Team:Fudan China/HP/Gold Integrated

Integrated human practice is about integrating human practices considerations into the design and execution of the project. In this part of the wiki, we will illustrate our work to improve our project with the idea we gained from the activity mentioned on the ‘human practice-general’ page

A guide on presenting an iGEM project
--An interpretation of the Bloom’s Taxonomy from an iGEM perspective

For both integrated human practice and public engagement & education, the first step is to let your audience outside your laboratory—your industry stakeholders or the residents from your neighborhood to understand what your project is about. In that way , the presenting of the iGEM project, serving as the start point of a successful communication, is the basis of a successful human practice.

As an active participant of iGEM conferences, our team this year gained a lot of experience in presenting an iGEM project to a larger audience. So we decided to go further in this part and develop a a theory around it, so that all the teams can benefit from it. During our preparation for presentations and also audience for other teams, we have felt the strong resemblance between presenting an iGEM project and education practice. So, with the hope of finding the perfect model for a typical iGEM presentation, we explored education theories and finally came up with a ‘iGEM presentation taxonomy’ briefly illustrated in the figure bellow.

The iGEM presentation taxonomy is an interpretation of the original version of the Bloom’s taxonomy and also a revised version of the Bloom’s taxonomy by Robert J. Marzano . We carefully dealt with the difference between presenting an project to people from different major background and teaching classes in a classroom by revising the highest level of the taxonomy. At the same time, we adopted the first several levels from the original cognitive domain, with the belief that these basic principles of how human beings know about the outside world can be applied to any information processing procedure at the onset. We also rewrote the situations defining each levels of the taxonomy, giving it a completely new interpretation aimed specifically at iGEM project presentation.

We hope that these works may lead to a better understanding of possible goals or outcome one may get when presenting the iGEM project, and that improvements may be made by finding out the additional goals one may want to achieve when comparing the existing goals and the possible goals listed in this taxonomy.

Here are the detailed illustrations of our work.

First we shall have a look at the right part of the figure, the box named ‘metacognitive system’. The idea comes from the revised version of Bloom’s Taxonomy by Robert J. Marzano, which indicates that mental process can be ordered in terms of control. That is to say, before we actually start our cognitive activities, we need first to decide whether or not we will engage in the speech the speaker is delivering. When it comes to presenting an iGEM project, it means that at the beginning, the speaker may need to stress on the importance and uniqueness of the project. So it would be helpful to show the seriousness of the problem the project is dealing with, and to clarify the research background of the project so that people doing research in similar fields may be interested.

Then we may come to the cognitive part of the process, which is illustrated by the large triangle in the middle in figure. It is further divided into four levels.

1. Retrieval

The retrieval here means the retrieval of knowledge about simple facts. The major mental activity in this stage is memory. It’s about the knowledge we have memorized and the knowledge we are yet to memorize.

Speakers working on this level will help the audience to recall simple facts like ‘an open reading frame starts to express when the inducer binds to the promoter’, and also introduce the basic feature of a new concept like ‘a recombinase reverses the DNA sequence between its action sites’.

The knowledge or fact we retrieve here will become the building block of the following stages.

2. Comprehension

Comprehension here includes the common ‘understanding’ process and also an additional ‘interpretation’ process, which means that the audience here are expected to take in what the speaker is explaining and convert it into something that is more meaningful to him/herself.

Speakers working on this level will give meanings to the knowledge building bricks retrieved in the first level. The basic knowledge here are organized in a certain relationship to express an idea the speaker want to express.

In an iGEM presentation, this is extremely important when the speaker tries to explain how their circuit work, for example ‘how does the combination of different promotors and recombinases produce a sequential memory machine’.

Most presentations may be considered successful when its audience reaches this stage.

3. Analysis

In contrast to comprehension, which emphasize on ‘comprehend all the knowledge and relationship as a whole’, analysis focuses more on breaking the whole project into basic elements again. Through evaluation of different basic element and their relationship, audience are supposed to understand why these elements are organized in this specific way instead of the many other random combinations.

Analysis prepares the audience for making creative changes on the existing project.

4. Inspiration

We have thought a long time about what should be the ultimate goal of an iGEM presentation, and finally we name the highest level of our taxonomy as ‘inspiration’.

After the entire preparing step mentioned above, the audience have converted a new and unfamiliar project into a dynamic part of their own knowledge system. From then on, the original project can be easily abstracted, broken down and forming into new ideas, and that is the most charming point of the communication.

References

  1. Bloom, Benjamin S., et al. Taxonomy of Educational Objectives. the Classification of Educational Goals: Cognitive Domain. Longman, 1984.
  2. Marzano, Robert J., and John S. Kendall. The New Taxonomy of Educational Objectives. Corwin Press, 2007.

A set of 3-D printed brick toy inspired by the iGEM taxonomy

When we look through the iGEM presentation taxonomy ourselves, we found that it is more difficult to help the audience go through the last two levels of the taxonomy with only a presentation alone. So, we came up with an idea that designing a 3-D printed brick toy may help with these process.

The brick toy is naturally composed of basic elements. They are designed to be easily pulled apart and recombined again and again, thus giving plenty of opportunities for the players to do the comprehension and analysis work. Especially for our recombinase-base system, which actually involves a turning and moving gene circuit itself, a brick toy helps to visualize the process how the circuit changing from one state into another. In that way, the players can easily check whether or not his/her new design can work properly, making the whole ‘inspiration’ stage more enjoyable.

We have brought the brick toy to the iGEM conference CCiC and also to our club fair. It received warm welcome there.

The brick toy is composed of the following parts.

Here is the base board where all the other parts can be put.

Here is the recombinase part, indicating the DNA sequence between two action site of one recombinase. These two triangles represents the action site of the recombinae.The part can be plugged on the base board and can be turned around. You can also plug two recombinase part together so that the sequence can be turned twice.

Here is the DNA sequence without recombinase action sites. These parts are the same as the recombinase part mentioned above, except that they do not have the triangles, so they do not turn under any circumstances.

Here is the promotor part. Promoters answers to inducers and start the expression after induction. The promoter part here has a track on both side which can hold the little patch indicating the inducer. When a patch is put on the track, it means that the promoter answers to the inducer.

The promoter can be plugged into the grooves at the side of both recombinase part and normal DNA sequence part mentioned above.

Here is the coding sequence part. It can be plugged into the recombinase part and the normal DNA sequence part mentioned above. The arrow at the front indicates the direction of the expression.

Here is the terminator part. It indicates the end of expression.

Finally, here is our circuit demonstrated by this model.

The white and black patch indicate the presence and absence of the clock signal. The yellow patch indicate the target signal.

The sewage plant visit and beyond

During the visit

Our project focuses on the construction of a new kind of cellular memory machine which is capable of recording the changes of a signal in an extended time period. This aspect of our memory machine can be extremely useful in monitoring the chemical changes in the environment. So we contacted one of the biggest sewage plant in Shanghai—Xinchu sewage plant and paid a visit there.

After talking to the workers at the sewage plant, we had some new ideas.



  • The biochemical reaction pool where all the microbes works hard to lower the COD value is exactly where we may put our engineered E.coli to do the monitoring work.
  • Although data like COD value and pH of the sewage is dynamically monitored, some other important data like the amount of heavy metal is more difficult to detect. So, When it comes to real world application, we may have a closer look on the monitoring of heavy metals.
  • The reaction pool is more than 10 meters deep, but the regular sampling of the sewage can only cover the several centimeters right beneath the surface. We can add a light sensitive part after our memory circuit, in that way, we may guide the engineered E.coli to collect the data at the bottom and swim up the surface to be collected.

After the visit

We cultured E. coli DH10B, the bacteria where we constructed our circuit in with 100%, 50%, 25% and 0% sewage in the culture system. At last they all survived and thrived. Even the group cultured with 100% sewage seemed to grow well.

The result showed that it is possible to put the bacteria directly in the reaction pool and collect the data later on.

In that way, we can make more improvements

  • A suicide gene may be attached to the end of our circuit, so that we can prevent it from spreading into the environment.
  • A special sequence served as the identity number of the E.coli may be add to the beginning of the circuit. So that if we put in the E. coli in batches, we can identify the data collected in each batch easily.