http://2010.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Liam+Wilson&year=&month=2010.igem.org - User contributions [en]2024-03-29T10:57:01ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:WITS-South_Africa/PhilosophyTeam:WITS-South Africa/Philosophy2010-10-27T21:37:51Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<div style="padding:40px;"><br />
<br />
<div class="heading"><br />
Human Advances <br />
----<br />
</div><br />
<br />
<div style="padding:4px;"><br />
<br />
<div style="width:880px;text-align:justify;float:left;"><br />
<br />
As the first South African iGEM team, it seems fitting to add to this debate by introducing the theory of '''ubuntu''' a means of furthering ethical debate around synthetic biology.<br />
<br />
[[Image:Ubuntu 904.jpg|400px|left]] I am not talking about this - though the penguin is very cute. <br />
<br />
<br />
<br />
I hope to answer the question ''''Should ubuntu be seriously considered when making policy?'''' I am of the opinion that applying the principle of ubuntu might prove to be good policy on both a macro and a micro level. On a micro level, adhering to ubuntu would make scientists and researchers more ethically sensitive. On a macro level ubuntu can maintain sound policy while preserving the importance of individual ethical conduct. <br />
<br />
Here is a biref sketch of my argument.- I will be raising raise some key of the main ethical concerns that are raised by our team's lactoguard device. I will then present a workable theory of ubuntu and apply it to these concerns, raised in order to see if doing so can provide constructive insights into how they could be resolved. it can address the issues raised. The paper will therefore be a philosophical 'case study' into bio-ethics.<br />
<br />
From this, I will hope to show that ubuntu can provide ethical guidance for synthetic biology, - as it provides both 'internal' and 'external' moral motivations for ethical conduct, and to present a convincing argument that . From this I hope to convince people that the following five 5 tenents of ubuntu can serve as good 'rules of thumb' for ethical conduct within the field:. They are: <br />
<br />
• Informal relations are important and have a role in our decision making. <br />
<br />
• Community members should show special ‘family-like’ concern for one another and that one’s actions reflect on the community as well as on the individual. <br />
<br />
• Every member of that community has a personal stake in its endeavours and should bear some of the responsibility for the community. Conversely, every member should also but also share in the fruits of its endeavours. <br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive from the community. Some members may be more reliant on the community that than others and some may be expected to contribute more. <br />
<br />
• Members of the community have access to the resources of that community and can make use of them in so far as they contribute to the community and are involved with it. They can also profit of from the communities resources, provided that the profit generated goes into supporting the community. <br />
I will not fully argue every point – a more comprehensive account is given in my longer paper ''Anticipating ethical with problems the possible development and distribution of Lactoguard in a South African context''. for everything here - one will need to read my full paper for a proper length explaination of everything I have brought up here. But I will not leave you in the dark - here are some bite- sized definitions and explainations that will give you so you can get an idea of what I am talking about and where my arguments will goare. I will also provide some links to external sites that might be of some help.: <br />
<br />
'''Ubuntu'''<br />
<br />
Ubuntu is a new field of study in analytical philosophy. I wager Tthis is probably because of the cultural isolation of the Apartheid apartheid years and the general social and political turmoil that has been experienced in on the African continent post-colonialisation Africa. Anyway, on to the positive matter - how do we define ubuntu? <br />
Metz describes ubuntu in terms of harmonious relations: ‘An action is right just insofar as it produces harmony and reduces discord; an act is wrong to the extent that it fails to develop community. <br />
<br />
Basically, ubuntu is a theory of right action - that it is, it a theory that tells us how to act in order to act in a morally good manner. If we compare Metz's conception of ubuntu with other normative ethical theories, we can see how different ubuntu really is. <br />
<br />
Deontologists maintain that an action is right if it is in accordance with some duty or moral rules, such it is wrong to murder. Consequentialists see the moral weight, that is, if the action is good or not, - as resting in the consequences of an action. For example, one might refrain from lying because by not lying one tends to promote good consequences. Consequentialism is often expressed by the saying 'The ends justifies the means'. <br />
By Metz's definition we can see that actions can be considered good because of both the duties that harmonious relations have attached to them - such as a duty not to lie or cheat – and . And they can also be considered good because of the consequences that it produces, - such as reconcilling with a person who has wronged you in order to promote harmony in your community. To put this in perspective, - these two schools are traditionally set up in opposition to one another. <br />
<br />
I will also argue that ubuntu also has an extra component to it. That component is virtue ethics. Virtue ethics is the oldest form of ethical debate in the 'western' tradition. It's roots are found in the dialogoues and ethical theories of Socrates, Plato and Aristotle. Virtue ethics is an ethical theory that take the view that it is the concept of virtue that should be of primary concern when analysising moral actions. Virtue is understood as character traits that are considered to be good. Ine of the major problems for virtue ethics is to account for how a person thinks in terms of moralit with refering to duties or concequences. I will this argument is unhelpful - we should instead <br />
<br />
I will argue in favour of Metz's conception of ubuntu as I believe it captures the 'Africanness' of ubuntu and is explicit enough to tease out the deontologist, consequentialist and virtue ethical elements of the theory. My contention is that the virtue component of ubuntu is not a distinct object in the ethical framework of the theory in the way that the concept of 'goodness' is considered in classical deontologist and consequentialist theories. Instead, I contendt that ubuntu fosters the development of a sensitivity to ethical situations within the individual in question which can be described as virtue. Ubuntu can therefore be considered to be, at least in part, a character trait. <br />
<br />
The Wwikipedia entry on ubuntu alludes to this the connection that I am trying to establish. <br />
<br />
http://en.wikipedia.org/wiki/Ubuntu_%28philosophy%29 <br />
<br />
Here is Desmond Tutu (who is perhaps one of the best exponents of ubuntu) describing ubuntu <br />
<br />
http://www.youtube.com/watch?v=ftjdDOfTzbk<br />
<br />
'''Should we take notice of ubuntu?'''<br />
<br />
I think that that we should. The use of ubuntu is not entirely unpreceidented at a policy level. The philosphy of ubuntu has provided a guiding influenced in the Truth and Reconciliation Commission, where the focus was not on punishing those responsible (on both sides) for the hideous crimes committed during the struggle against Apartheid. Instead, the focus was on communal harmony and reconcilliation. <br />
Desmond Tutu describes his view of restoritive justice: <br />
<br />
http://www.youtube.com/watch?v=MCEboJ1k5Ek&feature=related <br />
<br />
Here he is again talking about forgiveness: <br />
<br />
http://www.youtube.com/watch?v=NsXPZ3WPW0M&feature=related <br />
<br />
What would policy look like if it where to be informed by ubuntu? They could possibly look something like these very rough outlines: <br />
<br />
• Informal relations should play an important role in governing the industry. A person's work should be scrutinized by his peer's in an informal setting and those recognised as leaders to the best of their abilities. Scientific research and the commercialization of products and knowledge should be subject to the informal approval of peers. <br />
<br />
• Members of the synthetic biology community should show a special concern for one another. This concern should extends past beyond the professional relationships. All participants in the research, development, distribution and consumption of goods developed by synthetic biology should be considered part of the synthetic biological community. Also, all members of the community should bear in mind that their actions reflect on the community as well as on themselves. <br />
<br />
• Every member of the community has a personal stake in the community and should bear some responsibility for the ensring that it continues to flourish. flourishing of the community. Every member of the community should also share in the fruits of the community’s endeavours. An individual should bear responsibilty for the community to the extent that he or she is involved in the community. <br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more. This can be in the form of goods and resources not necessarily linked to work in the field of synthetic biologyical work. For example, some members may rely on the community to provide them with housing or food etc. <br />
<br />
• Members of the community have access to the resources and infomation of the community to the extent that they contribute towards the community. Ethically sensitive materials and infomation that the community possesses may be withheld from those outside the community and from those who do not contribute adequately. Mmembers of the community may also generate a profit by utilising the resources and knowledge of the community, - provided that part of the the profit is , in part, goes intouse to supporting the community. <br />
<br />
<br />
And here's the end result... enjoy the read<br />
[[Image:Anticipating moral problems of Lactoguard in a South African context2.pdf]]<br />
<br />
<br />
[[Image:DSC02492.JPG|400px]]<br />
<br />
Our resident philosopher, Liam, stops to ponder ethical theory<br />
<br />
</div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/PhilosophyTeam:WITS-South Africa/Philosophy2010-10-27T21:19:25Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<div style="padding:40px;"><br />
<br />
<div class="heading"><br />
Human Advances <br />
----<br />
</div><br />
<br />
<div style="padding:4px;"><br />
<br />
<div style="width:880px;text-align:justify;float:left;"><br />
<br />
As the first South African iGEM team, it seems fitting to add to this debate by introducing the theory of '''ubuntu''' to help further ethical debate around synthetic biology.<br />
<br />
[[Image:Ubuntu 904.jpg|400px|left]] I am not talking about this - though the penguin is very cute. <br />
<br />
I hope to answer the question ''''Should ubuntu be seriously considered when making policy?'''' I wish to answer this question in the affirmative and show that ubuntu would provide good policy on both a macro and a micro level. On a micro level, I believe adhering to ubuntu would make scientists and researchers more ethically sensitive. On a macro level I think that ubuntu can maintain sound policy whilst preserving the importance of individual ethical conduct. <br />
<br />
Sketching my argument briefly - I will be raising some key ethical concerns that are raised by our team's Lactoguard device.I will then present a workable theory of ubuntu and apply it to the concerns raised in order to see if it can address the issues raised. The paper will therefore be a philosophical 'case study' into bio-ethics. <br />
<br />
From this I will hope to show that ubuntu can provide ethical guidance for synthetic biology - as it provides both 'internal' and 'external' moral motivations for ethical conduct. From this I hope to convince people that 5 tenets of ubuntu can serve as good 'rules of thumb' for ethical conduct within the field. They are:<br />
<br />
• Informal relations are important and have a role in our decision making. <br />
<br />
• Community members should show special ‘family-like’ concern for one another and that one’s actions reflect on the community as well as the individual.<br />
<br />
• Every member of that community has a personal stake in its endeavours and should bear some of the responsibility for the community but also share in the fruits of its endeavours<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more.<br />
<br />
• Members of the community have access to the resources of that community and can make use of them in so far as they contribute to the community and are involved with it. They can also profit of the communities resources provided that the profit generated goes into supporting the community.<br />
<br />
I will not fully argue for everything here - one will need to read my full paper for a proper length explaination of everything I have brought up here. But I will not leave you in the dark - here are some bite sized definitions and explainations so you can get an idea of what I am talking about and where my arguments will go. I will also provide some links to external sites that might be of some help:<br />
<br />
'''Ubuntu'''<br />
<br />
Ubuntu is a new field of study in analytical philosophy. I wager this is because of the cultural isolation of the Apartheid years and the general turmoil on the African continent post-colonialisation. Anyway, on to the positive matter - how do we define ubuntu? <br />
<br />
Metz (2007) describes ubuntu in terms of harmonious relations: <br />
''An action is right just insofar as it produces harmony and reduces discord; an act is wrong to the extent that it fails to develop community''<br />
<br />
Basically, ubuntu is a theory of right action - that it is a theory that tells us how to act in order to act in a morally good manner. If we compare Metz's conception of ubuntu with other normative ethical theories we can see how different ubuntu really is.<br />
<br />
'''Deontologists''' maintain that an action is right if it is in accordance with some duty or moral rules, such it is wrong to murder. '''Consequentialists''' see the moral weight, that is if the action is good or not, as resting in the consequences of an action. For example, one might refrain from lying because by not lying one tends to promote good consequences. Consequentialism is often expressed by the saying 'the ends justifies the means'. <br />
<br />
By Metz's definition we can see that actions can be considered good because of both the duties that harmonious relations have attached to them - such as a duty not to lie or cheat. And they can also be considered good because of the consequences that it produces - such as reconcilling with a person who has wronged you in order to promote harmony in your community. To put this in perspective - these two schools are traditionally set up in opposition to one another. <br />
<br />
I will also argue that ubuntu also has an extra component to it. That component is '''virtue ethics'''. Virtue ethics is the oldest form of ethical debate in the 'western' tradition. It's roots are found in the dialgoues and ethical theories of Socrates, Plato and Aristotle. Virtue ethics is an ethical theory that take the view that it is the concept of virtue that should be of primary concern when analysising moral actions. Virtue is understood as character traits that are considered to be good. <br />
<br />
The entry goes further to note that: <br />
<br />
''The main problem for the approach is to account for how the virtous agent thinks, as courses of action are contemplated, without admitting that it will be in terms of duties, or consequences, which thereby regain a certain priority.''<br />
<br />
I will argue in favour of Metz's conception of ubuntu as I believe it captures the 'Africanness' of ubuntu and is explicit enough to tease out the deontologist, consequentialist and virtue ethical elements of the theory. My contention is that the virtue component of ubuntu is not a distinct object in the ethical framework of the theory in the way that the concept of 'goodness' is considered in classical deontologist and consequentialist theories. Instead I content that ubuntu fosters the development of a sensitivity to ethical situations within the individual in question which can be described as virtue. Ubuntu can therefore be considered to be, at least in part, a character trait. <br />
<br />
The wikipedia entry on ubuntu alludes to this connection that I am trying to establish.<br />
<br />
http://en.wikipedia.org/wiki/Ubuntu_%28philosophy%29 [[Image:HHDLPresentsLOTAwardToTuTuJune12006.jpg|250px|right]] <br />
<br />
Here is Desmond Tutu (who is perhaps one of the best exponents of ubuntu) describing ubuntu<br />
<br />
http://www.youtube.com/watch?v=ftjdDOfTzbk<br />
<br />
'''Should we take notice of ubuntu?'''<br />
<br />
I think that that we should. The use of ubuntu is not entirely unprecidented at a policy level. The philosphy of ubuntu has provided a guiding influence in the Truth and Reconciliation Commission, where the focus was not on punishing those responsible (on both sides) for the hideous crimes committed during the struggle against Apartheid. Instead the focus was on communal harmony and reconcilliation.<br />
<br />
Desmond Tutu describes his view of restoritive justice:<br />
<br />
http://www.youtube.com/watch?v=MCEboJ1k5Ek&feature=related<br />
<br />
Here he is again talking about forgiveness:<br />
<br />
http://www.youtube.com/watch?v=NsXPZ3WPW0M&feature=related<br />
<br />
What would policy look like if it where to be informed by ubuntu? They could possibly look something like these very rough outlines:<br />
<br />
• Informal relations should play an important role in governing the industry. A person's work should be srutinized by his peer's in an informal setting and those recognised as leaders of the field should assume responsibility for guiding and assisting those within the community to the best of their abilities. Research and commercialization of products and knowledge should be subject to the informal approval of peers. <br />
<br />
• Members of the synthetic biology community should show a special concern for one another. This concern extends past the professional relationships. All participants in the research, development, distribution and consumption of goods developed by synthetic biology should be considered part of the synthetic biological community. Also all members of the community should bear in mind that their actions reflect on the community as well as themselves. <br />
<br />
• Every member of the community has a personal stake in the community and should bear some responsibility for the flourishing of the community.Every member of the community should also share in the fruits of the community. An individual should bear responsibilty for the community to the extent that he or she is involved in the community.<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more. This can be in the form of goods and resources not necesarily linked to synthetic biological work. For example some members may rely on the community to provide them with housing or food etc. <br />
<br />
• Members of the community have access to the resources and infomation of the community to the extent that they contribute towards the community. Ethically sensitive materials and infomation that the community possesses may be withheld from those outside the community and from those who do not contribute adequately. members of the community may also generate a profit by utilising the resources and knowledge of the community - provided that the profit is, in part, goes into supporting the community.<br />
<br />
And here's the end result... enjoy the read<br />
[[Image:Anticipating moral problems of Lactoguard in a South African context2.pdf]]<br />
<br />
<br />
[[Image:DSC02492.JPG|400px]]<br />
<br />
Our resident philosopher, Liam, stops to ponder ethical theory<br />
<br />
</div></div>Liam Wilsonhttp://2010.igem.org/File:Anticipating_moral_problems_of_Lactoguard_in_a_South_African_context2.pdfFile:Anticipating moral problems of Lactoguard in a South African context2.pdf2010-10-27T21:16:35Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_AfricaTeam:WITS-South Africa2010-10-27T06:53:27Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
{{Template:Wits-South_Africa-Side_Banner}}<br />
<div style="padding:40px;"><br />
<br />
<div class="title"><br />
Our Project - Lactoguard<br />
</div><br />
<br />
<div style="padding:4px;"><br />
<br />
<div style="width:680px;text-align:justify;float:left;"><br />
<br />
<div class="title"><br />
So what is "Lactoguard?" <br />
</div><br />
<br />
[[Image:Bacteria.jpg|250px|right]] <br />
It is a whole-cell biosensor for the immediate, in vivo detection of '''Human Papillomavirus (HPV)''', and thus cervical cancer, in the form of an engineered commensal vaginal bacterium. It is a safe, low-cost and easy-to-administer machine intended primarily for women in resource-poor settings.<br />
<br />
The link between HPV and cervical cancer is well-established; and while there are vaccines available against HPV, they are limited (due issues around cost and accessibility) in their ability to prevent disease burden in developing countries, where 80% of cervical cancer deaths occur annually.<br />
<br />
This inspired the search for a method of detecting the virus that will alert an infected individual that they have been exposed. The machine also has the potential to be further adapted to neutralise the virus and prevent the infection from spreading.<br />
<br />
The chassis of our machine, <i>Lactobacillus gasseri</i>, is a predominant commensal vaginal microbe and is ideally situated to detect and deter HPV. Interbacterial communication is achieved by quorum sensing, which has been studied in detail in various organisms such as gram positive bacilli and thus we have elected to use one of these pathways as the means of propagating the response signal throughout the population. Each bacterium will produce a visible reporter on receipt of the signal which the infected woman would be able to detect without medical assistance shortly after infection.<br />
<br />
----<br />
<br />
<div class="title"><br />
Meet the team<br />
</div><br />
<br />
[[Image:wits_team.jpg|270px|left]]<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
Wits South Africa 2010 is the first team from Africa ever to particpate in the iGEM competition! We are very excited to be representing our country and continent and hope to pave the way for more African teams to get involved in Synthetic Biology and the iGEM competition.<br />
<br />
<br />
Our team consists of students from various disciplines such as molecular biology, mathematics, engineering and philosophy. Whilst the biologists will focus on building the machine in the wetlab, the mathematicians and engineers will model its predicted behaviour and effect in vivo whilst the philosopher will focus on the ethics of creating such a machine for medical application.<br />
<br />
For more information on the Wits South Africa team go to [https://2010.igem.org/Team:WITS-South_Africa/students Students].<br />
<br />
----<br />
<br />
<div class="title"><br />
Parts submitted to the Registry<br />
</div><br />
<br />
*'''[https://2010.igem.org/Project/Lac1/AraC_Promoter/ Lac1/AraC Promoter]''': The inducible promoter serving as a proxy for infection<br />
*'''[https://2010.igem.org/Project/PlcR-PapR_Fusion_Protein/ PlcR-PapR Fusion Protein]''': The positive-feedback signal-propagating quorum molecule<br />
*'''[https://2010.igem.org/Project/Venus/ Venus]''': The YFP variant used in fluorometric analysis<br />
*'''[https://2010.igem.org/Project/PlcR_Promoter/ PlcR Promoter''']: The PlcR-PapR fusion protein-responsive promoter<br />
*'''[https://2010.igem.org/Project/SpooA/ SpooA]''': The negative feedback regulator of the machine<br />
<br />
<br />
----<br />
<br />
<div class="title"><br />
What we achieved this year<br />
</div><br />
<div style="padding:2px;"><br />
<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
Although the development of biological machines and parts is an important part of the iGEM competition, there is more to iGEM than just biology. We really got into the spirit of the competition, which encourages a collaborative, multi-disciplinary and open-source approach. This is reflected not only by our team, which is composed of budding researchers from a variety of fields, but also by the fact that during the course of our project we reached out to the public and the media, as well as to other experts around the world. When designing our project we consulted a diverse group of scientists, both South African and international, for help in refining and tweaking our idea. Everyone whom we approached was happy to help and share their knowledge with us. We are very grateful to everyone who responded so positively with information, time and resources, even setting up Skype dates at awkward times, given time zone differences. A list of our partners and sponsors can be found at the bottom of this page. <br />
<br />
We also received a very positive response from the media, when it came to sharing our project idea and the concept of Synthetic Biology with the public. We were invited to be part of a 'Future Science' panel in a Reporting Science Conference held in September and discussed Synthetic Biology and the iGEM competition with a range of science journalists, science communicators and science and journalism students. Several South African newspapers and radio stations also covered our participation in the competition.<br />
<br />
Project-wise, we developed our biobricks, spent hours in the lab honing our skills (digesting, ligating and transforming until we could do it in our sleep!), dissected our machines and their uses from many different perspectives, from maths to ethics. We learnt the hard way that biology can be very unpredictable, revised our ideas over and over again, got up close and personal with our bacteria, and danced around the lab when we turned them pink. We explored avenues of science previously unknown to us and looked at our own familiar fields from a completely different perspective. We made rookie errors and leaps of faith and many, many agarose gels.<br />
<br />
<br />
In short, we had an absolute blast being part of iGEM 2010. <br />
</div><br />
<br />
<br />
<br />
----<br />
<br />
<div class="title"><br />
Where are you viewing from?<br />
</div><br />
<div style="padding:2px;"><br />
<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
The map below indicates where the people who view our wiki are from. This is a cool way to see how far our message is spreading!<br />
</div><br />
<br />
{{Template:WITS-South_Africa-Cluster-Map}}<br />
<br />
<br />
<br />
<br />
----<br />
<br />
<div class="title"><br />
Sponsors and Partners <br />
</div><br />
<div style="padding:2px;"><br />
<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
The Wits iGEM team gratefully acknowledges the contribution of the following sponsors and partners, who have contributed to our project and supported us. We would like to thank everyone for their assistance!<br />
[http://www.bipedbiotech.com/ BiPed Biotech] and <br />
[http://www.inqababiotec.co.za/ Inqaba Biotech]<br />
<p><br />
[[image:Inqababiotec.jpg]]<br />
<br />
[[Image:Biped_customLogo.gif]]<br />
<br />
<div style="padding:10px;"><br />
<br />
'''The University of the Witwatersrand - Faculty of Health Sciences, Faculty of Engineering and the Built Environment, and the Vice-Chancellor's Office (South Africa)<br />
<br />
The Council for Scientific and Industrial Research and everyone at the CSIR's Synthetic Biology research group (South Africa) <br />
<br />
The Antiviral Gene Therapy Research Unit, University of the Witwatersrand, South Africa<br />
<br />
Dr Digby Warner and Dr Edith Machowski (Molecular Mycobacteriology Research Unit, National Health Laboratory Service, South Africa)<br />
<br />
Dr Leonard Damelin (National Institute for Communicable Diseases, South Africa)<br />
<br />
Professor Beth Lazazzera (University of California, Los Angeles, USA)<br />
<br />
Professor Didier Lereclus (France)<br />
<br />
Dr. Paul W. O'Toole (University College Cork, Ireland)</div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/partsTeam:WITS-South Africa/parts2010-10-26T20:20:16Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
== Mission Statement ==<br />
Here at WITS, we’re serious about our synthetic biology; we like knowing that when you shove your (nitrile-gloved) hand into our box of bio bits you emerge with a fully-functional nut for your bolt. So, hence, therefore, as a result we have decided to provide the entire life cycle of our BioBricks - over and above their behavioral characterization. From their genesis to gene synthesis, we’re giving you it all: snapshots of their sequences to our many guesses at their gels. Finally, you can rest assured that they sit happy in their bubble-wrapped plasmid packaging as we submit them off into the great lake of science - The Registry. <br />
<br />
== List of Parts Submitted to The Registry ==<br />
<br />
=== Non-Composite Parts ===<br />
==== Machine 1 Parts ====<br />
*'''[https://2010.igem.org/Project/Lac1/AraC_Promoter/ Lac1/AraC Promoter]''': The inducible promoter serving as a proxy for infection<br />
*'''[https://2010.igem.org/Project/PlcR-PapR_Fusion_Protein/ PlcR-PapR Fusion Protein]''': The positive-feedback signal-propagating quorum molecule<br />
*'''[https://2010.igem.org/Project/Venus/ Venus]''': The YFP variant used in fluorometric analysis<br />
==== Machine 2 Parts ====<br />
*'''[https://2010.igem.org/Project/PlcR_Promoter/ PlcR Promoter''']: The PlcR-PapR fusion protein-responsive promoter<br />
*'''[https://2010.igem.org/Project/SpooA/ SpooA]''': The negative feedback regulator of the machine<br />
<br />
=== Composite Parts ===<br />
*'''[https://2010.igem.org/Project/Machine-1/ Machine 1]''': The entire composite of Machine 1 <br />
*'''[https://2010.igem.org/Project/Machine-2/ Machine 2]''': The entire composite of Machine 2<br />
<br />
<br />
<br />
<!--<br />
<div class="heading"><br />
'''Cassette 1 BioBricks'''<br />
</div><br />
*'''[https://2010.igem.org/Project/ Lac1/AraC Promoter]''': The inducible promoter serving as a proxy for infection<br />
*'''[https://2010.igem.org/Project/ PlcR-PapR Fusion Protein]''': The positive-feedback signal-propagating quorum molecule<br />
*'''[https://2010.igem.org/Project/ Venus]''': The YFP variant used in fluorometric analysis<br />
<br />
<div class="heading"><br />
'''Cassette 2 Biobricks'''<br />
</div><br />
*'''[https://2010.igem.org/Project/ PlcR Promoter''']: The PlcR-PapR fusion protein-responsive promoter<br />
*'''[https://2010.igem.org/Project/ SpooA]''': The negative feedback regulator of the machine<br />
--><br />
<br />
[[Image:DSC02496.JPG|600px|left]]</div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/partsTeam:WITS-South Africa/parts2010-10-26T20:19:32Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
== Mission Statement ==<br />
Here at WITS, we’re serious about our synthetic biology; we like knowing that when you shove your (nitrile-gloved) hand into our box of bio bits you emerge with a fully-functional nut for your bolt. So, hence, therefore, as a result we have decided to provide the entire life cycle of our BioBricks - over and above their behavioral characterization. From their genesis to gene synthesis, we’re giving you it all: snapshots of their sequences to our many guesses at their gels. Finally, you can rest assured that they sit happy in their bubble-wrapped plasmid packaging as we submit them off into the great lake of science - The Registry. <br />
<br />
[[Image:DSC02496.JPG|250px|right]] <br />
<br />
== List of Parts Submitted to The Registry ==<br />
<br />
=== Non-Composite Parts ===<br />
==== Machine 1 Parts ====<br />
*'''[https://2010.igem.org/Project/Lac1/AraC_Promoter/ Lac1/AraC Promoter]''': The inducible promoter serving as a proxy for infection<br />
*'''[https://2010.igem.org/Project/PlcR-PapR_Fusion_Protein/ PlcR-PapR Fusion Protein]''': The positive-feedback signal-propagating quorum molecule<br />
*'''[https://2010.igem.org/Project/Venus/ Venus]''': The YFP variant used in fluorometric analysis<br />
==== Machine 2 Parts ====<br />
*'''[https://2010.igem.org/Project/PlcR_Promoter/ PlcR Promoter''']: The PlcR-PapR fusion protein-responsive promoter<br />
*'''[https://2010.igem.org/Project/SpooA/ SpooA]''': The negative feedback regulator of the machine<br />
<br />
=== Composite Parts ===<br />
*'''[https://2010.igem.org/Project/Machine-1/ Machine 1]''': The entire composite of Machine 1 <br />
*'''[https://2010.igem.org/Project/Machine-2/ Machine 2]''': The entire composite of Machine 2<br />
<br />
<br />
<br />
<!--<br />
<div class="heading"><br />
'''Cassette 1 BioBricks'''<br />
</div><br />
*'''[https://2010.igem.org/Project/ Lac1/AraC Promoter]''': The inducible promoter serving as a proxy for infection<br />
*'''[https://2010.igem.org/Project/ PlcR-PapR Fusion Protein]''': The positive-feedback signal-propagating quorum molecule<br />
*'''[https://2010.igem.org/Project/ Venus]''': The YFP variant used in fluorometric analysis<br />
<br />
<div class="heading"><br />
'''Cassette 2 Biobricks'''<br />
</div><br />
*'''[https://2010.igem.org/Project/ PlcR Promoter''']: The PlcR-PapR fusion protein-responsive promoter<br />
*'''[https://2010.igem.org/Project/ SpooA]''': The negative feedback regulator of the machine<br />
--></div>Liam Wilsonhttp://2010.igem.org/File:DSC02493.JPGFile:DSC02493.JPG2010-10-26T20:18:20Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/File:DSC02496.JPGFile:DSC02496.JPG2010-10-26T20:17:17Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/SafetyTeam:WITS-South Africa/Safety2010-10-26T20:15:44Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
= Safety =<br />
<br />
1.Would any of your project ideas raise safety issues in terms of:<br />
* Researcher safety<br />
* Public safety<br />
* Environmental safety?<br />
<br />
<br />
2.Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes:<br />
* Did you document these issues in the Registry?<br />
* How did you manage to handle the safety issue? <br />
* How could other teams learn from your experience?<br />
<br />
<br />
3.Is there a local biosafety group, committee, or review board at your institution?<br />
* If yes, what does your local biosafety group think about your project?<br />
* If no, which specific biosafety rules or guidelines do you have to consider in your country?<br />
<br />
<br />
4.Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?<br />
<br />
<br />
<br />
Would any of your project ideas raise safety issues in terms of: <br />
* Researcher safety<br />
* Public safety<br />
* Environmental safety? <br />
<br />
T'''here were several safety considerations that related to our project'''<br />
<br />
== 1. General laboratory safety (Researcher safety) ==<br />
[[Image:DSC02470.JPG|400px|right]] <br />
Given that any laboratory can be a hazardous environment if the correct safety protocols are not adhered to, all team members who worked in the wetlab were briefed on laboratory safety. A departmental laboratory safety manual was provided and each person was expected to familiarise themselves with the contents of the manual as well as any specific safety rules pertaining to the laboratory which they were working in. <br />
<br />
A copy of the Departmental Safety Manual can be found here. <br />
<br />
== 2. Working with bacteria (Researcher safety) ==<br />
The initial cloning steps used construct the machine were all conducted using laboratory adapted strains of E.coli such as DH5α and XL1-Blue, which when handled, stored and disposed of in the correct pose no safety risks. <br />
The final constructs were electroporated into a model Gram-positive organism (Bacillus subtilis). Some work was also done on the final intended chassis (L.gasseri ADH). Both of these organisms are considered safe to handle and pose no risk to the researcher, although care was taken to handle, store and dispose of the bacteria in a safe and sterile way. <br />
<br />
== 3. Manipulating gene expression using quorum sensing (Environmental and public safety) ==<br />
Our project deals with quorum sensing mechanisms in Gram-positive organisms. We have designed a fusion peptide which directly upregulates gene expression when it binds to its cognate promoter. It has been suggested that our peptide can activate expression of 20 different genes. The synthetic fusion peptide is also expected to be much more effective at increasing gene expression than the natural quorum peptides it is derived from. There are several safety issues regarding this Biobrick:<br />
<br />
Firstly the quorum peptide we have selected activates virulence in Bacillus thuriengiensis and Bacillus anthracis. B.t is a soil bacterium which is pathogenic to insects and b,a is a human pathogen. It is possible that unintended exposure to our enhanced quorum peptide could increase virulence in these organisms. <br />
It is also possible that the peptide could activate gene expression by binding to promoters other than the one we intended it to, causing off target effects in lgasseri or other gram positives in the vaginal mucosa. <br />
Although the work done to test this mechanism thus far has not posed a safety risk, as no invivo work was conducted, and there was no possibility of the quorum peptide encountering any bacteria any than those we exposed it to in a sterile in vitro environment. <br />
However, if this work was to be developed further, the implications of this Biobrick part and how to ensure that it acts only on its intended target need to be carefully considered. <br />
<br />
'''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''<br />
If yes: <br />
* '''Did you document these issues in the Registry?''' <br />
* '''How did you manage to handle the safety issue?''' <br />
* '''How could other teams learn from your experience?''' <br />
<br />
The plCR-PapR quorum peptide is the only part which could raise a potential safety risk. It only poses a safety risk if it comes into contact with other Gram-positive organisms. The full potential risks were documented on this part’s page on the Registry. <br />
This safety risk was only theoretical due to the fact that we only worked with it in a very contained lab environment thus no special precautions needed to be taken. <br />
<br />
It is important to consider all the possible effects of a Biobrick part. Many transcriptional activators or regulators have off-target effects. It is important to build in regulatory mechanisms that can limit or control such effects, or to keep these possibilities in mind if any testing is to be undertaken outside of a controlled and sterile setting. <br />
Is there a local biosafety group, committee, or review board at your institution? <br />
Yes. We informed them of our project in its current form as well as the possible next steps that could be undertaken and they responded thus: <br />
The safety aspects pertaining to an engineered commensal bacterium would depend on what is being inserted into the bacterium (as the commensals themselves are safe for use) – presumably in this case a expression casette producing a colour reagent upon stimulus.<br />
One would question the possible toxicity of such a colour product if it is not one that has been tested for human use (many dyes of often used in patients to detect various disorders etc – so many are considered safe for in vivo use). Some dyes may perhaps cause allergic reactions in some individuals.<br />
I would hardly think mere manipulation of the commensal would turn the “good guy” into a pathogenic organism – there are many published articles that show very positive use of genetically engineered commensals so would support that this would be a highly unlikely event.<br />
<br />
This project is a proof-of-principle design therefore would need to be demonstrated as a workable in an in vitro system. If promising as a concept then issues pertaining to safety would become relevant. Then either further preclinical work could be done in an animal model to test for safety and efficacy in a cervical cancer/HPV challenge model; phase 1 safety trial in humans and so on.<br />
<br />
I think this is a great concept that should not to my mind present any major hurdles with respect to safety considerations; certainly at this early stage general safety rules of any basic laboratory would apply. <br />
<br />
The normal flora of the vaginal mucosa would present no problem. However, under conditions of altered flora such as in sexually transmitted diseases, bacterial species can be very altered. I don’t think the species you mention are generally around even under pathogenic conditions, but can’t be sure. <br />
It should also be kept in mind that there are some very unusual sexual practices (herbal, additives to dry the vagina etc) where some unusual “creatures” may be introduced (and I don’t mean the sexual partner – although that may be another story). <br />
<br />
Again, in terms of safety testing at a time of being introduced one would ideally first test in a normal healthy non-pathogenic setting; once safety shown this could then be tested in individuals with STDs or HIV-1 etc as these patient groups would be associated with distorted bacterial floras. <br />
<br />
http://web.wits.ac.za/Academic/Research/Biosafety.htm<br />
<br />
<br />
'''Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?''' <br />
<br />
'''How could parts, devices and systems be made even safer through biosafety engineering?''' <br />
Although</div>Liam Wilsonhttp://2010.igem.org/File:DSC02470.JPGFile:DSC02470.JPG2010-10-26T20:12:58Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/ModellingTeam:WITS-South Africa/Modelling2010-10-26T20:10:20Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
== Introduction ==<br />
<br />
The biological sciences have generally been qualitative fields of study. However, due to the "top up" approach of synthetic biology, the need for quantitative mathematical models naturally arises. These models allow the biological system to be simulated and are necessary if control of the system is desired. We attempt to model a genetically engineered system implemented in the bacterium ''lactobacilus gasserii'' that is capable of detecting the presence of a pathogen, expressing a reported and also signaling others cells of the presence of the pathogen. <br />
<br />
=== Project Outline ===<br />
<br />
The aim of our machine is to identify an infection of Human papillomavirus in vivo. From a modelling point of view the mechanism has a number of points of interest expounded on in the following sections.<br />
<br />
Extracellular Activity: Varying concentrations and effects of the genetic machine on the habitat outside the cell<br />
<br />
Intracellular Activity: Responses to inputs and outputs as well as feedback loops<br />
<br />
Intercellular Activity: A medium for communication between cells<br />
<br />
== Modelling ==<br />
The benefits of modelling reach far beyond a theoretical understanding of a system. Models allow us to determine how we hope a system will behave. From this and experimental findings we can go on to determine where assumptions and simplifications made are critically important, whether it be positively or negatively. <br />
<br />
=== Assumptions ===<br />
<br />
* Total number of receptors, both occupied and unoccupied, is constant. [[#References | [4]]]<br />
* System reaches a quasi-steady state. [[#References | [4]]]<br />
* The number of input molecules is much greater than the number of receptors so that the receptors are always operating at maximal capacity. [[#References | [4]]]<br />
* We assume the number of operator regions is small with respect to the total number of repressor molecules. [[#References | [15]]]<br />
<br />
\end{itemize}<br />
<br />
== Components of the Model ==<br />
<br />
=== Extracellular Model ===<br />
The extracellular model describes the change in substances outside of the cell. These fluctuations are modeled by a system of differential equations, which are likely to be non linear and of an order higher than one. This model will be used to try and describe each cell as a 'black box'. This will then be used to model the intercellular communication.<br />
<br />
=== Intercellular Model (Cell Communication) ===<br />
This portion of the model describes the behaviour of the cells as a network of communicating individuals. They communicate via a signalling process called quorum sensing.<br />
<br />
=== Intracellular Model (Genetic Circuit) ===<br />
The genetic circuit describes the biochemical reactions taking place inside the cell. The intracellular model describes the fluctuations in concentrations of each substance by modelling each chemical reaction by means of an appropriate kinetic law.<br />
<br />
The intra cellular model is based on the block diagram shown in the figure below.<br />
The concentration of the proteins in the model can be expressed in terms of three ordinary differential equations.<br />
<br />
[[Image:GeneCircuit.png|900px|center]]<br />
<br />
<br />
Block diagram of the genetic circuit. Green rectangles represent promoters. Yellow rectangles represent genes. Blue ovals represent repressor, inducer or activator proteins. Red squares are terminator sequences.<br />
<br />
[[Image:WitsModel.png|950px|left]]<br />
<br />
== Methods and Tools ==<br />
<br />
=== Extracellular Model ===<br />
We will model the effects of our machine on the extracellular habitat by means of a system of differential equations. Measurements of the built machine as well as findings from the intracellular model will allow us to tweak parameters of this system to attempt to accurately determine the behaviour of the system. We will use Matlab [[#References | [9]]] and Mathematica [[#References | [16]]] to help solve our system, to simulate and investigate the stability and properties of the system.<br />
<br />
=== Intercellular Model (Cell Communication) ===<br />
The network of cells and the communication between them is modelled in Matlab and its Simulink. [[#References | [9]]] We treat each cell in the network as a black box that produces an output given an input based on data obtained experimentally and in conjunction with the intracellular model. <br />
<br />
=== Intracellular Model (Gentic Circuit) ===<br />
The modelling of the genetic circuit is done in CellDesigner. [[#References | [2]]] [[#References | [3]]] [[#References | [14]]]. Through this application we can determine and specify all kinetic laws governing the system, on a reaction to reaction basis. We can also tweak each constant. These rate constants can be found in literature or experimentally if needs be. We can also provide simulations over given time periods with varying initial conditions for every component within the system.<br />
<br />
== Outcomes ==<br />
We hope that the mathematical model of our genetic machine will allow insight into the desired effects and working's of the biological parts. From the model one will be able to establish boundaries to work within and utilize this to determine and guide biological choices.<br />
<br />
== Results ==<br />
The figure below show the concentration-time plot of the machine. There is a leakiness inherent with most promoters wherein the gene's are transcribed at a low constant rate without being activated. This introduces the problem of identifying correct operation of our machine or ruling out false positives. However given the increase in efficacy in production in the presence of an inducer we can regard the basal rates as an acceptable level of noise. <br />
<br />
[[Image:UnactivatedBasal.png|950px|left]]<br />
<br />
This figure below shows the effects of adding our input molecule IPTG. It is evident that the basal transcription rate is acceptable.<br />
<br />
[[Image:ActivatedBasal.png|950px|left]]<br />
<br />
=== Discussion ===<br />
<br />
Experimental data will allow the model to be fit accurately. The efficacy of the promoters is increased substantially when in the presence of promoters, this allows us to guess, initially, that the basal rates are small and acceptable. The difficulty in this modelling is the behaviour of each genetic component, promoters for example, will behave differently from others and hence biological data is very specific and consequently is scarce in literature. Running experiments is the best way to generate accurate and applicable data, since the biology is known exactly. This is however a time consuming process and the results may vary.<br />
<br />
== Conclusion == <br />
<br />
[[Image:DSC02486.JPG|450px|left]]<br />
<br />
The foundation set in place by a mathematical model are unrivalled in providing an understanding and insight to the nature of a system. Although first guesses may not be accurate from experimental data [[#References | [13]]] we can determine whether the model is fundamentally correct and requires fitting to the data, or if there is a fundamentally flawed assumption that overlooks an important aspect of the system. The importance of modelling this system is that we can determine initially how we hope the system will behave. From these initial guesses and hopes we can make educated choices in selecting biological mechanisms to function in a desirable way. <br />
<br />
Although the derived kinetics used in the model are studied with respect to enzymatic reactions, the biological processes of gene expression and enzyme reactions have parallels that substantiate the use of these models. Literature, [[#References | [8]]] [[#References | [10]]] [[#References | [6]]], supports this assumption, by indicating similar behaviour and responses to activation although derived from a statistical perspective. This is promising outcome, and the prospect of better understanding the processes of genetic expression is a fruitful one. <br />
<br />
[[#References | [1]]]<br />
<br />
==References==<br />
<br />
1. de Jong, H. (2002). Modeling and simulation of genetic regulatory systems: a literature review. ''Journal of computational biology.''<br />
<br />
2. Funahashi, A. and Kitano, H. (2008). CellDesigner 3.5: A versatile modeling tool for biochemical networks. ''Proceedings of the IEEE.''<br />
<br />
3. Funahashi, A. and Kitano, H. (2003). CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. ''BIOSILICO.''<br />
<br />
4. Edelstein-Keshet, L. (1988). Mathematical Models in Biology. The Random<br />
House.<br />
<br />
5. Gardner, T., Cantor, C., and Collins, J. (2000). Construction of a genetic toggle<br />
switch in escherichia coli. ''Nature.''<br />
<br />
6. Jack D. Dockery, J. P. K. (2001). A mathematical model for quorum sensing in<br />
pseudomonas aeruginosa. ''Bulletin of Mathematical Biology.''<br />
<br />
7. Jeff Hasty, David McMillen, J. J. C. (2002). Engineered genetic circuits. ''Nature.''<br />
<br />
8. Marc A. Suchard, Kenneth Lange, J. S. S. (2008). Efficiency of protein production from mRNA. ''Journal of Statistical Theory and Practice.''<br />
<br />
9. MathWorks, I. (2008). Matlab. Version: 7,7,0,471(R2008b).<br />
<br />
10. Michal Ronen, Revital Rosenberg, B. I. S. and Alon, U. (2002). Assigning<br />
numbers to the arrows: Parameterizing a gene regulation network by using<br />
accurate expression kinetics. ''Proceedings of the National Academy of Sciences.''<br />
<br />
11. Michel Leno, O.-W. M. and Hache, J. (1992). Kinetic studies of cellular<br />
metabolic activity, specific igg production rate, igg mrna stability and accumulation during hybridoma batch culture. ''Enzyme and Microbial Technology.''<br />
<br />
12. Rubinow, S. (1975). Introduction to Mathematical Biology. Wiley-Interscience<br />
Publication.<br />
<br />
13. Sarah Lebeer, Sigrid C. J. De Keersmaecker, T. L. A. V. A. A. F. K. M. and<br />
Vanderleyden, J. (2007). Functional analysis of luxs in the probiotic strain lactobacillus rhamnosus gg reveals a central metabolic role important for growth and biofilm formation. ''Journal of Bacteriology.''<br />
<br />
14. The Systems Biology Institute, Tokyo, J. (2010). Celldesigner. Version: 4.0.1.<br />
<br />
15. Tyson, J. and Sachsenmaier,W. (1979). Depression as a model for control of the<br />
dna-division cycle in eukaryotes. ''Journal of Theoretical Biology,'' 79:275–280.<br />
<br />
16. Wolfram Research, I. (2008). Wolfram mathematica 7. Version: 7.0.0.<br />
<br />
<br />
<br />
<br />
= Modelling Presentation = <br />
Below is the PDF presentation that was presented within the School of Computational and Applied Mathematics as part of the Honours Degree.<br />
<br />
[[Image:IGEM_Presentation.pdf]]</div>Liam Wilsonhttp://2010.igem.org/File:DSC02486.JPGFile:DSC02486.JPG2010-10-26T20:06:55Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/File:DSC02487.JPGFile:DSC02487.JPG2010-10-26T20:03:51Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/Gram_positivesTeam:WITS-South Africa/Gram positives2010-10-26T19:52:00Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<br />
<div class="title"><br />
Gram Positive Bacteria<br />
</div><br />
<div style="padding:10px;"><br />
<div style="width:850px;text-align:justify;float:middle;"><br />
<br />
<br />
= '''Introduction''' =<br />
<br />
[[Image:DSC02608.JPG|300px|left]] <br />
<br />
We have been working on optimising a protocol for electro-transformations on several gram positive bacteria that can function as the chassis for our machine. <br />
Lange has been performing several test experiments by electroporating several potential gram positive bacteria (i.e. ''Bacillus subtilis''; ''Lactobacillus gasseri''and ''Staphylococcus aureus''). This is being done in preparation for electroporation of the machine constructs into either one of these gram positive bacteria; depending on the most efficient bacteria we have to work with.<br />
<br />
We are also testing the ability of transforming the above mentioned bacteria with two different shuttle-vector plasmids; namely: <br />
• pGK12<br />
• pNDW5<br />
Once we have established which plasmid is best to use for electroporation; the gene constructs will then be inserted into that plasmid and we will perform electroporations using that plasmid. Electro-transformation of the selected bacterium will be done with our machine constructs; and testing of transformants will be undertaken. Once this is achieved analysis of the machines’ functionality will be determined using fluorescence in situ hybridisation and other fluorescent techniques (i.e. fluorimetry).<br />
<br />
We plan to achieve a high efficiency of gram positive transformation by optimizing relevant protocols for electroporation and fluorescence analysis. <br />
<br />
<br />
== Why Electroporation? ==<br />
<br />
Electro-transformations are mostly used to transform bacteria using large amounts of plasmid DNA; this method involves the use of an electric pulse that creates temporary pores in the cell wall of bacteria allowing the bacteria to take up the plasmid.<br />
Initially this plasmid needs to be along the surface of the cell wall for instant incorporation of the plasmid into the bacterial cytoplasm when an electric pulse in administered. Protocols for electro-transforming different kinds of gram positive bacteria vary depending on the strain, or family of bacteria (i.e. Lactobacillus species have been shown to require different media for Electroporation).<br />
<br />
Electro-transformation of potential Gram positive bacteria<br />
The Gram positive bacteria that are being tested are:<br />
1. ''Bacillus subtilis''<br />
2. ''Lactobacillus gasseri''<br />
3. ''Staphyloccus aureus''<br />
4. An unknown Lactobacillus strain<br />
These bacteria have been selected because we would ideally like the chassis for our whole cell biosensor to be a gram positive bacterium. This being said; women have commensal lactobacillus gasseri bacteria within their vaginal mucosa. This bacterium provides the ideal target for genetically engineering ''L. gasseri'' to act as a proxy for infection and subsequently for amplifying the quorum signal and propagating the signal for infection across the population of bacterial cells.<br />
''B. subtilis'', ''S aureus'' and the LAB sp. Are also being used considering their gram positive properties. They are being tested to determine whether or not they could substitute ''L. gasseri'' as a chassis for our machine; only if Electroporation of ''L. gasseri'' fails.<br />
<br />
<br />
== pNDW5 Plasmid ==<br />
<br />
[[Image:PNDW5.png]]<br />
<br />
'''Figure 1: showing the pNDW5 plasmid map.'''<br />
<br />
The pNDW5 plasmid is derived from a combination of two bacterial plasmids hence a shuttle vector; whereby one is gram positive and the other gram negative (''S. aureus'' and ''E. coli'' respectively).<br />
The ''S. aureus'' plasmid pC194 and ''E. coli'' plasmid pEcoR251 were combined to form the pNDW5 plasmid. This pNDW5 plasmid has a separate pair of Ori and Rep for gram positive and gram negative bacteria. This plasmid contains ampicillin and chloroamphenicol resistance marker genes; therefore ampicillin and chloroamphenicol resistant transformants with this plasmid can be selected.<br />
The pNDW5 plasmid has an EcoRI suicide gene instead of a multiple cloning region; inside the gene are 4 unique restriction sites which allows for the positive selection of transformants with inserts. <br />
The plasmid has a PR promoter (phage λ promoter) whose original function is to drive the transcription of the Cro gene which allows for induction of phage from its lysogenic state in the E. coli cell. A large portion of this Cro gene has been removed which defers its functionality allowing the use of the PR promoter to drive expression of EcoRI without expressing the Cro gene.<br />
In pNDW5, a repressor can be used to stop transcription and expression of EcoRI suicide gene. The EcoRI suicide gene automatically kills the cell if no genes have been cloned. For testing the vector a mutant of this pNDW5 plasmid was used (denoted pNDW5*); which allowed testing for electro-transformation qualities in various potential gram positive bacteria (''B. subtilis, L. gasseri, S. aureus'' and a LAB sp).<br />
<br />
<br />
== pGK12 plasmid ==<br />
<br />
<br />
The pGK12 plasmid is also a shuttle vector; it can be propagated in both Gram-positive and Gram-negative bacteria and it carries erythromycin and chloroamphenicol resistance markers. This plasmid has 3 restriction sites; HpaII, NdeI and BpmI.<br />
<br />
<br />
<br />
= '''What has been happening in the lab''' =<br />
<br />
Electroporation of potential Gram positive bacteria<br />
The protocols for electroporating all gram positive bacteria used in our project except ''L. gasseri'' can be obtained from http://openwetware.org/wiki/Main_Page<br />
General Electroporation protocol<br />
• Preparing electro-competent cells<br />
• Overnight culturing in Luria Broth (LB)*<br />
• Inoculate x100 dilution of culture into LB with 1.9% glycine<br />
• Incubate at 37°C<br />
• Measure 0.D. 600 (range 0.7)<br />
• Harvest cells (centrifuge)<br />
• Wash cells (x2) in Electroporation buffer<br />
• Harvest cells and suspend in 1/100 volume of Electroporation buffer<br />
• 50µl transformation<br />
• Electroporator parameters vary depending on strain<br />
• Inoculate in LB and incubate for 3hours at 37°C on a shaker<br />
• Plate in Luria agar and appropriate antibiotic plate<br />
(Note: LB* = media may vary depending on bacterial strain or species)<br />
The tests that I am currently performing are as follows:<br />
<br />
<br />
----<br />
<br />
<br />
== '''Test 1. Electroporation of pNDW5* into a Lactobacillus sp.''' ==<br />
<br />
<br />
=== Methods ===<br />
<br />
The above protocol was administered for electroporating the unknown LAB sp. There were no changes made.<br />
Electroporator parameters: 1.5 kV; 200 Ω; 25µF<br />
<br />
=== Results ===<br />
Upon completing Electroporation the following assessments were made:<br />
The control and experimental plates had an equal number of colonies when chloroamphenicol (Cm) was used as a resistance marker at 20µg/ml. Hence secondary testing for the appropriate chloroamphenicol concentration was done.<br />
<br />
'''Table 1: LAB colonies in the control and experimental plates at increasing chloroamphenicol concentration.''' (Note: control plates are the LAB only; experiment plate has electroporated LAB). From these colonies further tests on transformants were done. <br />
Chloroamphenicol (Cm)<br />
<br />
[[Image:LAB_colony_numbers.png]]<br />
<br />
<br />
At Cm concentrations of 60 µg/ml the ratio of experimental colonies to control colonies was approximately 5:1. To verify whether these colonies were real transformants plasmid extractions were attempted from these cells. However no plasmid could be detected. These results also suggest that this LAB strain has inherent resistance to chloroamphenicol therefore it cannot be used to determine whether pNDW5 would transform the LAB sp. <br />
<br />
==== Transformation efficiency ====<br />
In order to determine the success of transformation, the concentration of DNA used for the transformation would be determined. There are two methods to do this. The first is to analyze band intensities after gel electrophoresis in comparison to a control band whose DNA concentration is already known. The alternative method is to measure DNA concentration with a spectrophotometer at 260nm. Transformation efficiency would be expressed as the number of transformants per µg of DNA.<br />
<br />
<br />
<br />
----<br />
<br />
<br />
== '''Test 2. Electroporation of pNDW5* and pGK12 into L. gasseri''' ==<br />
<br />
<br />
=== Methods ===<br />
<br />
- A standard curve for analysing the growth characteristics of ''L. gasseri'' was undertaken<br />
<br />
- The protocol for electroporating ''L. gasseri'' was obtained from Nickoloff, J.A. (2007). Electroporation Protocols for Microorganisms: chapter 20- Transformation of Lactobacillus by Electroporation. Methods in Molecular Biology 47: 201- 208<br />
<br />
- The appropriate media was made; preparation of competent cells and Electroporation was done using the above mentioned protocol with minor adjustments. The most common marker genes applicable to LAB are genes causing resistance to erythromycin (Ery) and chloroamphenicol (Cm).<br />
<br />
- The concentrations used for the antibiotic plates were as follows according to the above protocol:<br />
• Erythromycin (Ery) 1 µg/ml<br />
• Erythromycin 1 µg/ml and Chloroamphenicol 5 µg/ml<br />
• Chloroamphenicol (Cm) 5 µg/ml<br />
<br />
- The media used, Electroporator parameters and incubation styles are different for ''L. gasseri''<br />
• Media = MRS for broth and agar; Sucrose Media<br />
• Electroporation buffer = MRSSM (MRS in Sucrose).<br />
• Electroporator parameters: 1.5 kV; 800 Ω; 25µF<br />
• Growth = anaerobic chamber and not shaken<br />
<br />
=== Results ===<br />
<br />
The growth curve for ''L. gasseri'' is shown below:<br />
<br />
[[Image:L._gaseri_growth_curve.png]]<br />
<br />
'''Figure 1: The cfu/ml of ''L. gasseri'' over a time period of 5 hours. The graph suggests an exponential increase in the colony forming units/ml after 2 hours of incubation.'''<br />
<br />
[[Image:L._gaseri_O.D_600.png]]<br />
<br />
'''Figure 2: The O.D at wavelength of 600nm at time period of 6 hours. The O.D. was measured every hour. The gradual increase in O.D. is reflective of cell growth.'''<br />
<br />
<br />
'''Table 2: Shows the Electroporation colony numbers for the pGK12, pNDW5 plasmid and the control plate at the different antibiotic concentrations'''<br />
<br />
[[Image:Electroporation_colony_numbers.png]]<br />
<br />
'''Note:''' the 3 colonies in the Ery 1µg/ml control plate were all contaminants and were not ''L. gasseri''.<br />
<br />
<br />
It can be seen from Table 2 that the pGK12 Ery (1µg/ml) plate; and Ery 1µg/ml Cm 5µg/ml plate had colonies that were possible transformants growing on them and so plasmid preps were undertaken.<br />
The transformation efficiency could not be obtained for pGK12 because the original pGK12 DNA sample was either degraded or its concentration was very low. When the original pGK12 sample was transformed into ''E. coli''; colony numbers were low (2 colonies) whereas a control plasmid (pACYC184) gave a high number of colonies.<br />
pNDW5* shows 80 colonies on the erythromycin (1µg/ml) plate. This was obviously an error as pNDW5 does not confer resistance to erythromycin; therefore the colonies obtained shouldn’t have been observed here.<br />
The transformation efficiency could not be measured here due to the inconsistency of the pNDW5* results.<br />
<br />
<br />
----<br />
<br />
<br />
== '''Test 3. Electroporation of pNDW5* and pGK12 into B. subtilis and S. aureus''' ==<br />
<br />
=== Methods === <br />
The general protocol obtained from http://openwetware.org/wiki/Main_Page was used to electroporate pNDW5* and pGK12 into ''B. subtilis'' and ''S. aureus''.<br />
<br />
A few changes were made to the protocol:<br />
• media used = LB<br />
• Electroporation buffer = SHMG (sucrose, HEPES, magnesium chloride and glycerol) buffer<br />
• Incubation period = overnight for B. subtilis<br />
<br />
=== Results ===<br />
Electroporation of ''S. aureus'' has been successful whereby optimization is being done for ''B. subtilis''.<br />
Upon further optimization test 4 was conducted for transformation of ''B. subtilis'' by electroporation.<br />
there was no further experimental work done on ''S. aureus'' as ''B. subtilis'' was chosen an alternative model organism for ''L. gasseri''. pNDW5 was futher electroporated in Test 4. No further testing was done in S. aureus as B. subtilis was prefered as an alternative chassis for the Lactoguard machine.<br />
<br />
<br />
----<br />
<br />
== '''Test 4 Electroporation of machine cassettes in B. subtilis'''==<br />
<br />
=== Introduction ===<br />
<br />
''Bacillus subtilis'' is a gram positive soil bacterium from the genus bacillus. It has proven highly useful to genetic manipulation, and has therefore become widely adopted as a model organism for laboratory studies. It is also heavily flagellated, which gives ''B. subtilis'' the ability to move quite quickly. In terms of popularity as a laboratory model organism this bacterium is often used as the Gram-positive equivalent of ''Escherichia coli'', an extensively studied Gram-negative bacterium. <br />
<br />
It has proved useful in electroporating our machine constructs and has yielded good electroporation efficiencies for Machine Intermediates 1 and 2. Lactodetect and Lactoreport have also been successfully electro-transformed into ''B. subtilis'' as numerous transformants were present from colony plate counts however no empirical data has been calculated for these constructs.<br />
It is no surprise therefore that we have chosen to work with this bacterium as a model organism as an alternative to ''L. gasseri'' as a chassis for our Lactoguard Machine.<br />
<br />
=== Methods ===<br />
<br />
The general electroporation protocol was followed with minor adjustments.<br />
<br />
[[Image:Electroporation process.png]]<br />
<br />
'''Figure 1: Flow diagram representing the transfromation process of ''B. subtilis by Electroporation'''''<br />
<br />
''B. subtilis'' strains were grown overnight in LB broth at 37°C with vigorous aeration. The changes to the Electroporation protocol included:<br />
<br />
1. SOC Broth= pulsed cells were diluted in 2ml of this broth(contains 2% tryptone, 0.5% yeast extract, 10mM NaCl, 2.5mM KCl, 10mM MgCl2, 10mM MgSO4, 20mM glucose)<br />
2. 30% PEG6000 = Polyethyleneglycol (Electroporation medium)<br />
3. De – ionised water for the washes.<br />
<br />
=== Results ===<br />
<br />
The following constructs were electroporated.<br />
- Machine Intermediate 1 (LacI/ AraC promoter – mCherry – tt)<br />
- Machine Intermediate 2 (PlcR promoter – mCherry – tt)<br />
- pNDW5* vector (no “machine” genetic information; control)<br />
- Lactodetect ( LacI/ AraC promoter – PlcR –PapR – Venus- tt) in pNDW5<br />
- Lactoreport (PlcR promoter – PlcR-PapR- mCherry – PO Phage activator – tt – PO Phage promoter – E. chromi – SpooA – tt) <br />
<br />
==== Mass calculation for machine 1 and 2 intermediates ====<br />
Machine 1 intermediate DNA conc. = 52.2ng/µl; Machine 2 intermediate DNA conc. = 48.3ng/ml<br />
The volume used for electroporation was 5µl<br />
Hence: C = M / V whereby C is the concentration, M is mass and V is volume<br />
Mass of Machine 1 intermediate =C x V = 52.2ng/µl x 5µl = 261ng<br />
Mass of Machine 2 intermediate = C x V = 48.3ng/µl x 5µl = 241.5ng<br />
<br />
==== Electroporation Efficiencies for Machine intermediate 1 and 2 in B. subtilis ====<br />
Colonies from electroporation plates were counted and yielded the following:<br />
Machine 1 intermediate = 1300 transformants<br />
Machine 1 intermediate = 1300 colonies/261ng DNA = 1300/0.261µg DNA = 4980 colonies/ µg DNA<br />
<br />
Machine 2 intermediate = 1400 transformants<br />
Machine 2 intermediate = 1400 colonies/241.5ng DNA = 1400/0.2415µg DNA = 5797 colonies/ µg DNA<br />
<br />
pNDW5* = 0 transformants (No DNA control)<br />
The pNDW5* vector had no transformants as expected<br />
<br />
Electroporation efficiencies were not calculated Lactodetect and Lactoreport</div>Liam Wilsonhttp://2010.igem.org/File:DSC02608.JPGFile:DSC02608.JPG2010-10-26T19:50:33Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/PhilosophyTeam:WITS-South Africa/Philosophy2010-10-26T19:47:40Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<br />
<br />
[https://2010.igem.org/Team:WITS-South_Africa/Outreach Outreach].<br />
<br />
As the first South African IGEM team, it seems fitting to add to this debate by introducing the theory of '''ubuntu''' to help further ethical debate around synthetic biology.<br />
<br />
[[Image:Ubuntu 904.jpg]] I am not talking about this - though the penguin is very cute<br />
<br />
I hope to answer the question ''''Should ubuntu be seriously considered when making policy?'''' I wish to answer this question in the affirmative and show that ubuntu would provide good policy on both a macro and a micro level. On a micro level, I believe adhering to ubuntu would make scientists and researchers more ethically sensitive. On a macro level I think that ubuntu can maintain sound policy whislt preserving the importance of individual ethical conduct. <br />
<br />
Sketching my argument briefly - I will be raising some key ehical concerns that are raised by our team's lactoguard device.I will then present a workable theory of ubuntu and apply it to the concerns raised in order to see if it can address the issues raised. The paper will therefore be a philosophical 'case study' into bio-ethics. <br />
<br />
From this I will hope to show that ubuntu can provide ethical guidance for synthetic biology - as it provides both 'internal' and 'external' moral motivations for ethical conduct. From this I hope to convince people that 5 tenents of ubuntu can serve as good 'rules of thumb' for ethical conduct within the field. They are:<br />
<br />
• Informal relations are important and have a role in our decision making. <br />
<br />
• Community members should show special ‘family-like’ concern for one another and that one’s actions reflect on the community as well as the individual.<br />
<br />
• Every member of that community has a personal stake in its endeavours and should bear some of the responsibility for the community but also share in the fruits of its endeavours<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more.<br />
<br />
• Members of the community have access to the resources of that community and can make use of them in so far as they contribute to the community and are involved with it. They can also profit of the communities resources provided that the profit generated goes into supporting the community.<br />
<br />
I will not fully argue for everything here - one will need to read my full paper for a proper length explaination of everything I have brought up here. But I will not leave you in the dark - here are some bite sized definitions and explainations so you can get an idea of what I am talking about and where my arguments will go. I will also provide some links to external sites that might be of some help:<br />
<br />
'''Ubuntu'''<br />
<br />
Ubuntu is a new field of study in analytical philosophy. I wager this is because of the cultural isolation of the Apartheid years and the general turmoil on the African continent post-colonialisation. Anyway, on to the positive matter - how do we define ubuntu? <br />
<br />
Metz (2007) describes ubuntu in terms of harmonious relations: <br />
''An action is right just insofar as it produces harmony and reduces discord; an act is wrong to the extent that it fails to develop community''<br />
<br />
Basically, ubuntu is a theory of right action - that it is a theory that tells us how to act in order to act in a morally good manner. If we compare Metz's conception of ubuntu with other normative ethical theories we can see how different ubuntu really is.<br />
<br />
'''Deontologists''' maintain that an action is right if it is in accordance with some duty or moral rules, such it is wrong to murder. '''Consequentialists''' see the moral weight, that is if the action is good or not, as resting in the consequences of an action. For example, one might refrain from lying because by not lying one tends to promote good consequences. Consequentialism is often expressed by the saying 'the ends justifies the means'. <br />
<br />
By Metz's definition we can see that actions can be considered good because of both the duties that harmonious relations have attached to them - such as a duty not to lie or cheat. And they can also be considered good because of the consequences that it produces - such as reconcilling with a person who has wronged you in order to promote harmony in your community. To put this in perspective - these two schools are traditionally set up in opposition to one another. <br />
<br />
I will also argue that ubuntu also has an extra component to it. That component is '''virtue ethics'''. Virtue ethics is the oldest form of ethical debate in the 'western' tradition. It's roots are found in the dialgoues and ethical theories of Socrates, Plato and Aristotle. The Oxford dictionary of Philosophy has this to say about it:<br />
<br />
''The theory of ethics that takes the notion of virtue as primary, rather than a view either of the 'good', for the sake of which we act, or of duty, law, or reason thought as providing rules of action.'' <br />
<br />
The entry goes further to note that: <br />
<br />
''The main problem for the approach is to account for how the virtous agent thinks, as courses of action are contemplated, without admitting that it will be in terms of duties, or consequences, which thereby regain a certain priority.''<br />
<br />
I will argue in favour of Metz's conception of ubuntu as I believe it captures the 'Africanness' of ubuntu and is explicit enough to tease out the deontologist, consequentialist and virtue ethical elements of the theory. My contention is that the virtue component of ubuntu is not a distinct object in the ethical framework of the theory in the way that the concept of 'goodness' is considered in classical deontologist and consequentialist theories. Instead I content that ubuntu fosters the development of a sensitivity to ethical situations within the individual in question which can be described as virtue. Ubuntu can therefore be considered to be, at least in part, a character trait. <br />
<br />
The wikipedia entry on ubuntu alludes to this connection that I am trying to establish.<br />
<br />
http://en.wikipedia.org/wiki/Ubuntu_%28philosophy%29 [[Image:HHDLPresentsLOTAwardToTuTuJune12006.jpg|250px|right]] <br />
<br />
Here is Desmond Tutu (who is perhaps one of the best exponents of ubuntu) describing ubuntu<br />
<br />
http://www.youtube.com/watch?v=ftjdDOfTzbk<br />
<br />
'''Should we take notice of ubuntu?'''<br />
<br />
I think that that we should. The use of ubuntu is not entirely unprecidented at a policy level. The philosphy of ubuntu has provided a guiding influence in the Truth and Reconciliation Commission, where the focus was not on punishing those responsible (on both sides) for the hideous crimes committed during the struggle against Apartheid. Instead the focus was on communal harmony and reconcilliation.<br />
<br />
Desmond Tutu describes his view of restoritive justice:<br />
<br />
http://www.youtube.com/watch?v=MCEboJ1k5Ek&feature=related<br />
<br />
Here he is again talking about forgiveness:<br />
<br />
http://www.youtube.com/watch?v=NsXPZ3WPW0M&feature=related<br />
<br />
What would policy look like if it where to be informed by ubuntu? They could possibly look something like these very rough outlines:<br />
<br />
• Informal relations should play an important role in governing the industry. A person's work should be srutinized by his peer's in an informal setting and those recognised as leaders of the field should assume responsibility for guiding and assisting those within the community to the best of their abilities. Research and commercialization of products and knowledge should be subject to the informal approval of peers. <br />
<br />
• Members of the synthetic biology community should show a special concern for one another. This concern extends past the professional relationships. All participants in the research, development, distribution and consumption of goods developed by synthetic biology should be considered part of the synthetic biological community. Also all members of the community should bear in mind that their actions reflect on the community as well as themselves. <br />
<br />
• Every member of the community has a personal stake in the community and should bear some responsibility for the flourishing of the community.Every member of the community should also share in the fruits of the community. An individual should bear responsibilty for the community to the extent that he or she is involved in the community.<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more. This can be in the form of goods and resources not necesarily linked to synthetic biological work. For example some members may rely on the community to provide them with housing or food etc. <br />
<br />
• Members of the community have access to the resources and infomation of the community to the extent that they contribute towards the community. Ethically sensitive materials and infomation that the community possesses may be withheld from those outside the community and from those who do not contribute adequately. members of the community may also generate a profit by utilising the resources and knowledge of the community - provided that the profit is, in part, goes into supporting the community.<br />
<br />
<br />
[[Image:DSC02492.JPG|600px]]</div>Liam Wilsonhttp://2010.igem.org/File:HHDLPresentsLOTAwardToTuTuJune12006.jpgFile:HHDLPresentsLOTAwardToTuTuJune12006.jpg2010-10-26T19:47:02Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/PhilosophyTeam:WITS-South Africa/Philosophy2010-10-26T19:45:16Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<br />
<br />
[https://2010.igem.org/Team:WITS-South_Africa/Outreach Outreach].<br />
<br />
As the first South African IGEM team, it seems fitting to add to this debate by introducing the theory of '''ubuntu''' to help further ethical debate around synthetic biology.<br />
<br />
[[Image:Ubuntu 904.jpg]] I am not talking about this - though the penguin is very cute<br />
<br />
I hope to answer the question ''''Should ubuntu be seriously considered when making policy?'''' I wish to answer this question in the affirmative and show that ubuntu would provide good policy on both a macro and a micro level. On a micro level, I believe adhering to ubuntu would make scientists and researchers more ethically sensitive. On a macro level I think that ubuntu can maintain sound policy whislt preserving the importance of individual ethical conduct. <br />
<br />
Sketching my argument briefly - I will be raising some key ehical concerns that are raised by our team's lactoguard device.I will then present a workable theory of ubuntu and apply it to the concerns raised in order to see if it can address the issues raised. The paper will therefore be a philosophical 'case study' into bio-ethics. <br />
<br />
From this I will hope to show that ubuntu can provide ethical guidance for synthetic biology - as it provides both 'internal' and 'external' moral motivations for ethical conduct. From this I hope to convince people that 5 tenents of ubuntu can serve as good 'rules of thumb' for ethical conduct within the field. They are:<br />
<br />
• Informal relations are important and have a role in our decision making. <br />
<br />
• Community members should show special ‘family-like’ concern for one another and that one’s actions reflect on the community as well as the individual.<br />
<br />
• Every member of that community has a personal stake in its endeavours and should bear some of the responsibility for the community but also share in the fruits of its endeavours<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more.<br />
<br />
• Members of the community have access to the resources of that community and can make use of them in so far as they contribute to the community and are involved with it. They can also profit of the communities resources provided that the profit generated goes into supporting the community.<br />
<br />
I will not fully argue for everything here - one will need to read my full paper for a proper length explaination of everything I have brought up here. But I will not leave you in the dark - here are some bite sized definitions and explainations so you can get an idea of what I am talking about and where my arguments will go. I will also provide some links to external sites that might be of some help:<br />
<br />
'''Ubuntu'''<br />
<br />
Ubuntu is a new field of study in analytical philosophy. I wager this is because of the cultural isolation of the Apartheid years and the general turmoil on the African continent post-colonialisation. Anyway, on to the positive matter - how do we define ubuntu? <br />
<br />
Metz (2007) describes ubuntu in terms of harmonious relations: <br />
''An action is right just insofar as it produces harmony and reduces discord; an act is wrong to the extent that it fails to develop community''<br />
<br />
Basically, ubuntu is a theory of right action - that it is a theory that tells us how to act in order to act in a morally good manner. If we compare Metz's conception of ubuntu with other normative ethical theories we can see how different ubuntu really is.<br />
<br />
'''Deontologists''' maintain that an action is right if it is in accordance with some duty or moral rules, such it is wrong to murder. '''Consequentialists''' see the moral weight, that is if the action is good or not, as resting in the consequences of an action. For example, one might refrain from lying because by not lying one tends to promote good consequences. Consequentialism is often expressed by the saying 'the ends justifies the means'. <br />
<br />
By Metz's definition we can see that actions can be considered good because of both the duties that harmonious relations have attached to them - such as a duty not to lie or cheat. And they can also be considered good because of the consequences that it produces - such as reconcilling with a person who has wronged you in order to promote harmony in your community. To put this in perspective - these two schools are traditionally set up in opposition to one another. <br />
<br />
I will also argue that ubuntu also has an extra component to it. That component is '''virtue ethics'''. Virtue ethics is the oldest form of ethical debate in the 'western' tradition. It's roots are found in the dialgoues and ethical theories of Socrates, Plato and Aristotle. The Oxford dictionary of Philosophy has this to say about it:<br />
<br />
''The theory of ethics that takes the notion of virtue as primary, rather than a view either of the 'good', for the sake of which we act, or of duty, law, or reason thought as providing rules of action.'' <br />
<br />
The entry goes further to note that: <br />
<br />
''The main problem for the approach is to account for how the virtous agent thinks, as courses of action are contemplated, without admitting that it will be in terms of duties, or consequences, which thereby regain a certain priority.''<br />
<br />
I will argue in favour of Metz's conception of ubuntu as I believe it captures the 'Africanness' of ubuntu and is explicit enough to tease out the deontologist, consequentialist and virtue ethical elements of the theory. My contention is that the virtue component of ubuntu is not a distinct object in the ethical framework of the theory in the way that the concept of 'goodness' is considered in classical deontologist and consequentialist theories. Instead I content that ubuntu fosters the development of a sensitivity to ethical situations within the individual in question which can be described as virtue. Ubuntu can therefore be considered to be, at least in part, a character trait. <br />
<br />
The wikipedia entry on ubuntu alludes to this connection that I am trying to establish.<br />
<br />
http://en.wikipedia.org/wiki/Ubuntu_%28philosophy%29<br />
<br />
Here is Desmond Tutu (who is perhaps one of the best exponents of ubuntu) describing ubuntu<br />
<br />
http://www.youtube.com/watch?v=ftjdDOfTzbk<br />
<br />
'''Should we take notice of ubuntu?'''<br />
<br />
I think that that we should. The use of ubuntu is not entirely unprecidented at a policy level. The philosphy of ubuntu has provided a guiding influence in the Truth and Reconciliation Commission, where the focus was not on punishing those responsible (on both sides) for the hideous crimes committed during the struggle against Apartheid. Instead the focus was on communal harmony and reconcilliation.<br />
<br />
Desmond Tutu describes his view of restoritive justice:<br />
<br />
http://www.youtube.com/watch?v=MCEboJ1k5Ek&feature=related<br />
<br />
Here he is again talking about forgiveness:<br />
<br />
http://www.youtube.com/watch?v=NsXPZ3WPW0M&feature=related<br />
<br />
What would policy look like if it where to be informed by ubuntu? They could possibly look something like these very rough outlines:<br />
<br />
• Informal relations should play an important role in governing the industry. A person's work should be srutinized by his peer's in an informal setting and those recognised as leaders of the field should assume responsibility for guiding and assisting those within the community to the best of their abilities. Research and commercialization of products and knowledge should be subject to the informal approval of peers. <br />
<br />
• Members of the synthetic biology community should show a special concern for one another. This concern extends past the professional relationships. All participants in the research, development, distribution and consumption of goods developed by synthetic biology should be considered part of the synthetic biological community. Also all members of the community should bear in mind that their actions reflect on the community as well as themselves. <br />
<br />
• Every member of the community has a personal stake in the community and should bear some responsibility for the flourishing of the community.Every member of the community should also share in the fruits of the community. An individual should bear responsibilty for the community to the extent that he or she is involved in the community.<br />
<br />
• An individual’s contribution to the community does not have to be equal to the benefits that they receive the community. Some members may be more reliant on the community that others and some may be expected to contribute more. This can be in the form of goods and resources not necesarily linked to synthetic biological work. For example some members may rely on the community to provide them with housing or food etc. <br />
<br />
• Members of the community have access to the resources and infomation of the community to the extent that they contribute towards the community. Ethically sensitive materials and infomation that the community possesses may be withheld from those outside the community and from those who do not contribute adequately. members of the community may also generate a profit by utilising the resources and knowledge of the community - provided that the profit is, in part, goes into supporting the community.<br />
<br />
<br />
[[Image:DSC02492.JPG|600px]]</div>Liam Wilsonhttp://2010.igem.org/File:DSC02492.JPGFile:DSC02492.JPG2010-10-26T19:42:59Z<p>Liam Wilson: </p>
<hr />
<div></div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/The_ProblemTeam:WITS-South Africa/The Problem2010-10-26T19:42:02Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<br />
<div class="title"><br />
Problem Outline<br />
</div><br />
<div style="padding:10px;"><br />
{{Template:Wits-South_Africa_ribbon}}<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
<br />
<br />
=== Public enemy: Human Papillomavirus-induced disease ===<br />
<br />
Cervical cancer is the second most prevalent cancer in women worldwide and the ause of 250 000 deaths every year. Human Papillomavirus (HPV) has been established as the etiological agent of cervical cancer - in 100% of cases of cervical cancer, HPV DNA is present.HPV is a sexually transmitted infection – in fact it is the most common STI in the world! Its ubiquity is due to the fact that it is mainly asymptomatic in men and its effects are only seen long after initial infection in women. <br />
<br />
<br />
[[Image:Wits_Cervical_cancer.jpg|500px]] <br />
<br />
<br />
=== So what is HPV? And how does it cause disease? ===<br />
<br />
HPV is a ds DNA virus which is highly host and tissue specific. It infects non-keratinised, stratified squamous epithelium (mucosal skin cells with a high rate of cellular turnover. Over 100 strains of the virus exist, some of which have been implicated in 100% cervical cancer (high-risk strains such as type 16 and 18) or cancers of the vulva, vagina, penis, anus, and head and neck (tongue, tonsils and throat).Other strains cause infectious but benign genital warts. <br />
<br />
In most cases of infection, the body’s immune system recognises the infection and is able to clear it effectively. Most women who have been infected with HPV will never even realise it.However, HPV has developed methods of evading the immune system, including decreased antigen presentation and blunting of the interferon response. In some individuals, this results in the progression of cancer. Immunocompromised individuals are much more likely to be susceptible and risk factors such as smoking and fertility rate also contribute. <br />
<br />
<br />
=== Let’s talk about South Africa…===<br />
<br />
HPV is especially problematic in the developing world where access to regular health care is limited, such as South Africa<br />
In South Africa current estimates indicate that every year 5743 women are diagnosed with cervical cancer and 3027 die from the disease. About 21% of women in the general population are estimated to harbour cervical HPV infection at a given time<br />
Early detection and careful monitoring of disease progression is vital and this is often not possible for women living in rural or under resourced areas. WHO guidelines recommend that all women aged 18 – 69 have a pap smear every three years. Only 13.6% of women in South Africa are being screened for cervical cancer according to these guidelines!<br />
Click to download the WHO fact sheet on cervical cancer in South Africa. [[Media:Wits_who.pdf]]<br />
<br />
===Detection and diagnosis===<br />
<br />
There is no antiviral or cure for HPV infection. The only diagnostic for HPV does not detect the virus itself and will only detect an infection if it has actually progressed to cancer! This is the PAP smear - a histological investigation which looks for abnormal cell morphology which arise long after the initial HPV infection as a result of virally-induced oncogenic events. A smear can detect the pathology very (too) late. PCR can also be used to detect viral DNA – this is the current gold standard for HPV diagnosis but is strain specific and impractical to implement on a wide scale at this point. <br />
<br />
<br />
</div><br />
<br />
[[Image:DSC02488.JPG|600px|middle]]</div>Liam Wilsonhttp://2010.igem.org/Team:WITS-South_Africa/The_ProblemTeam:WITS-South Africa/The Problem2010-10-26T19:41:25Z<p>Liam Wilson: </p>
<hr />
<div>{{Template:WITS-South_Africa_Main_Menu_19_07}}<br />
{{Template:WITS-South_Africa_Main_Menu_0910}}<br />
<br />
<br />
<div class="title"><br />
Problem Outline<br />
</div><br />
<div style="padding:10px;"><br />
{{Template:Wits-South_Africa_ribbon}}<br />
<div style="width:680px;text-align:justify;float:middle;"><br />
<br />
<br />
=== Public enemy: Human Papillomavirus-induced disease ===<br />
<br />
Cervical cancer is the second most prevalent cancer in women worldwide and the ause of 250 000 deaths every year. Human Papillomavirus (HPV) has been established as the etiological agent of cervical cancer - in 100% of cases of cervical cancer, HPV DNA is present.HPV is a sexually transmitted infection – in fact it is the most common STI in the world! Its ubiquity is due to the fact that it is mainly asymptomatic in men and its effects are only seen long after initial infection in women. <br />
<br />
<br />
[[Image:Wits_Cervical_cancer.jpg|500px]] <br />
<br />
<br />
=== So what is HPV? And how does it cause disease? ===<br />
<br />
HPV is a ds DNA virus which is highly host and tissue specific. It infects non-keratinised, stratified squamous epithelium (mucosal skin cells with a high rate of cellular turnover. Over 100 strains of the virus exist, some of which have been implicated in 100% cervical cancer (high-risk strains such as type 16 and 18) or cancers of the vulva, vagina, penis, anus, and head and neck (tongue, tonsils and throat).Other strains cause infectious but benign genital warts. <br />
<br />
In most cases of infection, the body’s immune system recognises the infection and is able to clear it effectively. Most women who have been infected with HPV will never even realise it.However, HPV has developed methods of evading the immune system, including decreased antigen presentation and blunting of the interferon response. In some individuals, this results in the progression of cancer. Immunocompromised individuals are much more likely to be susceptible and risk factors such as smoking and fertility rate also contribute. <br />
<br />
<br />
=== Let’s talk about South Africa…===<br />
<br />
HPV is especially problematic in the developing world where access to regular health care is limited, such as South Africa<br />
In South Africa current estimates indicate that every year 5743 women are diagnosed with cervical cancer and 3027 die from the disease. About 21% of women in the general population are estimated to harbour cervical HPV infection at a given time<br />
Early detection and careful monitoring of disease progression is vital and this is often not possible for women living in rural or under resourced areas. WHO guidelines recommend that all women aged 18 – 69 have a pap smear every three years. Only 13.6% of women in South Africa are being screened for cervical cancer according to these guidelines!<br />
Click to download the WHO fact sheet on cervical cancer in South Africa. [[Media:Wits_who.pdf]]<br />
<br />
===Detection and diagnosis===<br />
<br />
There is no antiviral or cure for HPV infection. The only diagnostic for HPV does not detect the virus itself and will only detect an infection if it has actually progressed to cancer! This is the PAP smear - a histological investigation which looks for abnormal cell morphology which arise long after the initial HPV infection as a result of virally-induced oncogenic events. A smear can detect the pathology very (too) late. PCR can also be used to detect viral DNA – this is the current gold standard for HPV diagnosis but is strain specific and impractical to implement on a wide scale at this point. <br />
<br />
<br />
</div><br />
<br />
[[Image:DSC02488.JPG|500px|middle]]</div>Liam Wilson