CH391L/S13/Introduction

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== The Culture of Synthetic Biology ==
== The Culture of Synthetic Biology ==
-
On the one hand, synthetic biology has its roots in conventional fields of science, including molecular biology, metabolic engineering, protein design, and bioengineering. One could say that it is simply a clever re-branding of advances in those fields. On the other hand, much of the "newness" of synthetic biology has been due to the impact of a do-it-yourself (DIY) mindset associated with the open-source movement and even hacker culture that is not traditional to the field of molecular biology. The idea is that putting the tools in the hands of young and creative scientists will result in rapid and creative progress. This is a philosophy of the [http://igem.org iGEM competition], for example. Critics of this approach would content that such rapid progress and wide dissemination of these technologies without oversight risks having unintended adverse ecological and societal impacts. See the [[CH391L/S13/Ethics|synthetic biology ethics topic]].
+
On the one hand, synthetic biology has its roots in conventional fields of science, including molecular biology, metabolic engineering, protein design, and bioengineering. One could say that it is simply a clever re-branding of advances in those fields. On the other hand, much of the "newness" of synthetic biology has been due to the impact of a do-it-yourself (DIY) mindset associated with the open-source movement and even hacker culture that is not traditional to the field of molecular biology. The idea is that putting the tools in the hands of young and creative scientists will result in rapid and creative progress. This is a philosophy of the [http://igem.org iGEM competition], for example. Critics of this approach would contend that such rapid progress and wide dissemination of these technologies without oversight risks having unintended adverse ecological and societal impacts. See the [[CH391L/S13/Ethics|synthetic biology ethics topic]].
Links related to the flavor and hype of synthetic biology:
Links related to the flavor and hype of synthetic biology:
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* [[Media:16cribsheet.pdf|SEED Magazine's Synthetic Biology Cribsheet]]
* [[Media:16cribsheet.pdf|SEED Magazine's Synthetic Biology Cribsheet]]
* [http://www.fieldtest.us/bio.shtml Field Test Film Core Synthetic Biology documentary]
* [http://www.fieldtest.us/bio.shtml Field Test Film Core Synthetic Biology documentary]
 +
* [http://www.ted.com/talks/craig_venter_is_on_the_verge_of_creating_synthetic_life.html 2008 TED talk given by J.Craig Venter about the 1st Synthetic Genome Assembled ]
* [http://www.youtube.com/watch?v=ushmgPM7HT8 Imperial College iGEM team Wellcome Trust documentary (50 min)]
* [http://www.youtube.com/watch?v=ushmgPM7HT8 Imperial College iGEM team Wellcome Trust documentary (50 min)]
* [http://vimeo.com/19759432 E. chromi video]
* [http://vimeo.com/19759432 E. chromi video]
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|- bgcolor="lightgray"
|- bgcolor="lightgray"
! Year !! Event
! Year !! Event
 +
|-
 +
| 1970 || Discovery of first site-specific restriction enzyme <cite>Smith70</cite>
|-
|-
| 1972 || First publication on recombinant DNA <cite>Jackson1972</cite>
| 1972 || First publication on recombinant DNA <cite>Jackson1972</cite>
 +
|-
 +
| 1976 || First genome sequenced- Bacteriophage MS2 <cite>Fiers1976</cite>
 +
|-
 +
| 1981 || Introduction of phosphoramidite method of DNA oligonucleotide synthesis. <cite>Matteucci1981</cite>
 +
|-
 +
|1983 || First genetically modified plant is produced <cite>Fraley</cite>
|-
|-
|2000 || The "Repressilator" <cite>Elowitz2000</cite>
|2000 || The "Repressilator" <cite>Elowitz2000</cite>
|-
|-
-
| 2003 || First use of the term "BioBrick" <cite>Knight2003</cite>  
+
|2002 || Creation of the first synthetic virus <cite>Cello2002</cite>
 +
|-
 +
| 2003 || First use of the term "BioBrick" <cite>Knight2003</cite> First chemically synthesized bacteriophage  genome assembled <cite>Smith2003</cite>
|-
|-
| 2004 || First iGEM Jamboree
| 2004 || First iGEM Jamboree
|-
|-
| 2005 || "Adventures in Synthetic Biology" ''Nature'' Cover
| 2005 || "Adventures in Synthetic Biology" ''Nature'' Cover
 +
|-
 +
| 2006 || Human Genome Project completed <cite>Gregory2006</cite>
 +
|-
 +
| 2007 || First application of context-free grammars in CAD software for Synthetic Biology ([http://www.genocad.org GenoCAD]) <cite>Cai2007</cite>
 +
|-
 +
| 2008 || First synthetic genome assembled <cite>Gibson2008</cite>
 +
|-
 +
| 2010 || Creation of ''Mycoplasma mycoides'' JCVI-syn1.0, the first microbe with a self-replicating synthetic genome. <cite>Gibson2010</cite>
 +
|-
 +
| 2012 || Storage of digital information using DNA popularized in the media, ''Economist'' ([http://www.economist.com/news/science-and-technology/21570671-archives-could-last-thousands-years-when-stored-dna-instead-magnetic Archives Could Last Thousands of Years when Stored on DNA])
|}
|}
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** Ex: circuits, DNA computing, metabolic engineering
** Ex: circuits, DNA computing, metabolic engineering
** Rewriting biological sequences in ways that could not be achieved (quickly) by natural evolution
** Rewriting biological sequences in ways that could not be achieved (quickly) by natural evolution
 +
 +
== Synthetic Biology Workshops ==
 +
 +
* [http://meetings.cshl.edu/courses/2013/c-synbio13.shtml 2003 Cold Spring Harbor Laboratory Synthetic Biology Course]
== Synthetic Biology Conferences/Sessions ==
== Synthetic Biology Conferences/Sessions ==
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Looking over the schedules of recent conferences is an excellent way to find new topics of interest or finds labs that are involved in synthetic biology.
Looking over the schedules of recent conferences is an excellent way to find new topics of interest or finds labs that are involved in synthetic biology.
-
[http://sb6.biobricks.org/about/| SBx.0 Conference Series]
+
[http://sb6.biobricks.org/about/ SBx.0 Conference Series]
* Synthetic Biology 6.0 (2013) [http://sb6.biobricks.org/ main page]
* Synthetic Biology 6.0 (2013) [http://sb6.biobricks.org/ main page]
* Synthetic Biology 5.0 (2011) [http://sb5.biobricks.org/schedule/ schedule]
* Synthetic Biology 5.0 (2011) [http://sb5.biobricks.org/schedule/ schedule]
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ICBE—International Conference on Biomolecular Engineering
ICBE—International Conference on Biomolecular Engineering
*4th ICBE (2013) [http://www.aiche.org/sbe/conferences/international-conference-biomolecular-engineering-icbe/2013/icbe-conference-schedule schedule]
*4th ICBE (2013) [http://www.aiche.org/sbe/conferences/international-conference-biomolecular-engineering-icbe/2013/icbe-conference-schedule schedule]
 +
 +
==Read More==
 +
Special Synthetic Biology Edition in the [http://www.sciencedirect.com/science/journal/13675931/16/3 August 2012 Current Opinion in Chemical Biology ]
== References ==  
== References ==  
<biblio>
<biblio>
-
#Jackson1972 pmid=4342968
+
#Smith70 Smith H and Welcox KW. A Restriction enzyme from Hemophilus influenzae ☆: I. Purification and general properties. 1970. pmid:5312500 http://www.sciencedirect.com/science/article/pii/002228367090149X
 +
#Jackson1972 pmid=4342968 http://www.sciencedirect.com/science/article/pii/002228367090149X
//Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of ''Escherichia coli''.
//Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of ''Escherichia coli''.
#Elowitz2000 pmid=10659856
#Elowitz2000 pmid=10659856
 +
#Fraley  Fraley, RT et al. (1983) Expression of bacterial genes in plant cells. Proc. NatL. Acad. Sci. USA 80: 4803–4807  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384133/
#Knight2003 Knight, T. Idempotent Vector Design for Standard Assembly of Biobricks. 2003.
#Knight2003 Knight, T. Idempotent Vector Design for Standard Assembly of Biobricks. 2003.
  http://hdl.handle.net/1721.1/21168
  http://hdl.handle.net/1721.1/21168
 +
#Smith2003 pmid=14657399
 +
//Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides.
#Judson1979 isbn=0879694785
#Judson1979 isbn=0879694785
 +
#Gregory2006 Gregory et al. The DNA sequence and biological annotation of human chromosome 1. 2006.
 +
http://www.nature.com/nature/journal/v441/n7091/full/nature04727.html
#Andrianantoandro2006 pmid=16738572  
#Andrianantoandro2006 pmid=16738572  
// Synthetic biology: new engineering rules for an emerging discipline
// Synthetic biology: new engineering rules for an emerging discipline
#Benner2005 pmid=15995697
#Benner2005 pmid=15995697
// Synthetic biology
// Synthetic biology
 +
#Gibson2010 pmid=20488990
 +
<!--below:First publication of a CAD program for synthetic bio-->
 +
#Cai2007 pmid=17804435
 +
#Gibson2008 pmid=18218864
 +
#Cello2002 pmid=12114528
 +
#Fiers1976 Fiers, W et al. 1976. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene.
 +
http://www.regensci.org/twiki/pub/IGEM2009/BrainStorming/ms2article.pdf 
 +
#Matteucci1981 Matteucci MD and Caruthers MH. 1981. Synthesis of Deoxyoligonucleotides on a Polymer Support. http://pubs.acs.org/doi/abs/10.1021/ja00401a041?prevSearch=matteucci%252C%2Bcaruthers%252C%2B1981&searchHistoryKey=
</biblio>
</biblio>

Current revision

Contents

Introduction to Synthetic Biology

This quotation about the Molecular Biology revolution of the first part of the twentieth century sets the stage for synthetic biology.

It was a quarter-century ago that Watson and Crick, playing with cardboard cutouts and wire-and-sheet-metal models and sorting out the few controlling facts from a hotchpotch of data, elucidated the molecular architecture of the genetic material itself, the double-railed circular staircase of deoxyribonucleic acid. What has been learned in the years since is full of surprises, full of wit and beauty, full of the most gratifying illumination. The culmination is now approaching of the great endeavor of biology that has swept on for a century and a quarter—an achievement of imagination that rivals the parallel, junior enterprise in physics that began with relativity and quantum mechanics. Biologists' pursuit of complete and explicit understanding has begun to list the exact molecular sequences that encode the hereditary message, instruction by instruction; it has tweezed apart the springs and gears by which the message is expressed in the building of the cell, and the ratchets and pawls by which that expression is regulated; it has accustomed men to speak apparently without wonder of the structural transformations by which a single protein molecule, an enzyme, will break or build other proteins, or by which, for example, a molecule of hemoglobin will flex its broad shoulders and bend its knees to pick up oxygen.
To be sure, the discoveries have not produced the great practical payout that has repeatedly been anticipated for them. Biologists have no atomic power stations and no bombs to point to, or at least not yet. No baby has been cured of a congenital deficiency by insertion of a missing gene into its cells. There is no vaccine against human leukemia, not even a cure for hay fever. Though some of the rewards are at last imminent, most scientists have learned that they must speak guardedly and emphasize to laymen the gaps to be filled in.
The Eighth Day of Creation, Horace Freeland Judson, 1979 [1]

The Culture of Synthetic Biology

On the one hand, synthetic biology has its roots in conventional fields of science, including molecular biology, metabolic engineering, protein design, and bioengineering. One could say that it is simply a clever re-branding of advances in those fields. On the other hand, much of the "newness" of synthetic biology has been due to the impact of a do-it-yourself (DIY) mindset associated with the open-source movement and even hacker culture that is not traditional to the field of molecular biology. The idea is that putting the tools in the hands of young and creative scientists will result in rapid and creative progress. This is a philosophy of the iGEM competition, for example. Critics of this approach would contend that such rapid progress and wide dissemination of these technologies without oversight risks having unintended adverse ecological and societal impacts. See the synthetic biology ethics topic.

Links related to the flavor and hype of synthetic biology:

Timeline of Synthetic Biology

Year Event
1970 Discovery of first site-specific restriction enzyme [2]
1972 First publication on recombinant DNA [3]
1976 First genome sequenced- Bacteriophage MS2 [4]
1981 Introduction of phosphoramidite method of DNA oligonucleotide synthesis. [5]
1983 First genetically modified plant is produced [6]
2000 The "Repressilator" [7]
2002 Creation of the first synthetic virus [8]
2003 First use of the term "BioBrick" [9] First chemically synthesized bacteriophage genome assembled [10]
2004 First iGEM Jamboree
2005 "Adventures in Synthetic Biology" Nature Cover
2006 Human Genome Project completed [11]
2007 First application of context-free grammars in CAD software for Synthetic Biology (GenoCAD) [12]
2008 First synthetic genome assembled [13]
2010 Creation of Mycoplasma mycoides JCVI-syn1.0, the first microbe with a self-replicating synthetic genome. [14]
2012 Storage of digital information using DNA popularized in the media, Economist (Archives Could Last Thousands of Years when Stored on DNA)

What is synthetic biology?

Types of studies referred to as synthetic biology (and other fields that might also claim them).

  • "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."[15]
  • "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." [16]
  • Bottom-up assembly of genes, organelles and organisms.
    • In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.
    • Ex:Re-factoring and re-writing genomes from scratch.
    • Create chemical systems with biological behaviors (e.g., self-replication).
  • Application of engineering principles to biology.
    • Standardized parts that give predictable outcomes when put together in different combinations.
    • Instantiating algorithms and problems from physics and math into biology. (e.g., oscillators)
    • Ex: circuits, DNA computing, metabolic engineering
    • Rewriting biological sequences in ways that could not be achieved (quickly) by natural evolution

Synthetic Biology Workshops

Synthetic Biology Conferences/Sessions

Looking over the schedules of recent conferences is an excellent way to find new topics of interest or finds labs that are involved in synthetic biology.

SBx.0 Conference Series

ASM

Keystone

  • Keystone Conference: Precision Genome Engineering and Synthetic Biology schedule

ICBE—International Conference on Biomolecular Engineering

Read More

Special Synthetic Biology Edition in the August 2012 Current Opinion in Chemical Biology

References

  1. Horace Freeland Judson. The eighth day of creation. Plainview, N.Y.: CSHL Press, 1996. isbn:0879694785. [Judson1979]
  2. Smith H and Welcox KW. A Restriction enzyme from Hemophilus influenzae ☆: I. Purification and general properties. 1970. pmid:5312500 http://www.sciencedirect.com/science/article/pii/002228367090149X [Smith70]
  3. Jackson DA, Symons RH, and Berg P. . pmid:4342968. PubMed HubMed [Jackson1972]
    Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli.

  4. Fiers, W et al. 1976. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. http://www.regensci.org/twiki/pub/IGEM2009/BrainStorming/ms2article.pdf [Fiers1976]
  5. Matteucci MD and Caruthers MH. 1981. Synthesis of Deoxyoligonucleotides on a Polymer Support. http://pubs.acs.org/doi/abs/10.1021/ja00401a041?prevSearch=matteucci%252C%2Bcaruthers%252C%2B1981&searchHistoryKey= [Matteucci1981]
  6. Fraley, RT et al. (1983) Expression of bacterial genes in plant cells. Proc. NatL. Acad. Sci. USA 80: 4803–4807 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384133/ [Fraley]
  7. Elowitz MB and Leibler S. . pmid:10659856. PubMed HubMed [Elowitz2000]
  8. Cello J, Paul AV, and Wimmer E. . pmid:12114528. PubMed HubMed [Cello2002]
  9. Knight, T. Idempotent Vector Design for Standard Assembly of Biobricks. 2003. http://hdl.handle.net/1721.1/21168 [Knight2003]
  10. Smith HO, Hutchison CA 3rd, Pfannkoch C, and Venter JC. . pmid:14657399. PubMed HubMed [Smith2003]
    Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides.

  11. Gregory et al. The DNA sequence and biological annotation of human chromosome 1. 2006. http://www.nature.com/nature/journal/v441/n7091/full/nature04727.html [Gregory2006]
  12. Cai Y, Hartnett B, Gustafsson C, and Peccoud J. . pmid:17804435. PubMed HubMed [Cai2007]
  13. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864. PubMed HubMed [Gibson2008]
  14. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. . pmid:20488990. PubMed HubMed [Gibson2010]
  15. Andrianantoandro E, Basu S, Karig DK, and Weiss R. . pmid:16738572. PubMed HubMed [Andrianantoandro2006]
    Synthetic biology: new engineering rules for an emerging discipline

  16. Benner SA and Sismour AM. . pmid:15995697. PubMed HubMed [Benner2005]
    Synthetic biology

All Medline abstracts: PubMed HubMed
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