Bio-Based Ideas

Freely-Speaking: A note on end-of-life care of solar panels

2012-01-18T07:30:00.000-08:00

(Source: http://i-solarpanel.yolasite.com/)

Happy 2012 everyone!

A new year means fresh energy, and new goals. With respect to this blog it means more posts of interesting ideas and concepts and perhaps deeper discussions of ideas previously mentioned.

To start the year, I thought I would quickly make a mental note to myself about something I just listened to on "Deutschland Radio - Umwelt und Verbraucher" which translates into "German Radio - the Environment and the Consumer". Side Note: It's interesting that in the US, environmental protection and sustainability are often mentioned in conjunction with energy-independence, and security of the country while in Germany often times environmental protection and protecting the consumer are linked more often.

Anyway, the topic of discussion was what to do with solar panels after their useful time is up. The German and European answer: Come up with legislature that require solar panel manufacturers to take back and recycle an increasing amount of solar panels. This law would apply to all manufacturers including those from other countries.

Why was legislation required?

Apparently, industry was not able to come up with guidelines all would stick to on their own.

What is the rational for this legislation now?

The lifespan of solar panels is about 20-30 years. Some solar panels contain toxic substances (like heavy metals etc.). A take-back and recycling mandate on the manufacturers makes sure that these toxic substances are disposed of in a responsible manner. More importantly though, it ensures that valuable resources are conserved and reintroduced into the value chain rather than having to mine these increasingly rare resources anew. Solar panels are rich sources for silicon, aluminum and glass afterall.

My personal opinion

While in the US, we are still struggling to come up with any CONSISTENT long-term framework, and the discussion of what to do with solar panels at the end of their useful life has note even entered the discussion, I think it's great for a government to be capabble of thinking this far into the future. By blogging about this, I hope to contribute a teeny-tiny bit to a starting discussion of what to do about solar panels after we are done using them here in the US as well.

Solazyme powers first United flight with algae jet fuel

2011-12-03T18:35:00.000-08:00

"Today's historic flight with United marked a significant milestone in the history of aviation, and demonstrated the commercial applicability of our drop-in fuel," said Jonathan Wolfson, CEO, Solazyme. "The U.S. Navy has demonstrated the effectiveness of our fuel in multiple vessels over the past year, and we are honored to be working with industry pioneers such as United and Honeywell's UOP to see this important next step in the commercialization of our renewable fuels."

Solazyme's algae-derived renewable jet fuel, Solajet, was manufactured via Solazyme's proprietary fermentation process and renewable jet fuel processing technology from Honeywell's UOP. Solajet fully complies with the ASTM D7566 specification for Synthetic Paraffinic Kerosene from Hydroprocessed Esters and Fatty Acids, which specifies bio-based fuels intended to be blended with commercial jet fuel (Jet-A).

To date, Solazyme has produced and delivered the largest quantities of microbially-derived advanced biofuels in history. These deliveries include over 375,000 liters of in-specification marine diesel and jet fuel.

(Source: http://www.solazyme.com/media/2011-11-07)

In Other Words | Angela Belcher: Using nature to grow batteries

2011-10-01T00:55:00.000-07:00

Yet another interesting, TED talk!

Freely-Speaking: The Beginning of my Journey into the Bio-based Industry

2011-09-25T10:12:00.000-07:00

Today's blog post is not about any bio-based events, I attended. It's not about any great ideas, or moving news either. This time I thought I would just briefly touch upon what happened in the last few weeks.

For me the end of graduate school was also accompanied by some anxiety of what would come afterwards. But I also realized that it is an opportunity to make changes for the better in that I have a chance again to pick a direction I like. And so I searched every possibility that would bring me closer to starting a career in the bio-based biotechnology industry. The result? I am very happy to have been selected for a Molecular Biology internship for the next 3-4 months (until the end of November and the beginning of December)! I was told that quite a few people interviewed for this position but did not get it. Not knowing anyone at Amyris previously, I consider myself very lucky. Having been picked for this internship out of all the people is also both a humbling experience, and one associated with a bit of pressure to perform up to the expectations set. This being an internship, of course, is not a permanent situation. Talking to some friends and acquaintances, I have often received some hesitations of why I would want to do an internship after a PhD. After two weeks, I can say that instead of waiting for more permanent opportunities to arise, this was THE BEST decision, I have made so far.

The company I am interning for is called Amyris (which I had summarized before). They are known for making Artimisinin, an anti-malarial drug, more cheaply by reprogramming yeast instead of extracting that substance from rare plants. Amyris is also a renewable energy, and chemicals company. So this is the perfect match to learn the thought-processes and work-flow of a dynamically growing biotechnology company, and it's my opportunity to gain some real and meaningful industrial experience. A friend of mine said that the transition to industry from academia is quite drastic. After two weeks, I can confirm what he was saying. While things in grad school seem much more artisan (NOT a bad thing), in industry everything is more stream-lined. In grad school, if I wanted to run a gel, I made the gel. Here, at Amyris, every possible reagent and gel and everything is already made. You just need to do the experiment. With this stream-lining, of course come much higher expectations in terms of not just working hard, but getting most impactful actions and results in as short a time as possible. Make everything count! And so experiments need to scaled-up. Waiting times need to be minimized and filled with other meaningful actions. This is another reason, I am happy to have started the internship at Amyris rather than taking a bit more time to obtain an academic post-doc. Now this decision will not be right for everyone, but since I am sure about building up a career in industry, I think that for me this was the right decision.

The work culture itself at Amyris is quite amazing! I once visited Google, and have to say that in some regards it is very similar. People here work hard, but also know how to enjoy themselves. Everyone here is very motivated. People constantly talk to each other, and there is team-work all around. Although the background of everyone here is very diverse (people coming from all kinds of fields like infectious diseases or pharmaceuticals), I think what unites all people working at this company is the desire to make a difference - a relatively large, and immediate impact for the sake of our children's future. My Tai Chi teacher also told the students once that if you want to change in a certain direction, you should surround yourself with people of the same energy. I think I can do exactly that at Amyris. The people who work on the same project with me are all very knowledgeable, and smart. But in addition, they are also just down-to-earth and cool people with lots of patience to answer all my questions. All this makes learning and working here extremely enjoyable.

My supervisor also has high expectations - that at least is what my first impressions are and what I have heard. Thinking of the lessons my Tai Chi teacher gave me, I have realized that the lessons he taught me also apply here: Change brings challenge, challenge brings growth and, growth leads to success. In this light, I am embracing the opportunity that was given to me with this internship, and will work my butts off to rise to the challenge!

What will the future hold? Even my wife's best friend's mom could not foresee the future. So I guess I will worry about it when I get there :-)

Meanwhile, check back here occasionally, as I will continue to keep this site active!

Recap: SD-CAP 2011 - ”Fueling the Navy of Tomorrow – Moving Away from Petroleum" (Keynote) presented by General Kamin

2011-09-11T19:45:00.000-07:00

Recently, NPR radio was talking about a plan of how themilitary plan might become more sustainable and made the point that the planwas still nebulous apart from some general goals. This reminded me that I stillwanted to summarize some of the talks from the SD-CAP 2011 meeting I went toearlier 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 foreignoil within the NAVI.

He started by pointing out that with a large amount ofsubmarines, operational aircraft, and troops, the NAVI is very energy dependent– most of which comes from petroleum. To put things in perspective, the NAVIuses 25% of all the energy within the Department of Defense. The Department ofDefense 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 highlightthat the Navi has increased its budget for fuel from $ 1 billion to $ 5 billionlargely due to price increases, and notes that when prices increase in such anunexpected way, money spent on fuels cannot be used for other important issuessuch as maintenance, and troop security. The trends of increasing oil priceswill only continue in the future. Furthermore, protection of energytransporters is also costly and dangerous for the troops protecting theseconvoys. Thus, he concludes, it is a national security interest to find alternativesto oil.

General Kamin shared that within the Navy there is atransition in thought going on: Energy is no longer considered a commodity buta precious strategic resource. So as part of the Navy’s energy vision, it isseeking to reduce petroleum use by 50% which is approximately equal to 8million barrels by 2020.

To do so, the Navy is both seeking to reduce fuelconsumption, and also increase the use of biofuels. He illustrated a fewexamples of prototype projects that reflect the will of the Navy to implementthese changes, among them a prototype fleet of hybrid boats, and other hybridvehicles, as well as a prototype fleet that is experimenting with the use ofalgal fuel sources.

General Kamin then outlined more technical requirements andthe beaurocratic process of steps biofuel providers must go through to gettheir fuel certified by the NAVI so that the NAVI can start sourcing them.

Whether these prototypes that the general talked about ornot reflect a unified strategy to move the military of fossil fuels issubstantial or not in real terms, I think it is significant to note that thefact that generals are publicly talking about such issues reflects a change inattitude of what fossil fuels mean for the future of the military. Whether oneagrees on global warming or not, whether one agrees on the economic validity ofsustainability or not, it is interesting to observe that the military came to thesame conclusion that getting of the addiction to fossil fuels is something thatneeds to be addressed by thinking in terms of long-term safety of our nation.

In Other Words: Informational Videos - Fiorenzo Omenetto: Silk, the ancient material of the future

2011-08-04T11:44:00.000-07:00

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.

Freely-Speaking: A Bio-based Technique for Removing Bacteria

2011-07-31T16:19:00.000-07:00

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 bacteria from water treatment plants could theoretically make it back into the human intestines again if exposed to them (swimming in water streams, ingestion of fruits that were exposed to this water etc.). It is of course possible to try to remove bacteria from the water through several means (UV, chlorine, filtration), but these techniques tend to be rather expensive.

Within this framework, Forschung-Aktuell covered the research of Dr. Wolfgang Eichler, who proposed another approach: using ciliates, (single-celled eukaryotic cells that eat bacteria) to reduce the bacterial count of water coming out of water treatment plants. In initial tests under controlled conditions, his research group has found that a selected strain of ciliates was capable of reducing the count of E. coli bacteria by 25% per hour.

You can read the abstract of this research presented just recently here.

Freely-Speaking: Quick note on bio-based antennaes

2011-07-16T11:50:00.000-07:00

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 words, what they have created are tunable bio-based antennaes which could be used for more efficient usage of the available light spectrum in future solar panel designs as another blog at IEEE noted. Cool technology!

Freely Speaking: Human Cells Become Living Laser

2011-06-14T09:31:00.000-07:00

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 "Light Amplification by Stimulated Emission or Radiation". 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 not replace the entire traditional laser setup. It just replaces one component of the laser - the gain medium.

Interesting but what is this useful for?

The authors imagine possible uses for medical diagnostics or ways to study the state of individual cells. Purely speculating here, but I wonder if the property of these cells could be used somehow to further increase the spectrum and penetration of the usable light spectrum into photobioreactors growing photosynthetic organisms to increase efficiencies and eliminate dead spots. Like with the original invention of the laser, individual uses were hard to predict at the time. Nowadays, so many applications rely on lasers. Will the same thing be true for "living" or "bio-based" lasers?

Source:

You can read a commentary here: Nature News Commentary
The original article can be obtained here (subscription required): Original Nature Photonics Journal Article

In Other Words: Inspirational Videos - "Suzanne Lee: Grow your own clothes"

2011-06-12T12:42:00.000-07:00

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.

Freely Speaking: What is an Artificial Leaf?

2011-05-30T21:39:00.000-07:00

It's been a while again since I last posted here. Writing my thesis and preparing for the actual defense in July are taking most of my time. However, I wanted to at least share an interesting idea I came across in the last couple of months before this month is over.

And so today, I'll write about the artificial leaf which Professor Nocera at MIT was researching. It's been all over the science news: an alloy made of nickel and cobalt acts as a catalyst to split water into hydrogen and oxygen similar to what plant leafs do when they perform photosynthesis.

After the coolness of the words "artificial leafs" wore off, I started to wonder what is so special about an artificial leaf. After all, doesn't an artificial leaf just do electrolysis? Couldn't I just achieve the same by connecting solar panels to a container with water and two electrodes?

Apparently, the answer is yes and no. By applying a current to water, electrolysis could indeed be performed producing oxygen and hydrogen. The current produced could even come from the solar panels. However, Nocera's artificial leafs work slightly differently:

First: The nickel-cobalt alloy with the catalyst, can directly break water into hydrogen and oxygen without the need for any apparent electrodes. It's "wireless" electrolysis if you will.

Second: It's all about efficiencies. While photovoltaics could be used to split water, by itself this is not a very efficient process. The secret is in the catalyst which lowers the activation energy of splitting water sufficiently to make photo-catalysis (in this case we are breaking things down) feasible.

The Implications

One of the weaknesses of using photovoltaics is that electricity generation drops to 0 when there is no sun. Artificial leafs could fill this gap by storying part of the energy captured during the day in form of hydrogen and oxygen. In the evening, electricity could be generated again from the stored energy. Nocera has also stated that he hopes these materials are cheap enough so that people in 3rd world countries could easily and cheaply obtain artificial leaves that could be used to power a light source at night.

All in all, very cool research and technology. I will try to keep my eye on this for the future.

Sources:
http://news.cnet.com/8301-11128_3-20047814-54.html
http://www.eurekalert.org/pub_releases/2011-03/acs-dot031811.php

In Other Words: Informational Videos - "How to make things cleaner"

2011-04-16T13:52:00.000-07:00

I recently watched another great NOVA episode on "How to make things cleaner". This is a great episode containing many ideas that could fall into one of our often discussed "bio-based" ideas. It's a bit long, but totally worth it, so bring some time!

Watch the full episode. See more NOVA.

Recap: AWIS Biofuels Panel Discussion, March 2011

2011-04-08T19:03:00.000-07:00

I recently attended a panel discussion on career opportunities in the Biofuels business sponsored by the Los Angeles Chapter of AWIS. There were 2 representatives from Ceres, and 2 representatives from Sapphire Energy. The following are general meeting notes I took of that panel discussion.

First Richard Hamilton, President of CEO of Ceres, spoke. He started by outlining the challenges of the current fossil fuels. Oil prices are increasing because of increased demand from emerging countries (including India and China), reduced supply as an increasing number of known oil reserves have peaked in their oil production and not enough new sources start production. Furthermore, increased regulation due to environmental concerns and decreased political stability in key oil producing regions all contribute to the increasing oil price. Lastly, Dr. Hamilton pointed out that oil prices are also increasing as the dollar becomes more and more devalued.

When we consider that oil is also one of the biggest sources of our trade imbalance (something around 54%), a strong case can be made to reorient ourselves in our energy policy.

Dr. Hamilton pointed out that although President Obama was advocating for “clean electrons” (solar, wind, geothermal), carbon-based energy carriers should not be neglected because “electrons are not oil” (Personal Note: This was just to emphasize the easy confusion between clean electricity and cleaner, more sustainable fuels, as President Obama also included furthering biofuel development in his agenda.) In other words, while carbon-based fuels have a very high stored energy potential, electricity is a form of energy that must be used instantly. As a side remark, batteries of course exist, but currently the technology for storing a lot of electricity in a light and affordable battery does not exist on a large-production scale. Furthermore, oil is not just used for heating and transportation. Even if we, according to some Toyota projection, started to sell 100% hybrids in 2012, and 50% plug-in hybrids in 2013, we would not be able to become energy independent immediately. The increase in oil dependency would not increase quickly anymore and possibly even slightly fall, but the oil dependency remains. The reason for this is that unlike light transportation, heavy load transportation, air and ship transportation cannot be replaced with electric engines in the foreseeable future. Additionally, many products we use nowadays were derived from oil. Merely changing to electric transportation will not deal with these issues.

All these factors lead to the conclusion that the development of biofuels no matter what the source is becomes necessary. As he put it:”Every molecule of carbon is needed” to face the challenges coming from decrease abundance of fossil fuels.

Dr. Hamilton then proceeded to address a common concern: that energy crops are competing with food agriculture. His case against the energy crop “myth” was as followed:

Agriculture is not operating at its peak efficiency. Energy crops could be grown without competition to food crops if these inefficiencies were addressed. He mentioned CRPs (paying farmers in poor countries not to use their farm land) as one example of inefficiencies. (Personal Note: This argument is partially based on the assumption that increased efficiencies has no negative side-effects.)
Agriculture is not static either. By this he means that crop yields over the last thousand and especially last century have increased exponentially. He concluded that with research and development yields can still further be improved. (Personal Note: The graph seemed to suggest that crop yields will continue to grow at an exponential rate. Infinite exponential growth is very unlikely but the question is how long an exponential growth in yields can be maintained with continued research and development.)

As a result, Dr. Hamilton concluded that 10% of agricultural land can provide the bioenergy source of the world without competition to food agriculture. He claimed that the increase in basic food commodities is not due to energy crops, but can rather be attributed to increases in fossil fuels, and fertilizer prices and proceeded to show us a correlational chart which correlated the price of oil with the price of common food commodities. He then briefly touched on the two products that Ceres is marketing to meet the demand: sorghum and switchgrass. With this, Dr. Hamilton made the case for any form of biofuels setting up the stage for the other three talks.

Dr. Julissa Sosa, who is a Scientist, talked about the research that she is doing at Ceres. These include screening and selecting for grass strains that are hardier, that is, they can grow in more salty areas, or can grow in soils contaminated with heavy metals such as aluminum. Aluminum in particular is toxic to normal plants because it inhibits root growth, which is important for physical support through anchorage and access to water and nutrients. The rationale behind her research was that plants that can grow on marginal lands can be cheaply grown without competing with more valuable agricultural land.

Next Tracy Duong, a Scientist at Sapphire Energy, introduced her company. With an introduction that was very similar to Dr. Hamilton’s, Sapphire Energies justified its existence because they believe algae provide a more efficient platform for the production of biofuels. Notably, Sapphire Energies is rapidly moving towards commercialization. They are in the process of building a pilot algal biofuels plant which includes growth, and harvesting of “green crude”, which they hope to feed into existing refinery processes.

Lastly, Dr. Yan Poon, who is both a Section leader and Co-founder of Sapphire Energy, spoke in broad strokes of some of the research going on at Sapphire Energies. Briefly, they use insertional mutagenesis combined with selectional screens, as well as competition assays to select for algal strains that have properties they are looking for (salt and herbicide resistance for protection, easy settling (called bio-flocculation) for more efficient harvesting, high oil content or fatty acids for increased yields).

Action Plan to deal with global warming and climate change

2011-03-26T21:59:00.000-07:00

Goals:
1. Adapt and deal with symptoms (preparation, preservation, plantation, energy saving, etc)
2. Combat causes of global warming
2.1. Long-term impact (cut CO₂ emissions and remove CO₂ from atmosphere and oceans) ^(C,D)
2.2. Short-term impact
2.2.1. Reflect more sunlight back into space ^(D)
2.2.2. Reduce pollutants other than CO₂
2.2.2.1. Reduce emissions of chemical gases such as HFC, PFC, SF_6,, halon, CFC and HCFC ^(A)
2.2.2.2. Reduce emissions of CH₄, N²O, BC, CO, NO_x and VOC ^(B,C,E)
2.2.2.3. Produce extra OH ^(D)

This can be best achieved through:

A.		Protocols (Kyoto, Montreal, etc), standards and deposits (refunded at collection) on products containing inorganic pollutants
		Fees on nitrogen fertilizers and livestock products (where farmed) to fund local application of biochar
C.		Fees on burning fuel (where burned) to fund clean local alternatives (incl. EVs, solar cookers, WWS energy)
D.		Geoengineering (adding lime to seawater and aerosols to the atmosphere, carbon air capture, using UV light to stimulate methane oxidation, cloud brightening, etc; for more see the geoengineering group)
E.		Organic waste handling standards (e.g. the UNEP-proposed ban of open field burning of agricultural waste)

Color Use:

Blue		Goals
Purple		Inorganic waste policies (cycle A)
Green		Land use and organic waste policies (cycles B & E)
Orange		Geoengineering & energy-related policies (cycles C & D)
——>		Feebate policies

Acronyms and Abbreviations
BC	black carbon (or soot)
CFC	chlorofluorocarbon
CH₄	methane (or natural gas)
CO	carbon monoxide
CO₂	carbon dioxide
EV	electric vehicle
HFC	hydrofluorocarbon also known as freon, with the subclass HCFC
HCFC	hydrochlorofluorocarbon
H₂O₂	HOOH or hydrogen peroxide
NO	nitrogen monoxide (commonly known as nitric oxide)
NO₂	nitrogen dioxide
NO_X	nitrogen oxides (NO and NO₂, which cause O₃, smog and acid rain)
N²O	nitrous oxide
O₃	ozone
OH	hydroxyl
PFC	perfluorocarbon
SF₆	sulphur hexafluoride
UNEP	United Nations Environment Programme
VOC	volatile organic compound include CFCs, styrene, limonene and formaldehyde
WWS	WWS energy or Wind, Water and Solar Energy (water includes hydro, wave, tidal and geothermal)

Related Posts

Goals
Ten Dangers of Global Warming
America can win the clean energy race

A. Protocols, standards and deposit programs
A national bottle recycling bill
Green Refrigerators and Air Conditioners

B. Fees on nitrogen fertilizers and livestock products, funding biochar
Biochar
Afforestation - bringing life into the deserts
Save the Rainforest
Fees on Livestock to fund Biochar

C. Fees on burning fuel, funding clean local energy programs
Electric Vehicles - Frequently Asked Questions
SuperB Grid

D. Geoengineering
The Threat of Methane Release from Permafrost and Clathrates
Funding of Carbon Air Capture
Open letter on Arctic sea ice loss

E. Organic waste handling standards
Algae Bags

——>

Feebate policies

Feebates

Further reading
Posts at Gather

In Other Words: Informational Videos - "How Smart Are Animals?"

2011-03-18T08:18:00.000-07:00

On a slightly different angle of the bio-based theme, today's video pick is on "How smart animals are?", a 1 hour video from PBS' NOVAScience, which I have recently become a real fan of.

Watch the full episode. See more NOVA scienceNOW.

In Other Words: Inspirational Videos - "PBS Profile: Jay Kiesling"

2011-03-05T17:28:00.000-08:00

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 the entire American media landscape. A thriving democracy depends on a well-educated and informed general public, and so the services that public media provide, in my opinion, represent a rare beacon of light in support of our democracy in the ocean of sensationalist eye witness news reporting and opinionated quasi news shows on the major cable networks (Disclaimer: I don't think highly of the current quality of news coverage provided by most of the current US cable news outlets.). Right now public media (both radio and broadcast) are having their spring membership drive. No matter where you stand on the debate on whether to help fund public media federally, contributions from individuals like yourself are even more important this time around. And so, with the risk of sounding just like a member drive spokes person, I hope that you will consider doing the right thing.Thank you!

Watch the full episode. See more NOVA scienceNOW.

Journal Club:"Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen"

2011-02-20T12:00:00.000-08:00

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.

What did they do?

Image of Cow with Fistula. Source: Scientific American

The research group figured out a way to create a sealable opening into a cows stomach. They used this opening to insert bags containing switch grass (a target for the production of second generation biofuels) into the stomach of the cow which they were also able to remove after a given amount of time. They then broadly asked what kinds of bacteria are living in the cow rumen by sequencing the DNA extracted from the bags which they incubated in the cow's stomach. Because DNA pieces obtained through the current massively parallel sequencing technologies produce rather short fragments, it is initially very hard to assign a given piece of DNA to a given bacterial genome. Thus, the DNA soup obtained from this massive sequencing effort is called a metagenome. Although accurate assignment may not be possible with metagenomic analysis, there are still many questions one can ask.

The motivation behind the sequencing effort was to identify new possible enzymes that are capable of breaking down different forms of carbohydrates (cellulose in particular). They group was able to find many, many candidates. They tested a subset of these enzymes (90 candidates), and found that 53 of those enzyme candidates indeed had some sort of activity in their panel of 9 different carbohydrates - a very significant enrichment for proteins with carbohydrate activity. Although other papers have identified a slew of these enzymes already, it should be noted that their methologies allowed for identification of a whole set of new candidates by not relying on sequence identity but more so on the presence of certain typical functional domains.

Lastly, it should be again noted that metagenomics is messy because it is hard to tell which of the billions of short DNA sequencing reads belong to which species. Yet most remarkably, the research group was able to assemble and propose 446 draft genomes corresponding to 446 proposed new bacterial species. The group was able to do so because the coverage (how many times a particular region of the genome is captured by a snippet of DNA) was very high (53x). High coverage leads to a high likely hood that fragments overlap. These overlaps were exploited to assemble "scaffold assemblies" (essentially a larger continuous piece of DNA). Using something called TNF (tetranucleotide frequencies) and read coverage as a measure of abundance, the group was able to then bin individual contigs which is how they came up with the number 446. This number likely is an overall underestimation of the actual number of different bacterial species out there because there is a bias against rare species.

Why is this article important?

Firstly, there is a lot of technical detail hidden in this article that suggest a way to approach metagenomic analysis of such scale. Secondly, this article is a treasure box full of new enzymes that can be used to make biofuels production more efficient and thus more affordable. I suspect that any biofuels company out there will probably study this article in great detail. And lastly, the ability to culture a bacterial species had previously been a condition to study it including trying to sequence its genome. In this case, 446 brand new draft genome sequences were inferred from bacteria that had never been cultured before!

On a personal observational note, I find the recent trend in the articles that appeared in Nature and Science including our previous journal club in which we looked at the ability of two bacterial species to pass off electrons from one to another interesting because it reflects a transition in the field in which the importance of biological research is expanding out to other areas not limited to biomedical research. Exciting times are ahead of us!

In Other Words: "Testimony Before the Senate Subcommittee on Green Jobs and the New Economy"

2011-02-18T10:46:00.000-08:00

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 believe that these crises bring enormous opportunity, but only if the United States decides to get off the bench and join the green jobs race already being run by most of the other developed countries in the world. I am glad to share my and the Center for American Progress Action Fund’s perspective on green jobs and the global economy, and I look forward to your comments and questions.

In my testimony I will discuss the global clean energy marketplace, and specifically the work other countries are doing to become innovation leaders in the new green economy. As a contrast, I will point out where the United States has failed to pass policies and make investments in the “building blocks of innovation” that made us leaders in prior economic transformations, including our infrastructure, our workforce, our research and development capabilities, and our manufacturing sector. I will conclude by recommending several specific steps this Congress and administration can take to put America back on track to lead the clean tech revolution, just as we led the Industrial and high tech revolutions that came before. These recommendations include:
Stabilizing the market for green technologies by passing a national Clean Energy Standard
Crafting finance policies to make more public and private capital available to innovators to invent, commercialize, and produce green technologies
Modernizing our basic infrastructure to allow businesses to more effectively collaborate and compete in domestic and international markets
Investing more in science and math education and in workforce training to ensure we have workers able to participate in the technology-driven economy of the present and future
Promoting international trade policies that ensure access to foreign markets, and the free flow of goods, services, knowledge, and capital across borders.
Providing incentives, through competitions and other “race to the top” strategies, to lift up innovative energy solutions at the local, state, and regional level
Green jobs and the green economy
Amidst the Great Recession that swept the United States in 2007 and the high unemployment that we are still experiencing today, the set of industries and occupations often referred to as “green jobs” continues to hold the key to unlocking a better, stronger, clean energy economy for the country. And not only do these industries have the potential to employ many currently un- and underemployed workers across a range of skills and occupations, they can also help catapult the United States into a leadership position in one of the fastest growing sectors in today’s economy.
I want to emphasize that the phrase “green jobs” stands for much more than the jobs themselves—it also stands for a whole new set of industries and investments that will make us more competitive and our economy more sustainable. We are currently in the process of switching our entire energy infrastructure over from capital-intensive, risky, and often highly polluting energy sources to clean, labor intensive clean energy sources.
This is an economic transformation on the scale of the transition from horse-drawn carriages to engine-driven vehicles, or the Industrial Revolution, or the more recent high-tech revolution. In each of those eras, we talked about economic transformation, competitiveness, and overall job growth. We talked about the need to transition away from industries on the decline into the industries of the future. We did not sit around counting exactly how many jobs might be lost in agriculture if people moved to the cities to work in factories, or how many blacksmiths might be out of work with the advent of the automobile.
We saw these as transformative moments in American history, where we had the chance to move forward toward a more advanced age defined by stronger industries, better infrastructure, and a steadily growing middle class. And in fact, in each of these revolutions we saw workers applying current skills to new industries—blacksmiths using welding expertise to become auto mechanics, for example—along with new workers, especially women and immigrants, finding opportunities where before there had been none. Many of these workers ultimately enjoyed higher wages, longer-term job prospects, and a shot at the middle class as a result.
The move to a greener economy brings additional value in that it is focused on making the United States a more effective energy consumer, which ultimately will make us more productive and efficient. As we invent new renewable energy systems and energy efficiency improvements, we will apply these to our own businesses and industrial processes, making the U.S. economy run more smoothly with fewer dollars invested in energy consumption. Our energy bills will be lower and our productivity greater as a result. In this way, “greening the economy” will create benefits that go far beyond the individual sectors and occupations included in most definitions of “green jobs.”
The green jobs revolution has the potential to move us into yet another stage of American leadership, with the huge added benefit of combating the climate change that threatens not only this country, but the entire planet. But the potential will only become reality through political leadership and progressive action.
Competing with other nations for global leadership: Is the United States falling behind?
The global clean-tech market is expected to expand to at least $2.3 trillion by 2020, and America must compete for a piece of this pie. To compete in the global clean energy race, America must take a page from China’s playbook and begin to invest in the building blocks of innovation, like education and worker training, research and manufacturing, and infrastructure—the same building blocks that brought America to global leadership in past economic transformations.
The World Economic Forum, in its monumental "Global Competitiveness Report 2010-2011," underscores the importance of innovation as the basis for long-term economic growth:
Although substantial gains can be obtained by improving institutions, building infrastructure, reducing macroeconomic instability, or improving human capital, all these factors eventually seem to run into diminishing returns. The same is true for the efficiency of the labor, financial, and goods markets. In the long run, standards of living can be enhanced only by technological innovation. Innovation is particularly important for economies as they approach the frontiers of knowledge and the possibility of integrating and adapting exogenous, [or imported,] technologies tends to disappear.
We are bound by the reality that to be competitive in the 21st century global economy, we have to innovate. Across the globe, developed and developing countries are realizing what economists have known for years—that technological innovation, more than any other factor, fuels long-term economic competitiveness and growth, and that innovation in turn requires a robust and well-integrated foundation of education, research, and infrastructure.
Yet we are failing to take these lessons to heart.
In the United States, nondefense R&D spending as a percentage of all discretionary government spending has fallen from a high of 25 percent in the mid-1960s at the height of the Apollo space program, to between 12 percent and 13 percent since the early 1980s.
And investment in clean energy R&D is even further behind. Venture Capitalist John Doerr, an early investor in Google Inc. and other companies, worries that we are failing badly behind in the clean energy race because investments in R&D are completely inadequate to drive innovation and growth:
America spends only about $5 billion—about half a percent—per year on new energy R&D…Sadly, America spends more on potato chips than we do on our new energy R&D.
We have also fallen behind in providing investments for the stages of innovation beyond early-stage inventions. America still supports our national laboratories—though we will see whether the labs can emerge intact from the current budget battle—but we fall down on investing in turning these inventions into commercializable products that can in turn become part of an American export market. An essential element of innovation and competition is to nurture new technologies so that they can actually be built and commercialized. Many inventions require continued investment across the technology innovation cycle: from invention at the federal labs and publicly sponsored universities, to public-private partnerships aimed at commercializing and licensing new technologies, to technical assistance to make our manufacturers the most advanced and efficient in the world, and finally to deployment to bring these technologies to scale.
In particular, the link between innovation and manufacturing is an important one.
We all know that the U.S. manufacturing sector has experienced a long-term decline. The U.S. manufacturing capacity utilization rate hit a near all-time low of 65 percent last June. Overall, manufacturing now just makes up 12 percent of U.S. GDP, down from 28.3 percent at its high point in 1953. As American firms close their doors and investments increasingly flow to other countries, we need to amp up our game to remain competitive.
Some in Washington have intimated that the manufacturing sector is no longer necessary to American global leadership—that we can just as easily invent here and manufacture elsewhere without losing any competitive advantage. But research shows that the manufacturing sector, especially the advanced manufacturing industries that characterize clean tech manufacturing, is actually critical if America wants to stay innovative and globally competitive.
It turns out that it really does matter to our global leadership where our manufacturing jobs are located. According to Harvard economist Gary Pisano, when manufacturing moves overseas, America not only loses solid middle-class jobs and production prowess; we also lose the process innovation that comes from co-locating R&D, design, engineering and manufacturing. Pisano calls this combination of related skills and industries the “industrial commons.” He writes, “In addition to undermining the ability of the United States to manufacture high-tech products, the erosion of the industrial commons has seriously damaged the country’s ability to invent new ones.”
The upshot is that if we lose our ability to make things, we may well also lose our ability to invent them. Though it is difficult to measure the precise impact advanced manufacturing has on innovation, we know anecdotally that if we cede production on a process invented in the United States, we may lose future iterations of innovation in that process.
Solar panels are one example: invented in the United States at Bell Labs in 1954, production of solar PV panels has moved largely overseas (China is currently the world’s largest producer), and most new innovations in panel production, such as process improvements that make the panels far more powerful by altering their electrical properties, are happening outside the United States. This is less true for non-panel innovations, such as the holographic solar applications pioneered by small start-ups in Arizona and New York, possibly because these new innovations are still cutting edge and not yet in commercial production at any real scale. Once these technologies do scale up, however, they too may be produced and improved overseas.
One industry where the spatial relationship between manufacturing and innovation has actually been tracked and measured using empirical data is the optoelectronic industry (for example, lasers and fiberoptic telecommunications). In a recent set of studies, Carnegie Mellon engineering professor Erica Fuchs used a combination of simulation modeling and empirical data to demonstrate the impact of offshoring production on technological innovation. What she found was that when optoelectronic firms offshored production of their original designs to, for instance, Asia, they tended to produce those initial designs cheaply and efficiently. However, when these firms then began work on new and improved designs, they tended to lose valuable time and knowledge if their operations were offshore. The firms she studied were faced with a choice: whether to offshore their production and save labor and materials costs—often the most efficient solution in the short-term—or to take a longer-term view, keep emerging design and production domestic, and push forward new technologies that might keep them more competitive in the long run.
As Fuchs and others have pointed out, the workforce skills associated with these jobs are also at risk of moving overseas when advanced manufacturing migrates. That’s a problem for the United States for two reasons. First, it means we lose manufacturing jobs here, which are some of the best jobs for middle-skill American workers—those who have a high school education but lack a four-year college degree. These workers make up fully two-thirds of America’s workforce. They should not be left behind.
But it also means we lose actual skills, so that we are at risk of having to import workers into trades facing labor shortages due to the lack of trained, skilled workers in some critical industries. These range from engineering and science-based occupations, to trades such as machining, welding, and pipefitting. Maintaining this skill base in the United States is critical for our future competitiveness, but it is also essential if we are to keep our lights on and electricity flowing through the transmission grid. Fully half of America’s utility workforce is expected to retire in the next decade.
Other nations are not waiting around for America to act
America may be hesitant to throw itself into green jobs growth—the great economic engine of this century—but other countries are not. Countries such as China and Germany are now investing in many of the building blocks of innovation-driven economic growth that the United States has all but abandoned over the past several decades, and are focusing on clean tech industries as a critical part of their economic growth strategies. In a recent Center for American Progress report “Rising to the Challenge,” I and my co-authors argue that China in particular is actively and methodically building up the basic foundations for future economic growth while also ensuring a market for its current and future products and services at home and abroad. Commerce Secretary Gary Locke reports that China invests almost $12 billion monthly into its renewable-energy sector: “They’re doing this because they really want to be the world’s supplier of clean energy and they recognize this will support millions of jobs.”
In 2008, China’s gross national expenditure on research and development stood at roughly $66 billion, or about 1.5 percent of China’s gross domestic product. This is the highest investment level among developing economies as a percent of their domestic economy and ranks China fourth in the world in overall R&D spending behind the United States, Japan, and Germany.
Compounding this imbalance is that some of America’s political leaders seem intent on crippling us before we have even fully entered the global green jobs race. Just this week, the House Republican caucus put out a proposed spending bill for the remainder of fiscal year 2011 that waves the yellow caution flag that these legislators want to slow down—if not outright halt—the promise of America’s green jobs revolution and all the ensuing companies and jobs that would create. The proposed budget would slash clean-tech and energy investments by nearly 30 percent, devastating this growing but immature industry that struggled during the Great Recession. It would also dramatically disinvest in the solar, wind, wave, geothermal, and other renewable technologies that enabled the United States to get back in the clean energy race, and would cut funds to technical assistance to manufacturers and to job training programs working to prepare unemployed job seekers for the clean tech industries of the future.
The decision not to invest in the green economy comes at a cost. Already we have seen cutting-edge solar power manufacturing companies begin to close their doors, either permanently or to move to other countries with strong and dedicated clean energy markets. Evergreen Solar Inc., for example, recently announced plans to close its Massachusetts plant to put more funds into solar panel manufacturing in China. The company followed on the heels of SpectraWatt Inc. in New York and Solyndra Inc. in California closing some of their facilities. As General Electric Co.’s chairman and chief executive Jeff Immelt said at last year’s ARPA-E summit, those countries with strong demand for renewable energy products will naturally pull these companies into their borders because “innovation and supply chain strength gets developed where the demand is the greatest.”
Similarly, wind manufacturers in Iowa, once a state leader in this industry, have begun to lay off workers as new orders fail to materialize. Leading global financier Deutsche Bank decided to move billions of investment dollars out of the U.S. clean energy market, and into China and Europe as soon as it was clear there would be no comprehensive climate and energy legislation coming out of the 111th Congress. China and our other economic competitors in Asia, Europe, and emerging markets are not waiting for America to regroup.
All this points to one key question: Do we really want to be in the business of inventing the green technologies of the future, only to end up buying those technologies back from countries that have successfully commercialized, manufactured, and exported those technologies—and come up with successive waves of innovation that they can then also sell back to the United States? Do we want to be the world’s great clean technology consumer, while the rest of the world prospers? Is this the way to strengthen the American economy?
A lack of national leadership, but some hope from America’s cities and states
Contrary to critics intent on maintaining the carbon-intensive, fossil-fuel dependent status quo, we know that investing in the green economy does produce results, and that these investments are critical if America is to get back on the path to global leadership.
The evidence is ample. The American Recovery and Reinvestment Act of 2009, the largest single domestic investment in clean energy in U.S. history, jumpstarted our economy, saving and creating millions of jobs and providing successful clean energy incentives to spur business investment and help consumers lower their electricity bills. The Council of Economic Advisors’ recent quarterly report found that “the clean energy provisions of ARRA alone have already saved or created 63,000 jobs and are expected to create more than 700,000 by 2012.”
But ARRA funding is coming to an end, and businesses are beginning to worry that the United States will not make any further real commitment to moving America toward the green economic transformation already happening throughout the rest of the developed world.
Luckily our states and cities have surged ahead, and there is evidence at these sub-national levels of the great strides that our country can make when we harness our innovative and entrepreneurial spirit, along with our skilled workforce, to tackle the green jobs challenge. Because of these state and local efforts, such as Renewable Electricity Standards in place in 30 states, multiple building codes and energy efficiency investments, and creative “cluster-based” approaches combining research and development with regionally specific natural resources and competitive industries, the last decade has seen significant green jobs growth relative to the economy as a whole. A PEW Charitable Trusts study found that the number of green jobs in America grew about 2.5 times faster than job growth as a whole, growing 9.1 percent from 1998-2007.
California’s green economy in particular has shown high returns on investment. In the recent report “Many Shades of Green,” by the California-based nonprofit Next 10, researchers found using state employment data that from 2008 to 2009, California’s “core green economy” grew over three times faster than its traditional ‘brown economy.’ The report found that “between 1995 to 2008, green businesses increased 45 percent, and green jobs grew 36 percent while total jobs in the state grew only 13 percent.” Green manufacturing jobs alone grew by 10 percent in 2009 in California. Partly as a result of this expansion, 24 percent of green jobs were in manufacturing in California as opposed to 11 percent for the economy as a whole. And in November 2010, California voters overwhelmingly voted to continue growing this green economy, defeating the Big Oil-funded Proposition 23, which would have indefinitely stalled implementation of California’s landmark Global Warming Solutions Act, A.B. 32.
Michigan, too, is a striking example of how the clean energy economy can bring opportunity to one of the hardest hit regions of the U.S. In Michigan, total private employment dropped 5.4 percent from 2005 to 2008, while during the same period employment increased by 7.7 percent among 358 green-related firms counted in the study. As Michigan continues to struggle with devastatingly high unemployment rates, the green jobs sector remains both a growing source of jobs and a bright spot on the horizon.
In former subcommittee member Senator Voinovich’s state of Ohio, new Governor Kasich recently reversed his campaign promise to roll back the state’s Renewable Energy Standard after multiple business leaders contacted him to tell him how important green industries have been in the Toledo area in particular. The city, which ranked in the bottom 10 by per capita income in 2000, has seen a renaissance as a hub for solar innovation and production. More than 6000 individuals are employed in these industries in Toledo today, and the city is home to several major solar panel exporters including First Solar and Xunlight. Building on its existing manufacturing infrastructure and workforce skills in glass and auto parts, both industries that were on the decline, as well as its world-class universities and strong economic development agencies, Toledo managed to turn itself into a serious player in the global solar marketplace. The city stands as a testament both to the promise of new clean tech industries to revitalize aging industrial cities, and to the innovative spirit of America’s existing businesses and communities.
Preliminary research by the Apollo Alliance also highlights a promising advantage in inner-city areas in particular, where green jobs growth is rapidly outpacing overall job growth:
“While the number of inner-city jobs in the largest U.S. cities has grown by a scant 1 percent overall during the past decade, new research from Apollo, the Initiative for a Competitive City (ICIC), and Green For All, suggests that inner-city green jobs have grown by 11 percent, more than 10 times the rate of job growth overall.”
Green jobs have seen faster rates of growth throughout the country than the rest of the job market, and we need them to move the country forward as the transformation to a clean energy economy takes shape.
And lest we forget, the policies and investments put in place by ARRA and multiple states and cities have not just created jobs today, they have created new low-carbon infrastructure that will help our nation become more energy independent, cleaner, and healthier well into the future. Every million dollars invested in building a wind farm creates 5.7 permanent, direct jobs, to be sure—but it also creates a wind farm that will be in place for at least 30 years.
Green jobs protect Americans’ health while helping American business
The case for green jobs is integrally related to the case for solid, predictable environmental regulation—something that is on the minds of many here in Washington as the Environmental Protection Agency goes to the mat to defend its current plans to curb pollution in a number of sectors. As you know, the EPA has recently come under attack from politicians and dirty energy lobbyists, despite the trillions of dollars of health benefits it has generated since its creation. But the case for EPA authority goes far beyond the protection of public health and the environment, which Americans in great majority already support. New data shows that the EPA’s soon-to-be-finalized regulations create green jobs while also creating the business certainty and environment that American businesses need to invest in America.
A new report by Ceres and the PERI Institute at the University of Massachusetts, Amherst, finds vast economic benefits from two Clean Air Act rules expected to be finalized in 2011: the Clean Air Transport Rule and the Utility Maximum Achievable Control Technology, otherwise known as Utility MACT. The report outlines the jobs impact of “investments in pollution controls, new plant construction, and the retirement of older, less efficient coal plants as the country transitions to a cleaner, modernized generation fleet under new EPA clean air standards.” Key findings include:
Total employment created by capital improvements over the next five years is estimated at 1.46 million jobs, or about 290,000 jobs on average in each of the next five years.
Installing modern pollution controls and building new power plants creates a wide array of skilled, high-paying installation, construction, and professional jobs.
The American auto industry provides a prime example of how well-crafted rules can translate directly into new green jobs and industries. A new fleet of fuel-efficient vehicles would put auto workers and many others back to work while reducing dangerous carbon pollution, enhancing America’s energy security, and allowing the American auto sector to sell its new technologies on the global market.
The recent analysis “Driving Growth: How Clean Cars and Climate Policy Can Create Jobs,” conducted by the Center for American Progress, the United Auto Workers, and the Natural Resources Defense Council, found that strengthening automotive fuel efficiency standards through streamlined federal standards can spark the investment and innovation needed to reach new levels of efficiency while creating jobs. The analysis found that supplying the U.S. automobile market with more efficient cars could create up to 150,000 new jobs for U.S. workers by 2020 from improvements to fuel economy alone, all things being equal.
We need to let the EPA continue to do its job: creating green jobs, spurring innovation and investment, and strengthening the economy while protecting our health and the environment.
Harnessing the green economy to enhance American innovation and competitiveness
Innovation and investment are the essential building blocks of a strong U.S. economy, but we are no longer doing what we should to continue generating the ideas, goods, and services for which America is so well known. Instead, we are spending our time squabbling while Rome burns, by ignoring our crumbling infrastructure, by disinvesting in our workers and students, by chopping away at research and development funds, and by failing to take the necessary steps to put America into the global race to lead the green economy.
These are some of the progressive proposals that Congress dearly needs to take to heart to strengthen our economy:
Stabilize the market for green technologies by passing a national Clean Energy Standard, one that would set a target of 35 percent renewable and efficient energy by 2035, and a second target of up to 80 percent including a broader range of clean energy technologies.
Craft finance policies to make more public and private capital available to innovators to invent, commercialize, and produce green technologies. These include policies such as the Clean Energy Deployment Administration, the 1603 cash grant program for renewable energy developers, and the 48C program for advanced manufacturing. Each of these received bipartisan support in the last Congress.
Modernize our basic infrastructure to allow businesses to more effectively collaborate and compete in domestic and international markets
Invest more in science and math education and workforce development to ensure we have workers able to participate in the technology- and advanced-manufacturing-driven economy of the present and future.
Promote international trade policies that ensure access to foreign markets, and the free flow of goods, services, knowledge, and capital across borders
Provide incentives, through competitions and other “race to the top” strategies, to help our most innovative cities, states, and regions develop private-public partnerships to harness their best institutions, workers, and minds and find solutions to tomorrow’s energy challenges
The Center for American Progress has fleshed out many of these recommendations in a number of white papers and reports that are available on the CAP website at www.americanprogress.org. These include: “Helping America Win the Clean Energy Race,” “Rising to the Challenge,” “Cutting the Cost of Clean Energy,” “The Green Bank,” and “Rebuilding America.”
These steps would make great strides in boosting our national competitiveness and jobs growth in the short run and ensure our once-dominant position in science and technology, innovation and entrepreneurship, and job creation is not eclipsed by China in the 21st century. Government cannot do everything, but it can spur the private sector by ensuring a market for emerging technologies, and by creating incentives and evening the playing field for rising industries with great job potential. This will revitalize our entire economic engine and change how we are innovating new ideas, products, goods, and services.
Conclusion
We believe it is time that America fully join in the global green economic transformation. In fact, we want America to lead this transformation and to turn it into the great economic engine of future growth—much as we did during the Industrial and high tech revolutions. If we do not embrace a more sustainable growth strategy, we risk seeing jobs move overseas and our middle class decimated, even as we become more and more vulnerable to volatile energy and financial markets. If we do not lead in this green revolution, we risk becoming the great consumers of the 21st century, rather than its great innovators.
Investments in clean energy will do more than help some specific sectors add and maintain green jobs, though it has and certainly will continue to do so. Rather, by realigning America’s thinking toward a strong clean energy economy, we can strengthen the entire economy and ensure U.S. global competitiveness in decades to come.
President Obama reminded Congress during his State of the Union that the United States faces a real innovation challenge from China, Germany and other nations, much as it did in 1957 as the Soviet Union rocketed ahead of us in space exploration.
When the Soviets beat us into space with the launch of a satellite called Sputnik, we had no idea how we would beat them to the moon. The science wasn’t even there yet. NASA didn’t exist. But after investing in better research and education, we didn’t just surpass the Soviets; we unleashed a wave of innovation that created new industries and millions of new jobs.
This is our generation’s Sputnik moment. Two years ago, I said that we needed to reach a level of research and development we haven’t seen since the height of the Space Race. And in a few weeks, I will be sending a budget to Congress that helps us meet that goal. We’ll invest in biomedical research, information technology, and especially clean energy technology—an investment that will strengthen our security, protect our planet, and create countless new jobs for our people.
Our country needs a truly comprehensive clean energy investment agenda centered on groundbreaking policies and programs that reduce carbon emissions, increase public and private investments in clean and efficient energy technologies, and ensure broadly shared prosperity and sustainable economic growth. As President Obama said, this our Sputnik moment, and we must seize the opportunity it presents.
Thank you very much.
Kate Gordon is the Vice President for Energy Policy at American Progress.

In Other Words: Inspirational Videos - "Michael Pawlyn: Using nature's genius in architecture"

2011-02-10T09:26:00.000-08:00

I have been covered in work lately finishing up the last experiments for my thesis. So my blogging time has been less than I'd like to. Just to give a heads up, I recently read a review article on biofuels which I am planning on summarizing. However, today I wanted to introduce another angle on the "bio-based" theme by sharing with you another TED talk that talks about about bio mimickry. It very well summarizes some of what I have been thinking about and continue to be inspired about. Enjoy!

P.S.: I am curious to see what the readers of this blog think about this video and the posts in general. Feedback and general commentaries, as well as suggestions for future blog posts are always welcome!

News: USDA Starts Label for Bio-based Products

2011-01-20T13:54:00.000-08:00

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 encourage everyone in the bio-based industry to check out the official "Bio-Preferred" website created by the USDA.

Investigation: What sustainable biotechnology companies are there in California? Part II: Sustainable Products

2011-01-10T00:23:00.001-08:00

In my previous blog, I surveyed what companies are more closely associated with the biofuels field. Continuing on the survey for sustainable biotechnology companies in California, today, I want to cover companies that fall under the broad and often times overlapping category of industrial enzymes, bio-based chemicals and products.

Industrial enzymes are bio-catalysts often used to make other products the consumer ends up using. In the past, they have often been developed to substitute traditional chemical catalysts that can be toxic, and often are not specific enough. Sustainable chemicals and products often replace traditionally fossil-derived products and are usually the result of metabolic processes.

Amyris Biotechnologies: Amyris Biotechnologies, located in Emeryville, is the first sustainable biotechnologies company we will cover today. Founded in 2003, Amyris' first product was the production of synthetic Artemisnin, an anti-malarial agent, using a genetically engineered yeast-platform. Since then, Amyris has diversified its portfolio. Recently, the company has launched Biofene, which appears to be bio-based farnesene or a farnesene-derivative for which Amyris received the "2010 Product of the Year" award from Biofuel's Digest. Farnesene can be used in the manufacturing of a variety of applications such as lubricants, polymer additives, additives to cosmetic products, flavor and fragrances. Finally, on the biofuels side, the company was successful in converting their Biofene product into renewable diesel. In addition to Biofene, Amyris is working on other ways to obtain biofuels components from sugar cane (for example ethanol), and has partnered up with important bio-ethanol partners in Brazil including Crystalsev, and Santa Elisa.

Aurora Algae: After a recent reorientation, Aurora Algae, located in San Francisco and formally known as Aurora Biofuels, prides itself in being the "industry's first photosynthetic algae-based platform for pharmaceutical, food, fuel and aquaculture products". Aurora Algae is notably not focusing all their efforts on algal bio-fuels though it is still part of their longer-term strategy. Rather, its first approach consists of harvesting higher-value products from algae. At this point, the company focuses on omega-3 fatty acids which are naturally abundant in many algal species. The company plans on marketing these omega-3 fatty acids as pre-cursor products to the pharmaceutical industry and as food supplements to the general consumer. Algae are known to be good protein sources for many fish species. As part of the integrated production platform, Aurora Algae is also targeting the fish farming market by offering algal-based fish feed.

Codexis: Codexis, located in Redwood, is another exciting sustainable biotechnology company. Its strength lies in the development and optimization of an advanced proprietary directed-evolutionary-based platform. Codexis has leveraged this very special strength by offering services to custom manufacture bio-catalysts, pharmaceutical intermediates and metabolites, as well as offering screening panels. Interestingly, Shell and Codexis have formed a strategic partnership for the development of the next-generation biofuels.

Genencor: Genencor, located in Palo Alto, is an independent division of the Danish food-processing company Danisco. Genencor's expertise lies in the development and marketing of enzymes for various consumer and industrial markets. As a reminder, the advantage of enzymes, which are essentially bio-catalysts, are often significant reductions in energy use, reduction in the use of toxic chemicals, as well as much more chiraly specific complex products. With about a quarter of the world-wide industrial enzymes market, Genencor is the second largest company in the field only to be surpassed by Novozyme. As such the product line is too long to list in detail. But to name a few, consumers will likely have used some of Genencor's products without knowing if they use laundry or dishwashing detergents. Amylases, proteases and cellulases are often used in these products and allow for cold washes to still be effective. Genencor offers a wide variety of enzymes for agricultural and industrial uses including carbohydrate processing, water treatment, pulp and paper as well as textile processing. Genencor's approach to the biofuels market lies in the manufacturing of cost-competitive bio-ethanol using its expertise in industrial enzymes engineering.

Genomatica: Genomatica, based in San Diego, has an interesting history. Originally founded by Professor Bernhard Paalson, the company was offering its expertise and services in metabolic engineering and bioinformatics of microorganisms. It turned out that bioinformatics as a discipline did not by itself have a big enough market to support all the different specialty services. So the company has decided to apply its expertise in metabolic engineering to specialize in producing chemicals in a renewable that is bio-based way. Genomatica's first product currently in pilot-production stage is 1,4-Butanediol, or BDO which is has many uses including uses as a solvent or as a component in the manufacture of some types of plastics, elastic fibers and polyurethanes. The company states an interest in developing cost-competitive, bio-based isopropanol, butadiene and propylene in the future.

Micromidas: This start-up company, based in Sacramento, only recently hit my news screen. They came to the news because it is their goal to convert human waste streams to plastic products using their proprietary bacterial platform. I have not been able to find out much more about the company as they seem very new. As such I will follow this company with great interest to see their future progress.

Verdezyne: Verdezyne is a new privately held start-up company based in Carlsbad with goals similar to Genomatica but with its own niche. The company's slogan is all about "Green Chemistry" using a proprietary yeast production platform. When I had a chance to visit the company, I found that they essentially have two branches of research: renewable chemicals and renewable fuels. On the renewable chemicals front, Verdezyne is currently working on developing cost-competitive, bio-based adipic acids, which according to Wikipedia is the most important dicarboxylic acid on the market with many uses ranging from pre-cursors for nylon, to uses in medicine and food as gelling agents. On the biofuels front, Verdezyne seeks to produce ethanol from pentose and hexose sugars.

Verenium: Verenium is another specialty enzymes company similar to Genencor, but is based in San Diego. Verenium used to own and operate a pilot plant for the production of bio-ethanol from switch grass in partnership with BP. However, with the recent company reorganization due to the partial acquisition of Verenium's biofuels department by BP Biofuels, the company can now focus on its strength developing specialty enzymes. Verenium has four product columns. In the animal health and nutrition field, Verenium developed a phytase in collaboration with Genencor in order to increase the ability of feedstock to uptake phosphorous naturally contained in plants and hence reduce the use of phosphate rock normally used to enhance animal feed. Verenium offers various enzymes to enhance oil seed and grain processing efficiencies. On the emerging enzyme market, the company offers mannanases, and lyases. A product I particularly find interesting is a xylanase which the it says can improve pulp bleaching while reducing the need for toxic bleaching chemicals.

Closing Comments

These few blog posts are a work-in-progress. As I find out more about this field, I will come back to these blog posts and update them with some frequencies. Compared to the pharmaceutical industries, these companies represent just a small fraction of the total biotechnology world out there. However, it appears that there is a lot of exciting growth potential for all of these companies and the sustainable biotech field as a whole. Given the number of companies in this field in California, it appears that the unique combination of abundant finance, regulation and density of research institution serves as fertile breeding ground for innovations in bio-based cleantechnology field. The sampling of these very diverse companies in California gives just a small glimpse of the future. I hope that my survey also helped the reader understand some of the potential of this field and understand why I get excited and look forward to be part of this movement.

News: Biofuels Digest Awards for 2010

2010-12-31T09:54:00.000-08:00

It's the end of the year, and so many places look back onto the year and evaluate their accomplishments. So Biofuel's Digest, a leading biofuels news site, has looked at the industry and handed out a multitude of awards. The ones I consider the most important ones are:

Company of the Year: Solazyme
Tech of the Year (pilot): Lanzatech
Tech of the Year (demonstration state): Taurus Energy, Sekab
Tech of the Year (commercial stage): Renewable Energy Group
Product of the Year (fuel): Amyris (Farnesane)
Product of the Year (renewable chemicals): Genencor (Bioisoprene)
Product of the Year (bio-based products): OPX Biotechnology (Bioacrylic)

Of note also is that SG Biofuels (not to be confused with Sythetic Genomics) and Sapphire Energies mentioned in my previous survey also won some awards:

Plan for Scale: Sapphire Energy
Feedstock domestication project of the Year: SG Biofuels

There are more awards and honorable mentioning. 2010 has been an exciting year for the sustainable biotechnology industry and bodes well for the coming year! For the full article, go here: 2010 Biofuel Digest Awards

Investigation: What sustainable biotechnology companies are there in California? Part I: Biofuels

2010-12-30T23:49:00.000-08:00

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 the market at this time. As such most of these companies are start-ups that put a lot of their efforts into the development of a technology pipeline. Some may already be working on scaling-up production.

Next time, we will look at California-based companies in producing sustainable biochemicals, enzymes or products.

Companies I mainly found to work on biofuels:

Sapphire Energy: Sapphire Energy is located in San Diego, and its goal is to produce drop-in biofuels from oils produced in algae. The company has already succeeded in producing 91-octane gasoline in 2008, and tested algae-based jet fuels in 2009. Now Sapphire Energy is working on scaling-up the production capabilities. To this end, the company is constantly working on various technologies and has started to break ground for an “Integrated Algal Bio-Refinery” to be finished in 2014. To finance this big undertaking, Sapphire Energy has organized various sources of funding: Reputable investors such as Arch Venture Partners, The Wellcome Trust, Cascade Investment, Venrock have all invested into Sapphire Energy. Additionally, the company has partnered with Shell and has secured several government loan guaranties. Recently, Sapphire Energy has formed a strategic partnership with Monsanto. Although the company does not currently have any products on the market the prospects of this company are still very exciting.

Synthetic Genomics: Synthetic Genomics is the other biotech company in San Diego that works on algae. Although their goals are broader on stating a goal of producing sustainable chemicals using the same technology platform they are developing right now, their first stated emphasize is in the development of sustainable biofuels from algae. To this end, Synthetic Genomics has partnered with ExxonMobil, and is funded by Biotechonomy LLC, Draper Fisher Jurvetson, Plenus, S.A. de C.V., ACGT Sdn Bhd, and Meteor Group. What makes Synthetic Genomics interesting is the research agreement with the J. Craig Venter Institute which allows Synthetic Genomics exclusive access to new invention at the not-for-profit organization.

Solazyme: Solazyme, located in San Francisco, is the other major algal bio-fuels company that seeks to produce bio-based oils that could be used as fuel in transportation and other uses. However, their approach to this end is different in that the company hopes to bring down the cost associated with traditional growth processes by growing algae in large dark vats. Algae are fed sugars obtained from renewable sources and are then fermented to obtain oils and/or ethanol. Solazyme is in part funded by Braemar Energy Ventures, Harris & Harris Group, Lightspeed Venture Partners, The Roda Group, and VantagePoint Venture Partners. It appears that each of these bio-fuels companies is more closely partnered with one of the major energy company. In this case, Solazyme seems to have partnered up with Chevron.

Kent Bioenergy Corporation (added 2011/3/5): Another local company that has not been mentioned much in the regular news is Kent Bioenergy Corporation. It is another company based in San Diego, and according to their website, they have had many years of experience in the field of growing and harvesting algae. Being a bioenergy company, their goal is the development of algal-based biofuels. Not much public knowledge is available for this company. But appaerently, they have developed an efficient proprietary algae harvesting method that can make algae settle out of the solution and then be withdrawn by a conveyor belt at the bottom of the pond. Remember that algae harvesting through centrifugation is extremely energy intensive and expensive. So this company may have one of the key pieces to make biofuels development cheaper.

LS9: LS9, also located in San Francisco, advertises itself to be a leading biofuels company. However, unlike the above mentioned companies, LS9 relies mainly on modified microorganisms. Additionally, LS9 appears to be more diverse by also pursuing the development of sustainable chemicals. Like Sapphire Energy and Solazyme, LS9 is currently in the process of developing products for the market and is currently supported by a variety of venture capital firms: Flagship Ventures, Khosla Ventures, and Lightspeed Venture Partners. Additionally, LS9 has partnered with Procter and Gamble in order to speed up the development of sustainable chemicals.

SG Fuels (added 2010-12-31): SG Fuels is yet another biofuels company, based in Encinitas, with yet another approach. They call themselves energy crop company, and their approach entails the harvesting of optimized Jatropha seeds. To do so, the company has collected an impressive genetic library of variations that can be used to further increase the yield of oil from Jatropha seeds. The company claims that it can produce these oils at a cost of $1.40 a gallon or about $58 a barrel.

Ceres (added 2011-04-02): I became of this biofuels company which is based in Thousand Oaks when I recently attended an AWISE panel discussion on Green Energy Biofuels. Like SG Fuels, this company this company seeks to derive biofuels from a "crop". While SG Fuels has decided to focus its immediate efforts on Jatropha seeds, Ceres has instead focused on genetically manipulating various grasses which allow them to grow on marginal lands that are perhaps too salty or too polluted with heavy metals for other plants to grow. Ceres' current product portfolio consists of switchgrass and sorghum seeds.

Some Personal Comments

Although I have tried my best to extensively survey companies in this field, it may be possible that I have missed some. However, in other cases, I have decided to leave the names off for the next part which is focused on industrial enzymes and sustainable chemicals/products because often times, those companies have products in the mentioned categories. Unlike previously mentioned companies, biofuels is an extension of their current technology platform and only part of an overall product portfolio rather than the sole immediate goal. So we are looking differences in emphasize.

Looking at the different approaches each company is taking to solve today's energy bottlenecks makes me excited! Which one will ultimately succeed, I dare not want to say. However, it is my personal believe that in tomorrow's energy economy, an over-reliance on just one way just like with mono-cultures in agriculture is only a short-sighted solution. Given that energy needs are going to increase in the coming years thus driving energy prices higher, I think there is a place for all of these companies to grow synergistically together. I look forward to see (and hopefully be part of this) change!

If you feel that I should mention other companies, please feel free to contact me.

Sustainable Living – One Step At A Time: More Efficient Recycling

2010-12-28T21:34:00.001-08:00

It's been a while since last I talked about my families' path on going on a more sustainable life style. Today, I want to talk about recycling. Like many other houses in the neighborhood, we have 3 trash cans outside: One blue can for recycled goods, a green can for "garden" waste, and a regular black one for trash that will just go to the land-fill. We have in the past sort of haphazardly made use of these containers. I mean: the tons of spam we receive ends up in there, and cut grass goes into the green container. But really, a lot of other stuff just ended up in the black trash bin because it is just so much easier to throw everything into the same trash can in the kitchen. We had a nice and big 13 gallon trash can with a sensor, but since the cheap sensor recently broke, and the lid became suddenly useless, I decided to make recycling easier by purchasing a less technology-intensive trashcan (less complexity = less can break) that, however, has three compartments (http://www.kaboodle.com/reviews/trio-recycling-bin): one for recyclables, one for compostable waste, and one for normal waste.

We have been using this trash can for two to three months now. These are some of the observations I have made in the mean time: Specifically for the model we bought, it would have been nice for each of the compartments to be better labeled (like here: http://www.kaboodle.com/reviews/3-compartment-recycling-bin--stainless-steel) as the provided stickers easily fall off. Having made the purchase, we decided to just stick with it. But if I could start all over again, I would probably go with the second choice.

My Experience

More generally, three-compartment trash cans may have an overall larger capacity (~18 gallons) but since these are split between 3 compartments, each individual compartment fills up more quickly. The recycled compartment tend to be more bulky and therefore fills up most quickly. On the other hand, the compostable waste compartment fills up most slowly because unless you feed a large family, there is just not that much food waste which generally is also very compact. This actually tends to be a problem because if the food waste container is not emptied regularly, the moisture and warmth that can develop inside the bin can lead to unpleasant odors. We worked around the issue by just hanging much smaller grocery-sized bags into this compartment and just taking out these individual bags once every other day which coincides with whenever the recycling container is full. Lastly, I noted that if one were to always use new bags whenever each compartment was emptied, this would actually be contra-productive and potentially create more waste. To work around this potential problem, we decided to only sparingly change bags on the recycling compartment because most of the recyclable packaging material tends to be dry and clean anyway. The food waste container bag does get very messy and cannot be kept, but since we use much smaller bags, I hope that the impact remains small. The non-recyclable compartment does not always get messy depending on the waste that ends up in it. So I use judgment when I need to change it. Lastly, we are going to start using compostable/biodegradable bags (like these: http://www.biobagusa.com/catering.htm).

Well, what is the effect of all of this?

I have noticed that before changing to the 3-compartment trash bin, the oversized black trash bin completely filled up within a week while the recycle bin remained relatively empty. After these adjustments, the container barely reaches 1/3 of its capacity. The recycle bin, on the other hand, is full. So I think we are recycling much more efficiently now.

All this seems like a lot of work. Does it really change that much? Is it really worth it?

There are financial benefits to municipalities who adopt recycling programs. Although the exact financial benefits to the municipalities are debated. There seems to be a consensus that recycling can reduce costs to waste management (http://environment.about.com/od/recycling/a/benefit_vs_cost.htm) because recycled materials can be sold in bulk. I heard on NPR radio that in some cases recycled bins can make a small amount of money, while regular trash bins just cost money. According to the coverage, some cities have resorted to fining people who out of laziness only take out the regular trash bin. I have not had to confirm and backup this claim further though.

So why should one put in more efforts into recycling?

Simply said it's the right thing to do because it helps the environment by reducing the amount of waste that go to land-fills, increasing the amount of resources that can be reused, and thereby reduce the amount of new resources that have to be harvested or mined from the environment. It helps the municipality you live in save some money on waste management which will help you because savings in waste management are passed onto you in the form of fewer increased fees.

Recycling more efficiently is just another small step we can take to help reduce our impact on the environment. It is powerful though because with relatively little investment, and a small change in behavior, one can immediately make a personal contribution. In the end, I believe that it is the sum of small steps each of us individuals take that will make a difference. And so I hope, I have provided another small seed of an idea that can take hold in more people's mind in the future.

Journal Club:”Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria” - OR: How Bacteria Hook up to Share Energy

2010-12-11T23:44:00.001-08:00

Another curious observation made the science rounds the past week: wired, electric bacteria. Reading this article reminded me of a review article on dissimilatory bacteria I read before, and one of the most interesting talks I ever attended in my life titled "Eavesdropping on Bacterial Conversations".

What did they do?


Figure 1. Conceptual diagram showing electric symbiotic relationship between G. metallieducens and G. sulfurreducens. (Source: http://www.geobacter.org/)

Summers, who is Microbiologist working in the Lovley lab at the University of Massachusetts, was studying Fe(III) reducing bacteria in the soil. They wondered what would happen when Fe(III) reducing bacteria would deplete Fe(III) available in the soil. In order to study this question, the research group co-cultured two strains of geobacter bacteria: Geobacter metallireducens and Geobacter sulfurreducens. The research team thought that combining the former bacteria that can oxidize ethanol in order to obtain energy, but normally must pass obtained electrons onto Fe(III) which was not present in the solution, with the latter strain which cannot metabolize, but can reduce fumerate to succinate while consuming hydrogen released by the previous bacterial species, would lead to the formation of an electrical symbiosis. The effect where one bacteria lives off the products of another bacteria is called syntrophy, and the authors wondered how this might happen.

They hypothesized that together these two bacteria could metabolize ethanol completely. In order to select for those bacteria that were capable of doing so, nine co-cultures were grown together and sequentially transferred when each co-culture was able to metabolize at least 70% of the supplied ethanol.

After a few months, they observed red bacterial aggregates forming. The role of interspecies hydrogen transfer has been debated in the field. The group wanted to study importance of this function within these aggregates and therefore knocked out a gene required to make hydrogenase. To their surprise, knocking out hydrogenase function did not have any effects on ethanol metabolism efficiency, but it sped up the formation of the aggregates (21 days instead of 7 months). This observation suggested that alternative mechanisms for electron transfer must other than interspecies hydrogen transport.

Upon sequencing the genomes of the co-cultured bacteria, a single mutation in G. sulfurreducens encoding an enhancer binding protein gene was found. Expressing this mutation in wild type strains also reduced aggregate formation time down to 21 days suggesting that this mutation is sufficient to promote aggregate formation.

The mutation lead to increased expression of various targets amongst which is a pili-associated cytochrome c-type protein which normally promotes electron transfer to Fe(III) oxides. Knocking out the gene inhibited growth of the bacteria even after more than nine months. Thus, this observation strongly suggests that G. metallireducens is passing its electrons directly to G. sulfurreducens without a hydrogen intermediate, giving us a concrete example for a sort of electric symbiosis.

Why is this significant?

According to Ken Nealson, who was asked about this research by The New Scientist, there are potential far reaching implications of this kind of symbiosis for disease treatment and diagnosis. Professor Nealson also wondered if human cells in our body are wired like these bacteria. On a personal note, I also see potential applications for the environmental and/or sustainable biotechnology field.

In our next journal club we will look at an article analyzing the microbial community inside cow stomachs.

As usual, I encourage everyone to read the original article which can be obtained from here:

http://www.sciencemag.org/content/330/6009/1413.full.pdf

Journal Club:”A Bacterium That Can Grow by Using Arsenic Instead of Phosphorous”

2010-12-03T19:45:00.001-08:00

Since the previous journal club where we covered an article that looked at the microbial synthesis of alkanes, another a curious observation made the rounds in the science world. In the latest Science Journal, Felisa Wolfe-Simon et. al. report their successful isolation of a bacteria that can use arsenic instead of phosphorous.

The group isolated the bacterial strain called, GFAJ-1, by inoculating synthetic media containing glucose, vitamins and trace metals and varying concentrations of AsO₄^3- with sediments from Mono Lake which naturally contains high concentrations of dissolved arsenic (200 M) and performing many serial dilutions. GFAJ-1 was identified to belong to Halomonadaceae family of Gammaproteobacteria.

Various tests were performed to verify that these organisms could not only live but procreate in this environment. Among the remarkable features of this organism is the observation that arsenic can get incorporated into macromolecules most notably DNA where it replaces the need for phosphorous in the backbone. Despite similar chemical properties of AsO₄^3-and PO₄^3-down-stream processes can be affected by the presence of AsO₄^3-explaining the toxic effects of arsenate. It is even more remarkable that this bacterium can switch between the use of AsO₄^3- and PO₄^3-although it has to be noted that the organisms grow much faster in media containing phosphate instead of arsenate. Details on how arsenic was incorporated into macromolecules and how the organism can deal with varying concentrations of arsenic and phosphorus are currently unknown but will surely be part of future publications.

Why is this so important?

There has been the long-standing view that life on earth is mostly based on carbon, hydrogen, nitrogen, oxygen sulfur and phosphorus. The observation that phosphorus which builds the backbone of DNA can be replaced by arsenic expands the view of possible biochemistry that can take place in other parts of the universe.

From an environmental point of view, dissolved arsenic is toxic to most life due to the similar but but not quite identical properties of arsenic which allows some reactions to take place while inhibiting others. Could bio accumulation of arsenic by used to clean up arsenic contamination sites?

P.S (2011-02-18).: The journal club would not be complete if I did not mention that some people remain skeptical of the claim that arsenate can replace phosphate in these organisms. The criticicsm centers around some of the assumptions underlying some of their indirect methodologies. An alternative hypothesis was suggested: Rather than arsenate incorporation, some scientists hypothesize that arsenate is rather sequestered. Great claims require great proofs which in the minds of these scientists had not been brought forward. In response to the criticism the author decided to submit the strain to two publically available culture collection centers (the American ATCC and the German DSMZ) to allow for their more widespread studies.

Literature Cited:

Felisa Wolfe-Simon et. al. "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus."
Science Express, December 2, 2010, pp 1-9
Link: http://www.sciencemag.org/content/early/2010/12/01/science.1197258.full.pdf

In Other Words: Inspirational Videos - "Greg Stone: Saving the ocean one island at a time"

2010-11-07T20:20:00.000-08:00

TED talks are ever so inspiring. Earlier in the year, Sylvia Earle was speaking about the need to protect our ocean's resources. It appears that ocean protection is getting more on the radar screen of the general public. Today's post features yet another talk with a very inspiring story on protecting our ocean's resources.

In Other Words: From Poop to Plastics

2010-11-02T08:03:00.000-07:00

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

News Flash: German Electric Vehicle sets every-day driving record of 372 miles

2010-10-30T01:29:00.000-07:00

It's been interesting to observe how news of a EV from Germany has slowly spread across the ocean. Recently, according to a Deutsche Welle article, a modified Audi A2 which is all-electric, successfully completed 372 mile journey from Munich to Berlin on a single electric charge.

This is very significant because the range of electric vehicles has always been the Achilles heals of the technology. Electric vehicles in the past have been limited by the low energy densities of the battery making EVs of the past very heavy and limiting their range to about 60 miles. The upcoming Nissan Leaf which will rely on a compact Lithium Ion battery can reach distances of 62-138 miles depending on the driving style. Although a significant improvement good enough to satisfy the needs of 80% of US drivers, the range is still significantly shorter than what a typical car using the combustion engine can do (about 300-400 miles). The Audi A2 is the first vehicle that can produce these ranges under relatively normal driving conditions.

How did it manage to produce these ranges?

Details are still sparse. But two factors should be noted.

On the one hand, the Audi A2 is a rather compact car. Compact sizes cut down on weight and hence energy required to propel the vehicle.

The other factor is of course the battery technology. According to UPI, the battery manufacturer (DBM Energy), uses a technology they call "KOLIBRI AlphaPolymer Technology". DBM Energy notes on their website that although the battery uses lithium, the battery is not a lithium ion battery in a traditional sense: there is no danger of leaking liquids, toxic gases or explosions associated with lithium ion batteries. Instead, DBM energy states that their lithium polymer technology is a solid-state battery in which layers of a proprietary membrane and a special electrolyte mixture combine to produce leap-frogging energy density gains. The result: smaller, lighter batteries for a given energy requirement, fast recharge (as little as 6 minutes) using a regular power chord.

On a personal note...

As of late, there has been some discussion about the potential of German solar energy to overload the German grid. I am skeptical as to the powers that might have caused the stir up of this debate. However, this debate highlights an important point. Renewable energies by nature can be sporadic. If countries around the world would like to rely more on renewable energies, it becomes more important to store energy when it is produced in excess to tap into when energy demand outpaces production. I think this technology is quite exciting because battery technologies from DBM and other companies could also be applied to these challenges.

R&D News: Bio-Based Arsenic Sensors

2010-10-18T21:28:00.000-07:00

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. Using mass-spectrometry, it is possible to measure the amounts of arsenite in water samples. However, these technical solutions are very expensive because the equipment is expensive, and extremely sensitive requiring more money to maintain. Poor countries may not be able to afford these solutions. This is where Hauke Harms research comes in.

His research group was able to reprogram E. coli bacteria to emit a blue luminescent light when arsenite is present. They did so by inserting the gene to produce this luminescent light into the same operon (same set of instructions) that becomes active when arsenic is pumped out of E. coli cells as these bacteria do not like arsenic either. Instead of an expensive mass-spectrometer, one now only needs a cheap apparatus with a light sensor to detect the faint blue light. The researchers envisage that these bacteria could be placed onto paper strip tests similar to the way we measure blood sugar. After a certain period of time of exposing the strip to the water sample, the paper strip could be read by the much cheaper light sensor.

On a personal note, I think that applications from these sorts of bio-sensors are remarkable and exciting as their fields of application are wide-ranging extending all the way to the medical field.

For his research, Professor Hauke Harms recently received the "Erwin Schrödinger" Award for 2010.

Literature Cited:

An early paper on this topic from his research group can be found here:

Judith Stocker, Denisa Balluch, Monika Gsell, Hauke Harms, Jessika Feliciano, Sylvia Daunert, Khurseed A. Malik, and Jan Roelof van der Meer. "Development of a Set of Simple Bacterial Biosensors for Quantitative and Rapid Measurements of Arsenite and Arsenate in Potable Water."
Environ. Sci. Technol., 2003, 37 (20), pp 4743–4750
Link

The recent news were based on recent publication that further optimized storage and preservation of these bacteria:

Kuppardt A, Chatzinotas A, Breuer U, van der Meer JR, Harms H. "Optimization of preservation conditions of As (III) bioreporter bacteria."
Appl Microbiol Biotechnol. 2009 Mar;82(4):785-92. Epub 2009 Feb 6.
Link

Permaculture: nature is still smarter than us

2010-10-10T16:15:00.000-07:00

Permaculture

In the year 2010, there are many aspects of humans' daily life that would lead us to believe that we have dominated nature. Unlike the thousands of other species that have gone extinct, we have settled and thrived in almost every environment and every continent on this planet, aside from Antarctica. We have eradicated diseases like smallbox and subdued other diseases which previously decimated our populations on a massive scale (see The Black Death in the 1300s and Columbus' “discovery of the Americas in 1492). We have created chemicals that allow us to blast weeds and insects into submission and thereby cultivate thousands of acres of the same species on farmland; an environment that would be impossible in nature.

But nature is still smarter than us. A lot smarter. And we still have much to learn from its processes. Permaculture is the idea of mimicking the ways that ecosystems work in the context of essential human activities: house and settlement design, farming, and waste management. I just finished reading Introduction to Permaculture by Bill Mollison, which provides a fantastic introduction to the concepts of permaculture.

Why should I care? You may ask. I don't live on a farm. Whether you live in a rural, suburban, or urban area, this book will help you identify specific ways that you can be much more efficient and save yourself money while decreasing your adverse impact on the environment.

Some examples:

1) Composting your kitchen scraps and other organic waste, and using the compost to fertilize your garden.

- Benefit to the environment: organic waste is efficiently recycled on a local scale instead of 1) ending up in a landfill or 2) being trucked several miles to a compost center

- Benefit to you: no need to pay for fertilizers for your garden

2) Growing vines on the outer walls of your house for insulation

- Benefit to the environment: your house uses less energy to maintain a comfortable temperature

- Benefit to you: lowers your heating and air conditioning bill; makes your house look cooler (no pun intended)

But by far the most powerful knowledge in this book is how to grow your own food easily and efficiently. I'm going to delve into this in another post specifically on urban and suburban agriculture.

In Other Words: Inspirational Videos - "Mushrooms, the new plastics?"

2010-10-08T10:35:00.000-07:00

Journal Club: Microbial Biosynthesis of Alkanes

2010-10-02T22:30:00.000-07:00

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 described above often occurred next to each other and therefore likely form an operon which are genes that are expressed together at the same time. To test the above hypothesis, the authors expressed operones described above in E. coli which is known not to produce alkanes. Putting these two genes into E. coli enabled the organism to now produce alkanes and alkenes.

The take-home message: Gasoline and other fossil-based fuels to a large part consist of alkanes and alkenes. Although researchers were speculating about how these hydrocarbons could be produced in living organisms, this paper for the first time clearly identifies two protein classes that can actually synthesize the reaction which could form the basis for a bio-based way of fungible (directly usable) biofuels.

I encourage everyone to read this from source directly here:

http://www.sciencemag.org/cgi/content/short/329/5991/559

Freely Speaking: Random Thoughts on Words

2010-08-14T19:03:00.000-07:00

Introduction

Today I want to talk about something that would probably fall into the category of “organic ideas” rather than sustainable ideas. I want to plant a seed of thoughts by talking about something we seem to take for granted every day: Words. That was the title of the latest Radiolab episode I subscribe to. Now for those of you who don’t know, Radiolab is a radio show on WNYC hosted by Jad Abumrad and Robert Crowitch with the goal of asking big questions to stimulate the mind to grow. I consider them to be the “This American Life” of Science or better for the lack of any better words. There is also a really nice bonus video which I have embedded below. Anyway, watch the video, and if you find this blog interesting, I highly recommend that you listen to the podcast (, subscribe, and donate to the cause of public radio).

Source: http://www.wnyc.org/shows/radiolab/

Synopsis

In four acts, this time the show covered what importance words have on us in our daily lives. In the first act, Jad Abumrad interviews Susan Schaler, one of the first women to have learned sign language, about her discovery of a 37-year old deaf man who did not seem to know what language was, and we learn what transformational changes happened to the man as he learns that there is language for the first time in his life.

In the second act, Jad and Robert learn about an experiment in which mice have to find food located on one corner of a rectangular room where all but one wall is painted in the same color, the difficulties they have and implications this has on us humans.

In the next act, Jad and Robert listen in on a TED talk given by Professor Taylor a famous neuroanatomist, who lost her language as a result of a stroke, and then talk to her to learn about the experiences she went through as she regained her language abilities.

In the forth act, Jad and Robert discover what happens when a whole school of deaf children get together to play and learn: They invent their own language, and we learn about the changes that take place there over time.

We are then left with some thoughtful words as Jad and Robert revisit the Susan Schaler trying to learn how it was like for the deaf man before he learned a language.

Reflections

When I listened to this podcast, so many thoughts went through my head because this show seemed to link up so many ideas, I have always taken for granted. In the progress, there were a few simple truths I rediscovered for myself.

Where to start?

“Language is the key that opens door to success”, my dad always said. It’s true. Languages do not only transmit information. But the thinking of a culture is embedded in language. Hence learning different languages not only allows one to communicate information to another person, but can facilitate the learning of cultural values, and cultural thinking. It is true that languages change over time because individuals make changes to it in response to changes in the environment. But it is equally true that the changes in language represent changes in the collective mind. I was reminded of this when listening to how the deaf Nicaraguan children were able to come up with their own language, and how this language got refined within just one generation, allowing children of the younger generation to engage in more complex thought than their older brethren. Knowing one language will allow a person to think in one system. I am starting to see why it is so important to learn many different languages early on. Learning different languages enables the brain to think in different ways making it more flexible. Flexibility of course is important for surviving challenging situations.

But just as words and languages are one mode of thinking, Professor Taylor touched on something I think my Tai Chi sifu is trying to teach in his formless Tai Chi class. In meditation, one tries to calm the mind and naturally let the brain chatter disappear. Rather than thinking (which in my mind always involves words) about how to move in Tai Chi, he promotes experiencing the movements. It’s hard to explain in words, but the best I can describe this as is sensing each movement and being aware of them and their directions. My sifu always said that Western culture thinks too much with the right hemisphere by which he means that it is too reliant on analytical thinking which is often built on concepts and constructs drawn up by words. Although these words are powerful means to transmit information, they are also an intermediate construct to what is. They funnel the brain to think in a certain way – efficiency results from the funneling effect. My sifu has always promoted “more left hemispheric thinking”, more experiencing truths that is very similar to what Professor Taylor now seems to long for. That got me thinking: Can meditating monks induce this state of mind voluntarily? And what are the benefits?

Concerning, the remark that the Nicaraguan kids of the second generation were able to think more about thinking as a result of having several words that describe different thinking processes, I was thinking several things: Apart from words as they appear in spoken and written languages, there are other forms of “words” as well: the musical language, programming language, or mathematical language. In each of these cases, it may be hard to understand concepts in music, programming or math without knowing learning the language first.

On a related note, my sifu has always said: The mind affects the body, and the body affects the mind. This got me thinking: The normal mode is that a tired body breeds negative thoughts. But if the mind also affects the body, what would the effects of surrounding myself with positive language, with people who are positive, and who themselves use positive language be?

There is an old saying I learned about when I started this blog:

Watch your thoughts, for they become words.
Watch your words, for they become actions.
Watch your actions, for they become habits.
Watch your habits, for they become character.
Watch your character, for it becomes your destiny.

— Frank Outlaw

Thanks to Jad and Robert, I feel that I have gained a new appreciation for this saying and what my dad has always tried to teach me. I now better understand why language opens the door to success. Thank you all!

Sustainable Living - One Step at a time: Toilet Paper

2010-07-03T15:27:00.000-07:00

Introduction

It's been a while since last, I posted here.

Today, I want to introduce another blogging series which I call "Sustainable Living - One Step at a time"

In the past, I have often written and talked about interesting new technologies and ideas in the biological field, some of which could be used to reduce the impact human kind makes on the environment. Although many dedicated brains are tackling these interesting challenges, there are even more who are not working in these kinds of fields. What can other people do to reduce one's impact on the environment? Generally, by adapting a more sustainable approach of living. Because so many habits and other aspects of life would need to be changed, many people may not feel that it is worth pursuing these efforts because the perceived sacrifices would be too big. Alternatively, one may not know where to start. I do not exclude myself it the latter group.

So, instead of trying to do everything at the same time, I will in a less structured way chronicle how my family and I try to find a good middle ground towards a more sustainable live style - one step at a time. I hope that my discoveries will help others who want to make an impact on the environment but who may not work in such a field. In doing so, I may often talk about specific products. I don't mean to be an advertisement banner to these products but I do want to mention products I see to give specific practical examples of how small changes may look like.

Bath Tissues

I am sorry to start with something rather personal and potentially graphic :-) Today, I went to Costco to buy some cleaning supplies. We normally buy cleaning supplies there because bulk is cheaper. As I was standing in front of the Kirkland toilet paper, I thought that it's funny/ridiculous that most people right now are using fresh virgin paper once to do their business only to throw the toilet paper away afterwards. Although not universal, the use of toilet paper is certainly standard in the US. I do wonder how many new trees are cut down just so you can w--- y--- b--- ? I didn't know it then, but according to Wiki "one tree produces 100 pounds of toilet. An average American uses 50 pounds of toilet paper each year. According to the Census Bureau, there are about 307,006,550 in the US as of July 2010. Doing some rough math, this means that just for toilet paper 150 million trees are chopped down just for toilet paper production which is half of the entire US population - in other words: a lot of trees.

Right then, I realized that next to it, Costo was now also offering "Marcal small steps bath tissues". The same company offers other paper-based products, however, Costco does not offer them.

They claim that buying their products is "small step towards a greener earth". What makes this product greener? Bath tissues use 100% recycled paper. The paper is not whitened with bleach but some other means. Lastly, unlike Kirkland, four rolls are wrapped in one plastic wrapper, hence, slightly reducing type 4 plastic waste.

As a side note, it seems that local Marcal is based in the US. It appears that they are collecting, processing and shipping their paper within the US (New Jersey) unlike many other products that use cheap fast growing trees and processing from China.

The choice was clear to me. My first chronicled step towards a greener live style is simply to switch from regular bath tissues to those that are made from recycled paper.

In Other Words: Inspirational Videos - "Brian Skerry reveals ocean's glory -- and horror"

2010-06-05T11:57:00.000-07:00

As you all know, I have grown quite fond of TED talks. Today, I found Brian Skerry's tells a very visual story of the ocean - both good and bad. Although it's a bit long, I encourage everyone to watch and reflect on the talk.

Recap of SD-CAP Algal Biofuels Symposium 2010: Cyanobacteria – the other Algae by Susan Golden

2010-05-31T09:30:00.001-07:00

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 production. This is so because excess energy is stored in the form of glycogen and not lipids. Membranes of course consist of lipids, but different from other eukaryotic organisms, these are polar lipids! The other hurdle, comes from the fact that genetic models for cyanobacteria do not necessarily have qualities that would make them excellent production systems.

It is this challenge that the Golden Lab has decided to tackle by using a 2-pronged approach. Professor Golden spent most of the time outlining what she meant by this approach giving examples from her own lab. On the one hand, current model organisms are used to identify novel genes and pathways. On the other hand, her lab is working on identifying strains of cyanobacteria that would be suitable to serve as a production strain and use these naturally occurring strains to further evolve them to fully fit industrial needs.

Professor Golden points out that working with cyanobacteria unlike the eukaryotic counterparts is relatively easy because the full complement of molecular biological tools exist. These include: transformation (as mentioned before), conjugation, known regulated promoters, libraries of knockouts and overexpression genes, and all sorts of reporters (fluorescent, bio-luminescent, and chromogenic).

Using these tools, and Solexa sequencing technologies, 73 genomes have been sequenced with genome sizes ranging from 1.6 (marine environments) to 9.0 Mbases (complex habitats). There are some very impressive numbers to note:

Despite the fact that many eukaryotic and prokaryotic genomes are already known, 25% of each cyanobacterial genome is unique.

40% of all genes are still of unknown function or are hypothetical genes!

Using homology many pathways from other organisms can be transposed onto cyanobacterial metabolic networks. However, this will not get at the functions of unknown genes. To get at these, new technologies and systematic genetic approaches need to be used.

To give one specific example of work going on in her lab, she talked about the work on one by the name of Snechococcus elongates PCC 7942. This strain is an obligate phototroph meaning that it needs light to survive. This strain is known for the ease of transformation. Simply adding DNA to the liquid growth media can be enough for transformation to take place. Its efficient homologous recombination machinery makes gene knock-outs or knock-ins easy to perform similar to techniques available in the more studied baker's yeast. First, a random knock-out library was created using a modified E. coli transposon. To assay the lipid profile, a new high-throughput method to detect lipids was developed because the standard Nile red method absorbs the light spectrum that these cyanobacteria use to perform photosynthesis.

To modify the lipid profile, different saturases were inserted and assayed for any changes in the lipid profile. This approach led to the creation of cyanobacteria that can secrete fatty acids without further modification.

The Golden lab also looked for other traits using similar approaches to screen strains for changes in the carbohydrade profile, as well as looking for better harvesting traits such as better filamentation or settling.

Insights in the model organisms have then been applied to the collection, isolation, identification and characterization of possible production strains that were selected on the basis of tolerance to conditions that are less favorable to grazers such as high temperatures, salt, pH and light tolerance.

In summary, I got the following out of the talk amongst other points: Although much emphasize has been placed on eukaryotic blue-green algae, cyanobacteria should not be discounted in the biofuels and bioproduct discussion. Several traits including better molecular genetics tools seem to make cyanobacteria great production platforms for future products.

R&D News: Are we a step closer to recreate life?

2010-05-22T10:51:00.000-07:00


Paint-By-Numbers Statue of Liberty

In the latest Science Issue, the Venter Lab (Gibson et al. 2010) report that they have successfully created an "artificial genome" Mycoplasma mycoides which they transplanted into Mycoplasma capricolum cell to create a new Mycoplasma mycoides cell. In other words, they put the DNA of "A" into an organism of type "B". Just by doing so, they "converted" B into A. This begs the question....

So what?

The dream of creating artificial life - that is to say recreate life from scratch with inanimate starting components - has been the dream of some researchers that want to get at the question of:"What is life?" Of these researchers, Craig Venter probably has been the most recognized figure. Craig Venter claims that understanding how one can create life from scratch will also give us the ability to create purpose-driven life-forms. With the current oil spill an example comes to mind where one could create much better bacteria from scratch that would digest oil leaking from the ocean floor. But there are many other possible uses - both positive and potentially detrimental. Regardless, there is quite an intellectual challenge associated with trying to recreate life.

What exactly is needed and what obstacles need to be overcome?

Conceptually, the idea is simple. To make life, one simply should:

Make DNA.
Insert DNA into a "proto" cell - something with a plasma membrane around and other cell machinery. (This in itself is a challenge.)
Push the start button.

Until recently it wasn't clear that one could just change an organism by replacing the DNA. In a previous publication, the Venter lab tackled this question by demonstrating that one could take the genome of organism A, and when put into the nucleus of organism B, it would convert B into A simply said.

The difference between the previous publication and this one was that in this one, they used their own "test-tube" made DNA. This may seem trivial but in reality there are many challenges associated with this.

Making DNA: The first challenge is trying to string together 1,000,000 base pairs is not easy because we do not have the technology to do it. The Venter lab tackled this problem by inserting specially designed overlapping fragments of DNA into our baker's yeast and let the yeast cells figure out how to knit these overlapping DNA pieces together.
Getting DNA into the cell: The second challenge was trying to get the lab-created DNA into the second organism. It turns out that the recipient cell has its own defense mechanisms. DNA recognized as "foreign" gets cut into pieces on sight. So simply inserting freshly created lab DNA lead to failure because the recepient cell recognized the new DNA as foreign. To circumvent this problem, the Venter lab came up with two approaches. In one approach, they disabled the recipient defense mechanisms. Native DNA is distinguished from foreign DNA by the presence or absence of little tags on the DNA. In the second clever approach, Gibbs et. al. disguised the new lab DNA by putting on these tags (metyhl groups) at locations where they are also found in the "native" DNA.

Why did this appear in the Science Headlines?

This publication is a culmination of all the technologies developed in their lab in the previous steps. The important things to note are:

If we draw an analogy to computers, the Venter lab demonstrates that DNA is sort of like the software to run the hardware (the rest of the cell). So by inserting different sorts of softwares, we can make the hardware do different things. In this case we are not just talking about superficial changes, but about an entire change in the operating system.
Did we create artificial life? Well, not quite just yet. In an analogy, at this point, even if we still can't recreate our life-like artistic painting from scratch, we can at least assemble some of the pre-made components, and if we are given some sort of blueprint, we can now paint by numbers. Despite how belittling this may sound, this is a very significant step towards eventually creating our own paintings.

I encourage everyone to read the original which is linked in the Literature Cited section below.

Literature Cited:

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Science 21 May 2010:
Vol. 328. no. 5981, pp. 958 - 959

Recap of SD-CAP Algal Biofuels Symposium 2010: Where we are - where we are going

2010-05-14T10:58:00.000-07:00

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 growth in the energy market and fear of some analysts is that other developing nations may want to emulate the behavior of the United States, adopting an energy intensive economic model and hoping that this would lead to wealth. Professor Mayfield then diverts to distinguish between energy, as stored energy, and power which is electricity and analyzes current and future sources of energy who were it would. He argues that in many regards, we have already passed by peak oil production. On the other hand, energy demands are increasing. To give some numbers, the total energy reserves today are estimated to be about 2300 TW-year. Assuming 2-3% growth in the consumption, we would be out of fuel by 2099. If the rest of the world were to consume fuel at the rate the US is, we could run out of fuel by 2048. All these numbers serve to reinforce his main point which is that we are approaching the end of hydrocarbon era. Since the need to continued energy consumption will continue, the question is:

How will we replace this lost energy source?

There are no silver bullets, but one significant answer is the development of biofuels which Professor Mayfield defined as the biochemical conversion of sunlight energy into chemical energy. This is significant if we consider the following numbers:

- The world consumes 15 Terawatts (TW) energy. 80% of this energy is derived from fossil fuels.
- The sun provides 86,000 TW of energy every year.

If we can just harvest a fraction of this energy, it would appear that our energy problems would be solved. Professor Mayfield pointed out that there are many approaches and emphasized that each approach would have its limiting reagent. Those would be:

- The current use of petroleum is obviously limited by finite quantities
- 1st generation ethanol are limited by the competition with food resources
- 2nd generation fiofuels are limited by the quantity of easily recoverable plant waste material
- Electric batteries are limited by the amount of lithium which are only located in a few geographic locations.
- A hydrogen economy relies on abundant electricity supplies which themselves must be derived from a different source.
- Lastly, there are algae which at the current time are too costly because large-scale plants do not exist.

Although large-scale algal biofuels plant do not exist, proof-of-concept drop-in fuels have been developed for use in cars as demonstrated by the Algaeus car - the first hybrid car running on a bland of algae-based renewable gasoline – and a Continental Boeing 737 flight.

Professor Mayfield then talked about a possible algal biofuels production chain similar to what I have written about in my previous post.

He expanded on this by evaluating factors that need to be addressed to bring algal biofuels to a cost-competitive basis. Areas of focus include: Bio-prospecting better production strains, using engineering to improve reactor design and all processing steps along the way, using biological and agricultural techniques to create better algal strains by breeding-selection, and by finding and marketing co-products.
On the point of breeding and selection, Professor Mayfield made the point that current crops and livestocks are a result of a 7000 year domestication process recently further aided by advances in the basic sciences. This is important to note because no commercial system uses wild type organisms. In the algal field, it is possible to generate transgenic algae strains within weeks. On a personal note, I want to point out that although this is fairly good compared to generation and handling of transgenic mammalian cell lines, current technologies still rely on transformation of plasmid material! Techniques for permanent and targeted integration are still missing for most eukaryotic algae.

On the topic of algal bio-products, there are already many products derived from algae. As of today, these have mostly focused on high-value products with relatively limited markets including biomass, omega-3 fatty acids, aquaculture feed and b-carotene. Future products will target lower value products with larger markets. The biofuels market can be viewed as the most challenging but also most rewarding market.

He concluded by saying that much research remains to be done, but when coupled with the right economic and political framework – for example considering carbon capture and domestic waste water streams – the future for algal biofuels looks bright.

Recap of SD-CAP Algal Biofuels Symposium 2010: Research Dynamics.

2010-05-01T14:53:00.000-07:00

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 coincides with the onset of algal biofuels research significantly helped by significant increases in grants for biofuels development.

Professor Key then asked the question how an algal R&D pipeline can be built? A stable political framework that does not depend on the moods of each administration (see the changes in funding priorities from President Ford to President Reagan). It takes stable long-term commitment, and this long-term commitment should be funneled through the DOE, NSF, and USDA. Recent funding increases to these funding organizations as well as the structural reorganization initiated by Energy Secretary Steve Chu have been helpful in this regard. All this leaves the algal research community full of hope and energy for the future.

On a personal note, despite the impressive relative growth, even at the current maximum, there have only been 2000 publications in 2009 which is dwarfed by the number of publications in DNA replication or just yeast in the same year. This is not meant as a derogatory comment, but serves to emphasize that the algal research field is still at its inception. And this means that there is lot of growth potential.

The complete presentation can be obtained at the following location: http://algae.ucsd.edu/documents/SD-CABSymposiumKaySlides.pdf

Did/Do you know...?

2010-04-22T20:46:00.000-07:00

Today, I wanted to experiment with a more free-form way about little science factoids that may seem surprising. Today:

Schematic of a cell membrane.
Source: http://library.thinkquest.org/

Did/Do you know…what cell membranes are made off?

If you go back to your high school or basic college biology class, you may recall a picture showing that cell membranes are made off phospholipids.

All major examples taught in class – from animal, plants and microbial cell membranes to organelle membranes such as mitochondrial or ER membranes. The arrangement of phospholipid layers made complete sense: the lipid hydrophobic tails would be hidden within the bilayer of phospholipids while the polar hydrophilic heads would be facing the aqueous environment. For some reason, my brain made the connection: ALL membranes consist of phospholipids, but are they?

Apparently, this is not so when it comes to membranes of photosynthetic membranes according to the article titled “What Can Plant Models Teach Us About Lipid Trafficking?” written by Christoph Benning in ASBME Today. Instead, these membranes consist of galactoglycerolipids – or sugar lipids in other words.
Why do these membranes consist of sugar lipids rather than phospholipids you ask? Benning answers that when it comes to non-mobile plants (and aquatic environments for that matter), phosphorous used to be a precious and rare resource within the cell (before we started using synthetic fertilizers and using the oceans as dumps for unused phosphorous that is). Judicious use of this resource for other components such as energy transfer and copying of the cellular information material (DNA) had to be prioritized over other uses. Evolution responded by using galactoglycerolipids to conserve phosphorous.

What’s even more interesting is that the chloroplast has exported most of its DNA into the cell nucleus. In order for galactoglycerolipids to be assembled on the surface of chloroplasts, both the cell and the organelle have to work together to transport the lipid pre-cursors through multiple membranes to the chloroplast. How that’s done, however, remains a largely unknown mystery.

For tonight though, what I learned is: don’t let the brain fool you into a pattern. Question the obvious. The answers one gets may be surprising. And that wraps up tonight’s science factoid

Cited Literature:

Christoph Benning (2010). What Can Plant Models Teach Us About Lipid Trafficking?
ASBMB Today, April 2010, p.36

R&D News: Eco-Friendly Way of Degrading BPA-Plastics

2010-04-12T19:52:00.000-07:00

What was done?

I came across an interesting article yesterday titled “Biodegradation of Physicochemically Treated Polycarbonate by Fungi” published in Biomacromolecules. What this group essentially did was to isolate fungi from the environment by exposing them to conditions in which plastics were the only source of food. The group basically identified three fungi (Phanerochaete chrysosporium, Engyodontium album and Pencillium spp.) , and characterized some of the parameters by asking basic questions about:

Efficacy changes when fungal isolates were exposed to certain pre-treatments (either heat or UV light).
Growth of biomass (how much the fungi grew during this time)
How much extracellular protein was secreted and a crude determination of the class proteins released
Loss of mass of the piece of plastic
Changes in physical, chemical and surface properties.

Why is this important?

I asked myself the same question until I realized what plastic they were working with: Bisphenol A Polycarbonate or BPA containing plastics in other words. BPA is used to create clear, and shatter-free plastics.

For those who don’t know, BPA has recently entered the health news because of concerns on its effect on human health. The effects of BPA were first accidentally discovered in laboratory rats in which female mice all of a sudden had reproductive problems after changing the wash detergent used to clean the animal cages. The sudden effects puzzled the researchers until they were able to find the cause: The new detergents used in cleaning the animal cages dislodged BPA from the plastics. BPA was determined to be an endocrine disruptor in rats which means that it basically disrupts the hormonal cycles especially in female rats leading to fertility problems. The astonishing discovery was that the effects of BPA did not only affect the rat who was exposed to BPA, but that even the children of the mother were still affected. Although the plastics industry has officially stated that the human effects have largely been undetermined, many producers have voluntarily phased out the use of BPA due to pressure from consumer groups as well as the general scare within consumers.

What is the take-home message?

Although the use of BPA has been phased out, the question remains what will happen to all the plastics that have already been produced. What happens for instance when BPA leaches out of the plastics in land-fills and enters the ground water system where often times drinking water is drawn from? BPA has already been shown to have leached into the oceans where many scientists are very concerned about BPA's effects on marine life. This article crudely shows that we can safely bio-degrade BPA-containing plastics without releasing BPA to the environment. In previous articles, I have talked about how bacteria, or algae can be used to bioremediate (clean up the mess we produced) different sorts of pollutants. This article shows the potential of using certain fungi in the bio-degradation of BPA plastics.

Literature Cited

Trishul Artham and Mukesh Doble. "Biodegradation of Physicochemically Treated Polycarbonate by Fungi." Biomacromolecules, 2010, 11 (1), pp 20–28. Link: http://pubs.acs.org/doi/abs/10.1021/bm9008099

In Other Words: Inspirational Videos - "Test Tube Organs (Anthony Atala)"

2010-03-27T07:59:00.000-07:00

Introduction:

Today's post comes again from the famous TED series of talks. This is a great forum because many of the brightest heads come together at these talks to exchange the best ideas. If you want to learn more about what TED talks are, go here. Today's chosen video was just recently posted. Anthony Atala presents his institute's work on growing new organs.

Without further ado:

In Other Words: Inspirational Videos - "Sylvia Earle's TED Prize Wish"

2010-03-21T12:06:00.000-07:00

Introduction:

With some frequency, I want to introduce really good and inspirational videos without my own comments because the messages of these videos are much better than what I could say. Today's video posts without my comments comes from TED talk series. Sylvia Earle's TED Prize wish is to protect our oceans.

Without further ado:

R&D News: Biogas Reactor using Cow Stomachs

2010-03-14T12:49:00.000-07:00

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 cellulose.

There are a few ways one could go about solving this problem. One way, would be to sample the genomic diversity in the stomach of these animals, identify proteins that break down cellulose and then try to use optimized versions of the isolated protein in a large reactors containing sort of biochemical cocktail. Alternatively, one could take a particularly important gene and genetically engineer a crop to produce this gene which will aid in the break down of the plant material itself as reported two years ago [2]. In this case, the research team thought of simulating the entire cow stomach by taking the content of 4 cow stomachs (~ 400 L) and dumping it into a specialized 2-step reactor that emulates conditions inside cows.

In a cow stomach, plant fibers are converted into fatty acids. The cow saliva then absorbs the fatty acids and transport them to the blood where they are used by the body to generate energy. In the reactor, the saliva and blood are replaced by a special, secret liquid. This liquid transports the fatty acids to a second chamber where they are broken down into methane and carbon dioxide. Methane is then used for the generation of heat and electricity. So far the test reactor has been running for 2 years without the need of adding any more cow stomach contents.

There are a couple of significant points to note:

1.) The fact that the reactor has now been running for 2 years shows that the cow stomach biology can be preserved outside a cow's stomach which is good. Try imagining having to constantly add more content of cows!
2.) Compared to other processes, which may take up to 200 days for the break-down of a certain amount of hay, this process takes only 10 days. Since it's much faster, this will lead to potential savings in the size of a reactor.
3.) Lastly, the researchers imagine a highly modular architecture, meaning that their reactor design is highly scalable. Instead of having to plan for an eventual maximum capacities ahead of time when constructing one large reactor, using smaller reactors the capacity can more gradually be added as the need increases.

As I said, this is very interesting stuff. There are a couple of questions I had though when reading this article. Like:

What is this liquid made up off?
What cow processes are otherwise simulated?
What bacteria and what enzymes are involved here?
How efficient is this process compared to when this would take place inside a cow?
Can these processes be enhanced by enhancing the enzymes involved in the process?

News Source:

[1] Christoph Kersting. "Reaktor mit Kuhmagen". Forschung Aktuel. 10 March 2010. .Visited: 2010/03/14.
[2] Michigan State University. "Gut Reaction: Cow Stomach Holds Key To Turning Corn Into Biofuel." ScienceDaily 10 April 2008. 14 March 2010 /releases/2008/04/080408085453.htm>. Visited: 2010/03/14

Concept Discussion: What is the Bio-based Economy?

2010-03-07T23:01:00.000-08:00

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 resources:
Today's economy largely functions on non-renewable fossil resources. The clearest examples can be found in transportation and energy production: Up to this point, the majority of transportation depends on oil, and the major energy source for electricity generation is coal. Our dependence stretches far beyond the obvious as almost every single product we use came from fossil oil-derived products - from the plastic keyboard of the laptop I am typing on to the food we eat. The latter may seem surprising, but even modern agriculture relies on fossil resources which starts with the heavy overuse of synthetic fertilizers and pesticides used to grow the plants to all the fuel consuming equipment used to harvest, process and distribute the food. The impact of our reliance can be seen in the increased degradation of the environment.

In a biobased economy, the starting point for many industrial process would not be a fossil resource (i.e.: oil, natural gas, coal, uranium, phosphate) but resources that are renewable or can regrow. An examples of this are the plans to produce bio-ethanol from switch grass.

2.) Transition to bio-based manufacturing
The bio-based economy also relies on the increased use of bio-based manufacturing strategies. As the name implies, bio-based manufacturing relies on "living organisms" or the products produced from these organisms to manufacture what we desire. This idea is not actually a new one. Human kind has started to use these processes for many centuries to make basic food products such as wine, cheese, bread and yogurt. In the bio-based economy, the use of microorganisms as bio-refineries will be enhanced because bioinformatical and biotechnological techniques allow us to customize microbial organisms so that they can do things they were not able to do so before. Current examples include the manufacturing of a raw form of insulin from bacterial cells. On the horizon are the development of biofuels, and plastics from such organisms. It is important to note increasingly these processes are replacing traditional chemical processes which may often use toxic chemicals and use more energy. One particular example may be Verenium's enzymes that replace the use of chlorine in bleaching paper so that it has a nice white color.

Concept-wise, these descriptions may sound a bit dry. A picture may say more than a thousand words. So following, I found a video on YouTube that exemplifies some of the concepts mentioned above. The video needs to be taken with a grain of salt. It is a bit dated as it still promotes the use of first generation biofuels. Although it is a promotional video meant to attract potential investors to invest money into green-biotechnology in region of Europe, it is quite illustrative to imagine how a bio-based economy may affect us daily in the future.

Video 1. Towards a Biobased Economy.

The Bio-based Economy and the Sustainable Economy

The bio-based economy may often be mentioned in conjunction with a sustainable economy confusing some. It's important to note that these are note competing ideas. Rather both concepts are motivated from the realization that environmental degradation and depletion of fossil resources go hand in hand. Hence, both terms imply a reduction of fossil resource use and a reduction of our impact on the environment. While both terms may overlap by quite a bit, they put slightly different emphasize. The sustainable economy refers more to a framework of conditions that simply said state that we shall not:

take more from the environment than what it can replace.
put back more waste into the environment than it can deal with.

A bio-based economy more heavily emphasizes how we are going to get there by defining what sources and techniques may be used in the manufacturing of products that drive our economy. Both concepts are needed so that we can convert our often linear production processes (from raw material to waste material) to a more closed system in which the waste material of one processes becomes the input material of another.

P.S. (2011-02-18): I have since this article came out done a bit more research on actual companies that incorporate these values into their products. Feel free to read my investigations into California companies that:

1.) Seek to produce biofuels
2.) Seek to produce other bio-based products

Suggested Reading:

Although I did not specifically quote any specific passages this time, the following are sources I read to synthesize this blog post.

[1] Octave S, Thomas D. Towards an industrial metabolism. Biochimie. 2009 Jun;91(6):659-64. Epub 2009 Mar 28. Link.
[2] Wohlgemuth R. Locks and Keys to Industrial Biotechnology. N Biotechnol. 2009 Apr;25(4):204-13. Epub 2009 Jan 21. Link.
[3] OECD Document on "Bio-based Economy". Link.
[4] Bruce E Dale. Sustainability Analyses of the Biobased Economy. Link.

Concept Discussion: How Directed Evolution will Save the World

2010-02-22T00:59:00.000-08:00

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 Directed Evolution?

To discuss this idea, we need to briefly go over the basic concept of evolution. Without going into the philosophical implications of evolution, evolution relies on the following observations:

1.) Variation: Be it butterfly populations, birds, or humans, you will probably notice that even within one species, there are clearly observable differences ranging from appearance, or size to things less observable, like the proteins within each cell.Where the differences came from is subject to a different discussion.
2.) Natural Selection: The environment imposes certain pressures. In natural selection an environment may make it harder for predators to find and eat butterflies that have darkly colored wings compared to white wing.
3.) Adaptation: If the pressures mentioned above persist, this will lead a species to adapt. In our butterfly example, over time this allows for the darkly colored butterflies to become more dominant in the environment, and a defining character of that species.

Similarly, we can "evolve" a protein. This is done in the following ways.

1.) First, we need to introduce variations of the protein in question. To change a protein, we need to go back and change the blueprint which is the underlying DNA sequence. Although this sounds easy, choosing which mutations to try try out is not an easy task.Trying out all different possible combinations is not really feasible. To give an often cited example, take a protein with just 400 amino acids. If we imagine proteins to be just letters on a string, and if at a given position, we want to just change 1 amino acid with another, there would be 20 ways of doing so. If we were to try to change just change 400 positions with any of the 21 possible amino acids, there would be 20^400 different ways of doing so. These are unimaginably large numbers. To give a comparison of how much this would be, the estimated number of molecules in the entire universe is only about 4*10^79 [1]. So the number of possible mutations far exceeds the estimated number of molecules in the entire known universe!!! Therefore, choosing which mutations to try out gives directed evolution its direction so to speak. We will explore some ways of how mutations are chosen in future blog posts.
2.) The proteins are then expressed, and subjected to the "selection pressure" which is some desired criteria we wish the protein to have. Some examples of criteria are: specificity, how fast it processes, stability of protein, or the ability to work under certain temperature or pH conditions. Proteins that fulfill the criteria are then selected for.

Why aren't proteins designed rationally?

Let's take a chair as an example. Making a naturally occurring protein fit for a particular task would be akin to making an imperfect chair where for example not all the legs are even. In the perfect world, we would be able to see which leg was short and fix the problem in a very direct way. In the real world, our knowledge of protein structures is very incomplete. Many structures are unknown. And it takes significant efforts to find the structure of just one protein. Making a chair more stable without knowing which leg is short is difficult. Nature's way is to randomly slightly change copies of the chair of unknown structure and then to test for the stability of the chair. In another analogy, when ants follow a certain destination along a planned route, and find the route blocked, the ants natural instincts would be to find a detour around the blockage by randomly searching around the blockage. Natural selection can be compared to the ants way to find the way around a blockage given their limited knowledge.

Take Home Message

The use of enzymes can in many cases reduce the need for energy or replace toxic chemical reactions. By using bioprospecting, we turn to nature to find potential enzymes suitable for a given task. By using directed evolutionary algorithms, proteins can be improved for specific industrial use. Directed evolution can therefore contribute to reduction of the human impact on the environment by producing things in more sustainable ways. In future posts, we shall explore some of the algorithms with specific examples. But next time, we will see how directed evolution fits within the larger picture of a bio-based/sustainable economy.

Literature Cited:

[1] http://www.answerbag.com/q_view/41233

Phosphorus

2010-01-17T14:56:00.000-08:00

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 complex multi-cellular organisms such as plants and animals. For instance, the cell membrane containing each cell consists of phospholipids, and the backbone of the information carrying molecules DNA and RNA consist of phosphate groups as well. For this reason, plants require phosphorus when growing: They absorb it through the roots in the soil. Animals, too, require phosphorus. But different from plants which can derive the needed phosphorus from the environment, animals rely mostly on other animals or plants to take up phosphorus by eating them.

What is the link between fertilizers and phosphorous?

Knowing that phosphorus is an essential element of life probably makes it less surprising to find that it is part of any fertilizer.
The interesting question was to ask where the phosphorus comes from. Historically, animal or human feces were commonly used for fertilizers because they naturally contain phosphates (and other essential nutrients of course). In fact, it was through boiling, filtering and processing of about 60 buckets of urine, how Henning Schmidt discovered phosphorus back in 1669 [2]. Today, organic matter has in many parts of the world been superseded by the use of modern synthetic fertilizers which use phosphate rocks as a source for raw material, which, interestingly, are only found in a few countries such as China, Russia, Morocco and part of the United States [1].
Phosphate rock, just like coal, oil, and other forms of fossil fuels, is a non-renewable natural resource. And this is the crux of the matter: Because we rely so much on synthetic phosphate fertilizers, the rate at which we consume the phosphate rock is rapidly increasing while the natural stocks are decreasing. In this context, Hubbart’s name is frequently mentioned who first observed and predicted in 1949 that oil will at some time reach a maximal rate of production when about 50% of the resources are still in the ground, after which production rates will go down. However, if demands are going up at the same time and costs for the raw material will likely increase as well [3,4,5]. This, Hubbart called “peak oil”, but it appears that the same fate will be true for phosphate rocks as well: There will be “peak phosphorus” in form of phosphate rock deposits that are quickly declining. But there is one big difference, however: Unlike oil, where alternatives exist for sources, there is no alternative for phosphorus. It is essential for life.

“Where do eutrophication and algal blooms come from?”, you ask…

This leaves us with the question why algal blooms and eutrophication are happening more and more often? Ironically, it is in some parts due to excessive phosphorus leaking into water streams. Overfertilization, discarded animal feces, and human feces in large cities often lead to phosphorus leakage into the natural water cycle where they stimulate excessive algal growth. The problem is partly due to the current economic model which currently promotes a very linear and inefficient use of phosphorus. Simplified, phosphorus is added to plants, which will then be eaten by food stock animals or humans. Humans and animals then use some of the phosphorus for their own body and excrete the rest again. A lot of it nowadays is flushed away, into the waste water stream where it is not always cleaned before release. This leads to the aforementioned problems.

Synthesis

There are a couple of interesting observations to make:
1.)    The poorest agricultural lands are being exploited because those who can afford it first need to import phosphorus and from one of the other countries. The farmer then applies the fertilizer to grow crops, exports these crops (and thus part of the phosphorus goes away although it is most needed in the poorer country.
2.)    So ironically, although phosphate rock deposits are rapidly declining, the concentrations of phosphates in the water is partly to blame for current problems. What then is the solution to the dilemma? Instead of the often linear processes which includes mining/manufacturing/discarding, new methods of phosphorus recovery should be searched and applied.
3.)    Declining phosphorus reserves, and the resulting price increases will also affect 1st and 2nd generation biofuel production.

Literature Cited:

1.)    http://en.wikipedia.org/wiki/Phosphorus
2.)    http://en.wikipedia.org/wiki/Hennig_Brand
3.)    Cordell, D., Drangert, J.-O., and White, S., (2009) The Story of Phosphorus: Global food security and food for thought. Global Environmental Change, 2009. 19(2009): p. 292-305
4.)    http://www.energybulletin.net/node/33164
5.)    http://phosphorusfutures.net/peak-phosphorus

Journal Club:" Correlation of cellulase gene expression and cellulolytic acticity throughout the gut of the termite Reticulitermes flavipes."

2009-11-27T00:45:00.000-08:00

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 the energy required to get a given reaction started. Most organisms do not have the necessary enzymes to break down cellulose. However, there are some organisms that do have them. Among these organisms are the termites.

Curious to learn more about cellulases, the enzymes that break the links between each glucose unit, in termites, we picked an article with the following title:

“Correlation of cellulase gene expression and cellulolytic acticity throughout the gut of the termite Reticulitermes flavipes.”

The authors in this paper used metagenomics approach to identify four open reading frames, predicted genes, in the sequences of the recently sequenced Reticulitermes flavipes. They then showed by PCR that these open reading frames are also expressed. The four genes are called Cell-1, Cell-2, Cell-3 and Cell-4. Cell-2 in particular was found to have at least one intron due to the fact that the genomic DNA sequence was larger than the cDNA sequence. Cell-1 was found to be highly similar to other termite cellulases. The other cellulose genes were more similar to symbiotic cellulases, meaning that these cellulases are not produced by termites themselves but by their prokaryotic symbiotic partners. Aligning Cell-2 to Cell-4, showed that only Cell-2 was lacking certain “tunnel forming loops” which are characteristic of exoglucanase. Cell-2 was then characterized as an endoglucanase.

The authors then looked at expression of the cellulose genes. They found that Cell-1 was mainly expressed in the fore-gut and salivary glands, while the remaining cellulases are expressed in the hind-gut. Characterizing endoglucanases, exoglucanases, and xylanases with respect to the location showed a strong bias of endoglucanases for foregut regions (~65% of all occurances) vs hindgut regions (~27%). For exoglucanases, the picture was reversed 61.5% occurance in hindgut and only ~14.0% in the foregut. Xylenases, on the other hand, were almost exclusively found in the hindgut. Endoglucanses break internal bonds to disrupt the crystalline structure of cellulose and expose individual cellulose polysaccharide chains. Exoglucanases cleave 2-4 units from the ends of the exposed chains produced by endocellulase, resulting tetrasaccharides or disaccharide such as cellobiose. Xylenases degrade beta-1,4-xylan into simple wood sugar. The distribution of Cell-1 through Cell-4 therefore mimics the logical breakdown of complex wood material into simple sugars.

Although most of the findings were not too surprising, I enjoyed reading this paper for the well-written introduction, and the logical approaches biologists can take to perform a relatively simple characterization of novel genes using simple bioinformatical tools. Performing these kinds of characterizations can help in the further optimization of wood degradation processes.

News Flash: 30% Efficient Solar Power Silicon and Nitrite

2009-10-03T09:52:00.000-07:00

As reported by Greentechmedia on September 28th, Phoenix-based Rosestreet Labs Energy (RSLE) has successfully tested a new prototype of solar panels able to convert between 25-30% of sunlight into electricity. For comparison, the current maximum for conventional silicon-based solar panel is produced by SunPower can convert around 22.5% of sunlight into electricity. So the increases by RSLE represent a quantum leap in efficiency increases. The efficiency gains come at a cost of increased production costs. RSLE aims to lower production cost to below $ 1.50 per Watt by 2014 which is a goal already achieved by some solar panel manufacturers today.

RSLE claims to achieve this feat by combining silicon-based solar technology with other nitride-based alloys - in this case indium and gallium. The combination of silicon and indium and gallium nitride can make use of a broader spectrum of the visible light resulting in higher efficiencies. According to a 2005 press release, unlike conventional technology which is close to achieving the theoretical maximum, RSLE believes that their "Full Spectrum Technology" can reach efficiencies of up to 48%.

Plans for beginning of production of the HYBRID solar panels are set to start in the 4Q of 2010. In order to achieve this goal, RSLE has already received an undisclosed amount of funding from Sumitomo Chemicals and has started a Series A.

On a Broader Note

This news, and other recent news from many new start-up companies indicate that solar power generation is gaining momentum despite the current economic climate. Nanosolar or Prism Solar in particular represent technologies that potentially are disruptive in a sense that they can propel solar technologies into the main stream because their technologies can achieve such radical reductions in production costs through change in manufacturing or reduced use of resources.

On a personal note, I wonder if these technologies are compatible, and wonder what potential synergies can be achieved by combining the print-technology from Nanosolar, the nitrite alloy technology from RSLE and titanium dioxide nanostructures mentioned in my previous post for higher yields, with Prism Solar's solar concentration technology for reduced use of the raw material.

The combination of reducing the cost of electricity generation per Watt to be competitive with conventional energy sources, innovative financing options of through solar leasing (offered by companies such as Citizenre, SolarCity and other companies) as well as promotion of group discounts through block buying for residential applications (offered through companies such as 1bog) can sufficiently reduce the hurdles for entry into the solar market in the next few years. Bright times are ahead if political obstacles are removed and replaced with a reasonable and responsible regulatory framework that promotes the upgrade of the electrical grid.

Of Diatoms, Titanium Dioxide and A Bio-based Way to Increase Solar Power Efficiencies

2009-09-19T19:18:00.000-07:00

Prolog:

It has been a while since last I discussed a scientific journal paper. The following post is based on a paper published in the American Chemical Society NANO Journal (Vol.2, No. 10, pp 2103-2112) with the title “Metabolic Insertion of Nanostructured TiO2 into the Patterned Biosilica of the Diatom Pinnulario sp. by a Two-Stage Bioreactor Culvtivation Process”.

What have they done?

The Rorrer lab is a nanotechnology/biotechnology engineering lab. They manipulate various microorganisms so that the microorganisms produce substances that are of use to human kind. Their latest series of publications has focused on diatoms which are single-celled algae that are able to make silica shells with very intricate patterns (see below). The Rorrer lab has a significant body of work inducing a particular diatom by the name of Pinnulario sp. to incorporate optoelectronic substances into its frustules (outer shells) that it normally would not. Optoelectronic substances can transform, transmit or sense different forms of light.

Figure 1. Microscopy Image of Pinnulario sp. Go to London Natural History Museum Website

to read more about this organism. It's where this image is from.

In their latest work, Clayton Jeffryes et. al. have found conditions to cultivate these diatoms in such a way so that they incorporate titanium dioxide into the silica shell of the diatoms – something that these diatoms don’t do on their own. They did so by simply changing the media conditions. Initially, algal cells were starved for silicon dioxide. After starvation limited amounts of silicon dioxide mixed with titanium dioxide is fed back into the system. Under these “starved conditions” diatoms incorporate titanium dioxide into the frustules in addition to the normal silicon dioxide. When these diatoms are fixed onto glass slides and then gently washed with a detergent mixture (SDS/EDTA), the life cells are washed out of the silica shells, and the silicon/titanium dioxide skeleton is left behind.

Why is this significant?

The price per watt for solar panels is related to the cost for materials, manufacture, installation and maintenance and the amount of electricity that can be generated to payback the upfront cost. To increase distribution, the life-time cost for solar panels must come down. In different approaches, this could be achieved by reducing the use of the raw material through methods such as thin-film technology, and various light concentration technologies. Alternatively, the efficiencies of converting sunlight to electricity could be increased.

Titanium dioxide is known to be able to “trap” light particles called photons. The process of trapping these photons can dislodge additional electrons. In this way, small amounts of titanium dioxide can enhance photovoltaic properties of solar panels. The light trapping properties of titanium dioxide can be improved if titanium dioxide molecules are arranged in a certain periodic manner. However, this has been very difficult thus far. Using modified enzymes to precipitate titanium oxide out of solution has not thus far been successful in creating ordered titanium oxide structures. As an alternative, diatom frustules have been used as templates for “spraying on” titanium dioxide which requires much heat, and potentially harmful chemicals (titanium tetrachloride). This work by the Rorrer lab is significant because it describes a highly scalable, bio-based way of producing large of amounts of titanium dioxide that is arranged in a three-dimensionally ordered way.

Were this technology to be commercialized, at this time, it would still add too much cost to justify the increase. But one day, combining different technologies such as thin-film, light concentration with titanium dioxide doped bio-silica could make solar panels much more efficient than the mere ~ 20% current top-of-the line solar panel technology has to offer. The increased output could help to bring the cost of energy created per watt down sufficiently and make the dream of mostly relying on alternative energy sources come true.

Focus on Algae - Part II: Energy

2009-08-22T16:16:00.000-07:00

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 desired.

Figure 1. Modes of Algal Biomass Conversion adapted from Bet Wang et. al. (2008).

Using biochemical techniques or microorganisms, the algal biomass can either be fermented or anaerobically digested. The first can yield ethanol, acetone and butanol while the latter would produce methane and hydrogen [2].

There are several ways of thermochemically converting the biomass into usable fuels. Pyrolysis, the process of chemical breakdown at high temperatures (~ 500°C) in the absence of oxygen, can produce some oil and coal also known as bio-oil, and biochar to better distinguish their origins from the traditional fossil fuels. Gasifiers take the biomass or biochar and convert them into a combustible gas mixture (sometimes called syngas) under even higher temperatures (~800-900°C) but limited oxygen conditions. Liquefaction on the other hand, uses uses high pressure, but rather lower temperatures (~ 200°C) to convert the biomass or biochar into bio-oil. And lastly, purely chemical processes take advantages of the abundance of lipds in the cell membrane of the algae. Additionally, many algal species are known to accumulate various amounts of oils inside the cells. These amounts can vary anywhere from ~ 30-70% of the dry biomass [1].Using transesterification reactions, biodiesels can be produced [3]. It should be noted that many of these processes have occured naturally in the environment under geological conditions. This is what produced the fossil fuels. We are just enhancing the processes in controlled and optimized conditions using current biomass instead of biomass from the past.

Advantages of Using Algae for Biofuel Production

The advantages of using algae for biomass generation are plentiful. For one, algae have the advantage of not competing with valuable arable land and water needed to cultivate food crops. Depending on the type of algae used, fresh water may not even be needed. More importantly, although there are significant differences between different algal species, the generation time, that is the time it takes for an algae cell to divide, is much faster than for any other land-based plant. This can be as little as one hour! As a result, biomass can be generated much quicker than achievable with any land-based plant.

Figure 2. Integrated uses of Algal Biomass adapted from Yusuf Chisti (2008)

The methods mentioned above are not mutually exclusive. Rather, there is great potential to combine several processes into an integrated a pipeline which is where the greatest benefits of using algae for biofuel generation lie. One possible pipeline could start with waste water streams that are used to grow algal biomass while cleaning up the water and removing carbon dioxide in the process. Some of the biomass generated could be refed to the system while the majority is used for bio-oil, or biodiesel production through various extraction methods such as transesterification. The remainder after biomass extraction can still be used further downstream. The remainder of the biomass is still rich in nitrogen, phosphorous and protein sources which is ideal for animal feed (potentially posing some public concerns that need to be addressed) or fertilizer material. Alternatively, the biomass could be pyrolysed or anaerobically digested to produce biochar or biogas usable for cogenerating electricity and heat that the surrounding communities could use [3].

Challenges to Algal Biofuels

Despite the promises of algal biofuels, the current fraction of biofuels generated from different sources of algae is rather small as costs associated with the challenges and research to overcome them are still high.

The major challenges in algal biofuels come from dealing with sources of contamination that could out-compete the algae to be cultivated, and high energy costs associated with potential circulation of the system as well as biomass recovery. To bring down the cost, test sites need to be scalable which in itself can represent difficulties with some approaches. Research on all these fronts costs money a lot of money.

All these factors contribute to current cost of biofuel generation from algae. For only biodiesel production, the estimated current cost is estimated to be about $ 33 a gallon. However, the cost significantly comes down to about $ 5.50 when integrative approaches are used such as cogeneration of electricity and heat. A further cost reduction to about $ 3.50 can be achieved from selling algal byproducts such as animal feed, fertilizer materials, or other high-value products on the near-term [4]. Although much more manageable, this is still slightly higher than the current cost of diesel. But research to enhance efficiencies are being researched to lead us to price competitiveness.

Innovations in Algal Biofuels

Despite the challenges, many companies across the world are pushing forwards with their efforts to bring algal-based biofuels to the market supported by an increased effort of academic research, government subsidies, and changes in the regulatory-framework.

Current research is focused on finding more suitable algal species through bioprospecting. Genetic engineering can improve biomass generation, increase the oil content, or improve the sturdiness of algal species for a given condition. Up to now, the extraction process also killed the algae. But, as discussed on NPR's Science Friday show (3 July 2009), the possibility to develop technologies for "milking" the algae without killing is being researched.

On the industrial side, many companies are putting their ideas to the test by bringing their innovative approaches to the growing but challenging biofuels market. While Solazyme has adapted the approach of growing algae in completely dark vats and feeding them sugar [5], other companies such as Solix have worked on bringing improved bioreactors to large-scale [6]. Other companies, such as Sapphire Energy have focussed on directly extracting 'green crude oil' from algae [7]. There are also a couple of companies working on converting sewage water into biodiesel. A New Zealand company named, Aquaflow claims to have been the first company to successfully do so all the way back in 2006 [8].

By no means is this supposed to be an expansive list of current innovations in the field. But one thing is clear: Despite the 20 year history of research into algal biofuels, it only seems that now conditions and research have come far enough to seriously consider algae for biofuels. Which of these companies will eventually become successful is unknown at this time. Many hurdles remain. But the examples, hopefully, provide a glimpse to the bright future of algal biofuels and explain why there is so much excitement in the field.

Quoted Sources:

[1] Venice Seaport Eyes Algae for Energy Needs. Visited: 2009-08-21. www.reuters.com
[2] Bet Wang et. al. (2008) CO₂ bio-mitigation using microalgae. Appl Microbiol Biotechnol 79:707–718
[3] Yusuf Chisti (2008) Biodiesel from microalgae beats bioethanol. Trends in Biotechnology Vol.26 No.3
[4] Algae Biodiesel: It's $33 a Gallon. Visited: 2009-08-22. www.greentechmedia.com.
[5] Solazyme Produces World’s First Algal-Based Jet Fuel . Visited: 2009-08-22. www.solazyme.com
[6] Solix Biofuels Begins Large-Scale Production of Algae-Based Biofuels at Coyote Gulch Demonstration Facility . Visited: 2009-08-22. www.solixbiofuels.com
[7] Sapphire Energy turns algae to 'green crude'. Visited: 2009-07-20. www.sapphireenergy.com
[8] NZ company makes bio-diesel from sewage world first. Visited: 2009-07-21. www.nzherald.co.nz

What are Biofuels?

2009-08-09T20:09:00.000-07:00

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 the oil and burn it, we are releasing carbon dioxide that was removed from the atmosphere millions of years ago. The idea behind biofuels is that instead of releasing all the carbon dioxide stashed away millions of years ago, we become "carbon-neutral" by only relying on carbon sources that recently died to make gasoline.

Take corn for instance. When corn is growing, carbon dioxide is removed from the atmosphere as the plant incorporates the carbon into various cell components of the growing plant. Corn fermentation, the same process that also makes beer and fine wines, produces ethanol which can be used as a fuel to run cars. So when ethanol is burned in a car, the only carbon released into the atmosphere again in the form of carbon dioxide is the one that the plant absorbed before. Different plants can be used depending on climate and local geographical conditions. But the previous example, describe the basic idea behind the first generation biofuels. Theoretically, this describes a closed loop circuit which is close to carbon neutral because carbon dioxide released does not come from oil but from the plants we grew to make the fuel.

Disadvantages of First Generation Biofuels

In reality, however, especially corn-based ethanol has many problems. First, there are certain technical issues related to the inefficiencies of converting food crop into ethanol. Energy cost of production, and transportation of crops and fuel further reduce the theoretical yield and make these first generation biofuels less carbon neutral.

More importantly, there are concerns that high demand for energy crops could lead to increased deforestation because it may become more profitable to make more room for energy crops. Clearing of land for energy crops often happens in the form of burning forest land which releases more carbon dioxide than would be absorbed by growing just monocultures of corn. Scientist call this a "carbon debt".

Lastly, corn is also a food source for humans and other animals. Faced with limited arable land mass and water resources, increasing the demand for corn so that it can be used for fuel generation also increases the food price of these products. Because poor people can ill afford to pay more money for basic food sources, even small increases in the price can have devastating consequences on a families ability to buy basic sources of food in the third world.

Further research and careful policy making can potentially contain each of the above mentioned problems. In the next post, we shall look at the advantages one such approach and ask how algae can generally be used to solve some of the energy challenges we face today.

"Bio-based" Search Engines

2009-07-28T03:08:00.000-07:00

I am still working on the second part of the focus on algae, and between research, and moving to a new place, I am not finding just enough time to flesh out the article just yet. It will come though!

Instead tonight, I wanted to write an informal entry on a particular aspect of "bio-based" ideas: what anyone can do for environmental protection and conservation. In most of the industrialized world and beyond, internet access is pervasive. I find that I am spending quite a bit of time on the internet be it for email, searching information, social networking or gaming. I am sure others will have their own habits on the internet.

It's easy to forget that each action on the internet actually has an environmental cost associated with it. The computers used to read this blog use electricity. Games can be demanding on the graphics card which if high-end can use even more energy than the CPU itself. Beyond the borders of your own computer, each action one takes puts a certain work-load on server machines located somewhere else. And of course these server machines also consume varying amounts of energy.

With all the talk about carbon footprint, it may not be surprising to find that surfing the internet also has a carbon footprint. Searches especially despite the apparent simplicity can consume a lot of energy - sometimes as much as a 11 Watt light bulb in an hour!

For this reason, I just wanted to introduce two green search engines:

1.) Znout
2.) Forestle

These search engines don't actually use new algorithms that are more efficient or anything. In fact, Forestle is a custom search engine using the Yahoo! search engine, while Znout uses Google. What makes these custom search engines green though is what they do with the revenue generated by searches.

According to the website, Znout stands for "zero negative output" and is a CO₂ neutral Internet search engine that turns your web searches into green web searches by keeping track of energy usage, and carbon foot-printing and off-setting these by buying renewable energy credits at the end of each month.

Forestle goes a step further. In addition to purchases of renewable energy credits, Forestle uses ALL the revenue minus 10% for administrative costs by donating the remaining profits to The Nature Conservancy's "Adopt an Acre" program.

Because the search engines are based on the two main search engines - Yahoo! and Google -, the search results should be very familiar. Switching to these search engines is easy. They even have a search plug-in feature so that you can search from the comfort of your browser.

Anyway, give these search engines a try, and help save the environment while searching/browsing the internet with them.

Focus on Algae - Part I: Bioremediation

2009-06-12T18:24:00.000-07:00

After spending the last few blog posts on different aspects of dissimilatory bacteria, I want to switch the focus to a different class of organisms I have been interested in for a long time now. These are the algae. Algae comprise a large diversity of "sea weeds" and an even larger variety of single-celled organisms that mostly are capable of doing photosynthesis. They include the ordinary sea-weed, and make up a portion of the green slime found around the edges and the bottom of a pond. More exotic types of algae can live symbiotically - that is together with another organism in a mutually beneficial way. Lichens are an example of symbiotic relationship between algae and fungi. More information about the evolution and lineage of algae can be found in this wiki article.

Image via Wikipedia

Typically, these organisms are either not mentioned at all or only in conjunction with toxic algal blooms. But lately, algae, of course, have been in the news recently because of the promise of these organisms have for lessening the effects of global-climate disruption and energy dependency on other countries. In the next few blogs, we shall explore the different ways how algae can be used to combat the things mentioned above. We will start with waste water treatment.

Bioremediation in General

Waste water treatment is a wide field because waste water can come from a big variety of sources ranging from agricultural waste, to residential waste to specialty industrial waste. Within the scope of this overview it would be too much to go into details for all of them.

Typical residential waste water treatment consists of three stages. In the first two stages, large debris and physical matter are removed through a variety of filtration and sedimentation techniques. Generally, though contaminants in waste water such as excessive organic compounds (think of human or animal excretion), including excessive nitrogen or phosphate sources and heavy metals are not removed.

The third stage in waste water treatment deals with the above problems. Here, microbial organisms are stimulated to degrade these contaminants. This is either done by a process called "activated sludge" in which the waste water is aerated and mixed to stimulate the microorganisms to degrade the waste. Although very effective in waste removal, this process also takes up a lot of energy because it takes a lot of energy to continually mix large amounts of waste water. An alternative to activated sludge, are trickling filters. In this process, the waste water is drizzled over large pools containing many rocks. The rocks are colonized by a variety of bacteria, fungi and some algae. As the waste water slowly dribbles along the many layers of moist rocks, again microbial organisms degrade the waste.

Third stage water treatment has several disadvantages. As previously mentioned, third stage water treatment can be extremely energy intensive and therefore financially expensive. In addition, irregularities in the water conditions can lead to fouling. Communities surrounding the area may therefore experience bad odor on occasion. Lastly, waste water treatment itself produces waste which is known as "sludge". This sludge consists of water insoluble waste products the bacteria themselves excrete and a lot of dead cells from the dividing bacteria. The sludge is usually considered toxic as well and has often been discarded by dumping into land fill sites - an unideal solution.

Algal Use in Bioremediation

Instead of using mainly bacteria, it is also possible to use mainly algae to clean waste water because many of the pollutant sources in waste water are also food sources for algae. Nitrates, and phosphates are common components of plant fertilizers for plants. Like plants, algae need large quantities of nitrates and phosphates to support their fast cell cycles. Certain heavy metals are also important for the normal functioning of algae. These include iron (for photosynthesis), and chromium (for metabolism). Because marine environments are normally scarce in these metals, some marine algae especially have developed efficient mechanisms to gather these heavy metals from the environment and take them up. These natural processes can also be used to remove certain heavy metals from the environment.

The use of algae has several advantages over normal bacteria-based bioremediation processes. One major advantage in the removal of pollutants is that this is a process that under light conditions does not need oxygen. Instead, as pollutants are taken up and digested, oxygen is added while carbon dioxide is removed. Hence, phytoremediation could potentially be coupled with carbon sequestration. Additionally,Because phytoremediation does not rely on fouling processes, odors are much less a problem.

Of course, phytoremediation is not without problems. The main problem in phytoremediation is contamination and competition with bacteria. Eukaryotic algae have much larger genomes, and more complex cell machinery. Therefore, takes much longer for an algae to divide (a few hours) compared to bacteria in ideal conditions (less than an hour). If conditions are not carefully monitored, bacterial populations could out compete the algae and push them out of the water ecosystem at the treatment plant. Furthermore, algae although sturdy are more sensitive compared to bacteria. So water conditions have to be monitored carefully to not overexpose the algal populations to the pollution sources and thereby killing them.

Nevertheless, algae have several very exciting alternative uses that could theoretically be coupled to the remediation processes. We will go over some of these applications in the next section.

From "Eavesdropping on Bacterial Conversations" - Part II

2009-05-23T22:54:00.000-07:00

In the last part, we covered a important way of how bacteria communicate to each other through quorum sensing. The LuxI-LuxR system describes an interesting signaling system used by bacteria of the same species.

Professor Bassler's laboratory is especially known for her work on autoinducer 2 (AI-2) system which allows for inter-species communication. The discovery of AI-2, and its fundamental workings were a true scientific detective stories with twists and turns, and its implications are still being researched today.

Work on a different luminescent marine bacterium, Vibrio harveyi, revealed that regulatory apparatus for creating luminescent was more complex. It relied on two separate input signals: AI-1 and AI-2 which were recogized by two membrane spanning receptor kinases LuxQ and LuxN respectively. How AI-1 and AI-2 are involved for luminescence may be less important here except to say that both signals need to be present. While more information could be inferred about AI-1 in V. harveyri because its structural similarity to that of V. fisherii's autoinducer, the real mystery was how AI-2 worked. Three key realizations helped to establish the role of AI-2.

1.) Firstly, the realization that the LuxS gene is involved in catalyzing the last step in the creation of homocysteine along with pro-AI-2, helped to solve the mystery that AI-2 is derived from the ribose structure that is part of S-adenosylhomocystein (SAH). Because the derivative structures of pro-AI-2 is highly unstable in the environment, the mystery remained what AI-2 looked like.
2.) However it was possible to use AI-2 as a bait for pull-down and purification of its receptor counter-part which was hypothesized to exist. The Bassler lab was successful in its effort to identify this receptor now known as LuxP. Ultimately, this led to the first co-crystal structure of LuxP and AI-2. The structure of AI-2 opened up a new question: What stabilized the furansyl borate diester bonds at the unassigned electron densities? The team spent months puzzling over this because although carbon's electron densities were very similar, carbon does not form stable diester bonds.
3.) To solve the puzzle of the unassigned electron densities, the team had to discover the possibility of boron, which is abundant in the oceans, being in the position of the electron. Further experiments, in which cultures of V. harveyi were optionally exposed to boron confirmed that boron is needed for bioluminescence.

The mystery was solved. But what is the significance of AI-2?

Take-Home Message: Bacterial Esperanto and what's so important about AI-2

It was soon discovered that homologues of receptors like LuxP existed in most other eubacterial species as well. Furthermore, as mentioned before, because AI-2 has such unstable diester bonds, many different isoforms exist and interconvert within a solution with AI-2. Much work in other species soon confirmed that different bacterial species recognize and bind different isoforms of AI-2. That is highly significant because whereas the LuxI-LuxR genes describe a highly specific form of communication. The AI-2 secreted by V. harveyi can interconvert into a molecule a different bacterial species can recognize and understand. Hence, bacterial Esperanto is born. Bioinformatics analysis revealed that AI-2 diverse roles in signaling are associated with formation of biofilms and virulance offering new avenues of attack in treating bacterial diseases. Reagents could be developed that would destroy AI-2 type signals. This could reduce the virulence of a particular bacterium. Professor Bassler remarked that in many ways, nature is already exploiting these forms of communications for its own survival. Over time, many bacterial species have developed a variety of ways to eavesdrop, change or mute another bacterial specie's messages for its own uses.

Professor Bassler concluded by reflecting on the nature of multicellular eukaryotic organisms: There is communication between cells of the same type, cells of different types, and even organisms of different types. If simple, modern bacteria can talk to each other and form complex structures in biofilms, the assumption is not too far off that perhaps the basis for multicellularity could have been born in the bacterial kingdom.

From "Eavesdropping on Bacterial Conversations" - Part I

2009-04-04T17:32:00.000-07:00

Though many talks are interesting, once in a while there comes a talk in a graduate student's life that is so inspiring in both content and presentation. Today was one of these days. I attended the the "Intersectional Seminar Series" here at USC which is a seminar series meant to bring the different separate biology programs - Molecular and Computational Biology, Marine and Environmental Biology, Integrative and Evolutionary Biology and Neurobiology -together. Today's speaker was Bonnie Bassler from Princeton, and her talk title was "Eavesdropping on Bacterial Conversations". Today's blog entry is dedicated to the rich history of ideas she discussed in her talk. I apologize in advance to the longer than usual post and the higher than usual complexity as I try to accurately report back the ideas discussed in her talk.

To most lay people, the idea that simple, single-celled bacteria could use sophisticated means of communication may seem rather strange. But as early as 1979, Nealson and colleagues showed that a bacterial species with the name of Vibrio fisheri can communicate to other cells of each species to produce a light in a coordinated fashion. Vibrio fisheri are normally found in low abundance in almost all the world's oceans. The interesting thing is that these bacteria can detect each other. When the bacteria sense that enough of its brethren and sisters are around, all bacteria of that species start producing light. The picture to the left, taken from Science Daily, shows a flask of bioluminescent bacteria. Vibrio fisheri are also found living symbiotically within certain marine animals of the twillight zone (layer of ocean water receiving little light from 200-1000 m) where they are selectively captured and nurtured within the hosts "light organs" to serve many different purposes from blending with the environment, acting as an alarm system to serving to attract prey.

How does Vibrio fisheri know how many other cells are around it?

Two genes are responsible for this. The LuxI gene which is always expressed in Vibrio fisheri, produces a protein called Autoinducer synthase. This protein sythesizes a small molecule generally called the autoinducer which immediately diffuses out of the cell into the surrounding. For those interested, this small molecule is called N-3-oxohexacyl-l-homoserine lactone or OHHL for short. When there are very few bacteria around, the autoinducer leaves the cell too quickly to bind to the LuxR receptor, but when many surrounding bacteria are present, the concentration of the autoinducer increases. At some point, the concentration of the autoinducer reaches a point where the autoinducer cannot leave the cell quickly enough. Some autoinducer from the environment may even diffuse back into the cell. Another gene - the LuxR - gene produces the LuxR receptor protein. This protein can recognize the autoinducer and bind to it. Upon binding, the LuxR-Autoinducer complex activates transcription of a set of proteins that lead to bioluminescence. This is the way, the LuxI-LuxR gene pair works together to "sense" how many of its brethren and sisters are surrounding it.

This concept is known in to biologists as quorum sensing. And what was thought to be an isolated occurance in Vibrio fisheri has now been found to be a common mechanism employed by many bacterial species. And the genes controled by LuxI-LuxR-like gene pairs have many different fucntions often having to do with biofilm formation and virulence in disease causing bacteria. The interesting part to note are two aspects. Each bacterial species has:

1.) its own LuxI-LuxR-like gene pair. They are similar but not the same.
2.) Each bacterial species has a very similar but very specific autoinducer. The autoinducer of one species is not recognized by another species.

A side remark: The discovery that LuxI synthesizes a homoserine derivative is in itself an exciting discover. The LuxI and LuxR gene pairs exist in different operons for different species. Operons are sets of genes that are always turned on or off together. One of the remarkable insights was to recognize the significance of finding the LuxI gene within a set of other genes responsible for the synthesis of threonine if my memory serves me right. Homoserine lactone is a metabolite meaning that it is generated as a product of metabolism. Two other enzymes are responsible for the first two step. The LuxI gene acts in the third step of the reaction.

What's the Take-Home Message?

In this first part, the LuxI-LuxR gene pair describes a system in which bacteria of the same species can release small chemical molecules as a means to specifically talk to members of their own species.

What's up next?

Next time, I will try to accurately summarize a system that potentially allows bacteria of different species to talk to each other in what Professor Bassler called "bacterial Esperanto".

Supplemental Sources:

For the writing of this blog, to ensure factual accuracy, in addition to the intersectional seminar, I was using the following source:

Pappas, K.M, Weingart, C.L, Winans, S.C. (2004) Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling. Molecular Microbiology (2004) 53(3), 755-76.

http://animals.howstuffworks.com/animal-facts/bioluminescence.htm/printable

Part III: Dissimilatory Bacteria in Uranium Reduction

2009-03-28T13:25:00.000-07:00

Last time, we explored how dissimilatory bacteria can be used to generate electricity in devices called Microbial Fuel Cells. In part one, I mentioned that the dissimilatory properties of bacteria like Shewanella can potentially also be used for solving part of the problem of radioactive uranium contaminations. When I mentioned this idea to my friend who is a soil scientist, I realized that I did not know how these bacteria can be used to contain uranium contamination. Curious about how exactly this works, I found a review article titled “Uranium Reduction” in the Annual Review of Microbiology written by Judy D. Wall and Lee R. Krumholz (Vol. 60: 149-166, Oct 2006). Following is a summary of what I found.

Uranium is a metal with the symbol U on the periodic table. It has the atomic number 92 which means that it has 92 protons and electrons. In nature, occurs in three different forms U-238 (~ 99.238 %), U-235 (0.711 %), and U-234 (0.0058%) where each number refers to the combined number of protons and neutrons [1]. All forms are slightly radioactive, but it is the ability of this metal to react with any non-metal that makes this metal chemically very toxic [2].

Most people may not know that uranium contaminations are a problem. Part of it has to do with the fact that uranium is not rare being the 49th most abundant element in the earth crust. In recent years, with the advent of nuclear power, and nuclear weaponry, mining, refining, and nuclear testing has lead to different forms of environmental contamination in some areas. Just within the United States, the Department of Energy (DOE) has identified 120 sites covering 7280 km2 in 36 states and territories. This is about equivalent to the area of the entire urban area of New York City. Mining of uranium in Colorado, New Mexico, and Arizona for example has led to local contaminations of the water as uranium salts leach into the ground water.

The solution to soil and water contaminations is normally to employ microorganisms to bioremediate the contaminated area. Specialized bacteria are able to break toxic contaminants down into less toxic substances.

The problem with uranium and other heavy metals is the ability of these metals to form water soluble complexes and compounds with other non-metallic and organic substances that are often harmful to living organisms when consumed. Heavy metals being elemental also cannot be broken down any further. Because of that the only currently known strategic approach to bioremediation of heavy metals of contaminated soils is to decrease availability of the heavy metal to living organism (called bio-availability).

In water or soil sources, uranium is mostly present as soluble salts in form of uranyl (UO2+2) which has an oxidation state of U(+6). Many metals have the ability to assume different oxidation states. It turns out that when uranium has an oxidation state of +4 only it becomes much less water soluble. By changing the oxidation state, thus, uranium could be precipitated out of the water. As a reminder, dissimilatory bacteria are capable of externally passing electrons onto metal oxides. By gaining electrons, the metal oxide is reduced to a lower oxidation state. It turns out that a growing number of dissimilatory bacteria are capable of reducing uranium. Our friend Shewanella is one of them.

Many issues remain to be solved. Some include the possibility of redissolving precipitated uranium, and the question of how to sequester the precipitated uranium to to contain its spread, but the ability to use microorganisms to precipitate uranium out of groundwater represents an important step because this reduces the bioavailability of uranium to living organisms.

Part II: Microbial Fuel Cells (MFC)

2009-03-08T11:35:00.000-07:00

I can’t believe how fast time passes. I have been meaning on writing this post up for a long time now. In the last post, I just was introducing Shewanella onedeinensis and its ability to transfer electrons from a variety of organic substrates to metal oxides. Today, we shall look at one possible application for such a microbe: using bacteria to make electricity.

This is done through contraptions called Microbial Fuel Cells (MFCs) but to understand MFCs we need to first understand how fuel cells work. There is going to be some detail. But the take-home message here though is: We can use certain bacteria to make electricity out of waste.

A fuel cell is a device that produces electricity as long as one provides an external source of fuel and a source that accepts electrons known as oxidants. This is different from normal batteries because batteries simply release the electrical energy stored within them. They get tossed once they are used up. In the case of rechargeable batteries, energy must be put back into them first before they can be used again. A fuel cell will continue to work as long as the fuel is provided externally. In other words, a battery is an electrochemical storage device. A fuel cell is an electrochemical conversion device.

The diagram to the left is from a journal called "Emerging Environmental Issues" (Volume 10, 2005). The archetype of a fuel cell is a hydrogen fuel cell. Let’s look at how this fuel cell works going from left to right. In a hydrogen fuel cell, hydrogen flows into one side of the fuel cell (the anode side). Hydrogen consists of one positively charged particle (called proton) and one negatively charged particle (called electron). There is a special membrane that is able to separate electrons from protons and a solution that allows the protons to travel to the other side of the fuel cell (called electrons). This is an unstable state and for the reaction to become stable again, positive and negative charges must balance. The only way for the electron to catch up with the traveling proton is to travel through a wire to the other side. Hence, we have a flow of electrons – electricity that can be used to do work. At the other side, the oxidant is ready to accept the positively charged proton. 2 protons and 2 electrons combine with one oxygen atom to form water (H2O). In a nutshell, this is how a hydrogen fuel cell works.

Microbial fuel cells work in a very similar way. However, the fuel in this case is not hydrogen, it is a carbon source instead. Sugar is an example of a carbon source. Bacteria like our Shewenella that live on the anode are able to consume the sugars. Under anaerobic conditions, in the simplest case, these bacteria release a proton while depositing electrons externally onto the anode. Like with the hydrogen fuel cell, electrons and protons must combine with an oxidant at the cathode. In the process, electricity is created.

So why is this useful?

In many cases, urban waste waters contain many organic pollutants. These pollutants if released untreated into the environment can cause a lot of environmental damage. This is the reason why ideally waste water treatment is important, but can be very energy intensive because bacteria need to be constantly mixed and aerated in large tanks. What if instead of consuming a lot of electricity, we can use MFCs to clean up some of the waste in the water and at the same time generate part or all of electricity?

In reality, there are many challenges to make MFCs practical as discussed in review article titled “Towards practical implementation of bioelectrochemical wastewater treatment” (Trends in Biotechnology, Vol 26 No 8). Electricity generation in MFCs has been very small (< 1 amp/m2). In laboratory conditions, MFC performance has exponentially increased though. Over the last few years, it has reached 10 Amps/m2 and is likely to increase even more with more technological innovations. These, however, represent laboratory conditions only where optimal yields are obtained through use of special synthetic media in monocultures.

In waste water treatment, however, open souces of water means that organic food sources vary and are not optimal. Furthermore, monocultures cannot be maintained. There is much research done on this end. Research groups are experimenting with better anodes, MFC designs and ways to engineer “bacterial communities” to increase MFC performance in these scenario. And so I think it is only a matter of time until we will start seeing them used for waste water. Next time, we shall look at how these bacteria could be used in just cleaning up uranium waste.

Dissimilatory Bacteria - Part I: Model Species Shewanella oneidensis -Organism Introduced

2008-12-30T01:39:00.000-08:00

Today I came across a really interesting review article with the title “Towards environmental systems biology of Shewanella” that was published in the Nature Reviews journal (August 2008). I became interested in it because the organism has some very interesting properites. Furthermore, the review article shows how interdisciplinary fields such as biology, chemistry, bioinformatics, and engineering can work together to come up with new ideas. So in the next two posts, I will describe what these little organisms are and explore a few unique potential uses.

What is Shewanella spp?

Shewanella spp is a genus of many related microbes that lives in many aquatic and sedimentary ecosystems under aerobic as well as anaerobic conditions where it can use many carbon sources as its food. Although the microbes have been in culture collections since the middle of the 20th century, it was not until 1988 that work on a particular member Shewanella oneidensis MR-1 lead to the recognition for microbes in this genus to transfer electrons to solid a great variety of metal oxides (called reduction) when there is no oxygen (anaerobic conditions). There are a few other bacterial species that can do this, however, S. oneidensis are remarkably able to perform this task to metal oxides outside the cell which is known as dissimilatory.

The versatility of alternate electron acceptors in Shewanella species includes metal oxides (iron, manganese, urianium (IV), chromioum (IV), iodate, technetium, neptunium, plutonium, selenite, telleurite, and vanadate oxides) and some nitroaromatic compounds. The ability to use exotic substances such as uranium or plutonium oxides for example makes S oneidensis especially interesting for helping to cleaning up environments contaminated with radionuclides (a process called bioremediation). The fact that these microbes can be found in so many different environments begs the question.....

How is Shewanella oneidensis able to thrive in so many different environmental conditions?

In order to survive in many different conditions, it is essential that signals from the environment (such as temperature, moisture, availability of oxygen and nutrients) be transmitted to the inside the cell where decisions are made. This is done through specific receptors on the surface of the cell, transmitters of information on the inside of the cell and regulators throughout the cell and inside the nucleus. Usually one receptor can detect a specific type signal only (e.g.: pH, temperature, presence of oxygen etc.).

A high degree of flexibility in living environments suggests that S. oneidensis should have a high number of sensor-transmitter mechanisms. Indeed, through whole-genome sequencing and cross-species comparison, scientists have found that the S. oneidensis MR1 genome has 211 one-component systems, and 47 two-component systems. These one-component and two-component systems are different types of receptors-transmitter systems. One-component systems are receptors that can also transmit a signal inside the cell. Two-component systems have to work together to achieve the same result, but because of the combinatory nature are more flexible. To give some perspective on one particular example, while the garden-variety E. coli has one chemotaxis gene and five chemoreceptors (receptors with a particular shape or motif), S. oneidensis MR-1 has 3 sets of chemotaxis genes and 27 receptors.

A lot of work has been going on since 1988 with this species in trying to figure out how the organism works, and how to apply this to some practical problems. The review article mainly focused more on system-wide comparisons between Shewanella and other bacteria concerning transcriptional regulation, metabolic networks, and makes the point that a combination of in silico experiments and wet lab experiments are currently laying the groundwork for understanding this diverse genus.

Next time, we will explore how Shewanella can be used for practical purposes.

Source of Picture: http://gollum.stanford.edu/shewa/shewanella.jpg

Green Google

2008-12-27T12:40:00.000-08:00

As many of you have heard, Google has been very supportive concerning green energy. They have invested in several projects such as Prius Plugin Hybrids, Solar Panels on all their buildings, thermal energy, high-altitude wind energy extraction technologies, and Engineered Geothermal Systems, with more to come (e.g. ocean-generators). If you read this blog, you are probably interested in this field and Google probably offers one of the best opportunities to work closely with these green technologies.

"We are looking for a world-class team to lead this effort. We need creative and motivated entrepreneurs and technologists with expertise in a broad range of areas." (Joblist - click here)

Source: http://www.google.com/corporate/green/energy/

Science Team Announced

2008-12-20T11:25:00.000-08:00

What's new this week?

In a change from what I usually try to write about, significant announcements were made today that will affect the future of our capabilities in science and technology. This week President-Elect Obama has announced his science team in his weekly radio address. Without spin, it has been put up on YouTube:

My Own Observations

I do not want to read to much into these appointments as I believe the future actions of these appointees will speak more loudly than just their appointments. But I do have a few observations to make.

It appears that the coming administration will seek advice based on science, and pragmatism rather than ideology which is a stark contrast to the current Bush administration. While President Bush waited a year before filling the science advisor position late in 2001, President-Elect Obama has filled up the science advisor position before even officially taking office. This is important because under President George W. Bush, many of the important science policies were crafted already by the time the science advisor position was filled. Under the new administration, it looks like that the science team will be an integral part in coming up with policies as they are being crafted. The early appointment is unprecedented but has to be seen in the light that all his cabinet positions were filled early given the economic circumstances we find ourselves in.

In terms of appointments, with Stephen Chu (Secretary of Energy), John Holdren (Science Advisor), Harold Varmus and Eric Lander (Co-Chair for Council of Advisers on Science and Technology), and Jane Lubchenco (Head of the National Oceanic and Atmospheric Administration), strong, prominent scientists have been selected - 2 are Nobel Prize Laureates! The appointments come from the physical sciences (alternative energy sources in particular), life sciences (genomics) and climate research and suggest that these fields in particular will be emphasized.

I'll update this post later as I am finding out more information on each appointment, but meanwhile I wanted to share this bit with everyone as quickly as possible.

Diesel from Fungi!

2008-12-14T10:29:00.000-08:00

Recently, there has been a lot of talk about a fungus everywhere.

What's the deal with this fungus?

As we are turning to the future, we need to look for new ways to fund our energy demands. The November edition of the Microbiology Journal suggests one way this could be done. Professor Gary Strobel and his team publish their work on a new fungus which they name Gliocladium roseum (NRRL 50072). The special property of this fungus is that it can make diesel fuel called myco-diesel. (Myco is Latin for fungus.) It does so by breaking down cellulose which is the tough plant cell wall we use for everyday products like paper. Breaking down cellulose normally requires many toxic chemicals and a lot of energy. Therefore, it is quite remarkable that the fungus can make diesel without the need for toxic chemicals. This discovery is important because, in the future, we could use these fungi or the parts of it to make diesel without the need for oil.

Why does a fungus want to produce diesel?

Gliocladium roseum was isolated from the rainforests of the Patagonia region in South America. The moist, and warm conditions in the rain forests do not only promote dense growth and diversity, it also habours many infectious diseases. G. roeum is an endophyte which means that this fungus grows within its host plant Eucryphia cordifolia (ulmo).
Interestingly, it seems to do so without killing the plant. The researchers therefore hypothesize that, in fact, the relationship that this fungus has with its host plants is beneficial to both organisms (symbiotic): While the plant gives physical protection from the environment, the fungus helps the plant by producing these diesel components, which turn out to have anti-microbial properties. For those interested, among the many hydrocarbons this organisms produce are undecane, 2,6-dimethyl; decane, 3,3,5-trimethyl; cyclohexene, 4-methyl; decane, 3,3,6-trimethyl; and undecane, 4,4-dimethyl.

My Argument for Conservation

Apart from the ethical, and environmental reasons for preserving the environment, bioprospecting is the keyword. Prospecting is the act of finding something that will be beneficial or successful. Back in the colonial days, many prospectors went West to discover new rich lands. In the same sense bioprospecting is the act of looking to nature to find solutions to problems we have. Often times, we don't know how a given plant or organism would be useful right away, and this is why we catalog them. But it is ultimately through bioprospecting that some of the anti-cancer medicine we now use are found.
The recent discovery of Gliocladium roseum is the result of bioprospecting. Many future unknown benefits wait to be discovered. This is the dilemna we are facing right now throughout the world. Many of these habitats are in danger of being destroyed by the effects of humanity. Many areas are burned down for agriculture or for real estate. In the process, a lot of diversity that could hold the answer to many of our questions get destroyed without us even knowing.
I recently watched a CNN documentary special with Anderson Cooper called "Planet in Peril". It seems if people can be convinced that the natural habitat represents a valuable, renewable resource by discovering the use for some of these plants or organisms, a strong economic argument exists for preserving as many of our precious natural resources as possible while trying to learn how things are done the natural way. Watching the documentary, I gained a whole new appreciation for people who promote conservation efforts while working with the local population. I really recommend everyone to watch the documentary. This kind of work is tough! Therefore, I would encourage everyone to support any of those workers in any small way you can.

Obama's new Energy Secretary and EPA head

2008-12-12T14:15:00.000-08:00

The US has been abuzz with talk of Obama's picks for his cabinet. One very exciting guy coming up for Secretary of Energy will be Steven Chu, a strong advocate for alternative and renewable energy. He also happens to be a Nobel Laureate for Physics from 1997 (cooling and trapping atoms with lasers). Currently this guy serves as director for the Lawerence Berkeley National Laboratory, pushing the governmental institution towards becoming a world leader in biofuels, artificial photosynthesis, and solar energy technologies, focusing on using carbon-neutral sources.

One particular quote stands out to me: "If I were emperor of the world, I would put the pedal to the floor on energy efficiency and conservation for the next decade," he told Reuters in a May 2007 interview. This really excites me because I think he will be able to push the US towards the forefront of the climate change issue. Personally, I'm also proud that a Chinese-American will be spearheading the effort. It may send a message to China, as well, to push them to change their policies towards reducing greenhouse emissions.

Further quotes from Steven Chu about climate change can be found here.

Another important cabinet pick will be Obama's choice for the administrator for the EPA. Lots of names have been thrown around, but it sounds like he's recently settled for Lisa P. Jackson. Her record as former head of the New Jersey EPA seems fairly green, although critics have argued that her record shows neglect of hazardous waste sites and weakening proposals to enact safer groundwater quality standards.

We'll have to see how these appointments turn out, but so far, I'm fairly excited to see the people that Obama has put his trust in. Let's hope that trust is well placed.

Is cheap, unobtrusive hydro energy at hand? VIVACE - Hydroenergy without turbines!!!

2008-12-06T08:20:00.000-08:00

Today I came across a very interesting article suggesting a new way of generating hydro-electricity. The article caught my eye because "vivace" is Italian for quick, yet the article suggested that the water speed need not be quick. But let's back up for a bit.

What’s the scoop here?

The November 2008 edition of The Journal of Offshore Mechanical Arctic Engineering – I didn’t even know such a thing exists – showed that it is possible to generate electricity from vortex-induced vibrations (VIV). They devised a proof of concept machine which they called VIVACE which is short for Vortex-Induced Vibration Aquatic Clean Energy – quite catchy if you ask me. In short, this contraption can make electricity out of natural movements of the water.

Ehhh but what is a VIV again?

Those were the same questions I had when I read about the title because I am a Biologist and not an Engineer. To answer the first question, when air, or liquid passes by a cylindrical object vortexes are formed. Wikipedia again has a nice image of the beautiful vortexes you can get:

VIVs are the kind of vibrations that result from the vortexes you see above. Because this sounds a bit abstract, I searched for how VIVs actually look. I found a video that shows VIVs created by a stream of air.

VIVs are generally considered bad side-effects in many applications. It’s what civil engineers are concerned about when they build a bridge: The fast streams of water flowing around the legs of a bridge can create such vibrations. If the right frequency is hit, the signal can get so much amplified within the structure of the bridge that it will simply collaps. As a famous example, I found information on the Tacoma Narrows Bridge (again on Wikipedia) with a nice picture on what these vibrations can do to a bridge.

Airplane engineers are also concerned about these. When airplanes fly at high speeds, many vortices are generated along the span of the wing. VIVs can severely drag down an airplane, and in larger airplanes with long wings, these VIVs could in theory rip the wings off an airplane. This is not happening of course because airplane engineers are smart. Did you ever notice that the wings of an airplane has pointy extensions along the wing? These extensions were put there to redirect and reduce the amount of VIVs to mostly those flexible tips. Drag is reduced, and so is the vibration.

And how is VIVACE such a big deal?

Well, let’s think of how hydroelectric energy is normally generated. Hydroelectric energy makes use of water movements. Traditionally, in a river-setting for example, water from a higher elevation flows to a lower elevation, turning a turbine that runs the generator.

Tidal energy generators work in a similar way. These technologies though straightforward have a few disadvantages. First, they require relatively fast moving water (5 knots and above). Second, they may be quite obstructive. You may already have seen how big these dams are. In ocean environments, they may be harmful to marine life. Just try to imagine what will happen if fish get chopped off by the turning, spinning rotors.

Obviously, a lot of research is going on those fronts (like rotor design) too. But with VIVACE, no rotors are needed at all. No fish need be afraid of being chopped into pieces. And because VIVACE relies on tiny vibrations that are generated even when there is just a little water movement (2-3 knots), no fast streams are needed to generate electricity. If you wonder how such a contraption may look, gizmo.com has a nice concept art drawing which you can see below:

And there is a video of a working prototype on the newly formed company website:

What did I learn from here?

Who would have known that electricity can be generated from just vibrations. Energy is all around us. It will take a flexible mind to find these ways. A traditional argument against alternative energy sources has always been cost.

Cost and efficiency are always valid concerns. solar power currently costs 48 cents/kwh because of expensive material and production costs of solar panels. Furthermore, solar power can only be used during the day. Wind power now only costs about 8 cents/kwh, but has the disadvantage of not being reliable because the wind does not always blow. Just as a comparison, for coal this turns out to be about 4 cents/kwh. How well does VIVACE compare? The authors estimate that a VIVACE converter can generate electricity as cheaply as 5 cents/kwh.

Since "Change" was the slogan in a recent election campaign, it may be time to change the way we think about energy. As some have suggested already, there is no single magic energy source that will replace all others. Rather a healthy energy mix of renewable energy sources could compensate for the short comings of the other. For instance, often times when it's sunny, it's not windy. When it's windy, the weather is usually bad - at least that's what I observed in Germany. Combining solar, wind, and now hydro-electric energy like the VIVACE converter could perhaps provide us with enough clean energy for the future.

Collaborations

2008-12-04T17:16:00.000-08:00

Good ideas can develop when people cooperate, and work together as a whole towards a common cause by openly exchanging ideas and view points. As a Molecular Biologist, I am bringing in a certain view. But it is at the intersection of one discipline with others where many new innovative ways of thinking are born. For this reason, this site will henceforth be a collaborative-community effort in which we at the "Bio-Based" community will bring you news and views of things that could make this world a better place. In the coming days and weeks, look forward to contributions from my dear friends and colleagues who share the common vision of moving humanity forwards with innovative thinking and action.

Is the personal genome close? Single Molecule Real-Time Sequencing (SMRTS)

2008-11-29T08:17:00.000-08:00

So, I have always enjoyed explaining science to non-scientists. To help everyone understand these things better I want to organize these blogs into a short 1-3 paragraph description of what's new and cool for a fast overview, and a few more paragraphs below to give perhaps more background and details about the news. Please let me know if this works.

What's the short scoop?

Science Journal recently (November 20th 2008) published a report in which the authors show that they can perform "real-time DNA sequencing from a sinlge polymerase molecule". I am thrilled about this report! But why? This technology will make sequencing fast and cheap. For most people, it will be relevant to know that rapid and, in the future, affordable DNA sequencing opens the door for everyone get their own personal genome which can help with diagnosing and fighting diseases like cancer.

However, I am excited about this technology because I think that it will allow us to sequence all microorgansims in excotic environments a lot faster and a lot easier. The DNA from these microorganisms will serve as library of blue prints of building blocks for any given task - especially related to environmental protection? You want an enzyme that breaks down oil from oil spills? Look up what nature came up with! You want to find a better enzyme (protein that makes something happen without getting destroyed) for breaking down cellulose (for biofuels)? Look it up! Why should we reinvent the wheel when nature has provided us with millions of years of engineering expertise. Of course, it's not THAT easy, but the ability to sequence anything cheap and fast will bring us a long way along.

So what is DNA sequencing? Why is it so important?

Every cell in our body and in every other living organism has at some time DNA in it. DNA in our cells acts kind of like a library that contains all the blueprints for everything needed to build and run a new cell. Unlike English, the information is coded in long ladder-like structures (see Figure 1) that contain only 4 different kind of letters on the rungs usually abreviated as A, C, T and G. DNA sequencing means to determine the order of these letters on this string.

Figure 1. Schematic Picture of DNA taken from the US National Library of Medicine

Knowing this kind of information can be very useful. Many diseases arise when some of the letters change to something else (called mutation) changing the meaning of a word (or gene in the language of genetics). In some cases, this could tell the cell:"Start dividing and don't stop." This leads to big cell masses that destroy normal healthy cells. We call this cancer. So in a medical sense knowing where these mutations occur and what they are will help scientists and doctors understand what exactly is wrong with our cells and will help them to come up with ways to fix the problem through new drugs or therapies.

So what is the big deal about this feat in biotechnological engineering?

I don't think it would be helpful at this time to completely review the history of DNA sequencing. But if you are interested, you can read a good article about this at Wikipedia. Suffice it to say that previous techniques were indirect observations of sequencing and used to be slow and/or expensive process. The new technique will make sequencing MUCH cheaper because very few reagents are used. The other benefit is that it will be faster - much faster. To give some perspective, it took 10 years for the Human Genome Project to produce a first draft of the human genome using the old technique. According to a recent radio interview with one of the authors, this technology has the potential to resequence the human genome in 1 hour!

Technical Details

For those interested in more details, I recommend giving the article a read (if you have access). I wanted to find a publicly available image that captures the essence of this technique and found that there is already a wiki article on SMRTS which you can read if you don't have access to the actual article.

In short, single molecule sequencing relies on the following main innovations:

1.) To detect fluorescence of one single molecule, detection techniques had to be improved.
2.) Because the DNA synthesis rate of each polymerase is variable, it is essential to observe the activity of each polymerase on its own as otherwise the signal would appear fudged and would not be interpretable. Technologies had to be invented to be able to attach just one polymerase in one read out plate. They call this nanotechnological innovation zero-mode waveguide (ZMW) which I understand as making tiny wholes that are closer together than the wavelength of a given light used to scan for polymerase activity. It's basically one way that they try to address the challenge of putting only one polymerase in a whole so they can observe the activity of one polymerase.
3.) The fluorescent nucleotide (basic unit such as A, C, T, G) was reengineered in such a way that the florescent dye is not on the base (A, C, T, G) - the way it is done in the traditional ddNTP based techniques - but on the phosphate group that gets cleaved off. The benefit is that nucleotides labeled this way do not interfere with the polymerase in a meaningful way because the label is cleaved off upon incorporation. So in the end, the newly synthesized strand consists of "normal", untagged DNA.

Synopsis: Why I think it's cool.

The oceans, water-streams, soil, air and body are covered with millions of different bacteria that have been doing what they have. For the the most time though we have not been able to learn anything about these communities because typically one needs a lot of DNA from the same species to sequence it. It was expensive and cumbersome. With this technology we can, in the initial stages, take a scoop of ocean water and determine the DNA of all the organisms in that water easily. Doing this we can build a library of all the DNA sequences, cDNA sequences (and thus proteins). Having this information will make it easy for us to find proteins that do a particular function, and do it well for anything. I especially thinking of ways for breaking down waste such as oil, and heavy metals. The potential of use after sequencing are endless!

The Purpose

2008-11-27T10:54:00.000-08:00

Watch your thoughts, for they become words.
Watch your words, for they become actions.
Watch your actions, for they become habits.
Watch your habits, for they become character.
Watch your character, for it becomes your destiny.

— Frank Outlaw

Every blog has a purpose. For some it is to share one's personal life. For others it is to spread a political ideology. I have been blessed with the opportunity to listen to many different minds in science and talked to many whose conviction is that the path forwards in humanity requires us to rething everything we have done up to this point in order to make sure that future generations survive.

I have decided to dedicate my life to the service of this cause. I know I am not all-knowing nor claim to be. In all humility, keeping in mind the above quote, the purpose of this blog shall be to summarize and share information related to science, biotechnology, and the environment that I find interesting, and engage in an informed, reasoned discussion with anyone willing to learn. I look at this blog as a starting point to change my destiny.