5 ms·

PhD student working on the C4 rice project here. On the road right now but happy to answer questions when I can find a moment. I genuinely think C4 rice the be

by Blahah 12y ago

PhD student working on the C4 rice project here. On the road right now but happy to answer questions when I can find a moment. I genuinely think C4 rice the best shot we've got at alleviating a huge chunk of world hunger in one (extremely difficult) move. Some key points: - C4 plants (like maize and sugarcane) are generally about 50% more efficient at biomass accumulation than C3 plants (like rice and wheat). C4 rice could mean a yield increase for rice of up to 50% _with no increase in inputs_ - RuBisCO is by far the most abundant protein in plants. It accounts for the majority of the nitrogen required by C3 plants, and the inefficiency of C3 is the reason we have to use so much nitrogen fertiliser. C4 rice would require considerably less fertiliser than C3 rice. - C4 plants use CO2 much more efficiently that C3 plants. This allows them to keep their stomata closed much more of the time, so they lose less water through transpiration. This makes C4 plants much more water efficient - C4 rice could require much less water than C3 rice, meaning it could be grown on land that is currently unsuitable for rice production. - C4 is probably the most interesting example of convergent evolution we know about. It has evolved over 70 times independently. This is quite amazing - it's a complex trait that requires dozens of proteins to be organised in a particular temporal and spatial pattern, and needs a new cell type to be made. Yet it has evolved 70+ times. - We are using the recurrent evolution pattern as our 'way in' to the problem of figuring out how to control C4 at the molecular level. We analyse gene expression on a massive scale in C4 and C3 sister species from all the evolutionary origins of the trait. - This involves a lot of interesting software challenges that hn might be interested in. For example, we're working with so many species that we can't sequence all their genomes. But we can sequence their _transcriptomes_, which is all the genes that are expressed at a given time. The sequencing technology produces millions of tiny fragments of the original sequences, which have to be pieced back together to be useful (an NP-hard problem).

seanp2k2 12y ago
What is the plan to deal with the backlash from uneducated people screaming about how bad GMO is?
- JoshTriplett 12y ago
  A combination of education and (mostly) ignoring them, I would hope. Such screaming comes from people who expect to have food available for their next meal, and tends to evaporate when hungry.
  - icelancer 12y ago
    > ignoring them I couldn't agree more. I really hope this rampant science denialism that is getting traction in American society is just profoundly ignored by those in power.
    - kolev 12y ago
      I think your position is unscientific. First, there's enough food to feed everybody on this planet already, but the "economical science" is not in favor of distributing resources evenly. Second, it's highly unscientific to start feeding a large population with foods that haven't passed any testing, and, no, 5-10-year trials are not enough. So, instead of solving problems we've created, the only solution is change the system that's highly unfair and that's build around the idea that only a small percentage of the world population will live well, will be wasteful, and destroying the entire planet with it's pathological consumerism and the rest will be "servicing" them or, at least, not getting hold of their resources, but suffering from their unhealthy for the environment lifestyle. Also, although I understand the positive sides of the GMOs, introducing them to our ecosystem is something, which short- and long-term consequences we cannot predict. So, if you want to help the hungry, re-engineer the political and the economical system (like The Venus Project), which corrupt system allows this global unfairness and leave the organisms (in "GMO") alone! I personally don't mind planting GMOs on Mars, just not on Earth, please, or not outside of strictly-controlled environments!
      - Blahah 12y ago
        > it's highly unscientific to start feeding a large population with foods that haven't passed any testing It's not unscientific at all. Whether to perform extensive testing on foods is not a function of science but of public opinion. The science tells us that all plant-derived foods outside a very small group of sources are extremely likely to be safe for the vast majority of people. There are very few exceptions, but there are some, like potatoes and tomatoes, which are both derived from poisonous wild ancestors so new strains need to be checked for reversion to the wild state. I say 'the vast majority of people', because some tiny number of people can have allergic reactions to any food, whether derived from a GMO or not. We don't perform any testing at all on the majority of new foods introduced. This includes new plant strains bred by various mutagenesis strategies, where vast numbers of mutations are induced by chemicals or with x-rays. By comparison, GMO-derived foods receive extensive testing, but only due to public opinion, not because they are inherently more dangerous. They are in fact inherently more safe. In the process of producing a new strain by genetic modification, very few changes will be made to the genome, and they will tend to be highly predictable, whereas the conventional breeding process is highly unpredictable and introduces lots of unwanted effects. This has been demonstrated in dozens of studies. > So, if you want to help the hungry, re-engineer the political and the economical system This can only be said from a position of first-world comfort. It would be wonderful if we could solve the resource distribution problem. But let's not kid ourselves: it would be crazy to only try to fix the economics. What's the timescale on that change? A very long time. How likely is it to work? Not at all likely. Improving agricultural yields through technology is something we definitely can achieve, and the timescale is predictable. Hungry people will choose the technology that allows them to feed themselves now, not the promise that if the entire world economy changes they may one day get some food.
ak217 12y ago
I work at a company in the Silicon Valley that provides some of the computational firepower and software expertise used to analyze transcriptomes for this project. We're hiring engineers and scientists. Email in profile for more info on that, otherwise I'm happy to answer questions as well.
sdabdoub 12y ago
> we're working with so many species that we can't sequence all their genomes Are you talking about sequencing enough to get adequate coverage for reconstruction? Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild?
- csirac2 12y ago
  It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences of de novo species (these have no reference assemblies to go by). Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand... And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned). And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at. And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)
- Blahah 12y ago
  > Are you talking about sequencing enough to get adequate coverage for reconstruction? Yes. Assembling a genome requires a lot of sequencing data or different kinds, and is expensive. Genomes (especially in plants) can be huge. We're only interested, at least in this specific example, in the things that are expressed. These make up a small proportion of the genome, and so we sequence only those things. > Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild? Agriculture in general has a vast impact on the environment. This is true across the board - including organic, GMOs, 'conventional', etc. By its very nature agriculture is about shaping the environment so we can control a piece of it to optimise it for food production. Our responsibility is to try to predict and minimise the effects that might cause problems. So far, GMOs have proven to have relatively little effect on the environment (compared to other drivers of agricultural productivity, like pesticide and herbicide use, for example). In the case of C4 rice we can predict what the major potential issue might be: C4 rice plants might perform so well that they outcompete wild plants outside the field setting. `There are some technological tricks we can use to try to ensure plants don't do well outside the field.
Zaephyr 12y ago
Having no background in plants or genetics - In my experience most systems are a series of tradeoffs. Even though C4 has evolved over 70 times, are there advantages conveyed by C3 or is C3 just easier to evolve?
- Blahah 12y ago
  C3 is the ancestral system - 45 million years ago, all plants were C3. C4 is a relatively new evolutionary innovation. The evolutionary history goes something like this. 3.6 billion years ago, Earth's atmosphere was very rich in CO2 and had basically no O2. Then photosynthesis evolved in bacteria in the ocean, using the enzyme RuBisCO to trap CO2 into sugars. Those bacteria became incredibly successful and in the process released a lot of O2 into the atmosphere - over the next 2 billion years the atmosphere became oxygenated. Unfortunately, RuBisCO sometimes mistakes O2 for CO2 and accidentally creates a toxic product that wastes energy instead of storing it. So this new oxygen-rich atmosphere started to make photosynthesis more efficient. Eventually (42 million years ago) the atmosphere became so oxygen rich and CO2-depleted that this inefficiency was a major evolutionary pressure, and C4 started to pop up. There's very little compromise with C4 - it's just better in a very wide range of commonly occurring environmental conditions.
  - Zaephyr 12y ago
    That makes a lot sense and is pretty cool. Thanks!

by Blahah 12y ago

seanp2k2 12y ago

What is the plan to deal with the backlash from uneducated people screaming about how bad GMO is?

JoshTriplett 12y ago
A combination of education and (mostly) ignoring them, I would hope. Such screaming comes from people who expect to have food available for their next meal, and tends to evaporate when hungry.
- icelancer 12y ago
  > ignoring them I couldn't agree more. I really hope this rampant science denialism that is getting traction in American society is just profoundly ignored by those in power.
  - kolev 12y ago
    I think your position is unscientific. First, there's enough food to feed everybody on this planet already, but the "economical science" is not in favor of distributing resources evenly. Second, it's highly unscientific to start feeding a large population with foods that haven't passed any testing, and, no, 5-10-year trials are not enough. So, instead of solving problems we've created, the only solution is change the system that's highly unfair and that's build around the idea that only a small percentage of the world population will live well, will be wasteful, and destroying the entire planet with it's pathological consumerism and the rest will be "servicing" them or, at least, not getting hold of their resources, but suffering from their unhealthy for the environment lifestyle. Also, although I understand the positive sides of the GMOs, introducing them to our ecosystem is something, which short- and long-term consequences we cannot predict. So, if you want to help the hungry, re-engineer the political and the economical system (like The Venus Project), which corrupt system allows this global unfairness and leave the organisms (in "GMO") alone! I personally don't mind planting GMOs on Mars, just not on Earth, please, or not outside of strictly-controlled environments!
    - Blahah 12y ago
      > it's highly unscientific to start feeding a large population with foods that haven't passed any testing It's not unscientific at all. Whether to perform extensive testing on foods is not a function of science but of public opinion. The science tells us that all plant-derived foods outside a very small group of sources are extremely likely to be safe for the vast majority of people. There are very few exceptions, but there are some, like potatoes and tomatoes, which are both derived from poisonous wild ancestors so new strains need to be checked for reversion to the wild state. I say 'the vast majority of people', because some tiny number of people can have allergic reactions to any food, whether derived from a GMO or not. We don't perform any testing at all on the majority of new foods introduced. This includes new plant strains bred by various mutagenesis strategies, where vast numbers of mutations are induced by chemicals or with x-rays. By comparison, GMO-derived foods receive extensive testing, but only due to public opinion, not because they are inherently more dangerous. They are in fact inherently more safe. In the process of producing a new strain by genetic modification, very few changes will be made to the genome, and they will tend to be highly predictable, whereas the conventional breeding process is highly unpredictable and introduces lots of unwanted effects. This has been demonstrated in dozens of studies. > So, if you want to help the hungry, re-engineer the political and the economical system This can only be said from a position of first-world comfort. It would be wonderful if we could solve the resource distribution problem. But let's not kid ourselves: it would be crazy to only try to fix the economics. What's the timescale on that change? A very long time. How likely is it to work? Not at all likely. Improving agricultural yields through technology is something we definitely can achieve, and the timescale is predictable. Hungry people will choose the technology that allows them to feed themselves now, not the promise that if the entire world economy changes they may one day get some food.

ak217 12y ago

I work at a company in the Silicon Valley that provides some of the computational firepower and software expertise used to analyze transcriptomes for this project. We're hiring engineers and scientists. Email in profile for more info on that, otherwise I'm happy to answer questions as well.

sdabdoub 12y ago

> we're working with so many species that we can't sequence all their genomes Are you talking about sequencing enough to get adequate coverage for reconstruction? Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild?

csirac2 12y ago
It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences of de novo species (these have no reference assemblies to go by). Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand... And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned). And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at. And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)
Blahah 12y ago
> Are you talking about sequencing enough to get adequate coverage for reconstruction? Yes. Assembling a genome requires a lot of sequencing data or different kinds, and is expensive. Genomes (especially in plants) can be huge. We're only interested, at least in this specific example, in the things that are expressed. These make up a small proportion of the genome, and so we sequence only those things. > Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild? Agriculture in general has a vast impact on the environment. This is true across the board - including organic, GMOs, 'conventional', etc. By its very nature agriculture is about shaping the environment so we can control a piece of it to optimise it for food production. Our responsibility is to try to predict and minimise the effects that might cause problems. So far, GMOs have proven to have relatively little effect on the environment (compared to other drivers of agricultural productivity, like pesticide and herbicide use, for example). In the case of C4 rice we can predict what the major potential issue might be: C4 rice plants might perform so well that they outcompete wild plants outside the field setting. `There are some technological tricks we can use to try to ensure plants don't do well outside the field.

Zaephyr 12y ago

Having no background in plants or genetics - In my experience most systems are a series of tradeoffs. Even though C4 has evolved over 70 times, are there advantages conveyed by C3 or is C3 just easier to evolve?

Blahah 12y ago
C3 is the ancestral system - 45 million years ago, all plants were C3. C4 is a relatively new evolutionary innovation. The evolutionary history goes something like this. 3.6 billion years ago, Earth's atmosphere was very rich in CO2 and had basically no O2. Then photosynthesis evolved in bacteria in the ocean, using the enzyme RuBisCO to trap CO2 into sugars. Those bacteria became incredibly successful and in the process released a lot of O2 into the atmosphere - over the next 2 billion years the atmosphere became oxygenated. Unfortunately, RuBisCO sometimes mistakes O2 for CO2 and accidentally creates a toxic product that wastes energy instead of storing it. So this new oxygen-rich atmosphere started to make photosynthesis more efficient. Eventually (42 million years ago) the atmosphere became so oxygen rich and CO2-depleted that this inefficiency was a major evolutionary pressure, and C4 started to pop up. There's very little compromise with C4 - it's just better in a very wide range of commonly occurring environmental conditions.
- Zaephyr 12y ago
  That makes a lot sense and is pretty cool. Thanks!