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    Added: 25 February 2011

    • Abstract

      Scientists are inquiring the nature and Engineers are designing artificial technologies. Scientists are obtaining knowledge and engineers are using knowledge to design artificial systems. However, the technology is not enough for scientist to understand the nature and the data is not enough for engineers to design artificial systems.

      Their common goal is solving the problems in the world and making life easier. To achieve the goal, both obtaining knowledge and engineering it to produce artificial ones are vital. Their need to each other is increasing and destroying the boundaries between the fields. Herewith, new field are emerging like Nanotechnology and Synthetic Biology. The fields are suggesting innovative artificial solutions to our problems. Synthetic Biology is designing and constructing new biological parts, devices, and systems not the lives from scratch, and re-designing existing biological systems for useful purposes according to SynBio community http://syntheticbiology.org. The parts, devices, and systems are suggesting innovative solution for a broad application area from Bioenergy to Biomedicine. Day by day new ones are emerging.

      As the fields emerge, the knowledge to transfuse to next generations and between the knowledge staff is also increasing and getting more complicated. To overcome the problem we are designing a visual learning environment to give people basics about the field by uniting and improving number of resources.

      We are using multimedia Learning Approach and developing visuals to promote the learning. To visualize the concepts and provide self experience we are developing 2D, 3D animations, and simulations. To emphasize some texts and to apply dual coding principles we are using narration. Finally, to provide self test about basics we are asking a few questions on quizzes. Anyone interested in the field can learn the basics by following the guides in SYLLABUS.

    • Quick Links

      Part 1 Science and Engineering ......................... ||| Objective: Have an insight to the field.

      Part 2 Synthetic Biology Concepts ..................... ||| Objective: Learn the meaning of the basic concepts.

      Part 3 Synthetic Biology Standards .................... ||| Objective: Learn the basic standards and basic standardization progress.

      Part 4 Challenges in Synthetic Biology ............... ||| Objective: Aware the reality of the field and care about ethics.

      Part 5 Expert views and Editional Resources ..... ||| Objective: Improve your professional insight to the field.

      a) Expert views.

      b) Suggested Links and News.

    • Acknowledgments

      Developed by:
      • Bs. Muhammed Akif AĞCA, Bs. Ayub Rokhman WAKHID, Bs. Muhammad Fakhry SYAUQY

      Thanks to;
      Our Advisors :
      • Assoc. Prof. Dr. Kurşat Çağıltay, PhD Engin Küçükkaya
      Interviewees :

    • Page SYLLABUS Page
  • 1
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    Part 1 : Science and Engineering>

    • AN INSIGHT TO SCIENCE AND ENGINEERING

      Life Sciences have huge amount of data waiting to be interpreted and Engineering has perfect standards and computational methods to be applied. Scientists are continuing to find new data and engineers are continuing to develop new standards. However, scientists are complaining about the insufficiency of technology to find accurate data, engineers are complaining about unstandardized data to develop new standards for faster improvement as they did 1950s to circuit systems, which was the starting point of information era. In such a situation, scientists should be able to think as an engineer, to produce more standardized data. Engineers should be able to think as scientist to understand difficulties while looking for unknown by scientists. That is why the borders between each field are disappearing; anymore science engineering fields are emerging to find more standard data and develop new systems with the data.

      The scientists and engineers see the need of each field to each other. That is why integration of fields idea is very popular in these days, to suggest innovative solutions to each other and by the integration to problems in our life. The synthetic biology is the product of the idea. The field is aiming to design existing lives for desired functions and designing artificial ones by applying engineering principles to biology.

      In the field we need computational methods, statistics, machine learning approaches, artificial intelligence applications, standardization basics, design principles, and many fields can be applied to biology. In this wise, we can find artificial solutions to our problems in life and in industry. Even more, new industrial sectors can be found by finding innovative solutions from health to green energy. That is why we say “Industrial Revolution 2” is coming soon to find artificial solutions to our problems.

    • File Reading 1 - Science_and_Engineering File
    • File Reading 2 - Rethinking_science_technology_policy File

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    Part 2: SynBio Concepts

    • Biotechnology

      There are many different way to describe biotechnology. Many definitions are also exist regarding it. However, basically biotechnology came from the word bio which means life or living things and technology which is the practical application of science in commerce or industry. So we can say that basically biotechnology is the application of science approach to a living thing to manufacture new product. In the application, not only living things but also biological substances like enzymes can also be the object of biotechnology. The scientific application that we are talking about here is usually done by manipulating genes of a living organism or manipulating enzymes. Nowadays the manipulated genes are still limited to micro-organisms.
      Area of biotechnology

      Biotechnology often used in producing breakthrough in medical and agricultural areas. In medical areas it can helps in drugs production and synthetic hormones production. In agricultural areas in can help to increase the quality of food product. However, a lot of people do not agree in the use of biotechnology in most of the food products. It happens because scientist has not guaranteed 100 % that the product from biotechnology is safe for human’s health. Despite of this argument, the application of biotechnology is still spreading.

      Synthetic biology

      While Biotechnology comprises broader aspects, a new and more specific area was emerged. It is called synthetic biology. Different from biotechnology, this area has its own specific target which is designing or redesigning and constructing new biological functions, systems, or even organism.

      In the year of 1970s a common practice that was done was to take a particular DNA sequence that has a particular function from an organism and combine it with other organism’s DNA sequence so that the receiver organisms will be able to do a new biological function. However, this practice is really limited and expensive since it needs existing gene sequence and bacteria. This practice commonly still only conducted in micro organism level. The most use micro-organism for DNA implementation is E-coli bacteria.


    • Animations and Simulations

      Animation 1 Animation 2 Animation 3 Animation 4
      Transformation of a Trait Cloning Part An Application Area of Engineered Bacterias
      Objective: Understand transformation process Objective: Understand basics of cloning Objective: See an application area and understand how next simulation works Objective: See different applications of SynBio
    • References
      Biotechnology. (2008, February 6). Economist. Retrieved November 28, 2010, from http://www.economist.com/background/displayBackground.cfm?story_id=1055963
      Synthetic biology. (2011). In Encyclopædia Britannica. Retrieved from http://www.britannica.com/EBchecked/topic/1692043/synthetic-biology
      Synthetic biology. Bio-fiction. Retrieved November 28,2010,from http://www.bio-fiction.com/synthetic_biology.html
      Image from
      http://www.bioreactors.net/eng/ptemplate.php?img=bio.1.jpg&hedr=Biotechnology
    • More Resources:
    • File Reading 3 - Introduction to Biotechnology and Synthetic Biology File

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    Part 3: SynBio Standards

    • BioBrick

      Two or more different DNA structures are combined into a structure called BioBrick. The name is a trademark of BioBrick Foundation. BioBrick can be manufactured and then combined into living cells such as E. coli to make a new functional biological system. BioBrick is also considered as integrating engineering principles of abstraction and standardization into synthetic biology.

      One of the goals of the BioBricks project is to provide a workable approach to nanotechnology employing biological organisms. Another, more long-term goal is to produce a synthetic living organism from standard parts that are completely understood. (Alok, 2005)

      Each BioBrick part is a DNA sequence held in a circular plasmid. These sequences contain six restriction sites for specific restriction enzymes. This condition for the simple manufacture of larger BioBrick parts by arranging and modeling smaller ones in the way we want. In the process of chaining parts together, the restriction sites between the two parts are removed, allowing the use of those restriction enzymes without breaking the new, larger BioBrick apart. To make the assembly process happen, the BioBrick part itself must not contain any of these restriction sites.

      There are three levels of BioBrick parts: "parts", "devices" and "systems". "Parts" are the building blocks and encode basic biological functions (such as encoding a certain protein, or providing a promoter to let RNA polymerase bind and initiate transcription of downstream sequences); "devices" are collections of parts that implement some human-defined function (such as a riboregulator producing a fluorescent protein whenever the environment contains a certain chemical); "systems" perform high-level tasks (such as oscillating between two colors at a predefined frequency).

      All BioBrick formats proposed so far follow the same basic scheme where restriction and ligation of two BioBricks forms a new BioBrick:


    • Abstraction Hierarchy

      Based on syntheticbiology.org the definition of abstraction hierarchies is a human invention designed to assist people in engineering very complex systems by ignoring unnecessary details. If the process to design a biological system was to write down the string of nucleotides, it would immediately become unsustainable even for experts to design anything but very simple systems. Most people just aren't able to process that kind of detail all at once. If instead, an abstraction hierarchy is specified, it allows the designer of a biological system to ignore some of the operation details and focus only on the high-level design issues.

      All engineers from different branches take advantage of abstraction hierarchies to design and build complicated systems. For example, software engineers write in high level programming languages like C++ or Java which are designed to be easy for humans to read and write. These programs are then translated into lower level sets of instructions that are more easily translatable to bit strings that are machine interpretable and implementable. Thus, the people who write C++ programs do not need to know how to translate their programs to machine code and the people who work on instruction sets do not need to visualize all possible programs that the software engineer might write.

      In order to allow the engineering of very complex biological systems, abstraction hierarchies need to be developed for biological engineering. At this point, it is not necessarily clear which hierarchies are most useful and in fact it may be slightly premature to try and develop them. However, thinking about what an abstraction hierarchy in synthetic biology should look like might help us think about the "right" way to engineer biological systems and to design biological parts.

      Below several abstraction hierarchies are listed that might be appropriate for biological engineering. The abstraction hierarchies have been listed in chronological order of inception.



    • Animations and Simulations

      Animation 5 Animation 6 Animation 7 Animation 8
      Parts Introduction Assembly of Biobricks Abstraction Hierarchy of Biobrick Assembly Risks of Engineered Systems
      Objective: Learn the basics components of a part Objective: Learn the basics of biobrick assembly Objective: Learn the basics hierarchy of biobrick assembly Objective: Aware the risks of engineered systems
    • References:
      Jha, A. (2005). From the Cells Up. The Guardian. Guardian News and Media Limited.
      http://syntheticbiology.org
      http://openwetware.org
    • More Resources:
    • File Reading 4 - Synthetic Biology Standards File
    • Untitled 1

      Biobuilder.org Videos

      BioBuilder Animation 1 BioBuilder Animation 2 BioBuilder Animation 3 BioBuilder Animation 4
      Open Reading Frames Bacterial Gene Parts Part Genetic Digital Devices
      It’s not easy being green. It’s also not easy to figure out why Buddy is green, but Sally explains how open reading frames help. Not all apps are created equal. Dude gets lessoned on how to build a gene using the correct parts in the correct order. Dude cops an attitude. If we know the parts of a biological system, why can’t we design them to snap together like pieces from a model robot kit? Buddy’s growth is out of control. Sally shows Dude how the right device can be used as an on-off switch to keep Buddy from blowing up.
      BioBuilder Animation 5 BioBuilder Animation 6 BioBuilder Animation 7 BioBuilder Animation 8
      Abstraction Inverter DNA Synthesis Measurement
      iGEM team member Izzy tells Dude how her team’s project to detect arsenic in well water used the process of abstraction. Green light, go. Red light, stop. A transcriptional inverter may not work as fast as a traffic light, but Izzy helps Dude understand how this type of device can help him solve Buddy’s overgrowth. Order up! Dude is ready to string together his DNA design, but doesn’t know how. Izzy discusses what measurement data is available for biological parts, and Sally gives an overview of scientific measurements.
      BioBuilder Animation 9 BioBuilder Animation 10 BioBuilder Animation 11
      iGEM Biosafety Levels Cell Growth and Division
      Dude’s got the iGEM competition in the bag. At least that’s what he thinks. Dude’s plan to make viral cocoa beans using a BL4 virus gets Sally’s attention fast. Time to school Dude on the biosafety issues of synthetic biology. Izzy and Sally help Dude keep up with the cells growing in the lab. This video looks at the stages of bacterial cell growth, how to measure them, and launches the BioBuilder activity #1: Eau That Smell!

      Reference:

      Natalie Kuldell, Biobuilder.org animations. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://www.biobuilder.org/animations/ (Accessed June 13, 2011). License: Creative Commons BY-NC-SA


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    Part 4: Challenges in SynBio

    • Risks and Ethics in Synthetic Biology

      As understood from the name Synthetic Biology is focuses on to design artificial new live systems and modification of the existing one. Official community of Synthetic Biology defines the field as design and construction of new biological parts, devices and systems and redesign of existing biological systems for useful purposes (http://syntheticbiology.org/). That is the age of artificial live systems is starting. The engineers and scientists are coming together for the goal. Engineers are looking for more data to engineer the scientist are waiting for better technologies to see the nature to produce data to be engineered. By the way new integrative fields are emerging to achieve the goals. The more advanced technology the more problems of course. The progress can give unexpected results and can be used for de trop purposes. The workers of the field are not playing with toys they are playing with toxic proteins, pathogens, viruses etc. They may not be able to all possibilities of mutations and cannot guess all the results of course. Furthermore, the people are also not so different than the toys of scientists. They also can mutate and new BioHackers can emerge. Therefore, we have to be very careful about all possibilities. Safety issues should be specified in detail. It can be dangerous for researchers, public and environment. Security levels should be described very carefully, BioHacker can use the field for undesired purposes. Finally, international justice criterions have to be specified very carefully. Since the technology is not cheap all countries will not be able to develop own live machines and dependency to rich countries will increase. The issue needs to be evaluated carefully. Markus Schmidt and his team has implemented Synbiosafe project between January 1, 2007 and December 31, 2008 for detailed information abot the issues please check it http://www.synbiosafe.eu/.

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    Expert Views


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    Suggested Links and News


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