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Cellular Workers

In chemical engineering most processes depend on catalysts. For example ammonia is made from nitrogen and hydrogen with iron as a catalyst. Without the iron the reaction would proceed too slowly or need lots of expensive heat to be useful for the commercial production of ammonia. This is one of the simplest examples of the action of a catalyst. More complex products require many steps each generating nasty, unwanted waste and/or consuming energy. Another form of catalysis can be based on enzymes, specialized proteins. For example yeast turns sugar into alcohol with the aid of enzymes. Biocatalysis has many advantages over chemical: it operates at room temperature, takes place is benign water, and the unwanted products are usually biodegradable. As a whole biocatalysis is much more efficient than synthetic catalysis. Biocatalysis is today used to produce high-fructose corn syrup, the sweetener in most soft drinks, and aspartame, an artificial sweetener.

Companies are now making plastics via biocatalysis: Degussa and Cargill Dow are leaders. They concentrate on using non-traditional inputs such as vegetable fibers to produce traditional outputs, but with less input in natural resources, mostly fossil fuels.

There are several thousand known enzymes, but only a few are suitable for industrialization. Few are stable and many are difficult to produce or harvest. Stepping into the gap is Diversa, Avecia, and some other companies. They comb the world, concentrating on extreme environments such as deep-sea thermal vents and caustic-soda lakes, looking for microbes that produce enzymes that may be useful. They then extract the DNA that leads to the production of the desired enzyme, put it into a microbe that can be easily grown and maintained, and harvest the enzyme. One headache is distinguishing a useful enzyme from a sort-of useful enzyme. Thus these biocatalysts have to be carefully evaluated by comparing them to a more standard process to actually see if there is a gain.

One way around this is to genetically engineer an enzyme with the desired properties. Willem Stemmer of Maxygen has pioneered a technique of inducing mutations, selecting the best performers, and concentrating the mutations in a single offspring to have the best chance of producing a useful organism. This is called directed evolution with DNA shuffling technology. If that does not provoke a shudder, I am not sure what will. In the realm of pure research is the idea to create a desired catalysis from scratch. We do not really know how an enzyme's structure contributes to its function or how their interaction with other molecules speeds up reactions. At the moment we are moving towards a cellular work force to produce catalysts for chemical reactions.

Another example of cellular workers is occurring in the field of micro-structures. Dirk Volkmer is not actually using cells, but copies the technique of radiolaria to build micron scale structures out of silica. What might these structures be useful for? They can support catalysts. Their surface area is very high compared to their volume due to the large number of spikes and hollows. This is ideal for a catalyst as one wants the highest possible availability of the catalyst to mediate a reaction.

This column is based on two articles in the Economist. One is archived at Dirk Volkmer's site while the other, called Bugs as Catalysts, is from the 13 March 2003 edition, and is not available on line except to subscribers.

Roleplaying Ideas

Universal Solvent: An experiment in directed evolution with DNA shuffling has gone wrong. The enzyme that came out is some how a universal solvent and basically cuts through anything it comes into contact with. After rebuilding the lab subsequent batches are contained by magnetic suspension. It could be used for nefarious purposes by a biotech company trying to stave off bankruptcy and the party is called in to investigate the impossible crimes.
Negotiations: An experiment in directed evolution with DNA shuffling has gone wrong. At first everyone was pleased with the new batch of bugs that churned out an enzyme of tremendous value as it produced high quality plastic from organic waste. Lately production has fallen and the head of the project comes to the party telling them that the bioengineered bugs appear to be on strike and want to negotiate better working conditions. Can they please help? If communications can be opened what else would the bugs like to say?
Scratch that Industry: An experiment in directed evolution with DNA shuffling has gone right. Apparently the latest enzyme produces hydrogen from organic waste. The fossil fuel industry can read the writing on the wall and is determined to stop or steal this advance before they are completely wiped out. Perhaps an old friend has survived the initial raid and begs the party for help. Investigation reveals that the enzyme does not really work. What is really going on here?

Topics	Author	Date	Latest Reply
EMP doesn't work in space does it? (5) new	Ernest Mueller	02-29-2004 00:19	01-03-2006 22:38 new
Local expectations (1) new	Grop	01-16-2004 09:02	01-16-2004 09:02 new
What might be salavageable from an EMP? (3) new	Preserver	12-05-2003 12:31	03-03-2004 10:48 new
Heh... The perfect game system for this... (2) new	OneCrazyGuy	08-20-2003 09:17	03-03-2004 10:15 new
Three and only three (2) new	Stalkre	08-14-2003 14:31	08-18-2003 08:22 new
Dark Matter Nebula (1) new	TrueMortality	07-16-2003 04:22	07-16-2003 04:22 new
Haber-Bosch (2) new	Jon	06-26-2003 05:25	06-26-2003 05:26 new
Another kewl thing to do with enzymes (2) new	Dimitrios	06-25-2003 09:45	03-03-2004 10:17 new
EMP for space opera? (13) new	Michael	06-12-2003 02:18	08-20-2003 10:24 new
Popular Mechanics (1) new	PyroGod	06-11-2003 13:40	06-11-2003 13:40 new
Front panel link doesn't link to this column! n/t (1) new	Andrew Martin	05-17-2003 18:49	05-17-2003 18:49 new
Dark Energy Alternatives (6) new	Doctor TOC	04-14-2003 11:04	07-16-2003 16:46 new
Planetary (1) new	Sandy Antunes	04-04-2003 16:01	04-04-2003 16:01 new
Well, sort of (3) new	Wyrmwood	04-04-2003 08:34	04-16-2003 10:11 new
Terminology (10) new	Trevor Barrie	03-14-2003 09:52	07-16-2003 13:59 new
Um... (1) new	dasmen	03-13-2003 08:42	03-13-2003 08:42 new
Careful use of terms and claims (2) new	Scott Maxwell	02-14-2003 10:07	03-17-2003 21:41 new
Other Theories (2) new	Mortality	02-14-2003 04:50	02-14-2003 09:41 new
foot note #2 (1) new	Fil Kearney	02-14-2003 02:45	02-14-2003 02:45 new
Excellent column! (5) new	Thrain	02-13-2003 13:07	02-15-2003 03:48 new

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Cellular Workers

Cellular Workers

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Bleeding Edge Cellular Workers by Cyrus Ance Jun 25,2003	Cellular Workers In chemical engineering most processes depend on catalysts. For example ammonia is made from nitrogen and hydrogen with iron as a catalyst. Without the iron the reaction would proceed too slowly or need lots of expensive heat to be useful for the commercial production of ammonia. This is one of the simplest examples of the action of a catalyst. More complex products require many steps each generating nasty, unwanted waste and/or consuming energy. Another form of catalysis can be based on enzymes, specialized proteins. For example yeast turns sugar into alcohol with the aid of enzymes. Biocatalysis has many advantages over chemical: it operates at room temperature, takes place is benign water, and the unwanted products are usually biodegradable. As a whole biocatalysis is much more efficient than synthetic catalysis. Biocatalysis is today used to produce high-fructose corn syrup, the sweetener in most soft drinks, and aspartame, an artificial sweetener. Companies are now making plastics via biocatalysis: Degussa and Cargill Dow are leaders. They concentrate on using non-traditional inputs such as vegetable fibers to produce traditional outputs, but with less input in natural resources, mostly fossil fuels. There are several thousand known enzymes, but only a few are suitable for industrialization. Few are stable and many are difficult to produce or harvest. Stepping into the gap is Diversa, Avecia, and some other companies. They comb the world, concentrating on extreme environments such as deep-sea thermal vents and caustic-soda lakes, looking for microbes that produce enzymes that may be useful. They then extract the DNA that leads to the production of the desired enzyme, put it into a microbe that can be easily grown and maintained, and harvest the enzyme. One headache is distinguishing a useful enzyme from a sort-of useful enzyme. Thus these biocatalysts have to be carefully evaluated by comparing them to a more standard process to actually see if there is a gain. One way around this is to genetically engineer an enzyme with the desired properties. Willem Stemmer of Maxygen has pioneered a technique of inducing mutations, selecting the best performers, and concentrating the mutations in a single offspring to have the best chance of producing a useful organism. This is called directed evolution with DNA shuffling technology. If that does not provoke a shudder, I am not sure what will. In the realm of pure research is the idea to create a desired catalysis from scratch. We do not really know how an enzyme's structure contributes to its function or how their interaction with other molecules speeds up reactions. At the moment we are moving towards a cellular work force to produce catalysts for chemical reactions. Another example of cellular workers is occurring in the field of micro-structures. Dirk Volkmer is not actually using cells, but copies the technique of radiolaria to build micron scale structures out of silica. What might these structures be useful for? They can support catalysts. Their surface area is very high compared to their volume due to the large number of spikes and hollows. This is ideal for a catalyst as one wants the highest possible availability of the catalyst to mediate a reaction. This column is based on two articles in the Economist. One is archived at Dirk Volkmer's site while the other, called Bugs as Catalysts, is from the 13 March 2003 edition, and is not available on line except to subscribers. Roleplaying Ideas Universal Solvent: An experiment in directed evolution with DNA shuffling has gone wrong. The enzyme that came out is some how a universal solvent and basically cuts through anything it comes into contact with. After rebuilding the lab subsequent batches are contained by magnetic suspension. It could be used for nefarious purposes by a biotech company trying to stave off bankruptcy and the party is called in to investigate the impossible crimes. Negotiations: An experiment in directed evolution with DNA shuffling has gone wrong. At first everyone was pleased with the new batch of bugs that churned out an enzyme of tremendous value as it produced high quality plastic from organic waste. Lately production has fallen and the head of the project comes to the party telling them that the bioengineered bugs appear to be on strike and want to negotiate better working conditions. Can they please help? If communications can be opened what else would the bugs like to say? Scratch that Industry: An experiment in directed evolution with DNA shuffling has gone right. Apparently the latest enzyme produces hydrogen from organic waste. The fossil fuel industry can read the writing on the wall and is determined to stop or steal this advance before they are completely wiped out. Perhaps an old friend has survived the initial raid and begs the party for help. Investigation reveals that the enzyme does not really work. What is really going on here?