Share-Alike Genetic Engineering Intellectual Property Licenses

Posted by – November 9, 2008

A draft legal license for BioBricks was created early in 2008, though as far as I know, it has not been “tested” by industry use of the intellectual property (anyone know?).  Surprisingly, to me, the draft BioBrick license doesn’t contain any liability statements.  The BioBrick license attempts to solidify the “open source”ness of biological components.

Compare the BioBrick license to the original open source software license from MIT, below.

MIT License for Software (circa 1992?)

Copyright (c) [year] [copyright holders]

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.

The BioBricks license is simple and mandates only the sharing intent of the license.  Whereas the original MIT and GNU Copyleft licenses contain a significant statement of liability-reduction (which, as far as I know, hasn’t actually been tested in court, though is generally accepted), the BioBricks discussions don’t seem to mention liability at all.

Draft of the BioBricks Legal Scheme (January 2008)

1. You are free to modify, improve, and use all BioBrick parts, in systems with other BioBricks parts or non-BioBrick genetic material.
2. If you release a product, commercially or otherwise, that contains BioBrick parts or was produced using BioBrick parts, then you must make freely available the information about all BioBrick parts used in the product, or in producing the product, both for preexisting BioBrick parts and any new or improved BioBrick parts. You do not need to release information about any non-BioBrick material used in the system.
3. By using BioBrick parts, you agree to not encumber the use of BioBrick parts, individually or in combination, by others.

The BioBrick license seems similar to the Creative Commons Share-Alike license.  The legal scheme is based on the latest legal meetings organized by the BioBrick Foundation:

BioBrick Foundation / Samuelson Clinic Materials from March 2008 UCSF Workshop

  1. Legal Options Backgrounder & Draft BBF Legal Scheme: PDF
  2. Executive Summary of Findings: PDF
  3. Slides from March UCSF Workshop: PPT

Further BioBrick related legal documents are at Open Wet Ware: http://openwetware.org/wiki/The_BioBricks_Foundation:Legal

Open questions as of this writing:

  • Has liability been addressed in Biobricks?  (Especially considering the implications of biosafety that surrounds the field.)   By liability, this means a license term which boils down to: “The author of this BioBrick is not responsible if anything bad happens when/if anyone creates/clones/uses/modifies it.”
  • Has industry brought BioBrick technology to market which would “test” the BioBrick license?
  • What is the roadmap for future license drafts/official versions?

2008’s Thinking on Biological Engineering Business

Posted by – November 8, 2008

One set of perspectives on systems biology startup business for 2008.

Institute of Biological Engineering’s

Bio-Business Nexus 2008

From OpenWetWare

Presenter Title Presentation
Dr. Rob Whitehead North Carolina State University Office of Technology Transfer-putting ideas to work Media:1.Whitehead – IBE NCSU March2008.pdf
Michael Batalia, Ph.D. Avant-Garde Technology Transfer Leading Innovation at Wake Forest University Health Sciences Media:2. Batalia – 2008 IBE BioBusiness Nexus_MAB.pdf
John C. Draper, President, First Flight Venture Center Business Incubation, A Research Triangle Park Resource Media:3. Draper – IBE 13thAnnualConf-03062008c.pdf
Lister Delgado NC IDEA Grants Program Media:4. Delgado – NCIDEA Grants Program Overview – IBE Conference.pdf
Rob Lindberg, PhD, RAC The North Carolina Biotechnology Center Media:5. Lindberg – IBE 2008 BTD presentation 030708.pdf

Links

2007’s Thinking on Biological Engineering Business

Posted by – November 7, 2008

The presentations below were given at the  Institute of Biological Engineering annual meeting March 30, 2007 in St. Louis, Missouri, under the topic of BioBusiness.

The Mellitz presentation is very good reading.

BioBusiness Nexus Presentations 2007

Mellitz presentation: Commercialization of University IP: Translational Research in BME Leading to Company Formation

Nidus Center presentation

BioGenerator presentation: Bridging the Gap Between Technologies and Viable Companies

Akermin presentation: Biofuel Cells for Portable Electronic Applications

Chlorogen presentation: Production of a Human TGF-beta Family Protein with Potential as an anti-Cancer Therapeutic Protein From Plant Chloroplast

Kereos presentation: Targeted Imaging / Targeted Therapy

Apath presentation: Automated Antiviral Drug Screening Using Engineered Replication Systems

Orion Genomics presentation: DNA Methylation & Cancer

Sequoia Sciences presentation: Bringing Back Nature to Drug Discovery Natural Molecules in an Antibacterial Program

Somark Innovations presentation: BIOCOMPATIBLE RFID INK TATTOO

Web Seminar on Systems Biology: New Approaches, New Tools

Posted by – November 5, 2008

A 90-minute webinar (web seminar) on Systems Biology as a “new approach” in solving today’s health problems — includes summary of what systems biology is, how it is emerging as a current technology, and methods for addressing “systems medicine”.

Systems Biology: New Approaches, New Tools and Implications for Human Health Care

The original event was broadcast on:
Date: Thursday, October 30, 2008
Time: 1:00 PM EDT
Duration: 90-minutes

http://w.on24.com/r.htm?e=124050&s=1&k=7AE6968040C980E22D45F3994A29F4DA

Presentation is performed by the Institute for Systems Biology.  Partially sponsored by Agilent Technologies.

My brief overview

Initial introduction includes overview of technical & market drivers, and convergence of science & technology to create the emerging field.

“P4” Medicine: predictive, preventive, participatory and personalized medicine.

What are the top revolutionary technologies today which will drive the next several years of research?

  • High throughput and inexpensive DNA sequencing
  • Using nanotechnology to measure proteins from small amounts of blood
  • Information technology

System Biology’s largest “unsolved problems”

  • Validated datasets are unavailable – the massive amount of data is not fully used and systems for analysis are not fully developed
    • Open-to-the-public databases for research information is very important

      • “it must be freely and publically available to all, including industry. […] Those publishing articles must take the extra step to continue improving the data after simply being published” – Akhilesh Pandey, M.D., Ph. D., Associate Professor, John Hopkins University
  • Proteomics is still in its infancy
  • Sharing data is difficult
  • Building blocks are still being built; building blocks means specific databases for specialized data
  • Drug industry develops many new drugs; “but what we really need is” to identify specific drug targets for specific diseases/conditions, for screening
  • Lack of qualified people working in the field
    • “Biologists have to take second major in an engineering science” — Leroy Hood, M.D., Ph. D., President, Institute for Systems Biology

A typical Proteomics and Metabolomics workflow

  • Reduce complexity – Fractionation (mRP/UV); immunodepletion; MRP, OGE; sample preparation for membrane proteins
  • Profiling differences – Profiling (ToF); glycan profiling; metabolite profiling; biomarker discovery
  • Identifying Compounds – Identification (IT, QToF); PTM; glycan ID; metabolite ID; biomarker discovery
  • Characterizing differences – Characterization (QToF); intact protein; de-novo sequencing; protein complexes; membrane proteins; metalloproteins
  • Targeted quantitation – Validation (QQQ); biomarker screening by MRM; metabolite screening (UV, GC/MS, QQQ, ToF, QToF, IT, CE-MS, ICP-MS)

Discussed web site links

Towards a Market Model for Synthetic Biology

Posted by – November 4, 2008

If you ask most incumbents in the field of biology, they’ll likely say: “What exactly is synthetic biology?”

Maybe they should watch Drew Endy’s video on YouTube.

However, really, synthetic biology is the simple extension of modern biology.  Not too long ago, it wasn’t possible to “make” biology.  Now, it is possible (also known as: synthesis).  And the cost of synthesis keeps getting lower every year.  Some say the drop in the cost of synthesis looks curiously like the curves to Moore’s Law: doubling in technological capability every X months (where X is sometimes debated, usually quoted at 18 months, often misquoted as “every year”).

Synthetic biology is often compared to the computer industry, to leverage the historical perspective.

In the computer industry, there are three big pieces of the pie (usually seen as two; I want to purposely highlight as three).

  • Hardware companies
  • Software companies that sell source code (“source software companies” for the purposes of this article)
  • Software companies that sell binaries (“binary software companies” for the purposes of this article)

In the early days of the personal computer revolution, some bright guys saw that the hardware companies had a great product.. but software could be a much, much more profitable product:  with software, the cost of manufacturing is ZERO.  With hardware, the cost of manufacturing weighs down profits, so the maximum margin might be 20% to 30% for very glamorous products, and maybe 5% to 10% for less glamorous products.  These bright guys immediately bluffed their ways into IBM’s business center and negotiated what turned out to be one of the most profitable deals (if not the most profitable deal!) in the history of the world (Microsoft’s model).  In parallel to this, some other bright guys decided that they could instantly boost their overall profits by both building hardware and including all the fundamental software: hence, the first “personal computer systems company” (hardware plus all necessary software) was created (Apple’s model).

It’s worth keeping in mind at all times that the computer revolution existed before the “personal” computer revolution.  At that time, there were only mainframes (IBM: “big blue”).  During that time, though I’m not totally sure, I believe the market likely segmented like this:

  • Mainframe system companies (hardware + software)
  • Mainframe service companies (people required to run & maintain the machines)

Mainframe system companies charged heafty prices because they could: the only purchasers were governments and incredibly large (deep pocket) companies.  Yet the mainframe hardware business was killed by the personal computer market, which offered enough technology to the mass market to undercut most of the need for mainframes.  Of course, a mainframe company would never want to make a personal computer — it would erode their own profit potential (eventually, IBM caved in and created the IBM PC, but it was originally unsuccessful and only the reverse-engineered clones from other companies were accepted by the market).

The innovation in computer technology occurred so rapidly that unhealthy monopolies were created as a result. (Microsoft, AT&T, IBM)  In the case of AT&T, they were forced to split into different operations and allow more market competition (both the short and long term benefits of this forced split are still debated).  Microsoft avoided being split through government ignorance, entrenchment, lawyers, and luck.

Biology is a different from the story above. Biology does have “soft” ware, of a sort — it’s DNA.  The software is sometimes distributed as “source” code, of a sort — it’s as genes, protocols, primers and vectors.  The software is sometimes distributed as “binary” code, of a sort, too — it’s the modified microbes that “just run” when placed in the right environment.  But after this, the analogy kind of breaks down; the cost of manufacturing is never near zero.  Additionally, the fundamental “source” code can’t be protected under copyright, because it’s DNA.  And, the goverment has a heavy hand in determining what “software binaries” you can get ahold of in order to run.

Of course, I’m still a rank amateur at biology, though, currently, this is what others seem to see in biology.  And of course, I’m predicting the future, so maybe no one can definitely claim I’m incorrect.

  • Hardware companies, supplying machines and tools.
  • “Software” companies: supplying digital DNA sequences, cellular models (like BioBricks), and bioinformatics programs which simulate & verify the cellular models for fabrication.  Additionally, much of the intellectual property here will be public domain or Share-Alike licensed.
  • Fabrication companies: supplying physical biological material based on the digital sequences.  Most people will outsource fabrication to these companies and only the “large pharmas” will perform fabrication in-house.

Does this fit reality?  I say, no.  The fabrication companies will quickly starve, since the prices continue to fall — just like the DRAM computer companies closed with the falling prices of the transistor and transistor memory (Intel bailed out of manufacturing DRAM as Moore’s Law eroded their profits beyond repair).  The idealized “Software” companies can’t actually operate in the prescribed manner, because biology consists of chemicals, and such a company is not set up as a physical laboratory; the Share-Alike licensing will remove profit potential; and the company that sells the chemicals isn’t even on the map.

Here’s what seems to mirror the current market more closely.

  • Hardware companies: supply machines and lots of glass hardware.  Presumably lower profit margin except for large equipment sold to big pharma.
  • Wet Lab companies (biological engineers): supplying primers, enzymes, reagents, chemicals.  High profit margins, due to patent protection and high barrier to entry (requires highly specialized education and some number of years of experience).
  • Dry Lab companies (bioinformatics engineers): Design and supply digital DNA and cellular models, via computational models, and design bioinformatics progams and wet lab protocols for use.  Funky profit margin, because, if design is made Share-Alike, then profits don’t exist; if design is kept secret, then standards may not evolve well; and, the DNA intellectual property is already mandated as public domain.
  • Fabrication service companies: encompass limited rage of Wet Lab + Dry Lab, but don’t create their own protocols.  Margins vary, depending on level of the service.

The big winner right now seems to be the Wet Lab guys and the Hardware guys.  By leveraging patent protection, the Wet Lab competition is locked out of competing.  Although no one in the industry has anything nice to say about patents, everyone files them, and all investors demand them.  The Hardware guys currently have big profits, high prices, and little competition, as no one is forcing the prices down — sound familiar?  This should; it’s the same phenomenon that occurred in the mainframe days.

The shakeout seems to be that the Dry Lab guys, the Hardware guys, and the Fabrication guys will need to get together in some way.

Yet, there’s another interesting aspect of biology: organisms are different.  Each organism has it’s own unique pathways and in-compatibilities.  It is not possible, in general, to run “software” from one genetically engineered machine on another genetically engineered machine.  In fact, that’s why biologists usually argue against synthetic biology, claiming it will never work.

So rather than the universal “PC platform” that exists in the computer world (a derivative of both unhealthy monopolistic practices and the market requiring a common environment), the biological environments will number in the thousands.  Yeast grows differently than e. Coli, and both Hardware and Dry Lab are customized to individual species.  That could be the market segmentation: biological compatibility itself, creating multiple competitive hardware and “software” markets, with some market segments Share-Alike, and some not.

If someone has a crystal ball, let me borrow it for a second.

In-Depth Review, Part 3 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – November 3, 2008

In my previous write-ups of Part 1 and Part 2, I traced the Perl code and examples in the first half of the book, Beginning Perl for Bioinformatics, by James Tisdall, highlighting different approaches to bioinformatics in Perl.  As I mentioned before, Perl provides many different (and often stylistic) methods to solving a software problem.  The different methods usually differ in execution speed, code size, code scalability, readability / maintainability, simplicity, and advanced Perl symantics.  Since this is a beginning text, the advanced Perl isn’t covered.. that means templates, which could be useful for parsing bioinformatics data, are one of the topics not included here.

Often, the fastest code is the smallest code, and contains subtle code tricks for optimization. This is a perfect setup, because, in Chapter 8, Tisdall starts parsing FASTA files.  With Perl’s parsing engine, the subtly of the tricks leaves a lot of room for optimizing software.

FASTA & Sequence Translation

Tisdall offers a software problem based on the FASTA data, so time to solve it:

Tisdall: When you try to print the “raw” sequence data, it can be a problem if the data is much longer than the width of the page. For most practical purposes, 80 characters is about the maximum length you should try to fit across a page. Let’s write a print_sequence subroutine that takes as its arguments some sequence and a line length and prints out the sequence, breaking it up into lines of that length.

Compare his solution to mine:

# Solution by Tisdall
# print_sequence
#
# A subroutine to format and print sequence data

sub print_sequence {

    my($sequence, $length) = @_;

    use strict;
    use warnings;

    # Print sequence in lines of $length
    for ( my $pos = 0 ; $pos < length($sequence) ; $pos += $length ) {
        print substr($sequence, $pos, $length), "\n";
    }
}

The above is a straightforward, strings-based approach. I chose a regex approach, which took a couple minutes to work out, though should be faster during run-time:

sub dna_print {
  my $str = $_[0];
  do {
    $str =~ s/^([\w]{0,25})//;
    print "$1\n";
  } until (!length($str));
}

The above relies on the following method:

More

Witch Hazel? Triclosan? Horsetail Extract? Camellia Sinesis Leaf?

Posted by – October 29, 2008

Breeze by the cosmetics section of the department store next time. There is a 1+ billion-dollar market being bought and sold right under, and on top of, everyone’s noses, using mostly experimental organic chemistry, wrapped up in advertisements of sexualizing, anti-aging, softening, cleansing, wrinkle-reducing, organic, non-animal tested, oil-free, oil-reducing, oil-enhancing, whitening, darkening, clarifying, and most of all, “all natural”.

The cosmetics industry seems ripe for synthetic biology chemical factory creation. A short list of ingredients in skin care products, as some examples, are below (disclaimer: quoted from wikipedia).  Many of these ingredients do have supposed medicinal properties.. some are questionable.

Witch Hazel

Witch hazel is an astringent produced from the leaves and bark of the North American Witch Hazel shrub (Hamamelis virginiana) which ranges from Nova Scotia west to Ontario, and south to Florida, and Texas[1]. This plant, native to Canada and the United States was widely used for medicinal purposes by American Natives. The witch hazel extract was obtained by steaming the twigs of the shrub.

The essential oil of witch hazel is not sold separately as a consumer product. The plant does not produce enough essential oil to make production viable. However, there are various distillates of witch hazel (called hydrosols or hydrolats) that are gentler than the “drug store” witch hazel and contain alcohol.

Now for a PubMed article:

Highly galloylated tannin fractions from witch hazel (Hamamelis virginiana) bark: electron transfer capacity, in vitro antioxidant activity, and effects on skin-related cells, Touriño S, Lizárraga D, Carreras A, Lorenzo S, Ugartondo V, Mitjans M, Vinardell MP, Juliá L, Cascante M, Torres JL. Chem Res Toxicol. 2008 Mar; 21(3):696-704. Epub 2008 Mar 1.

Institute for Chemical and Environmental Research (IIQAB-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.    PMID: 18311930

Witch hazel ( Hammamelis virginiana) bark is a rich source of both condensed and hydrolizable oligomeric tannins. From a polyphenolic extract soluble in both ethyl acetate and water, we have generated fractions rich in pyrogallol-containing polyphenols (proanthocyanidins, gallotannins, and gallates). The mixtures were highly active as free radical scavengers against ABTS, DPPH (hydrogen donation and electron transfer), and HNTTM (electron transfer). They were also able to reduce the newly introduced TNPTM radical, meaning that they included some highly reactive components. Witch hazel phenolics protected red blood cells from free radical-induced hemolysis and were mildly cytotoxic to 3T3 fibroblasts and HaCat keratinocytes. They also inhibited the proliferation of tumoral SK-Mel 28 melanoma cells at lower concentrations than grape and pine procyanidins. The high content in pyrogallol moieties may be behind the effect of witch hazel phenolics on skin cells. Because the most cytotoxic and antiproliferative mixtures were also the most efficient as electron transfer agents, we hypothesize that the final putative antioxidant effect of polyphenols may be in part attributed to the stimulation of defense systems by mild prooxidant challenges provided by reactive oxygen species generated through redox cycling.

That doesn’t mean everyone should go rubbing witch hazel all over themselves..  though it does show that witch hazel does “something.”

Triclosan

Triclosan (IUPAC name: 5-chloro-2-(2,4-dichlorophenoxy)phenol) is a potent wide spectrum antibacterial and antifungal agent. Triclosan is found in soaps (0.15-0.30%), deodorants, toothpastes, shaving creams, mouth washes, and cleaning supplies and is infused in an increasing number of consumer products, such as kitchen utensils, toys, bedding, socks, trash bags, and some Microban treatments. Triclosan has been shown to be effective in reducing and controlling bacterial contamination on the hands and on treated products. More recently, showering or bathing with 2% triclosan has become a recommended regimen for the decolonization of patients whose skin is carrying methicillin resistant Staphylococcus aureus (MRSA)[1] following the successful control of MRSA outbreaks in several clinical settings.

Horsetail Extract

What! Yes, it says “Horsetail Extract” on the container. Though I didn’t find this as a real ingredient in wikipedia, I found it in the following patent.

United States Patent 5415861

Abstract: A method for reducing the visible size of facial skin pores by applying a novel composition which comprises an oil absorbing powder, a botanical astringent and a biological compound that alters the structure of the skin and/or the function of the sebaceous glands. […]

Horsetail extract (Equisetum arvense) is a preferred compound because it contains significant amounts (>8%) of organic silicones. These silicones are known to regulate collagen cross linking and improve the structural framework of connective tissues in the skin. Like the alternative compositions, Horsetail extract functions on and below the skin surface to reduce pore size with regular application.

Camellia Sinensis Leaf

Camellia sinensis is the tea plant, the plant species whose leaves and leaf buds are used to produce tea. It is of the genus Camellia (Chinese: 茶花; pinyin: Cháhuā), a genus of flowering plants in the family Theaceae. White tea, green tea, oolong and black tea are all harvested from this species, but are processed differently to attain different levels of oxidation. Kukicha (twig tea) is also harvested from camellia sinensis, but uses twigs and stems rather than leaves.

Tea extracts have become field of interest, due to their notional antibacterial activity. Especially the preservation of processed organic food and the treatment of persistent bacterial infections are being investigated.

  • Green tea leaves and extracts have shown to be effective against bacteria responsible for bad breath.
  • The tea component epicatechin gallate is being researched because in-vitro experiments showed that it can reverse methicillin resistance in bacteria like Staphylococcus aureus. If confirmed, this means that the combined intake of a tea extract containing this component will enhance the effectiveness of methicillin treatment against some resistant bacteria.

An amazing aspect of cosmetics is the historical basis for many of the ingredients, many of them in use for hundreds or thousands of years.

  • Category: Notes
  • Comments Closed

Next Generation Tech for DNA Sequencing

Posted by – October 24, 2008

Let’s say an organism is successfully modified and seems to be performing a portion of it’s synthetically designed biological tasks.  Several questions are raised:  has the organism evolved, during replication, from it’s original design?  Is the organism’s DNA actually the same as the desired engineered DNA?  Is there some mistake in the new organism’s DNA which could be improved?  If the organism doesn’t function properly, is it because of the designers’ mistake, or is it because of the random chance in nature?

These questions are usually answered by verifying the DNA of the organism — sequencing.  Today, verifying the organism’s sequence in a normal lab is done by a long process of diffusing the DNA through a gel and taking a UV picture of the result.  This is rather old (and annoying) technology.  Yet DNA sequencing is difficult because working with DNA poses several big technical problems.  What is the next generation technology for DNA sequencing which could improve this?

Here are some examples and some cool videos as well:

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“SynBioSS: The Synthetic Biology Modeling Suite”

Posted by – October 20, 2008

SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms. SynBioSS is available under the GNU General Public License. Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, and Yiannis N. Kaznessis, Bioinformatics 2008 24(21):2551-2553; doi:10.1093/bioinformatics/btn468

Sounds neat, let’s try it. Interestingly, the iGEM participants and biologists, in discussions of modeling, have thrown their hands in the air & state that it is difficult or impossible to model biology. Maybe SynBioSS can do the impossible?  Except: There is no specific installer available for OS/X (as of this writing) and it seems there are many assorted packages required.

Here are my install summary/notes/fixes for getting SynBioSS (version 1.0.1) running on OS/X (Leopard 10.5.5):
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Creating beneficial biological systems without cells

Posted by – October 19, 2008

In general terms, synthetic biology brings to mind using “BioBricks”, which are engineered genetic parts used to modify an organism, such as bacteria or yeast. The idea is to modify the organism to work to our advantage; for example, to eat sugar and produce biofuel — a pretty good tradeoff, considering the cost of gasoline and the cost of sugar. This is a top-down methodology: take an existing organism, modify it’s DNA, measure it’s behavior, and repeat the modification process until the desired “behavior” is measured.

Some synthetic biology research, however, doesn’t use traditional organisms at all. In fact, doesn’t even use “cells”. This might be called cell-free synthetic biology, or in vitro synthetic biology. This is a bottom-up approach: create the desired “behavior” from scratch. The idea has existed for some time; a good summary is Synthetic biology projects in vitro, Anthony C. Forster and George M. Church, Genome Res. 17:1-6, 2007: “Many biopolymer syntheses are already better scaled up in cell-free systems, such as linear DNAs by oligo synthesis and PCR, unmodified RNAs by in vitro transcription, and peptide libraries by in vitro transcription/translation. And engineering flexibility is much greater in vitro, unshackled from cellular viability, complexity, and walls.”

Synthetic Life

“How can I hack biology without using cellular organisms?”, you’re probably asking.

One proposed method for creating such cell-free synthetic biology projects (meaning: no bacteria, no yeast…  just… chemistry) is An integrated cell-free metabolic platform for protein production and synthetic biology, Michael C Jewett, Kara A Calhoun, Alexei Voloshin, Jessica J Wuu & James R Swartz, Molecular Systems Biology 4:220. These fully synthetic systems have significant environmental interactions in common with traditional bacteria:

It is striking to note that the Cytomim system closely mimics E. coli cellular metabolism. It is homeostatic in pH and [Pi], uses natural, non-phosphorylated energy substrates, provides a long-lasting ATP source, and fuels highly productive protein synthesis (up to 600 mg protein/l/h). In addition, each ribosome can polymerize approximately 10 500 amino acids (42 copies of chloramphenicol acetyl transferase, CAT), indicating that the Cytomim system is not limited by enzyme turnover (e.g. only one protein, or fraction of a protein, produced per ribosome). Furthermore, the specific oxygen uptake rate in the Cytomim system is on the same order as for intact E. coli cells.

As can be seen from the date of this publication (2008), this research is cutting edge. Prior work by the same primary author established this Cytomim system.

Digital-logic-like bistable circuit using synthetic biology without using organisms has previously been described in Construction of an in vitro bistable circuit from synthetic transcriptional switches, Jongmin Kim, Kristin S White & Erik Winfree, Molecular Systems Biology 2:68

The question by now might have changed.  Maybe at this point, you are asking, “Why should I use extensive trial-and-error while attempting to modify existing bacteria, when I can create exactly the proteins I need, from the ground-up, instead?”

That’s a good question for further research.

Word on the Street @ Synthetic Biology 4.0 – Day 3

Posted by – October 12, 2008

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

  • Venture capitalists and private investors are very interested in synthetic biology.  Significant buzz in the Bay Area regarding the term.  Large capital is required when making the transition from proven concept to, for example, a pilot plant for biofuel production.  Venture capitalists love to get excited because it’s their job to both get themselves excited and get others excited (excited enough to give them loads of money).
  • As on day2, a laboratory-proven “built from the ground up” organism (a thing, separate from other things, that eats, replicates, grows, and divides) may only be years away.
  • Very innovative solution proposed to slow the rate of spreading HIV, using synthetic biology to create a “get-the-HIV-away” preventative medicine.  Seemed very well received as a different track than current antiviral cures.
  • No one really knows how to model cells or modified cells.  (Again)
  • An interesting group at Cal Tech has proposed a method of designing, or compiling the design by converting a hardware netlist into DNA sequences, combinatorial logic which has unique signal outputs, thus eliminating the cross-talk problem; theoretically modeled up to 1,000 gates, currently tested up to 4 gates.
  • A cynical undergrad says that engineering biology will never work and will never be able to be modeled; though he has an iGEM project.
  • A Hong Kong local university biology professor also mentions that engineering biology will never work; it is too unreasonable to expect biology to behave under known rules: “biology is not like that.”
    • The word “never” in both cases might be very surprising to some, especially coming from two people in the field, one of whom has built Biobrick device(s).
  • DIY Bio is real!  Bio can be done as a hobby!  We want to let amateurs hack biology just like scientists do!  We need to apply rules to make it non-biohazard, and then just do it.”
    • Strongly contrasting opinion to the “it will never work” biologists.
  • Cells can be made to change shape dramatically with specific (laser) light input.  Very freakily amazing video.
  • Which opinion is more correct, that engineering biology will work or that it doesn’t or where we fall as of right now?
    • Drew Endy:  “The truth is somewhere in the middle.  Years ago, we had a lot of iGEM teams, and nothing worked.  Last year, we had let’s say 100 iGEM teams, and 10 teams had working devices.”  I conclude, the engineering process is improving through lab experience and raw data feedback.  Engineers eventually make nearly anything work (just ask Scotty).
    • Reshma Shetty (now at Ginko BioWorks): “It takes about 3 years to ‘get it’ [collect enough experience to be successful at creating biological devices].  Everyone seems to struggle until then.”
  • More back & forth related to the licensing issues of an “open source” biological library.
  • The Bay Area may have an accessible “Bio Fab Lab” in the years ahead, funded by public sources and aimed at improving the “open source” biological library.
  • Even the venture capitalists and synthetic biology company owners get history wrong; mistakenly stating facts.  “This is like the IBM PC architecture, completely open, and enabling things like the open source movement later”.. Wrong!; in fact, the IBM PC was completely locked down and very proprietary and backed by lawyers from the huge deep pockets of IBM — it was Compaq who, through a legal process of reverse engineering to work around the patent and intellectual property process, completely cloned the IBM PC firmware to a compatible version, thus inventing the clone-PC market (while IBM vehemently objected and litigated against).  Please read the history books (I would suggest Hackers, by Steven Levy, as a starting point). Most of the “this is like open source with computers” analogies are.. well.. off by a factor of two. At least a factor of two.
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 who aren’t familiar with synthetic biology, I will quote the Synthetic Biology 4.0 web site:

What are the applications of Synthetic Biology?

BioEnergy. Cells are being engineered to consume agricultural products and produce liquid fuels. British Petroleum and the US DOE granted $650 million dollars for research in the San Francisco Bay Area.

Drug Production. Bacteria and yeast can be re-engineered for the low cost production of drugs. Examples include the anti-malarial drug Artemisinin and the cholesterol-lowering drug Lipitor.

Materials. Recombinant cells have been constructed that can build chemical precursors for the production of plastics and textiles, such as Bio-PDO and spider silk.

Medicine. Cells are being programmed for therapeutic purposes. Bacteria and T-cells can be rewired to circulate in the body and identify and treat diseased cells and tissues. One such research program is the NIH-funded Cell Propulsion Laboratory at UCSF.

Synthetic Biology is a new approach to engineering biology, with an emphasis on technologies to write DNA. Recent advances make the de novo chemical synthesis of long DNA polymers routine and precise. Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells. With the development of this technology, there is a concurrent effort to address legal, social and ethical issues.

How is this different from genetic engineering?

Synthetic Biology builds on tools that have been developed over the last 30 years. Genetic engineering has focused on the use of molecular biology to build DNA (for example, cloning and PCR) and automated sequencing to read DNA. Synthetic Biology adds the automated synthesis of DNA, the setting of standards and the use of abstraction to simplify the design process.

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

In-Depth Review, Part 2 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – September 8, 2008

My Part 1 of 5 review of the book, Beginning Perl for Bioinformatics, by James Tisdall, left off at Chapter 8, just before Tisdall explains associative arrays, gene expression, FASTA files, genomic databases, and restriction sites.

Tisdall: “For simplicity, let’s say you have the names for all the genes in the organism and a number for the expressed genes indicating the level of the expression in your experiment; the unexpressed genes have the number 0. Now let’s suppose you want to know if the genes were expressed, but not the expression levels, and you want to solve this programming problem using arrays. After all, you are somewhat familiar with arrays by this point. How do you proceed?”

Perl’s associative arrays are one of the most powerful aspects of the language.  This is a good problem to examine using hashes.  Solutions to this kind of problem in other languages (C or matlab) might create an N-dimensional array (or even NxM) as a matrix representation of the problem.  In C, it might be solved using a lookup table possibly using a linked list, and the code to drive that needs to be written from scratch or borrowed from an external library.  Perl has a built-in method to solve these kinds of problems.

The solution is to use a hash:

$gene_name = "triA";
$level = 10;
$expression_levels{$gene_name} = $level;  # save 'level' on per-gene basis

This leads Tisdall to review biological transcription and translation, including code for DNA->RNA and RNA->protein data conversion.  The code is given in long form and then optimized in further examples for speed using associative arrays.  Recall the central dogma of biology:

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In-Depth Review, Part 1 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – September 6, 2008

As a specialized field, Bioinformatics is rather young.  It can be difficult to find universities which teach bioinformatics.  Bioinformatics can refer to many different types of tasks — from using programs and data without any computer science knowledge, to implementing database or web software, to writing data conversion programs which modify file formats between database storage methods, to writing algorithms for modeling and visualizing research problems.  Most of the work is described best as “computational biology”.

In the context of Perl (the famous computer language which runs underneath most web pages), Bioinformatics means computing text data retreived from biological databases.

The book, Beginning Perl for Bioinformatics, by James Tisdall, is for learning introductory software techniques in Perl, with a very brief biology review.  For biologists who have rarely programmed and need a starting language or need to learn Perl, this is a good place to start.  For technologists, note the copyright date on the book, to see how dated the information may be; since bioinformatics is still a young field, standards and technology are evolving rapidly.

Tisdall: “A large part of what you, the Perl bioinformatics programmer, will spend your time doing amounts to variations on the same theme as Examples 4-1 and 4-2. You’ll get some data, be it DNA, proteins, GenBank entries, or what have you; you’ll manipulate the data; and you’ll print out some results.”   (Chapter 4)

For software engineers or computer programmers, the biology field is also a completely new realm which is tough to get a handle on, and has it’s own language: Biology as a field (at least to me) has not yet differentiated itself between “soft, life science” and an engineering science.  For example, as a software engineer, the most basic software question is, “I need to write a look-up table for these elements, what are the all the possible strings for the field values?”  Yet this simple question can be very difficult to answer by consulting a biology textbook.  It is important to keep in mind that data manipulation for biology can involve massive amounts of information: also known as, very, very large strings; the strings represent DNA sequences which may range in practical usage from 10k to 100k.

Perl Bioinformatics Introductory Examples

The author states,

Tisdall: How do you start from scratch and come up with a program that counts the regulatory elements in some DNA? Read on.”

In chapter 4, there are the first simple Perl examples:  convert the DNA sequence to the corresponding RNA sequence.  In biology, the DNA uses A, T, G, C (representing the chemical names, of course); whereas RNA uses U instead of T.  Simple string manipulation provides the answer:  s/T/U/g;

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Biology & Life Science Textbooks for Download via NIH

Posted by – July 6, 2008

Resources at NIH and National Center for Biotechnology Information (NCBI):

Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.

Of particular educational interest is the NCBI Bookshelf, a growing collection of biomedical books with fully readable content online and that can be searched directly.  For example, Harvey Lodish Molecular Cell Biology (4th edition) is downloadable or searchable; although this is an older version than currently published (2000), it is useful.


The first book to be made available at NCBI was Molecular Biology of the Cell, 3rd edn, by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson, published by Garland Publishing, Inc. Molecular Biology of the Cell is one of the most widely used undergraduate textbooks in molecular and cell biology.

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.

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The World’s Smallest Organisms & Their Importance

Posted by – March 30, 2008

Biology is faced with the problem:  the field in general does not understand much of what it studies.  One method of solving this is to study the smallest organisms known, in an effort to “understand 100% of something small.”  This is a typical engineering approach, to understand the smallest system first, then work up to attempting to understand larger systems.  After understanding the organisms, of course, we have a better chance at modifying them (their DNA) into something useful (or, rather, something that actually lives at all).

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