GcatWiki - User contributions [en]

References

2014-06-25T14:09:52Z

Ckendig:

Applications of Genetically-Encoded Biosensors for the
Construction and Control of Biosynthetic Pathways [[File:Josh K. Michener.pdf]]

Synthetic RNA switches as a tool for temporal and spatial
control over gene expression [[File:Andrew L. Chang.pdf]]

Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein [[File:F. Ulrich Hartl.pdf]]

Soluable expression of recombinant proteins in the cytoplasm of E.coli [[File:Hans Peter Sørensen.pdf]]

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis [[File:Vierstra.pdf]]

Riboswitches, methods for their use, and compositions for use with riboswitches [[File:US.pdf]] (If wanted I can email. The file is too large)

Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942 [[File:Tozawa.pdf]]

Caffeine Riboswitch (possibly biosensor) [[File:Caffeine Riboswitch Paper.pdf]]

Emerging Applications of Riboswitches in Chemical Biology [[File:Emerging Applications of Riboswitches in Chemical Biology.pdf]]

Metabolic engineering of a reduced-genome strain of Escherichia coli
for L-threonine production [[File:Streamlining E. Coli Genome.pdf]]

SELEX (systematic evolution of ligands by exponential enrichment) to Identify Protein-Binding Sites on RNA [[File:SELEX to Identify Protein-Binding Sites on RNA.pdf]]

Philosophy of Biology References [[File:Philosophy_of_Biology_references_programmed_evolution.docx]]

File:Philosophy of Biology references programmed evolution.docx

2014-06-25T14:00:23Z

Ckendig: uploaded a new version of "File:Philosophy of Biology references programmed evolution.docx": Philosophy of Biology references

File:Philosophy of Biology references programmed evolution.docx

2014-06-25T13:56:14Z

Ckendig:

References

2014-06-25T13:52:58Z

Ckendig: Philosophy of Biology references

Ethics and Philosophy of SynBio

2013-06-28T03:10:40Z

Ckendig:

'''== Synthetic biology <--> philosophical questions ==
'''

Synthetic biological research is based on a whole suite of underlying philosophical assumptions. For instance, two of the central tenets of small systems synthetic biology are modularity and the standardization of functional parts.

So, where does the philosophy come in?, you may ask. Small systems synthetic biology is premised on the idea that the biological world has a particular structure and that structure is modular, e.g. that living organisms have a modular organization. The premise of biological modularity is an ontological claim.It is a premise about how the world is structured or organized. But it is a philosophical premise that can be tested in practice.

The concepts of modularity and standardization of parts used within synthetic biology both frame future investigations and serve to define it as a discipline.

In addition to ontological questions there are also epistemological questions (questions about the nature of knowledge--how do we acquire knowledge) and ethical questions (how should we act/behave):

''Epistemological questions''
What can synthetic biology tell us about how biological systems work or how they function?

''Ontological questions''
What kinds of things are synthetically produced pathways, parts, modules, or whole organisms?

''Ethical questions''
How should we act? What research should we pursue? How do we treat/behave towards the products of synthetic biology research?

Normative Ethical questions can be understood to come in three general varieties. Here's the simple taxonomy of ethical approaches:

Deontological approaches: duties or rules
Consequentialist approaches: consequences of actions
Virtue ethics approaches: moral character

For further elaborations see the Stanford Encyclopedia of Philosophy under "ethics" or James Rachels "Elements of Moral Reasoning"

'''Ethics and Philosophy of SynBio-- 4 case studies:'''

The 2013 GCAT SynBio Workshop Participants focused on 4 case studies:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator

In each, they identified philosophical and ethical issues, concerns, and impacts of this new synbio research and technology:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator

For each case, participants considered the following questions:

What can this tell us about how biological systems work or how they function? (ontological questions)

What kinds of things or entities could be produced—and how would you classify them? And on the basis of what methodology? (epistemological and methodological questions)

How should the products, pathways, platform technologies produced be developed or treated? What should they be used for—are there things they shouldn’t be used for? How do we treat/behave towards the products of these pathways or the data produced? (ethical questions)

Ethics and Philosophy of SynBio

2013-06-28T03:07:42Z

Ckendig:

'''== Synthetic biology <--> philosophical questions ==
'''

Synthetic biological research is based on a whole suite of underlying philosophical assumptions. For instance, two of the central tenets of small systems synthetic biology are modularity and the standardization of functional parts.

So, where does the philosophy come in?, you may ask. Small systems synthetic biology is premised on the idea that the biological world has a particular structure and that structure is modular, e.g. that living organisms have a modular organization. The premise of biological modularity is an ontological claim.It is a premise about how the world is structured or organized. But it is a philosophical premise that can be tested in practice.

The concepts of modularity and standardization of parts used within synthetic biology both frame future investigations and serve to define it as a discipline.

In addition to ontological questions there are also epistemological questions (questions about the nature of knowledge--how do we acquire knowledge) and ethical questions (how should we act/behave):

''Epistemological questions''
What can synthetic biology tell us about how biological systems work or how they function?

''Ontological questions''
What kinds of things are synthetically produced pathways, parts, modules, or whole organisms?

''Ethical questions''
How should we act? What research should we pursue? How do we treat/behave towards the products of synthetic biology research?

Normative Ethical questions can be understood to come in three general varieties. Here's the simple taxonomy of ethical approaches:

Deontological approaches: duties or rules
Consequentialist approaches: consequences of actions
Virtue ethics approaches: moral character

For further elaborations see the Stanford Encyclopedia of Philosophy under "ethics" or James Rachels "Elements of Moral Reasoning"

'''Ethics and Philosophy of SynBio-- 4 case studies:'''

The 2013 GCAT SynBio Workshop Participants focused on 4 case studies:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator

In each, they identified philosophical and ethical issues, concerns, and impacts of this new synbio research and technology:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator

For each case, participants considered the following questions:

What can this tell us about how biological systems work or how they function?
What kinds of things or entities could be produced—and how would you classify them? And on the basis of what methodology?
How should the products, pathways, platform technologies produced be developed or treated? What should they be used for—are there things they shouldn’t be used for? How do we treat/behave towards the products of these pathways or the data produced?

Ethics and Philosophy of SynBio

2013-06-28T00:38:43Z

Ckendig: Created page with " '''== Synthetic biology <--> philosophical questions == ''' Synthetic biology research is based on a whole suite of underlying philosophical assumptions—that the world is ..."

'''== Synthetic biology <--> philosophical questions ==
'''

Synthetic biology research is based on a whole suite of underlying philosophical assumptions—that the world is organized in a certain way –that is- that living organisms have an organization that is modular is one that is central to the functionality of small systems synthetic biology. The premise of biological modularity is an ontological claim.It is a premise about how the world is structured or organized. But it is a philosophical premise that can be tested in practice.
In addition to ontological questions there are also epistemological questions (questions about the nature of knowledge--how do we acquire knowledge) and ethical questions (how should we act/behave):

''Epistemological questions''
What can synthetic biology tell us about how biological systems work or how they function?

''Ontological questions''
What kinds of things are synthetically produced pathways, parts, modules, or whole organisms?

''Ethical questions''
How should we act? What research should we pursue? How do we treat/behave towards the products of synthetic biology research?

Normative Ethical questions can be understood to come in three general varieties. Here's the simple taxonomy of ethical approaches:

Deontological approaches: duties or rules
Consequentialist approaches: consequences of actions
Virtue ethics approaches: moral character

For further elaborations see the Stanford Encyclopedia of Philosophy under "ethics" or James Rachels "Elements of Moral Reasoning"

'''Ethics and Philosophy of SynBio-- 4 case studies:'''

The 2013 GCAT SynBio Workshop Participants focused on 4 case studies:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator

In each, they identified philosophical and ethical issues, concerns, and impacts of this new synbio research and technology:

Landmine detection

Synthetic artemisinin

Arsenic biosensor

Bacterial oscillator