Bio-Based Ideas

I just watched this documentary created by people at the Wired Magazine. This documentary conveys some of the challenges our world will need to face by 2050 and presents some inspiring approaches to tackling some of these challenges. Interestingly, in the first part, Professor Jay Kiesling gets a few minutes of face time to talk about synthetic biology and its contribution to the transportation energy field. Enjoy!

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.

Here is an interesting Tech Talk on Algae Pods which has a significant amount of research done already.  

Cover of Science Issue 335. It has been a while since we have done a journal club , and so today I thought I would write about an article I recently read. Adam J. Wargacki, who works in Yasuo Yoshikuni's group, recently published the above titled paper. In light of problems associated with the use of fossil energy sources (cost, scarcity, environmental impact, and geopolitical considerations), the search for new energy sources is starting to become more important. The paper in discussion today proposes that a coupled system consisting of brown macroalgae and engineered bacteria could be used. Of course there are more traditional biofuel feedstock sources such as corn and sugarcane. There a couple of hurdles such as the debate about “food versus fuel” and technical hurdles such as the degradation of lignocellulosic matter that need to be solved. We have previously discussed how microalgaecould get around the difficulties of corn and sugarcane in the production of bioefu...

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

Recently, NPR radio was talking about a plan of how the military plan might become more sustainable and made the point that the plan was still nebulous apart from some general goals. This reminded me that I still wanted to summarize some of the talks from the SD-CAP 2011 meeting I went to earlier this year. The first talk came from the keynote speaker, General Kamin, who was talking about the NAVI’s efforts on reducing the dependence on foreign oil within the NAVI. He started by pointing out that with a large amount of submarines, operational aircraft, and troops, the NAVI is very energy dependent – most of which comes from petroleum. To put things in perspective, the NAVI uses 25% of all the energy within the Department of Defense. The Department of Defense itself uses 93% of all the energy the government is using. Because the price for energy was low historically, efficiency has not been an issue until now. General Kamin went on to highlight that the Navi has increased it...

You may remember that a while ago I blogged about a research group that found a way to produce biogas reactor using the content of a stomachs cow . One of the questions, I had back then was what kinds of bacteria were in the cow's stomach fluids? Today, we'll look at a  massive Science article from January 28 with the title "Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen" from the Rubin Lab with Matthias Hess and Alexander Sczyrba as the primary authors recently hit the science world, and gives us that answer.

I have previously talked about the similarities and differences between the sustainable economy and the bio-based economy . As I am working on completing my PhD in 2011, I have started to look towards the next step. My goal for 2011 is to start a career in the sustainable biotechnology field, and so I have surveyed my options in California. In my survey on this topic, I have found that the sustainable biotechnology companies can be divided into three areas of activity: biofuels, industrial enzymes, and bio-based biochemicals. Perhaps the most visible field area of sustainable biotechnology is the biofuels field given the increased need to develop alternatives to fossil fuels. Because of the large potential market in this area, it may not be too surprising to learn that nearly every company in this field is involved in one form or another. This part will focus on companies that mainly are associated with biofuels development. They are characterized by mostly not having any products on...

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...

I found these news rather intriguing: According to "Forschung Aktuel" [1],  a German-based science radio news show, there is a research group in Germany that is trying to develop an integrated 2-step biogas reactor. Normally, this would not be really that big of a news but what they use as a source for biogas generation and how they do it is very intriguing. In the quest for renewable non-fossil-based resources, cellulose, the sturdy sugar based plant material, is often considered the holy grail for energy generation as it is in this case. The question is how to generate energy efficiently from cellulosic containing material because as mentioned in a previous post , it is difficult to break down cellulose into usable sugar molecules using traditional mechanical and chemical processes. For this reason, research scientists have looked to nature like the gut of termites and other wood-eating insects, and in this case the stomach of the cow for inspiration on how to break down ...

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...

Introduction In my previous posts, I have talked about ways of using different microorganisms to produce different things that are of use to humans. Two specific examples were diesel from fungi, or oils from algae. There are many other examples, some of which I hope to cover in my future posts. At the current time, the main challenge to many of these by-products is that they are not produced at efficiencies and quantities that allow for economical use. So how would you make fungi produce more biodiesel? How would you make the breakdown of cellulose happen faster? How do you increase oil production in algae? Although each of these questions, involves a deep understanding of complex cellular networks, at the base of each of these problems is a protein that carries out a given task. Increasing efficiencies of these proteins can help to increase the yields of the desire products. Today, we will look at one way, how proteins can be "engineered" by asking: What is Directe...

The fact that our overreliance on fossil fuels is quickly draining easily accessible resources is becoming more known in the public. Now there is talk on several scientific and environmental radio shows that warn of declining phosphorus reserves. The concern over a possible phosphorus shortage may seem contradictory to observations of increased algal blooms and eutrophication of inner water streams – a phenomenon where increased chemical nutrients in the environment lead to algal blooms and suffocation of aquatic life with detrimental  consequences to the environment – which at least in part are caused by increased bio-available phosphorus. All this lead me to the question: Is there really a phosphorus shortage? Phosphorus is the 15th element on our periodic table. In nature phosphorus never exists in its elementary form due to its reactivity [1]. Phosphorus is one of the essential elements of life because it is part of many structures in living cells from simple bacteria to c...

It has been a while since the last contribution to this site. Today’s blog entry shall be a summary of a journal article that a couple of friends and I started recently to educate ourselves on topics related to bio-based ideas that are of interest to us. Recently, I came across a general article in the Scientist that talked about biofuels production. The article mentioned integrated biofuel productionpipelines that could include the breakdown of agricultural waste products containing cellulose . Cellulose is a complex sugar, meaning that it consists of long-chains of individual simple sugar units such as glucose . The glucose that is released from the breakdown of cellulose could be used for bioethanol production. But it turns out that cellulose is a very sturdy material that is difficult and energy intensive to break down. One way to reduce the cost of break-down would be to rely on enzymes that are known as biological catalysts. Catalysts can reduce the activation energy which is ...

In the last focus section , we discussed how algae can be used to treat waste waters and mitigate CO2 in the process. Today's post will explore how algae can be used for energy generation. As already mentioned in the last time, biofuels have become very visible as of late due to environmental, economical and geopolitcal reasons. If at the heart of traditional biofuel generation lies in the creation and decomposition of biomass, then it would be easy to substitute corn or other less controversial land-based plants with algae. Although a lot of attention is paid to the use of algae in biofuel generation, and this article also mainly focusses on this aspect, it should be noted that algae can also be used to generate electricity by direct combustion of the biomass. Plans for these kinds of schemes are already on the way in Venice and a few other European locations [1]. Algae and Biofuels What happens to the biomass after it has been created depends on the type of biofuel that is de...

Introduction With prices for crude oil spiking in the recent past, and an unstable Middle East and intensifying effects of climate disruptions, the Obama administration and governments around the world have been promoting the development, and deployment of newer, more sustainable forms of energy generation, amongst which are biofuels . What are Biofuels? At the heart of every hydrocarbon based fuel (gasoline, diesel, kerosene, coal) are anaerobic degradation processes of organic material. For fossil fuels , the source of organic material comes from planctonic life, plants, and animals that lived and died millions of years ago. For biofuels, the source of organic material comes from planctonic life, plants or other sources of much more recent origin. The important concepts to note are: 1.) Building up organic matter removes carbon dioxide from the atmosphere. 2.) Burning hydrocarbon based fuels releases the carbon originally tied up in the form of carbon dioxide. So when we pump up t...