One of the major drawbacks of the open air pond system for industrial scale algae growth is the engineered strain’s inability to compete with wild types. This is because the lab trained algae spend all its energy resources producing oil instead of growing as fast as possible. So what is needed is a strain that can grow fast enough to push out the native strains and still produce the desired oil.

One possible way of achieving this is to rearrange one’s thinking about algae production. Instead of viewing the algae as biomass to be harvested, one could see them as solar powered bioreactors. What I mean by this is: have the oil production as an inducible trait and view the oil production as a byproduct of an algae bioreactor. This will allow the oil production to only occur when the engineered strain is at critical mass, and after it has grown fast enough to out-compete the wild type.

Of course this idea has a few technical hurdles (such as the oil produced would need a mechanism to be excreted into the media). But I see this post as more of a brainstorming exercise rather than trying to actively generate a solution. I would be interested in what the sustainable biotech community thinks.


Macroalgal Culture

June 26, 2008

Robert I and have been discussing the issues around macroalgal culture.  He found this cool like to a patent for a cultivation truss:

I would like to know if anyone knows about species selection or condtion optimization for this type of aquaculture.  The best contact I know of for this is Greg Mitchell, at Scripps Oceanography in SD, but I dont want to bother him with basic reserach questions.

The reason that this came up was becuase Robert and I were discussing open ocean algal biofuel cultivation strategy.  Ecological issues seem to detract from the feasibilty of microalgal culture, and larger species seem to be more containable.

Any comments?

Hello Blogosphere

June 23, 2008

Hey all you sustanible biotechers,

Because we all share the urge to make this world a cleaner, more energy-efficent place for our future generations to enjoy,  voice your ideas and challenge the thoughts of others regarding how to gain ground against (hopefully reversible) impending global sickness.

I believe that sustainability issues are not addressed at KGI as they should, and this forum will gather the ideas of all interested parties so we can express this issue for all to see.  Having a class in this issue would bring new business practices to light, and teach future leaders of biotech how to manage in a sustainable manner.  

News Source:

I will function to consolidate news I feel is interesting to the group and would like others’ input.  This is kind of like a think-tank idea. 

Thanks to Cyrus for setting all of this up!




Sorry I dissappeared for a while. First there was the end of the semester with finals and all of the projects we do at KGI coming due. Then I started my summer internship. I ended up working at Genentech down in Oceanside, CA (Northern San Diego County). Now you might be asking yourself, “What the heck is Cyrus doing working at a pharma biotech company?!” Well, in looking around for internships, I realized that a lot of the opportunities in the small biofuel type startups were lab related (for the scientists). I have always considered myself an engineer and my primary interest is in large scale manufacturing. Not just what bugs to grow or the theory of fermentation or bioseperations but how do you actually run a large plant? What are the systems needed and how are every day operations managed? So when I saw an opportunity to work in the state of the art manufacturing plant of the original biotech company, I jumped at the chance. I am doing a project in data management and automation of the plant which means I get a good overview of all the systems running in the plant. In fact I can see the status in real time of all 18,000+ sensors, valves, pumps, etc in the plant and also see what they have done since the place opened. So one thing I will have a good grasp on is how you put one of these $700 million dollar plants together and that is something that all those biofuel startups will need to know when the time comes to build their plants. Besides, Genentech is a pretty cool company. It’s probably one of the only traditional medicinal biotech companies I would consider working for long term. Plus, you get tons of free food!
Stay tuned for updates. In mid August, I will be attending the annual meeting of the Society for Industrial Microbiology wich is going to have all sorts of cool workshops and talks on metabolic engineering, biofuels, and even bionanotechnology systems. There is even a couple of talks on CHO cell culture by KGI’s very own Matt Croughan. I plan on providing full coverage of cool stuff I run across there.

The Killer App

April 22, 2008

A large well lit room contains hundreds of long tanks.  Pipes strung above the tanks lead down to valves and outlets into the tanks.  The whole operation hums with the high tech feel of a computer chip factory.  The tank closest to you suddenly springs to life.  The clear water that was originally in it is now being injected with a cloudy white liquid and heaters around it are being activated to warm the tank.  Unseen, the tank is being injected with bulk sugars and cellulose from recycled and reclaimed consumer and industrial products as well as several species of engineered microbes.  The microbes go to work communicating with each other and assembling the bulk sugars in and around a translucent tissue scaffold submerged in the tank.  Over a few hours, different microbes and enzymes are injected into and filtered out of the tank and slowly a large structure takes shape in the tank.  Finally, what emerges is a log, not just any piece of wood but the equivalent to a 36”x36”x20’ 2000 year old clear heart piece of Redwood.  This wood will match any old growth forest product but it was produced in less than a day from recycled waste and no logging has taken place.

Do I expect to see this in my lifetime?  Maybe, maybe not.  What it does illustrate is the direction I would like to take industrial biotechnology.  That is, into the realm of true industrial nanobiotechnology, where bioprocessing, high throughput robotics, microfluidics, nanotechnology, and tissue engineering all merge to give us advanced capabilities of using engineered microbes and enzymes to create complex structures.  Sure, such a thing may never prove possible or economically feasible but it will be fun to try.  I look forward to the day when industrial biotechnologists are exploring tissue engineering like our medical counterparts, or when alternative to current liquid bioprocessing like solid-gas phase bioprocessing or super-critical fluids are regularly used to create highly efficient enzymatic catalysts (1).  I also look forward to the day when bioprocess engineers get to create processes with multiple strains of microbes working in concert through quorum sensing. 

In all this I believe our field of industrial biotechnology will be called mature when we can not just process or recycle but up-cycle.  That is, take some waste created from everyday human doings and use the machinery of life to create something much more complex out of it.  Right now we sort of down-cycle or at best side-cycle.  We are working on breaking stuff down into simpler units or maybe units of equivalent complexity.  This is unlike nature in that it is very good at increasing complexity.  Redwood trees take simple units (CO2, water, trace nutrients) and over many, many years turn them into that wonderful structure with all its beauty and complexity.  I’m not expecting to replace Redwood trees; I just eventually want to give them a good rest.



(1)   Biocatalysis in non-conventional media—ionic liquids, supercritical fluids and the gas phase. S. Cantone, U. Hanefeld, A. Basso, Green Chem., 2007, 9, 954–971.


Grand Display

April 15, 2008

OK, so this post dosen’t have really anything to do with sustainable biotechnology other than I guess you could say that it is an awesome example of nature’s own biotechnological wonder. I finished all my work (and my taxes) on Sunday so I could take off and shoot the flowers in the desert north of KGI at the Antelope Valley Poppy Preserve. It takes a fair bit of time to get there but it’s totally worth it! I bet only a small fraction of the millions of people in the Los Angeles area know what happens just to the north every Spring. To get there from KGI you take the 210 West to the 5 North to the top of the Grapevine. Turn East onto highway 138 and drive till the world turns Orange then take a right. It’s just that easy.

 Hills near Gorman

The hills near Gorman just after you turn off Interstate 5.

Poppy Preserve looking West

A sea of Orange at the Poppy Preserve.

Mt. Baldy from the North

The North side of Mt. Baldy from the Poppy Preserve. KGI is directly on the other side of that mountain.

Poppy Preserve from the top.

Other stuff besides California Poppies grow there too. They are just harder to find.

PS. If anyone wants to see the rest of my photography check out my gallery ( and my regular site ( They have lots of stuff taken on my adventures around the state of California and the US. As you can tell I am way big into mountain adventure. All you KGI people who are into mountain biking, skiing, mountaineering, or anything else having to do with adventure in the great outdoors be sure to look me up and we’ll go get into some trouble.

Most people who know me know that I love to cook.  A while ago I learned about El Bulli, a restaurant located on Spain’s Costa Brava.  It is repeatedly voted the best and most innovative restaurant in the world and is lead by sort of a mad scientist chef named Ferran Adria who combines the deterministic knowledge of science with the art of cooking to create what has become known as Molecular Gastronomy.  He frequently uses industrial food ingredients in innovative ways to form edible art.  One of his most famous inventions is “El Bulli” style caviar.  This caviar is formed by combining a flavored liquid with Sodium Alginate.  This mixture is then dropped one drop at a time into a solution of Calcium Chloride.  When the drop hits the solution, the strong attraction of the Chloride ions pulls the Sodium ions out of the caviar liquid.  This void is then replaced by the Calcium ions which have a 2+ charge instead of a 1+ charge like the Sodium.  This increase in the charge causes an instantaneous cross linking of the Alginate polymers causing the drop to solidify into something that looks a lot like caviar; only it is flavored what ever the original liquid was. 

Here, I create a dessert Nigiri with Strawberries and caviar made from Balsamic vinegar.  First, gather the ingredients.  You will need Balsamic vinegar and some sweet Mirin for the caviar liquid, some large Strawberries, and a bowl of water with a strainer that can fit inside of it.  You will also need a “flavor injector” type food syringe which you can buy at most any well stocked cooking store.


You will also need some pretty unique ingredients which you can order from Will Powder.  They are food grade Sodium Alginate, Calcium Chloride, and Sodium Citrate.  For the caviar liquid you will want about a half cup or so of Balsamic vinegar and a tablespoon of sweet Mirin to add some sweetness.  To this liquid, first add a teaspoon of Sodium Citrate.  Alginate dosen’t work optimally in acidic liquids so you add this as a buffer to get a more neutral pH.  Next, get a teaspoon or so of the Sodium Alginate and very slowly wisk it into the liquid.  You should only add a little bit at a time otherwise the powder will clump into one big ball. 


Now, prepare the Calcium Chloride solution by dissolving a heaping teaspoon of it into a pint or so of cold water.


Suck the caviar liquid up into the syringe and move over to the Calcium Chloride solution.  Position the tip of the syringe about an inch above the surface of the solution.  If it is too low, drops will not form properly and if it is too high the impact of the drop on the surface will distort the drop into a flat disk.  Drop by drop, add the liquid into the solution.  Leave for a few minutes and you will have Balsamic caviar.


Remove the caviar with the strainer and rinse gently under cold water. 

Make Nigri pieces with sushi rice and rub a little Wasabi on them (trust me, it works).


Then add some thin slices of Strawberry and top with the caviar.  Presto, an innovative, unique dessert!


I can tell right about now that you are asking “This is a blog about sustainable biotechnology.  What could dessert sushi possibly have to do with sustainable biotechnology?”  It turns out that it has a whole lot to do with it!  Immobilization of cells and enzymes in bioprocessing units is an active area of research.  This immobilization facilitates easier handling of the cells or enzymes including bioseperations.  In the latest Journal of Industrial Microbiology, a team if Chinese researchers reports on a diesel fuel desulfurization process using exactly Sodium Alginate “caviar”(1).  New regulations for diesel fuel require strict limits on the amount of sulfur compounds that can be present in the fuel.  This team used Pseudomonas delafieldii bacteria isolated from the waste pools of Chinese oil fields which eat the sulfur in diesel fuel.  They made the Alginate spheres containing this bacterium instead of Balsamic vinegar.  This allowed desulfurization of the fuel while allowing easy separation and decontamination of the fuel once the process is complete.  There are a bunch of other applications of immobilization of cells and enzymes out there which I will leave to the reader’s curiosity.


(1)   Improvement of biodesulfurization activity of alginate immobilized cells in biphasic systems. Y.G. Li, J.M. Xing, X.C. Wong, W.L. Li, H.S. Gao, H.Z. Liu, Industrial Microbiology & Biotechnology, Volume 35 Number 3.