Category: Notes

Word on the Street @ Synthetic Biology 4.0 – Day 2

Posted by – October 11, 2008

Word on the street from Synthetic Biology 4.0..  take a word or leave a word.

  • Tom Knight mentions it will be another 10 years before an untrained hobbyist can order a BioBrick off the shelf, stir things up, and have them work like a can currently be done for a hobby electronics kit, noting they (the engineers! Applying proper engineering design rules!) have only been at system-level design biology for a couple years.  He suggests anyone interested should do iGEM, using borrowed or scrounged equipment if necessary, but doesn’t know about the startup costs involved.   (Budget would be good to know.)
  • Various MIT people again mention the way to get started from scratch in synthetic biology is through iGEM.
  • Big open questions (and significantly opposed views) regarding the licensing surrounding biobricks or “open source” parts libraries.
  • While everyone bandies about the phrase “open source,” it seems no one actually understands what open source means (or that there are two major camps in open source:  viral innovation-stifling copyleft GPL in which all your work must also be disclosed, and more open Apache/BSD which allows your work to remain private).  A point was made that the intellectual property could be released as public domain, yet authors rarely chose to do so, instead adopting a more complex license.
  • I didn’t realize this before, though apparently there is a “humanist” group which is reporting pseudo-scientific fluff regarding genetic engineering & synthetic biology.  I won’t name them as they don’t deserve air time based on the couple sensationalistic & skewed articles they’ve written.
  • A very small minority of specialists believe in just going skunk-works style, ignoring the assumed difficulty of engineering biology.  That means, setting up startup-like garage operations while maintaining control of everything.
  • Laboratory-created self-mobile molecular machines (aka: synthetic life) is closer to reality than anyone might guess.  Mix the right things into the right places and things which previously were inert will start to move on their own.
All quotes above are not to be taken literally.  Any resemblance to actual persons is entirely coincidental.  The contents of this article and this web site (web log) are Copyright with All Rights Reserved.  No content may be used without explicit written permission.  (This is to prevent quoting out of context.)

For those unfamiliar with synthetic biology, this video by Mac Cowell shows Drew Endy explaining the field:

Word on the Street @ SB 4.0 – Day 1

Posted by – October 10, 2008

Word on the street from Synthetic Biology 4.0..  take a word or leave a word.

  • DIY Bio such as Garage Hacking Biobricks – it’s not for grandma or the kids or even the DIY hackers.  It’s not an issue with access to tools, access to research, access to equipment, or access to a lab.  It’s lack of experience which will hamper any real results from the “I want to do DIY Bio”.  It could take an untrained bio hacker “years” to complete a simple new project since the design will be full of dead ends, whereas the trained (postdoc) scientist would complete similar tasks in a couple months.
  • Standard biological parts won’t solve everything, they could solve some things.
  • At least the belief that there’s a lot of doubt that standard biological parts could ever come to fruition, especially considering everyone sends everything to “the registry” which presumably can’t handle the burden of filling in all the gaps in everyone’s parts.
  • Hong Kong’s Ministry of Finance says he likes synthetic biology and believes in pledging lots of resources to the field even though he says he doesn’t really know what it is; the venture capitalists tell him it’s a good idea.
  • Free t-shirts.
  • Free Biobricks Foundation stickers.
  • Biologists are touchy about the “god” subject and about the “what is life?” subject.  Funny, I don’t know a single astrophysicist who is touchy about the “is the earth flat?” subject.
  • Some people adamantly believe that Biobricks are way too much baggage to be carrying around to solve an enzymatic problem (“we don’t need all these stinkin’ genes”).
  • Lots of software aided design tools for point-click-drag-drop-the-Biobrick-done!  Somehow, if it were really that easy, I would have expected the “grandma can DIY bio” argument to hold.
  • Students originating from foreign countries and heading to the U.S. to study biology have big visa issues.  Security level orange!  Banana-smelling e. coli detected!  We have an issue possibly brewing from the baker’s yeast!
  • Certain venture capitalists looove synthetic biology, and believe it is a far different capitalizing model than traditional genetic engineering or chemical engineering fields.
All quotes above are not to be taken literally.  Any resemblance to actual persons is entirely coincidental.  The contents of this article and this web site (web log) are Copyright with All Rights Reserved.  No content may be used without explicit written permission.  (This is to prevent quoting out of context.)

Happy Protein Families :-D

Posted by – October 10, 2008

A fun card deck from GeneArt at SB4.0.

Synthetic Biology Conference 4.0 (2008) Agenda

Posted by – October 8, 2008

The Synthetic Biology Conference for 2008 is in Hong Kong.

The agenda can be found here: Synthetic Biology Conference 4.0 Agenda

7th Annual International Symposium Addressed the Engineering through Systems Biology

Posted by – May 30, 2008

2008 SYMPOSIUM
Systems Biology and Engineering
Sunday, April 20 and Monday, April 21 2008

7th Annual International Symposium Addressed the Engineering through Systems Biology

The Institute for Systems Biology and the University of Washington College of Engineering will hold the 7th annual symposium, Systems Biology and Engineering, on April 20-21, 2008. This year’s symposium is a two-day event gathering the most influential researchers transforming biology into an integrative discipline investigating complex systems with this year’s focus on the areas of biological imaging, single-cell and single-molecule experimentation and synthetic biology.

  • Category: Notes
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Synthetic Biology Conference 3.0, 2007

Posted by – December 13, 2007

The Synthetic Biology Conference for 2007 (aka: SB3.0) was held in Zurich; download the conference proceedings.

Many of the talks are available for viewing online.

Video: Welcome to SB 3.0, by Sven Panke, ETH Zurich

NCBI BLAST: Basic Local Alignment Search Tool

Posted by – November 6, 2007

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NCBI BLAST
Basic Local Alignment Search Tool

From The NCBI Handbook,
Section 16. The BLAST Sequence Analysis Tool, by Tom Madden

Summary

The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA.

Basic Local Alignment Search Tool (BLAST) (1, 2) is the tool most frequently used for calculating sequence similarity. BLAST comes in variations for use with different query sequences against different databases. All BLAST applications, as well as information on which BLAST program to use and other help documentation, are listed on the BLAST homepage. This chapter will focus more on how BLAST works, its output, and how both the output and program itself can be further manipulated or customized, rather than on how to use BLAST or interpret BLAST results.

  • Category: Notes
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Synthetic Biology Conference 2.0 – video excerpt

Posted by – July 29, 2006

The Second International Conference on Synthetic Biology (SB2.0) took place on May 20-22, 2006, at the University of California, Berkeley. The conference brought together a diverse group of participants from a variety of disciplines, including some of the world’s leaders in biological engineering, biochemistry, quantitative biology, biophysics, molecular and cellular biology, bioethics, policy and governance, and the biotech industry. A collaborative effort of Berkeley Lab, MIT, UC Berkeley, and UCSF, the conference sought to promote and guide the further, constructive development of the field.