CH391L/S12/Introduction - Revision history

Jeffrey E. Barrick: /* References */

2012-02-11T23:50:17Z

References

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	#Judson1979 isbn=0879694785		#Judson1979 isbn=0879694785
	#Andrianantoandro2006 pmid=16738572		#Andrianantoandro2006 pmid=16738572
		+	#Benner2005 pmid=15995697
	#Fouchier2012 pmid=22267586		#Fouchier2012 pmid=22267586
	</biblio>		</biblio>

Jeffrey E. Barrick: /* Types of Studies */

2012-02-11T23:49:48Z

Types of Studies

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	* "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."<cite>Andrianantoandro2006</cite>		* "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."<cite>Andrianantoandro2006</cite>
-	* "Synthetic biologists come in two broad classes. One uses unnatural molecules to	+	* "Synthetic biologists come in two broad classes. One uses unnatural molecules to reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The other seeks interchangeable parts from natural biology to assemble into systems that function unnaturally." <cite>Benner2005</cite>
-	reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The	+
-	other seeks interchangeable parts from natural biology to assemble into systems that function	+
-	unnaturally." <cite>Benner2005</cite>	+
	* Bottom-up assembly of genes, organelles and organisms.		* Bottom-up assembly of genes, organelles and organisms.
	** In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.		** In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.

Jeffrey E. Barrick: /* Types of Studies */

2012-02-11T23:49:27Z

Types of Studies

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	* "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."<cite>Andrianantoandro2006</cite>		* "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."<cite>Andrianantoandro2006</cite>
-		+	* "Synthetic biologists come in two broad classes. One uses unnatural molecules to
		+	reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The
		+	other seeks interchangeable parts from natural biology to assemble into systems that function
		+	unnaturally." <cite>Benner2005</cite>
	* Bottom-up assembly of genes, organelles and organisms.		* Bottom-up assembly of genes, organelles and organisms.
	** In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.		** In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.

Jeffrey E. Barrick at 03:25, 5 February 2012

2012-02-05T03:25:43Z

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		+	[[Category:CH391L_S12]]
	== What is Synthetic Biology? ==		== What is Synthetic Biology? ==

Jeffrey E. Barrick: /* References */

2012-01-30T18:39:40Z

References

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	#Andrianantoandro2006 pmid=16738572		#Andrianantoandro2006 pmid=16738572
	#Fouchier2012 pmid=22267586		#Fouchier2012 pmid=22267586
-	~~</biblio>~~
	</biblio>		</biblio>

Ben Slater: Added example of bioterrorism-related controversy in the "Challenges" subsection.

2012-01-30T05:27:37Z

Added example of bioterrorism-related controversy in the "Challenges" subsection.

←Older revision		Revision as of 05:27, 30 January 2012
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	*Evolutionary breakdown of engineered systems.		*Evolutionary breakdown of engineered systems.
	*Escape of recombinant organisms and synthetic genes from the laboratory.		*Escape of recombinant organisms and synthetic genes from the laboratory.
-	*Misuse of tools for bioterrorism.
	*Debate over genetically modified foods.		*Debate over genetically modified foods.
		+	*Misuse of tools for bioterrorism.
		+
		+	====Recent Controversy in H5N1 Transmissibility Studies====
		+	Recent research has shown that reassortant viruses with the avian H5N1 protein HA (haemagglutinin) are transmissible among ferrets. It is unknown whether they are transmissible to humans.<cite>Fouchier2012</cite> In order to prepare a presention to the public regarding the benefits of such research, researchers "have agreed on a voluntary pause of 60 days on any research involving highly pathogenic avian influenza H5N1 viruses leading to the generation of viruses that are more transmissible in mammals. In addition, no experiments with live H5N1 or H5 HA reassortant viruses already shown to be transmissible in ferrets will be conducted during this time."<cite>Fouchier2012</cite>
		+
		+	They face an uphill battle in trying to convince the public that these studies are worth the risk, as synthetic biology is one of the most high-risk/high-reward fields. The risk of outbreak must be balanced against the greatly enhanced understanding of viruses that comes with such studies.

	== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==		== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==
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	#Judson1979 isbn=0879694785		#Judson1979 isbn=0879694785
	#Andrianantoandro2006 pmid=16738572		#Andrianantoandro2006 pmid=16738572
		+	#Fouchier2012 pmid=22267586
		+	</biblio>
	</biblio>		</biblio>

Jeffrey E. Barrick: /* Types of Studies */

2012-01-26T19:46:44Z

Types of Studies

←Older revision		Revision as of 19:46, 26 January 2012
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	** Instantiating algorithms and problems from physics and math into biology.		** Instantiating algorithms and problems from physics and math into biology.
	** Ex: circuits, DNA computing, metabolic engineering		** Ex: circuits, DNA computing, metabolic engineering
		+
		+	==== Program from Synthetic Biology Session for ASM 2012 ====
		+
		+	ASM is the [http://www.asm.org/ American Society for Microbiology].
		+
		+	[[Image:CH391L_S12_ASM2012Program.png]]

	=== Challenges ===		=== Challenges ===

Jeffrey E. Barrick: /* Hype and Substance */

2012-01-23T19:49:53Z

Hype and Substance

←Older revision		Revision as of 19:49, 23 January 2012
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	Like many new scientific fields (think nanotechnology), synthetic biology has been subject to a large amount of hype. Some even criticize it for not being anything new, but just a rebranding of other fields (recombinant DNA technology, metabolic engineering, etc.). There's not doubt that some of the flavor of the research question and new connections between forged between different fields are new. There are even some tremendous successes that can be claimed by the field of synthetic biology (full genome synthesis and engineering organisms to make certain new compounds). But, there are also many notable projects that turned out to be far more intractable than anyone imagined and have faltered partway through. An important aspect of this course will be analyzing and evaluating both types of outcomes and thinking about where synthetic biology will have the most impact in the future.		Like many new scientific fields (think nanotechnology), synthetic biology has been subject to a large amount of hype. Some even criticize it for not being anything new, but just a rebranding of other fields (recombinant DNA technology, metabolic engineering, etc.). There's not doubt that some of the flavor of the research question and new connections between forged between different fields are new. There are even some tremendous successes that can be claimed by the field of synthetic biology (full genome synthesis and engineering organisms to make certain new compounds). But, there are also many notable projects that turned out to be far more intractable than anyone imagined and have faltered partway through. An important aspect of this course will be analyzing and evaluating both types of outcomes and thinking about where synthetic biology will have the most impact in the future.

		+	Very cool links giving the flavor of synthetic biology:
	* [[Adventures\|Adventures in Synthetic Biology]]		* [[Adventures\|Adventures in Synthetic Biology]]
		+	* [[Media:16cribsheet.pdf\| SEED Magazine's Synthetic Biology Cribsheet]]

	=== Types of Studies ===		=== Types of Studies ===

Jeffrey E. Barrick: /* Cartagena Protocol on Biosafety */

2012-01-23T19:39:18Z

Cartagena Protocol on Biosafety

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	== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==		== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==

-	The Cartagena Protocol on Biosafety is an international treaty that addresses many of the concerns of biotechnology and synthetic biology.	+	The Cartagena Protocol on Biosafety is an international treaty that addresses many of the concerns of biotechnology and synthetic biology. It formalizes and updates many guidelines in the tradition of the [http://en.wikipedia.org/wiki/Asilomar_Conference_on_Recombinant_DNA\|1975 Asilomar Comference] where concerns about recombinant DNA were first addressed by scientists.

-	"The Protocol will enter into force on September 11, 2003. Although the United States is not a Party to the CBD and therefore cannot become a Party to the Biosafety Protocol, the U.S. participated in the negotiation of the text and the subsequent preparations for entry into force under the Intergovernmental Committee on the Cartagena Protocol. We will participate as an observer at the first Meeting of the Parties (MOP1), scheduled for February 2004 in Kuala Lumpur, Malaysia." http://www.fas.usda.gov/info/factsheets/biosafety.asp	+	Statement by the U.S. government: "The Protocol will enter into force on September 11, 2003. Although the United States is not a Party to the CBD and therefore cannot become a Party to the Biosafety Protocol, the U.S. participated in the negotiation of the text and the subsequent preparations for entry into force under the Intergovernmental Committee on the Cartagena Protocol. We will participate as an observer at the first Meeting of the Parties (MOP1), scheduled for February 2004 in Kuala Lumpur, Malaysia." http://www.fas.usda.gov/info/factsheets/biosafety.asp

	[[http://www.twnside.org.sg/title/lavanya-cn.htm News article on U.S. trade concerns]]		[[http://www.twnside.org.sg/title/lavanya-cn.htm News article on U.S. trade concerns]]

Jeffrey E. Barrick: /* Challenges */

2012-01-23T19:31:17Z

Challenges

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	*Misuse of tools for bioterrorism.		*Misuse of tools for bioterrorism.
	*Debate over genetically modified foods.		*Debate over genetically modified foods.
-
-	~~Berkeley Center for Synthetic Biology~~
-
-	~~http://www.nature.com/nchembio/journal/v3/n9/full/nchembio0907-527.html~~

	== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==		== [http://bch.cbd.int/protocol/ Cartagena Protocol on Biosafety] ==