User:NKuldell/Q/A working page 4 - Revision history

Nkuldell: /* Q: Who is investing in this and what do they see as the pay-off? */

Nkuldell — Fri, 29 Sep 2006 13:26:09 GMT

Q: Who is investing in this and what do they see as the pay-off?

←Older revision		Revision as of 13:26, 29 September 2006
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	The groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.		The groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

-	Currently much of the investment in the field is from the venture capital community into startup companies (e.g. [http://www.codondevices.com/ Codon Devices]). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [http://www.codondevices.com/] [http://www.syntheticgenomics.com/ Synthetic Genomics, Inc.], another startup by J. Craig Venter, ~~believes~~ "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [http://www.syntheticgenomics.com/about.htm]	+	Currently much of the investment in the field is from the venture capital community into startup companies (e.g. [http://www.codondevices.com/ Codon Devices]). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [http://www.codondevices.com/] [http://www.syntheticgenomics.com/ Synthetic Genomics, Inc.], another startup by J. Craig Venter, is founded on the idea that "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [http://www.syntheticgenomics.com/about.htm]

	The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. [ftp://ftp.cordis.lu/pub/nest/docs/synthetic_biology.pdf pdf] The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit [http://www.gatesfoundation.org/ Bill and Melinda Gates Foundation] has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [http://www.gatesfoundation.org/globalhealth/pri_diseases/malaria/announcements/announce-041213.htm].		The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. [ftp://ftp.cordis.lu/pub/nest/docs/synthetic_biology.pdf pdf] The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit [http://www.gatesfoundation.org/ Bill and Melinda Gates Foundation] has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [http://www.gatesfoundation.org/globalhealth/pri_diseases/malaria/announcements/announce-041213.htm].

Nkuldell: /* Q: Does the community include garage inventors? */

Nkuldell — Fri, 29 Sep 2006 13:24:11 GMT

Q: Does the community include garage inventors?

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	===Q: Does the community include garage inventors?===		===Q: Does the community include garage inventors?===

-	Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting, of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) ~~through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]~~. More sophisticated methods are needed if the goal is to grow hybrids, for example a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3]. Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...	+	Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting [http://www.make-digital.com/make/vol07/?pg=78], of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]). More sophisticated methods are needed if the goal is to grow hybrids, for example a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3]. Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

	Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.		Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.

Nkuldell at 13:21, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 13:21:41 GMT

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	Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. More specific is the definition offered by[[http://syntheticbiology.org/\| syntheticbiololgy.org]] which describes synthetic biology as		Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. More specific is the definition offered by[[http://syntheticbiology.org/\| syntheticbiololgy.org]] which describes synthetic biology as
	A) the design and construction of new biological parts, devices, and systems, and		A) the design and construction of new biological parts, devices, and systems, and
-	B) the re-design of existing, natural biological systems for useful purposes~~. One of its goals is programmable behavior in living cells~~.	+	B) the re-design of existing, natural biological systems for useful purposes.

	===Q: Do engineering lessons really transfer to biology?===		===Q: Do engineering lessons really transfer to biology?===
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	===Q: How is synthetic biology different from existing, related fields like genetic engineering?===		===Q: How is synthetic biology different from existing, related fields like genetic engineering?===

-	Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? ~~Throughout recorded history, people~~ have been ~~modifying~~ genetic material ~~via breeding and genetic crosses~~. ~~With the~~ advent of recombinant DNA technology, more methodical ~~combination~~ of DNA segments ~~became possible~~. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. ~~These two technologies of sequencing~~ and synthesis ~~are key~~ enabling ~~technologies of~~ synthetic ~~biology~~. [[User:NKuldell/Q/A Read more\| Read more]]	+	Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Breeding and genetic crosses have been used to modify genetic material throughout recorded history. The advent of recombinant DNA technology 30+ years ago allowed for more methodical combinations of DNA segments. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. Sequencing and synthesis enable cellular programs to be both read and written, thus enabling synthetic biologists to try to program the behaviour of living cells. [[User:NKuldell/Q/A Read more\| Read more]]

	===Q: What questions or applications are being addressed by synthetic biology?===		===Q: What questions or applications are being addressed by synthetic biology?===
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	===Q: Does the community include garage inventors?===		===Q: Does the community include garage inventors?===

-	Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting, of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]. More sophisticated methods are needed if the goal is to grow a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3]. Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...	+	Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting, of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]. More sophisticated methods are needed if the goal is to grow hybrids, for example a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3]. Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

	Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.		Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.
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	===Q: Does synthetic biology bring with it new risks not associated with existing, related fields?===		===Q: Does synthetic biology bring with it new risks not associated with existing, related fields?===

-	The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. ~~If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something with biological materials.~~ Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses.	+	The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses.

	Understanding that synthetic biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly. A full day of relevant discussion was programmed into the UC Berkeley hosted conference, [http://pbd.lbl.gov/sbconf/agenda.php Synthetic Biology 2.0, day 3]. Consequently, the Goldman School of Public Policy report [http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf PDF link] and a draft declaration from the conference [http://hdl.handle.net/1721.1/32982 pdf article] have been prepared. Additionally, some researchers within the community have self-organized to form a "synthetic society working group" [http://openwetware.org/wiki/Synthetic_Society], allowing scientists and engineers to engage with scholars expert in considering societal issues associated with emerging technologies, community leaders, and interested individuals. Finally, a report is anticipated from an ongoing project, sponsored by the Department of Energy and bio-era, that considers the impact of the genome synthesis and design [http://bio-era.net/research/add_research_17.html].		Understanding that synthetic biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly. A full day of relevant discussion was programmed into the UC Berkeley hosted conference, [http://pbd.lbl.gov/sbconf/agenda.php Synthetic Biology 2.0, day 3]. Consequently, the Goldman School of Public Policy report [http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf PDF link] and a draft declaration from the conference [http://hdl.handle.net/1721.1/32982 pdf article] have been prepared. Additionally, some researchers within the community have self-organized to form a "synthetic society working group" [http://openwetware.org/wiki/Synthetic_Society], allowing scientists and engineers to engage with scholars expert in considering societal issues associated with emerging technologies, community leaders, and interested individuals. Finally, a report is anticipated from an ongoing project, sponsored by the Department of Energy and bio-era, that considers the impact of the genome synthesis and design [http://bio-era.net/research/add_research_17.html].
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	<i> would a "read more" section useful to summarize regulatory framework from these sources: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution, how do these regulations differ for research in an industry setting. </i> <br>		<i> would a "read more" section useful to summarize regulatory framework from these sources: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution, how do these regulations differ for research in an industry setting. </i> <br>

-	===Q: What ~~are the existing barriers~~ to ~~the risk of potentially harmful~~ synthetic biology ~~products~~?===	+	===Q: What's to keep someone from using synthetic biology to harm others?===

-	To date, release of synthetic biology products is regulated by laws that regulate more conventionally produced agents. For example, the US Food and Drug Administration [http://www.fda.gov/] is established to insure only safe and effective medicines are available to the consumer, and synthetic organisms that produce a drug (such as the yeast programmed by Jay Keasling's group to manufacture precursor of the anti-malarial drug artemisinin) are subject to the same scrutiny. Similarly, the US Environmental Protection Agency [http://www.epa.gov/] is charged with protecting both the environment and human health and any synthetic organism constructed for intentional release into the environment (it's worth noting that no synthetic biology products like this currently exist) would be similarly overseen and regulated.	+	"DNA on demand" technology significantly lowers barriers to potentially dangerous substances in the hands of miscreants. Most companies check sequence requests to look for ones that might encode dangerous substances. Companies can and have refused to synthesize such DNA. It is unclear, however, if the synthesis orders were placed by miscreants or by researchers with legitimate scientific interests. Thus, synthesis technology seems ripe for abuse but there is no evidence supporting or denying the misappropriation of the technology.
-		+
-	There may be additional and different risks associated with synthetic biology, if it successfully enables the rapid and facile design and construction of biological materials. Access to the required technology and reagents may be more widely distributed, thus construction of harmful products, intentionally or unintentionally, may be more possible. Consequently, the synthetic biology community is engaged in open and active dialogs to anticipate and address the impact of engineered organisms, and to enable only responsible efforts.	+
-		+
-	~~<i>A~~ "read more" answer could included mention of barriers in place to regulate research labs and commercial fabricators. Could also bring in surveillance ideas to monitor SB biohackers and any means of restricting products from overtly malicious agents (if there is evidence for this). </i>	+
-		+
-	~~===Q: Is there evidence of interest in synthetic biology capabilities in the part of terrorists?===~~	+
-		+
-	~~Facile DNA synthesis is a key enabling technology for synthetic biology, but~~ DNA on demand significantly lowers barriers to potentially dangerous substances in the hands of miscreants~~. DNA synthesis companies have a record of synthesis orders but it’s not clear how or if that information would be shared~~. Most companies check sequence requests to look for ones that might encode dangerous substances. Companies can and have refused to synthesize such DNA. It is unclear, however, if the synthesis orders were placed by miscreants or by researchers with legitimate scientific interests. Thus, synthesis technology seems ripe for abuse but there is no evidence supporting or denying the misappropriation of the technology.	+

	<i>Still to add to answer: the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Thus part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start </i>		<i>Still to add to answer: the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Thus part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start </i>

Nkuldell at 13:08, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 13:08:17 GMT

Nkuldell at 02:17, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 02:17:04 GMT

←Older revision		Revision as of 02:17, 29 September 2006
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	Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)		Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

-	===Q3: How quickly is the field moving towards its goals?===	+	===Q: How quickly is the field moving towards its goals?===

	Though not all dedicated to enabling synthetic biology efforts, a timeline of relevant events include:<i> dates, landmarks still needed</i>		Though not all dedicated to enabling synthetic biology efforts, a timeline of relevant events include:<i> dates, landmarks still needed</i>

Nkuldell at 02:16, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 02:16:10 GMT

Show changes

Nkuldell at 02:10, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 02:10:00 GMT

Show changes

Nkuldell at 01:32, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 01:32:21 GMT

←Older revision		Revision as of 01:32, 29 September 2006
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	==Part 1: Defining the field and its capabilities==		==Part 1: Defining the field and its capabilities==
-	~~Q1: What is synthetic biology?~~
-	~~Q2: How is synthetic biology different from related fields like genetic engineering?~~
-	~~Q3: Can engineering lessons be applied to biology?~~
-	~~Q4: Have primitive life forms or viruses been through synthetic biology?~~
-	~~Q5: What applications are being addressed by synthetic biology?~~
-	~~Q6: How quickly is the field moving towards its goals?~~
-	~~End Q: where can I read more?~~
-

	===Q: What is synthetic biology?===		===Q: What is synthetic biology?===
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	Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Throughout recorded history, people have been modifying genetic material via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology. [[User:NKuldell/Q/A Read more\| Read more]]		Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Throughout recorded history, people have been modifying genetic material via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology. [[User:NKuldell/Q/A Read more\| Read more]]
-
-	~~===Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?===~~
-
-	Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.
-
-	Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)


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	Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.		Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.

		+	===Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?===

		+	Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.
		+
		+	Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

	===Q3: How quickly is the field moving towards its goals?===		===Q3: How quickly is the field moving towards its goals?===
Line 59:		Line 49:
	One oft cited paper by Carlson <cite>Carlson</cite> looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems. Related reference, not oft cited, is Zwick (2005) Technology: a genome sequencing center in every lab.		One oft cited paper by Carlson <cite>Carlson</cite> looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems. Related reference, not oft cited, is Zwick (2005) Technology: a genome sequencing center in every lab.

-		+	===Q: Where can I read more?===
-		+
-	===Where can I read more?===	+

	Some recent reviews are listed here. More are in the pipeline. <br>		Some recent reviews are listed here. More are in the pipeline. <br>
Line 70:		Line 58:
	*Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7		*Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7
	*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"[http://www.bioinfo.de/isb/2006/06/0038/]		*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"[http://www.bioinfo.de/isb/2006/06/0038/]
-
-

	<b>Reviews in the lay press include </b><br>		<b>Reviews in the lay press include </b><br>
Line 77:		Line 63:
	*Tucker & Zilinskas, The New Atlantis, Spring 2006 [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]		*Tucker & Zilinskas, The New Atlantis, Spring 2006 [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]
	*''Custom-Made Microbes, at Your Service'' by A Pollack NYT Science section January 17, 2006 [http://www.nytimes.com/2006/01/17/science/17synt.html link]		*''Custom-Made Microbes, at Your Service'' by A Pollack NYT Science section January 17, 2006 [http://www.nytimes.com/2006/01/17/science/17synt.html link]
-


	==Part 2: Defining the community==		==Part 2: Defining the community==

-	===Q1: ~~What~~ is ~~the nature of~~ the synthetic biology community?===	+	Q1: How organized is the synthetic biology community?
		+	Q2: Who speaks for the community?
		+	Q?: Is community distinct from genetic engineering community?
		+	Q?: add outreach/awareness question?
		+	Q?: add biohackers question?
		+	Q?: what groups are closely following synthetic biology and its implications?
		+	End Q: where can I read more?
		+
		+
		+	===Q1: How is the synthetic biology community organized?===

-	~~Like most emerging research fields, the synthetic biology community is loosely defined with no single unified voice.~~ Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held ([http://openwetware.org/wiki/Synthetic_Biology:Synthetic_Biology_1.0 Synthetic Biology 1.0] at MIT and [http://pbd.lbl.gov/sbconf/ Synthetic Biology 2.0] at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.	+	Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held ([http://openwetware.org/wiki/Synthetic_Biology:Synthetic_Biology_1.0 Synthetic Biology 1.0] at MIT and [http://pbd.lbl.gov/sbconf/ Synthetic Biology 2.0] at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.

-	~~Yet in~~ some ways the synthetic biology is quite organized given that it is in its early stages. For instance,	+	In some ways the synthetic biology is quite organized given that it is in its early stages. For instance,
	#An NSF-funded effort called SynBERC was launched in August of 2006 [http://www.synberc.org/index.html]. SynBERC (Synthetic Biology Engineering Research Center) initiates a multi-institutional, collaborative effort to lay the foundations for engineering with biological substrates.		#An NSF-funded effort called SynBERC was launched in August of 2006 [http://www.synberc.org/index.html]. SynBERC (Synthetic Biology Engineering Research Center) initiates a multi-institutional, collaborative effort to lay the foundations for engineering with biological substrates.
	#A [http://syntheticbiology.org community website] exists that can be edited and revised by anyone in the field.		#A [http://syntheticbiology.org community website] exists that can be edited and revised by anyone in the field.
Line 94:		Line 88:
	#UC Berkeley is archiving their [http://webcast.berkeley.edu/courses/archive.php?seriesid=1906978261 synthetic biology seminar series] online. [[User:NKuldell/Q/A Read more\| Read more]]		#UC Berkeley is archiving their [http://webcast.berkeley.edu/courses/archive.php?seriesid=1906978261 synthetic biology seminar series] online. [[User:NKuldell/Q/A Read more\| Read more]]

-	===Q2: Who speaks for the ~~field~~? ===	+	===Q2: Who speaks for the community? ===
	There is no single spokesperson.		There is no single spokesperson.
	*Authors of recent review articles are key workers in synthetic biology.		*Authors of recent review articles are key workers in synthetic biology.
Line 115:		Line 109:
	*[http://pbd.lbl.gov/sbconf/agenda.php Speakers]		*[http://pbd.lbl.gov/sbconf/agenda.php Speakers]

-		+	A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing.
-	A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing ~~(see Part 2, Question 1)~~.	+

	==Part 3: Possible future benefits of synthetic biology==		==Part 3: Possible future benefits of synthetic biology==

Nkuldell at 01:21, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 01:21:53 GMT

←Older revision		Revision as of 01:21, 29 September 2006
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	===Q: What is synthetic biology?===		===Q: What is synthetic biology?===

-	~~The~~ application of engineering principles to biology.	+	Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. According to [[http://syntheticbiology.org/\| syntheticbiololgy.org]] synthetic biology is
		+	A) the design and construction of new biological parts, devices, and systems, and
		+	B) the re-design of existing, natural biological systems for useful purposes.
		+

	===Q: Do engineering lessons really transfer to biology?===		===Q: Do engineering lessons really transfer to biology?===

Nkuldell at 00:27, 29 September 2006

Nkuldell — Fri, 29 Sep 2006 00:27:59 GMT

←Older revision		Revision as of 00:27, 29 September 2006
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	==Part 1: Defining the field and its capabilities==		==Part 1: Defining the field and its capabilities==
		+	Q1: What is synthetic biology?
		+	Q2: How is synthetic biology different from related fields like genetic engineering?
		+	Q3: Can engineering lessons be applied to biology?
		+	Q4: Have primitive life forms or viruses been through synthetic biology?
		+	Q5: What applications are being addressed by synthetic biology?
		+	Q6: How quickly is the field moving towards its goals?
		+	End Q: where can I read more?

-	===Q1: What is synthetic biology?===	+
		+	===Q: What is synthetic biology?===

	The application of engineering principles to biology.		The application of engineering principles to biology.

-	===Q2: Do engineering lessons really transfer to biology?===	+	===Q: Do engineering lessons really transfer to biology?===

	The engineering of biology is currently very hard to do, largely because engineers do not welcome uncertainty and unpredictable behavior but the biological world is full of these. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Existing descriptions of basic cellular activities and genetic codes do not allow biological activities to be predictably combined in novel and re-useable ways.The difficulties facing those who wish to engineer biology are concisely described by Endy <cite>Endy</cite> and Knight <cite>Knight-MSB-2005</cite>.[[User:NKuldell/Q/A Read more\| Read more]]		The engineering of biology is currently very hard to do, largely because engineers do not welcome uncertainty and unpredictable behavior but the biological world is full of these. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Existing descriptions of basic cellular activities and genetic codes do not allow biological activities to be predictably combined in novel and re-useable ways.The difficulties facing those who wish to engineer biology are concisely described by Endy <cite>Endy</cite> and Knight <cite>Knight-MSB-2005</cite>.[[User:NKuldell/Q/A Read more\| Read more]]

-		+	===Q: How is synthetic biology different from existing, related fields like genetic engineering?===
-	===Q2: How is synthetic biology different from existing, related fields like genetic engineering?===	+

	Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Throughout recorded history, people have been modifying genetic material via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology. [[User:NKuldell/Q/A Read more\| Read more]]		Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Throughout recorded history, people have been modifying genetic material via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology. [[User:NKuldell/Q/A Read more\| Read more]]
		+
		+	===Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?===
		+
		+	Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.
		+
		+	Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)
		+
		+
		+	===Q: What questions or applications are being addressed by synthetic biology?===
		+
		+	Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.
		+	Other successful efforts in synthetic biology involve metabolic engineering of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16330045&query_hl=4&itool=pubmed_docsum] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast <cite>Ro-Nature-2006</cite>, an achievement that may allow cheap and clean production of this precursor for an antimalarial drug.
		+	Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.
		+
		+

	===Q3: How quickly is the field moving towards its goals?===		===Q3: How quickly is the field moving towards its goals?===
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	*Tucker & Zilinskas, The New Atlantis, Spring 2006 [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]		*Tucker & Zilinskas, The New Atlantis, Spring 2006 [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]
	*''Custom-Made Microbes, at Your Service'' by A Pollack NYT Science section January 17, 2006 [http://www.nytimes.com/2006/01/17/science/17synt.html link]		*''Custom-Made Microbes, at Your Service'' by A Pollack NYT Science section January 17, 2006 [http://www.nytimes.com/2006/01/17/science/17synt.html link]
-
-	~~===Q3: What questions or applications are being addressed by synthetic biology that aren't being explored or built using other technologies?===~~
-
-	Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.
-	Other successful efforts in synthetic biology involve metabolic engineering of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16330045&query_hl=4&itool=pubmed_docsum] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast <cite>Ro-Nature-2006</cite>, an achievement that may allow cheap and clean production of this precursor for an antimalarial drug.
-	Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.
-
-
-	~~===Q5: Some people may foresee a day when synthetic biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?===~~
-
-	Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.
-
-	Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

←Older revision		Revision as of 13:08, 29 September 2006
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	Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. More specific is the definition offered by[[http://syntheticbiology.org/\| syntheticbiololgy.org]] which describes synthetic biology as		Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. More specific is the definition offered by[[http://syntheticbiology.org/\| syntheticbiololgy.org]] which describes synthetic biology as
	A) the design and construction of new biological parts, devices, and systems, and		A) the design and construction of new biological parts, devices, and systems, and
-	B) the re-design of existing, natural biological systems for useful purposes.	+	B) the re-design of existing, natural biological systems for useful purposes. One of its goals is programmable behavior in living cells.

	===Q: Do engineering lessons really transfer to biology?===		===Q: Do engineering lessons really transfer to biology?===
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	===Q: What questions or applications are being addressed by synthetic biology?===		===Q: What questions or applications are being addressed by synthetic biology?===

-	Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.	+	Some synthetic biologists are combining genomic information and synthesis technologies <b> to re-write the genetic code </b> from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.
-	Other successful efforts in synthetic biology involve metabolic engineering of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16330045&query_hl=4&itool=pubmed_docsum] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast <cite>Ro-Nature-2006</cite>, an achievement that may allow cheap and clean production of this precursor for an antimalarial drug.	+	Other successful efforts in synthetic biology involve <b> metabolic engineering </b> of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16330045&query_hl=4&itool=pubmed_docsum] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast <cite>Ro-Nature-2006</cite>, an achievement that may allow cheap and clean production of this precursor for an antimalarial drug.
-	Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. ~~Other~~ efforts ~~are focused on trying~~ to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.	+	Finally, synthetic biology can provide a framework for discovery-driven biologists who might like <b> to test their existing models by building them </b> from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. More futuristic are related efforts to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.

	===Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?===		===Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?===
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	===Q: How quickly is the field moving towards its goals?===		===Q: How quickly is the field moving towards its goals?===

-	Though not all dedicated to enabling synthetic biology efforts, a timeline of relevant events include:~~<i> dates, landmarks still needed</i>~~	+	Though not all dedicated to enabling synthetic biology efforts, a timeline of relevant events include:
	*Restriction enzymes, 1970 Werner Arber, Dan Nathans and Hamilton Smith		*Restriction enzymes, 1970 Werner Arber, Dan Nathans and Hamilton Smith
	*Dideoxy Sequencing, 1977 Frederick Sanger		*Dideoxy Sequencing, 1977 Frederick Sanger
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	A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing.		A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing.

-	~~===Q: Is the synthetic biology community distinct from the genetic engineering community?===~~
-
-	The answer to this question is likely to vary depending of the section of the public questioned. An interesting experiment would be to provide a five minute description of synthetic biology, without specifically differentiating it from other fields, and then ask how synthetic biology compares to genetic engineering. It seems likely that
-	*For the average person in society with little or no formal training in biology, synthetic biology would be seen as indistinguishable from genetic engineering and the communities would overlap completely.
-	*For the average biologist, a distinct approaches of the two fields would be seen, but perhaps considered a subtle one, with some community overlap .
-	*For the average funding agency or administrator, given the fact that the risks, benefits and applications are qualitatively similar, synthetic biology and genetic engineering might be viewed as one field with one set of workers.

	===Q: Is the synthetic biology community developing and operating awareness efforts?===		===Q: Is the synthetic biology community developing and operating awareness efforts?===
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	*methodical and discipline-specific curriculum, for example [[http://openwetware.org/wiki/Keasling%3A_Synthetic_Biology_Class at UC Berkeley]] and [[http://openwetware.org/wiki/BE.109%3ASystems_engineering at MIT]], is being developed to train university students in synthetic biology		*methodical and discipline-specific curriculum, for example [[http://openwetware.org/wiki/Keasling%3A_Synthetic_Biology_Class at UC Berkeley]] and [[http://openwetware.org/wiki/BE.109%3ASystems_engineering at MIT]], is being developed to train university students in synthetic biology

-	===Q: Does the community include garage inventors ~~with new reagents for biohacking~~?===	+	===Q: Does the community include garage inventors?===

-	~~Synthetic~~ biology may offer a new toolkit for the longstanding and common human drive to manipulate nature. ~~For example, what if~~ in ~~addition~~ to ~~the pears growing on~~ a backyard pear tree~~, there could also be apples,~~ two kinds, and ~~perhaps~~ a branch filled with quince~~. This unnatural tree could be made (indeed, has been made!~~[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]. ~~What~~ if the goal ~~was~~ to grow a pear tree with apple-flavored, quince-shaped fruits~~? Hybrid~~ traits require ~~more sophisticated methods, such as~~ cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3=], or recombinant DNA technology, ~~the method used to generate~~ the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for ~~biohacking~~ expand ~~considerably~~ with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...	+	Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting, of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [[http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]. More sophisticated methods are needed if the goal is to grow a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3]. Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

-	Deliberately mischievous ~~biohacking~~ is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have ~~plenty~~ to ~~use~~ for ~~mischief~~. It's hoped that better responses ~~to mischief~~ will also emerge, rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts ~~to guard against their mis-use~~.	+	Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.

-	<i> "read more" section might further explore "biohacking" as biological counterpart of a computer virus in the human environment </i>	+	<i> "read more" section might further explore "biohacking" as biological counterpart of a computer virus in the human environment. </i>

-	===Q: ~~what~~ groups are closely following synthetic biology and its implications?===	+	===Q: What groups are closely following synthetic biology and its implications?===

	Emerging technologies, including synthetic biology and its implications, are being followed and reported in the academic press. For example the European Molecular Biology Organization ("EMBO") published a special issue of EMBO Reports dedicated to science and security issues [http://www.nature.com/embor/journal/v7/n1s/index.html]. The lay press has also taken an interest in this area, for example the recent issue of MAKE magazine (volume 7) dedicated to backyard biology and garage biotechnology. Finally, many social organizations, including "watchdog" groups seeking vigilant oversight of the work and inclusion in the regulatory dialog, are interested and following development of this field. See for example their open letter to the synthetic biology community: [[Image:Macintosh HD-Users-nkuldell-Desktop-OpenLetter061805.pdf]].		Emerging technologies, including synthetic biology and its implications, are being followed and reported in the academic press. For example the European Molecular Biology Organization ("EMBO") published a special issue of EMBO Reports dedicated to science and security issues [http://www.nature.com/embor/journal/v7/n1s/index.html]. The lay press has also taken an interest in this area, for example the recent issue of MAKE magazine (volume 7) dedicated to backyard biology and garage biotechnology. Finally, many social organizations, including "watchdog" groups seeking vigilant oversight of the work and inclusion in the regulatory dialog, are interested and following development of this field. See for example their open letter to the synthetic biology community: [[Image:Macintosh HD-Users-nkuldell-Desktop-OpenLetter061805.pdf]].

-	===Q: ~~where~~ can I read more?===	+	===Q: Where can I read more?===
	BBF, SynBERC, Synthetic Society		BBF, SynBERC, Synthetic Society