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Revision as of 11:23, 20 October 2009

Team:USTC/Human Practice

How do We Explain E. ADEM to 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 much stronger feelings 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 be 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 risks while we are striving for this final purpose. It is the positive safety measures and prudent thinking that is being cried for. We are striving for the ability to control what we would create as urgently as we are striving for the benefits which would come along with the final purpose.

Safety

Experimental Safety

• Just like any other practical activity 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 may be worn in some certain circumstances,eg. when using a UV lamp.
    

• Work Safety in our lab is categorized into three 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 using 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 employed the gene of Activation-Induced Deaminase (AID) as the functional part 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：As we have described above, the most potentially dangerous part in our project is the variation function. If the variation function should become out of control, the living system with unknown random muation sites would be a great threat to both the human living 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 body.
    • 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.

Comments from the College Committee

The college committee members: Congzhao Zhou, Haiyan Liu, Jiarui Wu took part in the work of topic picking.

Security

BioBrick Security

Project Security

• Open Wet Ware：E.ADEM is now 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 "evolve" anything. Based on our work started from iGEM competition, the project should continue with the inspiration and perspiration from students or researchers with the similar interests all around the world. 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, too.
• Disadvantage：However, there are some conundrums of "open" and security.

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