Molecular Farming
is all about producing specific molecules from plants, using genetic modification techniques. It's about directed evolution, using a plant to express a gene that may come from another organism. It's a new term to me, though I've been interested in the field for decades.
The idea of expressing genes that may have come from other organisms in plants is not new, but the capacity to overcome some of the "natural" barriers to such a move are recent discoveries.
I'm enjoying reading "Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins: . Since I'm not a molecular biologist, it takes me a while to understand this paper, lots of looking up unfamiliar techniques and terms. Fun to learn, as I do know a fair amount about some of the science underlying this work.
Here is the reference to the paper, it is available for free.
PNAS vol. 106 No. 16 6579-6584 by Ralph Bock, et al
http://www.pnas.org/content/early/2009/03/27/0813146106.full.pdf
Researchers in Germany took a few genes from a phage that infects the bacteria causing bacterial Pneumonia, put them into e.coli for amplification, then using a toxin shuttle, they blasted them into chloroplasts and then reproduced the plants. In short, they have a new route to produce antibiotics.
The novel idea was to make the injected genes in such a way that the e.coli didn't completely express the genes. Without this "stop" in the gene replication, the phage gene that produces the chemical that kills the pneumonia will also kill the e.coli....but with the modification, the e.coli bacteria produces many clones of the gene that can then be passed on to the plant.
Injecting the amplified genetic material into plant plastids put them into a different environment and they then express the gene. This strategy takes advantage of the differences between bacteria and higher plants.
At the same time, before it becomes medicine, there is a lot of work to do. The understanding of how to take this path and the skills to carry out each step technically require the highest level of understanding and scientific laboratory support. Nevertheless, once the tough work is done in the lab, it is likely that the farm could produce tons of product. Continued agricultural practice is not without special technical issues such as how long a pure "high-expression" plant could last outside the lab. It is possible that this could completely change the economics of certain pharmaceutical substances.
While there is no way to know if this line of work is going to result in a medically useful product, it would be smart to invest in the basic scientific research that underlies these processes, and to develop the technology to extend the capability.
Awesome research, such a privilege to be alive and to encounter such work!
Friday, February 19, 2010
Wednesday, December 30, 2009
Algae have great potential in the quest for biofuel, but the basic research needed to support the farming of algae is starving. Recently several start-up companies have failed, and energy research in this area is not funded at a level that will support the development of basic research and applied research.
Wired magazine has a piece that reports the latest gloomy developments (Wired Magazine December 2009-How Algal Biofuels Lost a Decade in the Race to Replace Oil* By Alexis Madrigal ), pointing out that venture capitalists are pulling back from funding development efforts as the prospect of profits recede toward the horizon. Alexis also reports that collections of algae that were studied are now lost since the money to renew the cultures collected has vanished. This is a tragic loss since without the culture lines that were studied, much of the research knowledge was lost with them.
This is a classic example of where government funded research into the basic science can be effective, as a base level of knowledge and a community of scientists and technologists are necessary before a new industry can develop. It also highlights that without a congressional sponsor or "angel" who keeps the research funding going in the U.S. budget, science suffers.
The model to date is that small start up companies are formed to develop commercial technology, but this model usually results in the scientific knowledge being viewed as "intellectual property" that is proprietary.
When government research done through Universities and the energy research national laboratories produces a corpus of knowledge that is part of the public commons, this process can seed a real diffusion of the knowledge necessary to make a viable industry. Unfortunately the greed apparent in the current model is antithetical to the development of a critical mass of basic scientific knowledge that would enable such a transition from lab to farm.
While large energy companies have announced large programs to make biofuels, many sound more like PR campaigns than viable commitments to do the research needed to understand culture, genetics, and extraction of useful products from algae grown as an agricultural crop.
We need to better understand how communities of algae can be kept going for long periods of time, and to conserve the many species of algae that are endangered as global warming dries up the pond scum that nurtures these beings. Indeed there may be species living in some puddle that can produce pharmaceuticals, feed-stocks, biofuels, and sequester Co2 efficiently from the coal that we continue to burn in excess. We should make the basic science available to the public, and encourage the private firms that are experimenting with the technologies to publish more of their research.
When one of the start-up firms goes belly up, perhaps the government could purchase the research and make it available to the research community. It is important to learn from the failures as much as to publicize the successes. When we loose the story of the failures, so often the history is just going to be repeated elsewhere. Since failure of a start up may be a convolution of management failures along with scientific and technological failures, the gleaning of this knowledge is a research topic that demands a multidisciplinary case study if we are to learn useful lessons from the failures. Such research is properly conducted by University teams, and funded by government or foundations.
I hope that Stephan Chu as Energy Secretary will have the vision to fund the basic science needed to understand this ancient plant family better. While I can't predict where the research will lead, I know that growing a crop of new scientists and technicians who will build the intellectual commons where algae knowledge is a public resource is a good investment for our future.
Bruce Bagnoli
Wired magazine has a piece that reports the latest gloomy developments (Wired Magazine December 2009-How Algal Biofuels Lost a Decade in the Race to Replace Oil* By Alexis Madrigal ), pointing out that venture capitalists are pulling back from funding development efforts as the prospect of profits recede toward the horizon. Alexis also reports that collections of algae that were studied are now lost since the money to renew the cultures collected has vanished. This is a tragic loss since without the culture lines that were studied, much of the research knowledge was lost with them.
This is a classic example of where government funded research into the basic science can be effective, as a base level of knowledge and a community of scientists and technologists are necessary before a new industry can develop. It also highlights that without a congressional sponsor or "angel" who keeps the research funding going in the U.S. budget, science suffers.
The model to date is that small start up companies are formed to develop commercial technology, but this model usually results in the scientific knowledge being viewed as "intellectual property" that is proprietary.
When government research done through Universities and the energy research national laboratories produces a corpus of knowledge that is part of the public commons, this process can seed a real diffusion of the knowledge necessary to make a viable industry. Unfortunately the greed apparent in the current model is antithetical to the development of a critical mass of basic scientific knowledge that would enable such a transition from lab to farm.
While large energy companies have announced large programs to make biofuels, many sound more like PR campaigns than viable commitments to do the research needed to understand culture, genetics, and extraction of useful products from algae grown as an agricultural crop.
We need to better understand how communities of algae can be kept going for long periods of time, and to conserve the many species of algae that are endangered as global warming dries up the pond scum that nurtures these beings. Indeed there may be species living in some puddle that can produce pharmaceuticals, feed-stocks, biofuels, and sequester Co2 efficiently from the coal that we continue to burn in excess. We should make the basic science available to the public, and encourage the private firms that are experimenting with the technologies to publish more of their research.
When one of the start-up firms goes belly up, perhaps the government could purchase the research and make it available to the research community. It is important to learn from the failures as much as to publicize the successes. When we loose the story of the failures, so often the history is just going to be repeated elsewhere. Since failure of a start up may be a convolution of management failures along with scientific and technological failures, the gleaning of this knowledge is a research topic that demands a multidisciplinary case study if we are to learn useful lessons from the failures. Such research is properly conducted by University teams, and funded by government or foundations.
I hope that Stephan Chu as Energy Secretary will have the vision to fund the basic science needed to understand this ancient plant family better. While I can't predict where the research will lead, I know that growing a crop of new scientists and technicians who will build the intellectual commons where algae knowledge is a public resource is a good investment for our future.
Bruce Bagnoli
Thursday, December 24, 2009
Climate warming drives sea level rise and that may trigger increased seismic and volcanic activity. As the weight on the continental margins shifts as sea level rises, we may begin to see responses from the earth that could include earthquakes.
A recent article in the San Francisco Chronicle explained how scientists have discovered that tides, and the gravitational tugs of the sun and moon can trigger small, long duration low magnitude seismic action deep in the earth along the San Andreas Fault in California.
San Andreas found extremely sensitive...by John Wildermuth
This activity is below the level that generates most of the earthquakes that we feel, but as it moves, it puts strain on the levels closer to the surface and may create the conditions for a larger quake. The research was reported here:
Tremor-tide correlations and near-lithostatic pore pressure on the deep San Andreas fault by Amanda M. Thomas, Robert M. Nadeau & Roland Bürgmann,Nature,Volume 462 Number 7276,page1048
I speculate that similar mechanisms may respond to the shift in the weight distribution as glaciers melt, ice sheets move, and sea level rises. Indeed the geological record has hints that this may have happened during earlier climate shifts. There is no way to predict the magnitude of the effects that will be experienced as a consequence of the redistribution of so much mass but the forces involved are huge and even slight shifts in the earth can have huge consequences for our society.
Increased volcanism could be beneficial as it can send clouds of gasses that provide short term cooling as happened when Mt. Pinatubo exploded a few decades ago. Of more concern is the increased seismic activity that may be triggered.
More research is needed, and funding for both deep earth science and modeling that would simulate the redistribution of mass as the climate warms could help us understand the changes in store as we experience the climate change already "in motion".
A recent article in the San Francisco Chronicle explained how scientists have discovered that tides, and the gravitational tugs of the sun and moon can trigger small, long duration low magnitude seismic action deep in the earth along the San Andreas Fault in California.
San Andreas found extremely sensitive...by John Wildermuth
This activity is below the level that generates most of the earthquakes that we feel, but as it moves, it puts strain on the levels closer to the surface and may create the conditions for a larger quake. The research was reported here:
Tremor-tide correlations and near-lithostatic pore pressure on the deep San Andreas fault by Amanda M. Thomas, Robert M. Nadeau & Roland Bürgmann,Nature,Volume 462 Number 7276,page1048
I speculate that similar mechanisms may respond to the shift in the weight distribution as glaciers melt, ice sheets move, and sea level rises. Indeed the geological record has hints that this may have happened during earlier climate shifts. There is no way to predict the magnitude of the effects that will be experienced as a consequence of the redistribution of so much mass but the forces involved are huge and even slight shifts in the earth can have huge consequences for our society.
Increased volcanism could be beneficial as it can send clouds of gasses that provide short term cooling as happened when Mt. Pinatubo exploded a few decades ago. Of more concern is the increased seismic activity that may be triggered.
More research is needed, and funding for both deep earth science and modeling that would simulate the redistribution of mass as the climate warms could help us understand the changes in store as we experience the climate change already "in motion".
Friday, December 11, 2009
Kindness has a universal quality, a warmth made all the more important in it's rarity. It's a situational thing, a recognition of an opportunity, a conscious choice from an intuitive, emotional knowing rooted in shared values.
Kindness brings light to a darkness sometimes colored by despair, and a reward not sought. Kindness crosses species, and may be observed amongst "animals" as well as humans.
So practice systematic kindness and random acts of beauty!
Kindness brings light to a darkness sometimes colored by despair, and a reward not sought. Kindness crosses species, and may be observed amongst "animals" as well as humans.
So practice systematic kindness and random acts of beauty!
Thursday, November 26, 2009
In a short video available on Google Video, the Cambodian Norry railroad story is presented in an enjoying short video..
Bamboo Railway - Battambang, Cambodia
The story of how the Cambodian people could recycle pieces from the weapons of a genocidal war to fashion a working means of communication with the help of critical U.N. technical assistance in the form of gasoline engines shows how U.N operations can be effective with little cost. This railway operation benefits from the Cambodian ingenuity and cooperative values.
The very simple design of the rail car is economical in use of materials, only the basics beyond the gasoline engine. It's one use of gasoline where its an amazing and appropriate energy source. These engines are simple, rugged, and effective. The use of a stick on the axle as a brake is, perhaps, not enough safety for me however.
One wonders what they will do when the supply of abandoned battle tanks runs out that provide the wheels for the Norry. The absence of bumpers requires a certain fatalism from the passengers. Low speeds and the lack of rail traffic make this system practical.
Since the car must be taken off the tracks when a "REAL TRAIN" comes along or one Norry must pass the other, the design has parts that can be moved by at most two people, even one. Obviously the passengers are expected to help with taking the car on and off the tracks..... This limitation in the design is quite a challenge. The bamboo in the car platform deck is a locally grown resource and lightweight
I found this web video after following a link from a Facebook posting to a video by Gib Cooper where a Mexican master craftsman shows how to bend bamboo culms with heat. From there the YouTube suggestions with keyword bamboo had this video. I love railroads and bamboo, so I went there. What a gem!
The vision to create this informal rural rail system had huge and lasting beneficial impact on the lives of the survivors of the Khemer Rouge genocide. The U.N. is a vital part of our international community when it acts in this way. A catalyst and an enabler of the things that make life better.
Bamboo Railway - Battambang, Cambodia
The story of how the Cambodian people could recycle pieces from the weapons of a genocidal war to fashion a working means of communication with the help of critical U.N. technical assistance in the form of gasoline engines shows how U.N operations can be effective with little cost. This railway operation benefits from the Cambodian ingenuity and cooperative values.
The very simple design of the rail car is economical in use of materials, only the basics beyond the gasoline engine. It's one use of gasoline where its an amazing and appropriate energy source. These engines are simple, rugged, and effective. The use of a stick on the axle as a brake is, perhaps, not enough safety for me however.
One wonders what they will do when the supply of abandoned battle tanks runs out that provide the wheels for the Norry. The absence of bumpers requires a certain fatalism from the passengers. Low speeds and the lack of rail traffic make this system practical.
Since the car must be taken off the tracks when a "REAL TRAIN" comes along or one Norry must pass the other, the design has parts that can be moved by at most two people, even one. Obviously the passengers are expected to help with taking the car on and off the tracks..... This limitation in the design is quite a challenge. The bamboo in the car platform deck is a locally grown resource and lightweight
I found this web video after following a link from a Facebook posting to a video by Gib Cooper where a Mexican master craftsman shows how to bend bamboo culms with heat. From there the YouTube suggestions with keyword bamboo had this video. I love railroads and bamboo, so I went there. What a gem!
The vision to create this informal rural rail system had huge and lasting beneficial impact on the lives of the survivors of the Khemer Rouge genocide. The U.N. is a vital part of our international community when it acts in this way. A catalyst and an enabler of the things that make life better.
Thursday, November 19, 2009
My grandmother said that the hardest part of growing older was loosing friends. She lived to be 102, and by then, had lost all her friends though she still had our family. She passed away while my mother was in Europe with her husband, and I think that she had to go when Mom wasn't there. They were very close, and even though Grandmother lost some of her cognative powers as she aged, that love never faded.
For me, growing older has been good in some ways, as I'm married again, and happier than before. My values are more clear, as what's important comes through the noise as I age. Indeed Grandmother was right, friends are so important, and making new ones is both a pleasure and a challenge.
With my first wife, there was a time of closeness, family, learning and the shared dreams. The shared visions and values were corroded as fundamental incompatibilities in our core values came through, turning raw emotional sores into deep wounds.
My own immaturity was a factor in some dumb choices when I was young, but I did the best that I could and many of my choices were good. Now 60, my first wife died some 27 years after we divorced. She left me and precipitated a crises in my life, upending my story, in a painful episode that cauterized some aspects of me. It also caused me to seek counseling and to question many of my assumptions, and I changed in some important ways. Fortunately we were able to forgive each other before she passed away, and she was honest about some things that I suspected but never knew that happened during our marriage. She confirmed that my intuition was right, that my deepest self knew what I didn't want to know. She was able to grow and before she passed away, she was able to bring love to the forefront, and to give her daughter that unconditional love that is the gift that never dies.
So for me, living long enough to get some perspective on those painful events so long ago, to forgive and be forgiven, to learn and to understand has been a great gift. I learned about some of my unrealistic expectations and choices, and how some of my values and choices meant so much to those around me. That validation of who I am and my worth has been a comfort, and one that could only come with the perspective of time.
Even under the stress of loosing my marriage, I held to certain core values and personal decisions about how I would live my life. Those core values have been life saving, in ways that I never imagined. Indeed, it was only later that I learned that a slightly different choice could have been deadly for me, as I could have been exposed to disease that later killed her. Of course, her passing was the confluence of many things, and the lifelong alcoholism wasn't going to "work out". It's not a feeling of superiority that I'm talking about, rather the experience of amazing grace.
The grace that got me through those tough times and is with me today. The grace that got me through being with my dear partner Peggy when she passed away from cancer and the grace that lead me to open my heart again to my wife today. Amazing grace, thanks for the grace in my life! Thanks for this morning, for this breath. Thanks.
As the American Indians pray, "all life is sacred".
for all my relations,
thanks.
For me, growing older has been good in some ways, as I'm married again, and happier than before. My values are more clear, as what's important comes through the noise as I age. Indeed Grandmother was right, friends are so important, and making new ones is both a pleasure and a challenge.
With my first wife, there was a time of closeness, family, learning and the shared dreams. The shared visions and values were corroded as fundamental incompatibilities in our core values came through, turning raw emotional sores into deep wounds.
My own immaturity was a factor in some dumb choices when I was young, but I did the best that I could and many of my choices were good. Now 60, my first wife died some 27 years after we divorced. She left me and precipitated a crises in my life, upending my story, in a painful episode that cauterized some aspects of me. It also caused me to seek counseling and to question many of my assumptions, and I changed in some important ways. Fortunately we were able to forgive each other before she passed away, and she was honest about some things that I suspected but never knew that happened during our marriage. She confirmed that my intuition was right, that my deepest self knew what I didn't want to know. She was able to grow and before she passed away, she was able to bring love to the forefront, and to give her daughter that unconditional love that is the gift that never dies.
So for me, living long enough to get some perspective on those painful events so long ago, to forgive and be forgiven, to learn and to understand has been a great gift. I learned about some of my unrealistic expectations and choices, and how some of my values and choices meant so much to those around me. That validation of who I am and my worth has been a comfort, and one that could only come with the perspective of time.
Even under the stress of loosing my marriage, I held to certain core values and personal decisions about how I would live my life. Those core values have been life saving, in ways that I never imagined. Indeed, it was only later that I learned that a slightly different choice could have been deadly for me, as I could have been exposed to disease that later killed her. Of course, her passing was the confluence of many things, and the lifelong alcoholism wasn't going to "work out". It's not a feeling of superiority that I'm talking about, rather the experience of amazing grace.
The grace that got me through those tough times and is with me today. The grace that got me through being with my dear partner Peggy when she passed away from cancer and the grace that lead me to open my heart again to my wife today. Amazing grace, thanks for the grace in my life! Thanks for this morning, for this breath. Thanks.
As the American Indians pray, "all life is sacred".
for all my relations,
thanks.
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