Bio-Based Ideas

Have you ever wondered what other countries outside of the US are thinking about the biobased economy? Following is a word-for-word copy of what the "German Bioeconomy Council" thinks should be the road ahead. You can access the original document here: http://biooekonomierat.de/fileadmin/Publikationen/Englisch/Strategy_paper.pdf Decided at the 8th session of the Council, 14.5.2014 Preamble A sustainability-oriented bioeconomy can contribute vital solutions to the serious ecological and economic challenges of the future. However, such a bioeconomy will not develop automatically. Regulatory, social and technology policies are needed to move towards an ecologically sustainable economy that is based on innovation, renewable resources and efficient production processes. The Bioeconomy promotes process and product innovations with consumption and societal expectations in mind.

This year, I had the opportunity to attend the Synbiobeta 2013 Conference. Synbiobeta is an organization with the mission of fostering a community, and ecology of people, organizations and companies involved in synthetic biology. The conference was divided up into several sessions. In the next few posts, I will try to summarize what I thought was noteworthy during the meeting. We'll start with session 1.

As of late, Amyris has been in the news quite a bit. Another article surfaced in the Washington Post just a few days later titled "Companies rush to build ‘bio-factories’ for medicines, flavorings and fuels" . For the most part, the article echoes the content found in the New York times article. However, I wanted to emphasize the following bits:

Another interesting and inspiring talk from TED related to bio-based ideas was posted not too long ago.

This video made me go, "hmmm, very interesting!". It reminded me of a talk by Cheryl Hayashi at Cal State Fullerton in which she talked about properties of spider silk. Anyway, the reason I am posting this video here is because silk is another one of those bio-based materials that although known for a long time, have huge potential for alternative uses in the future.

Example of how ciliates look (Source: http://www.woodrow.org) This week, DW Radio covered an interesting topic in their science news radio show. In light of the recent EHEC outbreak in Germany, experts have been trying to trace the source of this deadly outbreak. For those who do not know what EHEC is, it stands for Enterohaemorrhagic Escherichia coli. In other words, these special strains of E. coli are very tough bugs that can cause intestinal bleeding - obviously not desirable and potentially dangerous. The search for possible sources has lead back to water treatment plants because the majority of water treatment plants treat water according to ecological aspects only, that is to say, they ensure that nutrients and waste in the water do not exceed certain levels. Many German water-treatment plants do not specifically try to reduce the number of bacteria in the water. That part is left to water companies that produce drinking water. The result is that high concentrations of...

With my thesis defense coming up this Monday, I really did not have as much time to share all the interesting things I came across lately. But I did not want to miss the chance to make a quick note to myself and the readers of this site of an interesting paper, titled "DNA-based programming of quantum dot valency, self-assembly and luminescence" just published in Nature Nanotechnology . Grigory Tikhomirov et al. report "the self-assembly of quantum dot complexes using cadmium telluride nanocrystals capped with specific sequences of DNA. Quantum dots with between one and five DNA-based binding sites are synthesized and then used as building blocks to create a variety of rationally designed assemblies, including cross-shaped complexes containing three different types of dots...Through changes in pH, the conformation of the complexes can also be reversibly switched, turning on and off the transfer of energy between the constituent quantum dots." In other w...

This is just a quick note on what's caught my eye in the last day or so: Two researchers from Harvard Medical School and Massachusetts General Hospital in Boston successfully created what they call a "living laser". How did they use a living cell as a laser? I realized that I didn't exactly how a laser worked so I looked it up on Wiki. According to Wikipedia , "Laser" stands for " L ight A mplification by S timulated E mission or R adiation". To build a laser, you basically need a light source, some device that absorbs the original light source and then emits an amplified signal also called "gain medium". The key to lasers is that the light is uniform and does not scatter all over the place - it's one bundle of light. This is performed be some complicated sets of optical mirrors. Normally, crystals (like ruby) are used for the gain medium, but in this case, a kidney cell expressing GFP was used. So technically, a cell does n...

This is a brief post while I am still mostly writing my thesis. I found another TED video with an interesting way to combine fashion with bio-based products - very interesting indeed.

I would like to thank Wilbert Escorcia , who recently also joined this blogging site, for having shown me the PBS site as another great source of information on the internet. He shared with me the profile of one of the people who are and will likely make a big difference in the sustainable biotechnology field: Jay Kiesling, founder of Amyris Biotechnologies , which was originally known for a bio-based method to efficiently and affordably produce artemisinin, an anti-malarial drug. Amyris Biotechnologies was a company I previously wrote about in my coverage of bio-based companies in California . On a Personal Note: Before, we dive into the video, I would just like to throw in a personal note. In light of the latest discussion about federal funding for public media on capitol hill, I think it is important to emphasize that the unique service public broadcast and radio provides - namely to inform and educate affordably, and broadly - is almost completely absent anywhere else in...

As an intermediate update, I wanted to post something I came across a few days ago: A testimony before the senate subcommittee on green jobs by Kate Gordon from the Center for American Progress Action Fund. I have reposted the exact content here only to make sure that her words do not get lost as often can happen when one only provides a link, and I do think what she has to say is important. I encourage everyone to go directly to the source and read it there. Mr. Chairman and members of the committee, thank you for inviting me to testify before you today. The issue of green jobs and trade is critical in light of the triple crises America faces: an economic crisis that has left 14 million people unemployed; an energy security crisis that leaves us vulnerable to every international incident and natural or man-made disaster; and a climate crisis that threatens the very planet we live on. In true American entrepreneurial spirit, we at the Center for American Progress Action Fund...

I have been for a while thinking now that it would be good to have a clear labeling system for products that are produced in a sustainable way from sustainable raw materials (which usually means bio-based). Well, today the USDA announced that a new, voluntary "Bio-preferred" label system was introduced that clearly labels bio-based products which the USDA defines as "those composed wholly or significantly of biological ingredients – renewable plant, animal, marine or forestry materials." The USDA hopes that the labeling system acts as a low investment high marketing return measure to promote the increased sale and use of these products in the commercial market and for consumers who wish to make educated and sustainable purchasing choices for their families. The labeling system is a small part in an overall strategy to decrease dependence on foreign oil, and increase the creation of domestic, green jobs.   For further details and regulations about the detail, I ...

I recently came across an interesting article posted at Discover which talked about a company by the name of Micropidas . It seeks to convert human effluent into a polyesterbelonging to polyhydroxyalkanoates or PHA family. Why is this important? Plastics often times are derived from oil. Using this bio-based approach cuts that out. In this case, there is an added benefit: they produce plastics while cleaning up the water. And lastly, Micropidas claims that the plastic produced is actually bio-degradable! I haven't had time to research this in more detail, but thought I would share this here.   To read the full, article please go here: http://news.discovery.com/tech/poop-plastic-puts-waste-to-work.html

Recently, “Forschung Aktuell” , a science news radio show on Deutschland Radio, highlighted some interesting research by the German scientist Hauke Harms on his approach to affordable solutions to detect arsenic in drinking water which is a common problem in some parts of the world. I was interested to learn how arsenic is sometimes found in drinking water. According to the show, arsen naturally exists in the environment as arsenopyrite. Natural processes can erode these layers and transport them down the river. There, arsen can react with organic matter that is commonly dumped into the river in heavily populated areas without proper waste water treatment to form arsenic. These arsenite containing waters can sink all the way into the ground water. Arsenite is a big problem because it is a non-biodegradable toxin which can cause cancer and other serious diseases as it accumulates in our bodies. To address this problem, one needs to have means to measure the presence of arsenite. Usi...

I recently read an article titled  “Microbial Biosynthesis of Alkanes” that appeared Science (Vol. 329, 559, 2010) was published by Andreas Schirmer et. al. By comparing nine cyanobacteria known to produce hydrocarbons (alkanes, and alkenes) to one species known not to produce any hydrocarbons, genes that exist only exist in the 9 other species. The genes that were identified this way became likely candidates for the alkane biosynthesis pathway. Two classes of proteins were identified: short-chain dehydrogenases or reductases, and the ferritin-like or ribonucleotide reductase-like proteins. Previously, it was predicted that alkane biosynthesis happens by decarbonylation of fatty aldehydes. The authors speculated that the dehydrogenase-like gene could encode a protein that initiates the reduction of a fatty acid intermediate while the ribonucleotide reductase-like protein could complete the decarbonylation reaction.  The authors noted that the gene pair classes describe...

There is one more talk I want to summarize because I thought it was really good: Susan Golden's talk about cyanobacteria was very educational because she reminds us all that when talking about algae not every algae is eukaryotic. According to her, cyanobacteria belong to the prokaryotic kingdom. There is a large variety of them out there with very unique metabolic processes and physiologies that can be exploited. Some fix nitrogen, others produce hydrogen, or other secondary products. Many are individualistic, while some form filaments that can be beneficial for harvesting. From a technological perspective, some cyanobacteria are very easily transformable – that foreign pieces of DNA can easily be absorbed into these organisms. From a research perspective, there are 10 genetic model systems providing a wealth of tools and information for further research questions. There are, however, challenges when it comes to working with cyanobacteria to extract oils for biofuels productio...

This is still from the SD-CAP Symposium. Another talk I wanted to summarize was Professor Stephen Mayfield's talk titled "Where we are - where we are going" The presentation slides can be found at the following location for anyone interested: http://algae.ucsd.edu/documents/SD-CABsymposiumMayfield.pdf Professor Mayfield’s talk was more of an overview talk meant to introduce the audience to the topic of algal biofuels. It could be divided into 2 parts: the problem, and the solution. The Problem Professor Mayfield started by making the point that between 1900 and today energy has been a rapidly growing market reaching $5.8 trillion today from just $ 0.4 billion. The future energy market is predicted to double in value within just ten years. There is an interesting correlation between energy use and wealth of a nation. The United States according this chart is one of the wealthiest nations in the world while also using proportionally more resources. The future growt...

Last week, I had the fortune of attending the Algal Biofuels Symposium held by the San Diego Algae Biotechnology Center which was founded by Professor Mayfield and his colleagues. The next few posts will focus on what happened at this symposium. Source: http://notafreemason.files.wordpress.com/2008/01/algae-oil.jpg The introductions were held by Professor Steve Kay, who is the Dean of Biology at the University of California, San Diego. Professor Kay noted that algal research has been steadily rising since the early 1990s again. Since the 2000s the growth curve of algal research resembles that of an early exponential growth as determined by number of publications with the keyword "algae". Key to this resurgence in algal research has been the advance of technologies in molecular biology, sequencing, and bioinformatics. Of note is that there has been an explosion in algal biofuels research since late 2008. The exponential growth exponential growth in algal research coincid...

Introduction I was recently asked why this site is called "Bio-Based Ideas". So I thought I would give a brief answer before leading into today's post. There are several reasons for naming this site the way it is. For one, having been trained as a biologist, I write what I know and am interested in. Naturally, many of the posts discussing ideas come with a biological slant. I wanted to make that clear in the title of the blog. But "bio" also comes from Greek meaning "life". And just as life organically grows and evolves, the posts here are meant to capture the richness of diversity of ideas. Lastly, it is my personal belief that the richness of biological ideas will have an increasing impact on our societies especially in this century. And so today with the last post on directed evolution in mind , I want to discuss: What is the bio-based economy? There are two basic ideas the bio-based economy relies on. 1.) Transition to biobased, renewable r...