Team:TUDelft/Meetings

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Contents 1 Meeting 25 1.1 Agenda 1.2 Ethical question 2 Meeting 24 2.1 Agenda 2.2 Ethical question 3 Meeting 23 3.1 Minutes 3.2 Agenda 3.3 Ethical question 4 Meeting 22 4.1 Agenda 4.2 Ethical question 5 Meeting 21 5.1 Agenda 5.2 Ethical question 6 Meeting 20 6.1 Agenda 6.2 Ethical question 7 Meeting 19 7.1 Agenda 8 Presentation EWI Bas 9 Meeting 18 9.1 Agenda 10 Meeting 17 10.1 Agenda 11 Meeting 16 11.1 Agenda/Minutes 12 Meeting 15 12.1 Agenda/Action Points in the meeting: 13 Meeting 14 13.1 Agenda: 14 Meeting 13 14.1 Agenda: 15 Meeting 12 15.1 Agenda: 16 Meeting 11 16.1 Agenda: 17 Meeting 10 17.1 Agenda: 18 Meeting 9 18.1 Agenda: 19 Meeting 8 19.1 Agenda: 20 Meeting 7 20.1 Agenda: 21 Meeting 6 21.1 Agenda: 22 Meeting 5 22.1 Agenda: 22.2 Report: 23 Meeting 4 23.1 Action points: 24 Meeting 3 25 Meeting 2 26 Meeting 1 27 Introduction meeting

Meeting 25

• Wednesday October 22th 12:30-13:30
• Kluyverlab room D

Agenda

• Talk about ...
• Steven's Question of the week!

Ethical question

The question of this week is very short:

Which of the ethical issues we discussed the past weeks do you think are nice to present at the Jamboree?

Meeting 24

• Thursday October 16th 12:30-13:30
• Kluyverlab room C

Agenda

• Talk about results from the lab
• Talk about modeling results
• Talk about one of Steven's proposed questions (see below)
• Talk about filling up the poster / presentation
• Progress on Shirts by Emrah!

Ethical question

Last week we discussed a more theoretical philosophical model on our attitudes towards nature. In this week’s session our opinions also play a central role. It appears that all of us have very different attitudes towards the goals of the project, the values that play a role and the responsibilities we have, while at first, in the very first value sensitive design session, we appear to have quite similar ideas. Time to reflect upon the Value Sensitive Design within iGEM. The question of this week:

Was value sensitive design useful and can it, should it, and if yes, how should it return in future project of the TU Delft or any other iGEM team’s project?

It appears that at first, the team was somewhat sceptical about the incorporation of ethical issues in very early stages of design, especially when no real project has been selected. Then, after the project was determined, no ethical review was carried out this year. For a complete ethical analysis of the iGEM project, including ethics at this decision making step is also necessary.

For future projects, introducing ethics may be interesting, also since the benefits are recognized by the students and supervisors. An ethical "review form" was suggested as a suitable format to ensure moral issues are considered in all stages of design. To incorporate it in the whole competition, is probably still a bridge too far, at least at this moment.

Meeting 23

• Wednesday October 8th 12:30-13:30
• Kluyverlab room C

Minutes

• Abstract, Areas to be evaluated (action man:Ruud)
• Reminder of deadlines!!
• Prepare to do lists (Oscar, Rad, Steven(?))
• Experimental part: Oscar presented the sonification results: it works smoothly, successive sonication do not (yet) degrade the proteins. As further experiment, the change in enzyme levels in time will be monitored.
• Costumes: White shirt, dark blue sweater. Banner on the back, logo in front. Sizes are noted down (action man: Emrah)

Agenda

• Requirements list from iGEM - to be updated
• Progress on experimental and modeling work
• Talk about one of Steven's proposed questions (see below)
• Talk about filling up the poster

Ethical question

In 1989 the Dutch philosopher Zweers discusses the attitudes people have towards nature. This coincides with the naturalness issue we discussed within the iGEM project. We are making (more or less) artificial systems based on (more or less) natural "biological" components. Zweers states there are generally six attitudes of man towards nature:

• The despot, ruling the earth as he sees fit;
• The enlightened ruler, where men is somewhat dependent on what nature offers, but nature can still be shaped;
• The steward of the earth, where one treats the earth as if it was not his own property, with respect for nature;
• The partner, working together with nature, but giving nature its own status next to mankind, where nature and mankind cooperate;
• The participant, placing nature "above" humans, where people are only part of nature;
• The "unio mystica", where nature is something spiritual and mankind lives in "unity" with nature.

The question of this week:

Where do you recognize yourself in this model? What if you do not consider nature, but biotechnology? Does this make a difference?

In discussing this topic we very soon started to discuss whether what is "natural" is also "good" per se (see also the naturalistic fallacy of [http://en.wikipedia.org/wiki/G.E._Moore GE Moore]). It was also felt that there can be a different attitude in different situations with different fields of nature. This could be the basis of misunderstandings between different stakeholders in discussions on biological topics.

We also recognized that in biological design, one tries to sell products as if it has the "unio mystica" character, while in early biological design, the researchers are "despots". Somewhere in between a developer needs to think of the ethical issues that may play, and address them properly. What "properly" exactly implies remains unclear for now.

Relations were made between the "perfect" character of nature, the creation of life within a Christian reference, whether a "God" made mankind and afterwards the world for mankind to use, evolution, etc.

Meeting 22

• Wednesday October 1st 12:30-13:30
• Kluyverlab room C

Agenda

• Requirements list from iGEM
• Progress on experimental and modeling work
• Talk about one of Steven's proposed questions (see below)

Ethical question

Last week we discussed who is ultimately responsible (legally and morally) for safety, security, etc. The Dutch VSNU (Vereniging voor Universiteiten - Association of universities in the Netherlands) also published on moral responsibilities of university researchers ([http://www.vsnu.nl/web/show/id=92096/langid=42 link]). The question of this week relates to the relation between natural scientists and social scientists, or, to put it bluntly: the relation between ethics and science. In the individual interviews carried out within the project, you all have different opinions on how ethics should be addressed in scientific practice. Some stated that ethicists should "tickle" scientists, others state that scientists should consider ethics themselves. All of you stated that at some point, cooperation between ethicists and scientists is necessary. The question of this week:

How would you like to see ethics incorporated in your daily work and how do you see ethicists and scientists work together in this?

Main conclusions for this question:

• Intensive ethical awareness creation is important at the beginning of a project. Ethical issues first have to be "officially" introduced, hereafter they can be more easily discussed.
• Weekly questions within the iGEM group are appreciated as a method to integrate ethics in daily scientific practice
• The condition is that the ethical question asked is relevant to the researchers. Scientific knowledge is expected from ethicists, likewise ethical knowledge can be expected from scientists.
• Students from other disciplines (not biotechnology) have not experienced intenstive ethical surveys in their field of education, but do feel that moral issues need to be considered.

Meeting 21

• Wednesday September 24th 12:30-13:30
• Kluyverlab room C

Agenda

• Requirements list from iGEM
• Progress on experimental and modeling work
• Talk about one of Steven's proposed questions (see below)
• Status last thermosensitive part

Ethical question

Last week we discussed whether or not application in society should have a focus in scientific design processes. We got wound up in a discussion on what the goals of iGEM are for MIT and for us, and we decided that before any product can be applied in society, in any shape or form, first other issues need to be considered, like safety, security and liability. The question of this week regards these issues in respect to the responsibilities of MIT, the TU Delft and ourselves:

Who should be responsible for safety or security, and why, and who should be liable in case of " emergency"?

See Safety section for an answer to this question.

Meeting 20

• Wednesday September 17th 12:30-13:30
• Kluyverlab room C
• Maaike Muller (Journalist of the campus journal) will NOT visit the meeting...

Agenda

• Progress on experimental and modeling work
• Talk about one of Steven's proposed questions (see below)
• Status last thermosensitive part

Ethical question

Among you there are persons who think that in a good science project, not only the fundamental science counts, but also the implementation of the eventual products, or, in short: what it means for society. But what does this mean for iGEM? Do we have to consider the impact on society of any application (without further definition of end products)? To what extent do we have to take issues relating to commercialization into account? It is already clear that all of you have different opinions on this matter. But this doesn't mean we can't think about the main question for this week:

Which advise can we give to the iGEM organizers at MIT on this matter?

See ethical conclusions for an answer to this question.

Meeting 19

• Wednesday September 10 12:30-13:30
• Kluyverlab room E

Agenda

• Progress on experimental and modeling work
• Paper on RNA thermometers
• Status of the DNA orders

Presentation EWI Bas

• Tuesday September 9, 12:30-13:30
• Shannon-zaal EWI, 10th floor, out of the elevator, at the end of the hallway to your right.

Meeting 18

• Wednesday September 3 12:30-13:30
• Kluyverlab room C

Agenda

• Progress on experimental and modeling work

Meeting 17

• Thursday August 28 12:30-13:30
• Kluyverlab room E

Agenda

• Progress on experimental and modeling work
• Outcomes of the meeting with Peter Leon
• Comments for wikipage
• How do we quantify the output?

Meeting 16

• Wednesday August 20 12:30-13:30
• Kluyverlab room C

Agenda/Minutes

• Stabs: ordered, received (9 stabs), already growing in a culture, the plasmids of which is going to be isolated. (courtesy of Ruud)
• Transformation: final checks to make sure sure that the problems are on the DNA. (+) control works fine, (the problem is not on the transformation protocol) put the DNA in a gel, got unclear/weird images. It looks like with the IGEM protocol (includes a heating step up to 42oc), you loose DNA but many impurities under the form of chopped off protein. In time DNA denaturates. Plans: There is one more thing to test: to transform the DNA we received to test promotor strength.
• PCR: Ruud is setting up/checking available PCR protocol. 95-50-75 protocol with Taq polymerase seems expectedly working. Plans: Put the genes into a vector (from stabs)
• New sequence design: Bastiaan made an additional sequence design that would allow to be activated starting from ~27oC. He got the green light to order it together with an additional sequence (to be activated at ~32oC). Where to order? (Action man:Bastiaan)
• How to test the temperature? We have a meeting with Peter Leon Hagedoorn. The outcomes of this meeting will be reported.
• Modeling work: The coloring pathway is curated. Found a parameter set for which the system is stable. Bifurcation analysis is carried out to find out parameter regions for which the system is locally stable. BRENDA is checked for nominal values of the a number of parameters in the pathway. Most values lie between 0.001-0.034. Matlab freaks have practical problems in generating random numbers within this region. Plans: make the enzyme variable, (currently constant). Check the literature for temperature enzyme activity relations.
• Questions: -What is actually in the vector? (from Steven to the Pipette nerds)

-How do you plan to integrate (plug in/adapt not Runge-Kutta), the Temperature dependence of the enzyme activity? Put a switch.

• Additional remarks: Janine said: "Disregard my remarks".

Three distinct words from Domenico: Document, document, document

Meeting 15

• Wednesday August 13 12:30-13:30
• Kluyverlab room C

Agenda/Action Points in the meeting:

• Trip to Groningen: it was a nice, introductory meeting with the Groningen team. we'll arrange a similar one somewhere in September.
• Webpage: Ethics sub-part is nicely filled (courtesy of Steven). Lab-notebook should be filled (almost) day-by-day. Separate remarks made for Experimental-Modeling wiki sub-parts.
• New advisor: Ali Mesbah is the new advisor. He will supervise/advise the modeling works, mostly ODE modeling part
• Orders: Having problems in the transformations, stabs will be ordered (Action man: Ruud). Further oligos will be ordered since these are delivered faster (Action man: Bas).
• Project Proposal: This version is highly improved (courtesy of Ruud). Marco still had comments.
• Travel: We are staying in Holiday-Inn Somerville

Meeting 14

• Wednesday August 6 12:30-13:30
• Kluyverlab room C

Agenda:

• progress of lab work
• modeling
• travel arrangements

Meeting 13

• Thursday July 31 12:30-13:30
• Kluyverlab room C

Agenda:

• progress of lab work
• project description
• modeling

Meeting 12

• Thursday July 24 12:30-13:30
• Kluyverlab room C

Agenda:

• Modeling fo the RNA switches. Planning of the experimental work.

Meeting 11

• Wednesday July 16 12:30-13:30
• Kluyverlab room D

Agenda:

• We got final a project. We have now to work it out...

Meeting 10

• Wednesday July 9 12:30-13:30
• Kluyverlab room C

Agenda:

• Final Brainstorming (... the previous one was not that final after all...).

Meeting 9

• Wednesday July 2 12:30-13:30
• Kluyverlab room B

Agenda:

• Final Brainstorming.

Meeting 8

• Thursday June 26 12:30-13:30
• Kluyverlab room C

Agenda:

• Brainstorming with the advisors.

Meeting 7

• Wednesday June 18 12:30-13:30
• Kluyverlab room B

Agenda:

Discussion with Ibo van der Poel on value sensitive design and related ethical issues.

Meeting 6

• Wednesday June 11 12:30-13:30
• Kluyverlab room B

Agenda:

• Brainstorming with the advisors.

Meeting 5

• Wednesday June 4 12:30-13:30
• Kluyverlab room D

Agenda:

• Primer on Molecular biology and modeling in a nutshel.
• Report about the teacher'workshop in Paris (Domenico).
• Update on systematic classification of previous year iGEM projects.

Report:

• Primer on Molecular biology and modeling in a nutshel.

The team members in "need" will have a separate session. Valencia link for some courses: [http://openwetware.org/wiki/Intertech:iSB2008:Materials Synthetic biology course-Valencia]. Nice course organized in 3 parts: training for biologists, training for engineers and training in syntetic biology. The students will meet tomorrow at 14:00.

• Report about the teacher'workshop in Paris (Bastiaan).

Everyone was very motivated, we also met members of the team from Groningen (NL). An introduction was given in which we were told we are at the beginning of a new era. We should not exppect to solve large problems like cancer but start out slow and easy. Some teams are larger than ours (12 members) and some are already working with parts in the wet lab.

The main wiki page should be the WiKi on iGEM. Two weeks before the Jamboree this will be locked! If nothing is there it will not be evaluated! Also be sure we have all information on the wiki before this closing date.

In general: Documentation is one of the most important parts of the iGEM project!

Beware errors are possible in the current DNA archive. Be sure to check by restriction analysis if you have the correct construct! If we foind an eronous construct the correct one can be dsipatched quicklly

www.partsregistry.org : large source of information on the parts, also protocols for extracting the DNA from the provides folder and making compentent cells. Registering parts: Start registration from the start of developement or even generation of the idea.

We have to impress/stunn/amaze the Judges: generate a novel and original idea (poineering, cutting edge, ambitious). Split the idea in steps/milestones and work on one step at the time (kind of modular organisation of the project).

Teams are invited to contribute to an inter-lab comparisson within iGEM.

Many protocols can be found on openwetware, however be aware the ones in the iGEM registry are tested and proven to work, using other protocols are on your own account (if you do, document/report)

Building on previous projects is encouraged, as long as you document it well and be sure to refer/acknowledge iGEM and the specific team.

• Update on systematic classification of previous year iGEM projects.

Most of them are done.

• Brainstorming next week

As a starting point use the classification of the previous iGEM projects. Members should present ideas to the advisors next meeting, prepare a few ppt slides/wiki entries.

Meeting 4

• Wednesday May 28 12:30-13:30
• Kluyverlab room D

Action points:

• Systematic classification of iGEM projects of previous year. Apparently a webpage already exists on openwetware that has initiated this effort; therefore we will add on that. Bastiaan will take the lead: he will assign each student a bunch of projects to claasify. This will facilitate the discussion with the advisors.
• Add a description of your competences/expertise on the wiki, so that it is clear what is your contribution to the project (Ruud, Rad, Farzad, Steven).
• A planning will be posted on the webpage so that we know when everyone is available (Oscar). (*Filippo Menolascina 05:19, 29 May 2008 (EDT): we could use gmail calendar integration supplied by OWW to work out this...some other users have implemented it. Oscar, if you need help tell me!)
• Have a look at the synthetic biology course of the [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology Imperial College] (all).
• Have a look at the experimental protocols for DNA extraction (Ruud).

Meeting 3

• Thursday May 22 12:30-13:30
• Location: let us meet at room D. From there we will head to the garden since no room is available... :)

Meeting 2

• Wednesday May 14 12:30-13:30
• Kluyverlab room D

Meeting 1

• Thursday May 8 12:30-13:30
• Kluyverlab room D

Introduction meeting

• Thursday April 24 17:00-18:00
• Kluyverlab room D

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