In the course of my blog postings, the National Academy of the Sciences report Rising Above the Gathering Storm has been cited frequently. The report's recommendations led mostly to the drafting of the 2007 America COMPETES Act. Rising Above the Gathering Storm however, focused mostly on the physical and engineering sciences, so another, slightly less known report was drafted: A New Biology for the 21st Century; which naturally (pun intended) focuses on the life sciences. I have drafted a summary of the report, as seen below, and will conclude with some thoughts of my own on the topic of synthetic biofuels.
A New Biology for the 21st Century - A Summary
What is the “New Biology?”
At its core the “New Biology” is about integration, integration of the many sub-disciplines of biology, and integration into biology of physicists, chemists, computational scientists, mathematicians, and engineers. It is not just the disciplines that need to be integrated; Interagency co-leadership of projects will be needed to help New Biology reach its full potential. It’s important to remember that inter-agency collaboration is not just about funding: the expertise, and individual knowledge possessed by each agency will be required to solve society’s greatest problems. Furthermore, the New Biology is characterized by a shift in higher-education. Interdisciplinary programs that expose students to the wide array of subjects that the New Biology will need to draw from will become critically important. It is well to keep in mind that a New Biologist will not be a dilettante flittering from subject to subject, rather, he or she will have a deep knowledge in one subject, and a working fluency in several others. Finally, New Biology is more akin to the Moon Challenge, or the Human Genome Project, in a sense that it would be problem-driven science, as opposed to individual investigator driven. However, great emphasis in the report is placed on the fact that New Biology will in no way replace basic research, rather basic research is crucial to the flourishing of New Biology.
The Great Challenges of Society
The NAS uses four great challenges to society to explain the potential of New Biology.
· Food Production
· Ecosystem Preservation & Restoration
· Sustainable Energy
· Health
Food Production
The Challenge: Producing enough food to feed the world’s 8.4 billion people by 2030, while allowing crops to adapt to climate change, and making sure there is enough land for ecosystem services and energy production.
The New Biology Approach:
· Understanding Plant Growth
o A deep understanding of both plant genomics and development (the part’s list and the instructions, respectively) will lead to comprehensive, and safe plant bio-engineering.
o We lack a fundamental knowledge in plant development. We have some parts lists, but no instructions.
o A deeper understanding of genomics and development combined with advances in breeding and engineering, will make it faster and less expensive to develop plants with desired characteristics (i.e. extreme climate tolerance).
· Genetically Informed Breeding
o New quantitative methods are being developed to allow scientists to target genome differences between plant parents, and to decide which genes bestow the desired trait.
o With this technology scientists can examine at the seed level which would be plants have the desired trait, rapidly expanding the speed, and power of plant breeding to bring about desired traits. (Old methods required waiting for the next generation to check for desired traits).
· Transgenics and Genetic Engineering of Crops
o Adding genes to plants from other species may lead to some important breakthroughs
o For example some desert plants follow C4 photosynthesis which allows them to photosynthesize in dry environments. If we could figure out a pathway to allow current C3 plants switch to C4, then that could lead to increased food production in changing climate, and environmental conditions
· Biodiversity, Systematics, and Evolutionary Genomics
o Greater understanding of biodiversity, and the gene pools that come along with it will provide a sort of warehouse for plant “parts”. Tapping into this warehouse will allow plant engineers, and breeders to help crops to adapt to climate change, and increase production
· Crops as Ecosystems
o Plants do not grow in vacuums, they grow in complex ecosystems with interactions among insects, microbial communities, birds etc. Understanding these interactions will have huge benefits to crop production in an uncertain climate future.
o New Biology is especially well poised to take on this challenge, because the knowledge must come from a wide array of scientists. Ecologists, microbiologists, hydrologists, environmental engineers, and computational scientists will all be required for such a study.
Ecosystem Preservation & Restoration
The Challenge: Sustaining the productivity of Earth’s ecosystems in the face of a changing climate.
The New Biology Approach:
· Monitor Ecosystem Services
o The goal of monitoring ecosystem services is to provide an accurate assessment of the services, and the ability to figure out when such services are at risk.
o Obtaining both intensive (lots of varied information) and extensive (across a wide variety of ecosystems, and across a large expanse of land) ecosystem monitoring will require an inter-agency effort, and the combined efforts of engineers, ecologists, statisticians, and computational scientists. Both types of collaborations are key principles within the New Biology.
· Advance Understanding of Ecosystem Restoration
o Holds the possibilities of both restoring ecosystems, and engineering ecosystems to help mitigate climate change.
o Right now very few techniques in the restoration ecologists toolkit. Need an integrated approach to ecosystem restoration.
· Integrate Basic Knowledge about Ecosystem Function with Problem Solving Techniques
o The new biology could lead to a new field of ecosystem engineering, which would be the equivalent of an MD-PhD in the medical world.
o
Energy
The Challenge: Rapidly expand the availability of sustainable, alternatives to fossil-fuels.
The New Biology Approach:
· Identifying and Optimizing Sources of Biomass for Biofuel.
o Corn cannot be our biofuel source forever, and must be supplemented and eventually replaced with either direct sugar crops (sugarcane or sweet sorghum), or cellulosic materials (switchgrass, miscanthus, or agricultural byproducts).
· Identifying and Optimizing Microbial Biocatalysts
o Microbial biocatalysts offer a promising way to make cheap biofuels quickly. Using genomic and metabolic research, organisms are being found to act as micro-factories, to produce the biofuels of the future.
o Collaborations among microbiologists, and evolutionary geneticists required.
· Approaching Biofuel Production as a Systems Challenge
o Collaboration across a wide variety of scientists will be needed to meet the energy challenge
o However not all these collaborations need to be physical, information technology allows for virtual collaboration which will be crucial for projects of this size.
Health
The Challenge: Developing healthcare to meet every individuals needs…and genome.
The New Biology Approach
· The Genotype-Phenotype Challenge
o Understanding how our genotype, environment, and microbial genotype inside of us, affects our phenotype is crucial to individualized medicine.
o The time is fast approaching where it will be economically feasible to sequence the genomes of every patient that arrives at the hospital
o However the challenge is much more than that, because we have to deal with environmental factors, epigenetics, and microbial communities within the human body.
o Once those areas are fully fleshed out, truly individualized medicine, rather than medicine based on statistical probabilities will arrive in America’s hospitals.
o New Biology, with its emphasis on problem driven, collaborative, interdisciplinary science is uniquely positioned to take on this challenge.
· Understanding Networks
o Understanding protein interactions, nerve cell interactions, developmental processes, etc. Is critically important to reaching the goal of individualized medicine.
o Collaborations among teams of scientists in many disciplines, is the best way for such a challenge to be met.
· Studying Complex Systems Directly in Humans
o Work with model organisms has been very productive, advances in imaging, high-throughput technologies, and computational biology have made it possible to compare and relate model system information directly with the human system.
o Another approach to the genotype-phenotype challenge is direct read outs of proteomes (all the proteins in a sample) and metabolomes (all the metabolites in a sample). The technology to acquire such read outs is currently expensive, and cumbersome, however it is being increasingly being used to analyze, blood, sweat, and urine.
o Such readouts could be used to design tailor-made drugs (i.e. adjustments made based upon how each individual would metabolize each drug).
o Such a task dwarfs the complexity of the Human Genome Project. Perfect for the New Biology to take on.
· A Systems Approach to the genotype-phenotype challenge
o A broad inter-agency approach is needed to solve the genotype-phenotype challenge
Conclusion
What is the New Biology?
· Collaborative Science
o Interagency
o Interdisciplinary
o Multi-University
o Public-Private Groups
· Problem Driven Science
o Letting the Challenges Drive the Science
o Basic, Investigator Driven research still plays a major role
· New Biology Education
o Interdisciplinary Studies
o Working fluency in several disciplines, deep knowledge in one
· The New Biologist may not even be a biologist!
o Physicists, Engineers, Computational Scientists, Statisticians, etc. who collaborate with other scientists on life systems.
If you managed to make it through the summary, Bravo, I commend you. The full 115 page report was not at all times a joy to get through but the writing inside I think is important. Some of the items the report touches on I consider so obviously beneficial to the enterprise of science that I wonder if it's unnecessary to give them their due praise, but interdisciplinary work among the sciences, and mission driven studies I think are crucial to the next generation of science.
Now for a little bit on Synthetic Biofuels
A New Biology for the 21st Century does gloss over a few issues. If you take a look at the Energy section again, it refers to "biocatalysts" for creating biofuels. What does this mean? They are referring to the concept of using algae or some other living organism, genetically engineering it to take even more CO2 from the air, and then using them to create a petrol substitute. While I must admit this is a very cool (and theoretically carbon neutral) idea, the specifics concern me. Namely, where is the natural resource infrastructure to support such an industry? Algae require quite a bit of water and nutrients and aren't exactly something you can just introduce into an ecosystem. Maybe the concerns are premature for a technology in an infant stage, and I'm surely not calling for a cessation of research into algae biofuels (I believe my earlier statement was it is "very cool") but resources are resources and where are they going to come from? Jim Thomas, a member of a technology watch-dog group actually summarized my concerns pretty succinctly.
...And the point is this: any meaningful assessment of synthetic biology as a technology has to grapple with the socioeconomic impacts of the industry that it gives rise to...And I think in the process, it might become like the petro-economy. Trying to guarantee the supply of sugar or cellulose or algae for the vats of synthetic organisms pumping out product will require a massive reorganization of natural resources, a grabbing of land and stripping away of plant matter and water and nutrients that could affect every part of the planet...
However, Jim and I differ in two senses: 1) I do not have (though I wish I did) his flair for the dramatic, and 2) I don't think the research should stop, I think algae biofuels have huge potential benefit. I do think, however, that we need to be aware of, and plan out a way to manage and mitigate any negative socio-economic impacts of the new technology. This does not have to be like the hey-days of synthetic chemicals where we place pound after pound of toxic chemicals into the soil without a single afterthought to the consequences. President Obama actually initiated a presidential commission to examine synthetic biofuels and other synthetic biology issues, so I think the groundwork is being laid to avoid at least some of the more egregious mistakes of the past. I personally think looking to an independent-ish third party like the National Academies to do a report on the potential consequences and benefits of such technology would be a great supplement to the presidential commission. We should be examining these issues now, before synthetic biology really takes off, so we have the appropriate structure to work through any issues, before the Rachel Carson of the 21st century has to write another book.
Just some food for thought.
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