From 2009.igem.org

Revision as of 16:59, 21 October 2009

Team:USTC/Human Practice

How do We Explain E. ADEM to Mr. Darwin?

Mr. Darwin

Dear Mr. Darwin:

You have already known about Synthetic Biology, don't you? [http://dsc.discovery.com/technology/slideshow/synthetic-biologists-darwin.html] I'm gonna talk to you about our novel project in Synthetic Biology field. Since it is based on and closely related to the Evolutionism, I think you'll be interested.

As you have known, the same stuff called DNA stores all the secrets of life and dominates the features of creature individual. Synthetic Biologists are changing the DNA sequence 'designing and synthetizing' the new forms of life. But we are trying something new. We choose to do 'synthetizing and evolving' in a living creature. It sounds crazy, you may say, as other people may think.

We not only want to give evolution a direction but also try to make the process automatic as the first steam locomotive in the world of synthetic biology. It seems that we are employing one of the most powerful forces in the nature to creat what we want, perhaps a living thing. This prospect may leave many people jittery. I don't know whether you were jittery or not when you discovered the most deeply covered secret of evolution. We now find we can employ or even 'control' evolution. What I am sure is that you certainly had a much more profound insight about the power of the evolution than us after seeing the fossils in person on the voyage of the Beagle.

We have thought about this question seriously. The final purpose of our project is to evolve anything including a system--a system that holds the potential to become a new form of life. Is it true that when we finally reach this destination we will have the chance to play God?

We are not fearing the possible godlike power; we are fearing the inability to control it. We agree with what Pro. Caplan once pointed out:'It is hard to credit the view that God would give us the abilities to make new life forms and then argue that to do so crosses a line that God does not want crossed. If one takes a more secular view the fact that human beings can mimic random processes that allowed life to emerge is not especially threatening to faith in the divinity.'

However, as for the inability to control the power, there are serious potential perils while we are working for this final purpose. It is the positive safety measures and prudent thinking that are being cried for. We are striving for the ability to control what we would create as urgently as we are working for the benefits which would come along with the final purpose.

Safety

Experimental Safety

• Just like any other practical activities in school science, all microbiology investigations require the user to adopt good laboratory practice. The preliminary experiment training made sure that every one of us get familiar with the whole system of basic microbiology investigations and get adroit skills especially for those in related majors.
• Several regulations has been set to guarantee personal protection.
  
  • Food or drink should not be stored or consumed in a laboratory or prep room that is used for microbiology.
    
  • No-one should lick labels, apply cosmetics, chew gum, suck pens or pencils or smoke in a laboratory or prep room.
    
  • Facilities should be provided within the laboratory or prep room for hands to be washed with soap after handling microbial cultures and whenever leaving the lab.
    
  • Paper towels or some other hygienic method should be used for drying hands. If contamination of the hands is suspected, then they should be washed immediately with soap and water.
    
  • Cuts or abrasions should be protected by the use of waterproof dressings or by wearing disposable gloves.
    
  • Safety glasses should be worn in some certain circumstances,eg. when using a UV lamp.
    

• Work Safety in our lab is categorized into two levels as follows:
  • Level 1: organisms we work with have little known risk and are observed in the closed containers in which they are grown. Microbes (K12) we growing is tested as non-risk and harmless, furthermore, by culturing closed containers which are taped before examination and remain unopened unless the cultures inside have been killed by the autoclave sterilizer. We made every effort to exclude any possibility of unsafety.
  • Level 2: biological reagents we use are considered on environmental and human safety. We choose GelRed[http://www.biotium.com/product/price_and_info.asp?item=41001&Sub_Section=09A] instead of EB as our nuleic acid stains.

E.ADEM Safety

• BioBrick
  • 

    

    Quorum Sensing
    AID-related Safety Problem: In our project, we employ the gene of Activation-Induced Deaminase (AID) as the functional section in the Variation Function which is responsible to change the evolution objects. The AID works on single DNA and inverts the base C to U by deamination. There are some potential dangers of the use of AID since it works on a relatively large scope and the spread of its gene may cause some unpredictable results.
  • Quorum-Sensing Safety Problem: Quorum-sensing device used to calculate population size and average score may lead to the formation of biofilm[http://en.wikipedia.org/wiki/Biofilm]. Quorum sensing allows bacterial cells to collaborate in a way that benefits an entire biofilm population. Biofilm enable bacteria to survive unpredictable environmental stressors such as temperature changes, desiccation, ultraviolet rays, and so on. This means that biofilms would do harm to many industries that involves a water-based process: nautical shipping, paper manufacturing, cooling systems, drinking water facilities, health care, medical devices, and food processing. Many methods aimed to eliminate the biofilm focus on interfering with quorum sensing. That way, the spread of the quorum-sensing device would cause some troubles related to food safety or other industries.

• System
  • 

    

    Mutation
    Restore the System：The most potentially dangerous section in our project is the variation function. If the variation function should become out of control, the living E.colis with unknown random mutation sites would be a great threat to both the human bodies and the environment. To avoid such kind of hazard, we have designed a supervising system and a suicide switch for our future work in order to restore the whole system as an emergency aid.
    • Supervise the Mutation：By measuring the mutation rate using a report gene, we can approximately learn the mutation situation inside the E.coli bodies.
    • Suicide Switch：When the variation part comes into dysfunction which can be monitored under the supervising system, we need a suicide switch to destroy the deviated system. Such devices are avaibable in Standard Parts.

Comments from the College Committee

College committee members: Congzhao Zhou, Haiyan Liu, Jiarui Wu took parts in our work of topic picking and judged the project E.ADEM as exercisable. Otherwise supervision was token all along the project to ensure every detail of safety.

Security

Security

BioBrick Security

Dilemma

Dilemma comes when we try to discuss whether offers of biobricks should be free or strict. On one hand, we worry all the time that our biobrick may someday be misused to cause disasters for the things we create are unnatural and with risks of out of control. In this way, we carefully select our offers and also understand completely when our ask of biobricks were turned down during our work. Well, on the other hand, we experience at first hand how strict regulations can delay and even destroy scientific research. You can imagine our dismay when some certain raw materials we need were checked and delayed by the Customhouse and we can only faute de mieux.

suggestion

Several possible solutions were approached in our discussion which we hope will improve the situations of dilemma described above.

• Those who own biobricks have responsibility to ensure safe conservation and appropriate use.
• Those who ask for biobricks should provide offical certification of their ability to handle a safe experiment as well as detail plans they will do with the biobricks.

Project Security

• Open Wet Ware：E.ADEM will soon be available on the OpenWetWare[http://openwetware.org/wiki/Main_Page]. The ultimate goal of Automated Directed Evolution Machine is to construct a robust system that can universally "evolve" anything. Based on our work started from iGEM competition, the project should continue with the inspiration and perspiration from students and researchers all around the world with the similar interests. We are anticipating your participation!
• Advantage：Open Wet Ware offers a development method for E.ADEM that can harness the power of distributed peer review and transparency of process, just as the open source system does in the field of software development. Actually, iGEM community has created a good environment for "open-source" path by building bridges among different labs. We are glad to promote this sharing atmosphere and reap benefits from it as well.
• Disadvantage: However, there is an ultimate conundrum between "open" and security. It is entirely possible that the E.ADEM would be used for destructive purpose. Unlike the open source software, the bio-engineering products are related to the bioweapons. The open accesses to the core information would also lead to malign use of those knowledge. We call for pertinent regulations and propose our suggestions as follows.

Regulation Suggestion

We held a discussion on this open-security delima and generated some suggestions for this issue.

• Precaution
  • A declaration is extremely necessary: The declaration should include not only the authorship but also the committement not to misuse the project. We will declare those issues in our project. Obviously, a general declaration for all the iGEM projects is needed.
  • The registration information for OpenWetWare should be audited under a strict standard: Although an extensvie group of users means a large influence, the armory of synthetic biology world without any fence would be a threat to our society since none can guarantee all the prospective users are research-oriented.
• Sanction: Given the unpredictability and severity of crimes in biology field, the levels of punishment are hard to define. However, any possible damage should have a punishment level in the scope of legal regulations.

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