecture (for more information, go to the Market Watch website and company's website). The service, Moab Viewpoint(TM), gives organizations operating the world's leading supercomputers to provide resources as services for computational challenging environments without require users to understand the system architecture.

Cloudy Computing with a Chance of Services

Illustration from Infreemation

Today's computing perspective has shifts to a new edge where resources especially information is shared through a very large and unlimited network of internet. All computer scientists are already aware (or at least realize the situation) of the computing evolution starting from stone-aged batch computing to the well-known mainframe and client-server architecture, just before the internet is introduced and become one of necessities in our life nowadays. Eventually, people who are severely use the internet facility, specifically, to their everyday businesses, understand the important of this technology and starting to explore the essential part of their major activity - service. From this starting point, the cloud computing has become the recently 'new kid in the block' which most people would like to think the technology that may change the world entirely.

In general, cloud computing technology do not provide physical infrastructures to its customers. This means that there are no more paying any hosting servers from third-party companies. Instead, this technology utilizes a same model that people already use in utility services such as electricity, room renting and prepaid billing. In other words, those who use this technology are only subscribe for the resource that he or she need only (so, we only need to spend for the service that we use). In the technical point of view, a large number of intangible computer resource sharing are exploited which consequently produce a very high computing power that manage to support high computational burden. Moreover, increased high-speed bandwidth provides valuable aid in order to improve and maintain the communication of different nodes (particularly for a network of computer nodes that link from diverse regions). This is an important point due to the fact that this technology is built in an architecture that involves communication over application programming interfaces (APIs) for instance web services.

Now, let us see how actually cloud computing is so related to services. In this part, it would be more appropriate if we can see through applications that we used everyday so that we can see (or at least imagine) how this technology is very near to and important for us. Cloud computing composes three main service models: cloud software as a service (SaaS), platform as a service (PaaS) and infrastructure as a service (IaaS). SaaS is the nearest model to everyday use applications such e-mails, online shops and social networking. Thus, this model deals with the use of browser-level applications without concerning or perhaps need users to manage cloud infrastructures including storage and operational systems. On the other hand, PaaS is much a like utilizing services such provided by well-known giant Google in implementing the cloud infrastructures. One of the great example is a bag-full set of Google applications (Maps, Calendar etc) that can be embedded into users applications (hand phones, even personal websites). Last but not least is IaaS which implemented greatly by people who involves in serious works such as researches and big-budget projects. This is due to the fact that this model provides capability to exploit infrastructures that permits users to develop applications that may use the processing power of the large scale computing facility. For instance, many bioinformatics projects deals with high dimensional dataset and diverse possibility results that require development of high computing applications. In addition, graphic visualization and animation industry such as Malaysia's most popular 3D cartoon, Upin and Ipin, and a number of online games developed by companies from Taiwan and Korea are usually make use this model very well.

The Rise of Synthetic Biology: Human-made cell version 1.0

Recently, scientists at J. Craig Venter Institute, led by genetics pioneer, Dr. Craig Venter himself, have successfully created a very first synthetic bacteria cell that can survive and replicate itself based on an artificial DNA sequence which may lead to the production of advanced artificial life (Hornyak, Crave CNET News, 2010: article). This synthetic cell, which named Mycoplasma mycoides JCVI-syn1.0, is produced from Mycoplasma capricolumgenetic code formed by millions of DNA base pair, sequenced as chemical DNA fragments together with yeast and E.coli bacteria and then injected to empty Mycoplasma mycoides bacteria (see video). Many articles discussing about this breakthrough have suggested that this remarkable finding may led to more outstanding discoveries not only to global health care, especially in vaccine, but also may contribute to sustainable environment and technology.