Indeed, abundance is irrelevant. "Coverage" is key. Coverage is the number of times that a part of the sequence is represented. Having more sequenced DNA increases the coverage, but a more important parameter is diversity. Whether it is inter- or intra-species diversity, having different sequences means you are less likely to run into that sequence again.
The most interesting metagenomic projects have been the low-diversity ones, where coverage is high enough to recreate the microorganisms there. In Banfield's pioneering work on the microbes composing biofilms growing on the acidic drainage from abandoned mines (aka "acid mine drainage"), near-complete genome sequences were obtained for the two most abundant constituents (of six total, I believe). Contrast this with Venter's simultaneously-published Sargasso Sea metagenome (sequencing the microbes caught in filters from deep sea water, erroneously purported to have low-diversity due to low mixing of waters): most sequences were never encountered a second time, after a ridiculous amount of sequencing.
To do a good metagenome study, you have to pick the environment cleverly. Getting the genome sequence of enrichments of unculturable microbes that are environmentally relevant (eg Annamox, Mark Strous), or the termite hindgut (Hugenholtz/Leadbetter).
As sequencing costs go down and throughput goes up, metagenomics is going to become more prevalent and inexpensive. LARGE LARGE LARGE datasets will be generated. While this scale of data has never posed a problem for you Slashdotting types, it becomes a matter of "what is the scientific question?" What are you looking for? Interesting things will be turned up by metagenomics, but few will ever thoroughly mine their metagenomic data for interesting information. On the applied realm, this may actually be a moot point. "Functional metagenomics" is already a normal strategy for drug discovery (cloning random bits of environmental DNA into a model organism and performing a clever screen)
Moreover: Growing algae in vessels means that there will be no runoff; much less fertilizer would need to be used (zero if you use nitrogen-fixing cyanobacteria or purple photosynthetic bacteria), and indeed this prevents pollution of the soil. Soil is not even a factor, since one would be concerned with reactors or ponds. The most effulgently-illuminated locations tend to have the least amount of arable land, so algal aquaculture does not compete with nearby plant-based agriculture (food production), potentially enhancing it with cell waste as fertilizer). If the process is done in sealed bioreactors, then water use is greatly improved since evaporation would be contained. There is major promise in the culturing of halophilic algae because few other things will grow in saline water, thus reducing problems of contamination.
MAJOR PROBLEM: self-shading. Unicellular photosynthetic microorganisms are rarely grown in monocultures in the environment; rather they are in competition for light with other species of phototrophs and of non-phototrophs that can scatter the light. Thus almost all photosynthetic microorganisms have evolved mechanisms to "hog" the light. (This is referred to as a "large light-harvesting chlorophyll antenna size", or simply "antenna"). An individual cell harvests more light than it really needs to do photochemistry, then quenches the excess excitation energy that it does not need. In a pure culture of a microalga (as envisioned for algal-aquaculture), cells increase their antenna size to try and capture as much light as possible; thus, light rarely penetrates the surface layers of the reactor. This is "self-shading".
This can be circumvented by either using shallow path-length reactors (arrays of tubes is one idea, or flat panel reactors) or by employing strains of algae that have decreased antenna sizes. A decreased antenna size sounds counterintuitive; less chlorophyll means less photosynthesis capable of being performed! But no, this only goes for lower light intensities. Antenna mutants saturate at higher light intensities than cells with normal (large) antennae. Efficiency PER CULTURE goes up (although efficiency per cell is probably lower).
Global Energy Network Institute, a Bucky Fuller-inspired nonprofit that studies the efficacy of hooking up and decentralizing the world's energy grids.
One large advantage is to offset peak loading (say, a dam in India at night can help supply energy to American daytime activities) or between hemispheres to offset seasonal variations. They have collected tons of facts about the energy available, but I was never one for remembering facts so check out the website.
This article's topic would support this idea even more.
Peace.
What did you think of Richard Dawkins? I am almost done with his "Unweaving the Rainbow" where he attempts to distinguish good poetic science from bad poetic science. It is often interesting, but it jumped from fluffy and easy-to-understand (for an aspiring scientist, myself) to a mode that needs much more thinking. I often found myself disagreeing with him, and even feeling he was arrogant. But that's what popular science writers are, thinking that the pride of being a poet is even more enhanced by possessing "objective" scientific knowledge. it's all subjective, no matter which way you look at it.
Slashdot Mirror
Indeed, abundance is irrelevant. "Coverage" is key. Coverage is the number of times that a part of the sequence is represented. Having more sequenced DNA increases the coverage, but a more important parameter is diversity. Whether it is inter- or intra-species diversity, having different sequences means you are less likely to run into that sequence again. The most interesting metagenomic projects have been the low-diversity ones, where coverage is high enough to recreate the microorganisms there. In Banfield's pioneering work on the microbes composing biofilms growing on the acidic drainage from abandoned mines (aka "acid mine drainage"), near-complete genome sequences were obtained for the two most abundant constituents (of six total, I believe). Contrast this with Venter's simultaneously-published Sargasso Sea metagenome (sequencing the microbes caught in filters from deep sea water, erroneously purported to have low-diversity due to low mixing of waters): most sequences were never encountered a second time, after a ridiculous amount of sequencing. To do a good metagenome study, you have to pick the environment cleverly. Getting the genome sequence of enrichments of unculturable microbes that are environmentally relevant (eg Annamox, Mark Strous), or the termite hindgut (Hugenholtz/Leadbetter). As sequencing costs go down and throughput goes up, metagenomics is going to become more prevalent and inexpensive. LARGE LARGE LARGE datasets will be generated. While this scale of data has never posed a problem for you Slashdotting types, it becomes a matter of "what is the scientific question?" What are you looking for? Interesting things will be turned up by metagenomics, but few will ever thoroughly mine their metagenomic data for interesting information. On the applied realm, this may actually be a moot point. "Functional metagenomics" is already a normal strategy for drug discovery (cloning random bits of environmental DNA into a model organism and performing a clever screen)
Moreover: Growing algae in vessels means that there will be no runoff; much less fertilizer would need to be used (zero if you use nitrogen-fixing cyanobacteria or purple photosynthetic bacteria), and indeed this prevents pollution of the soil. Soil is not even a factor, since one would be concerned with reactors or ponds. The most effulgently-illuminated locations tend to have the least amount of arable land, so algal aquaculture does not compete with nearby plant-based agriculture (food production), potentially enhancing it with cell waste as fertilizer). If the process is done in sealed bioreactors, then water use is greatly improved since evaporation would be contained. There is major promise in the culturing of halophilic algae because few other things will grow in saline water, thus reducing problems of contamination. MAJOR PROBLEM: self-shading. Unicellular photosynthetic microorganisms are rarely grown in monocultures in the environment; rather they are in competition for light with other species of phototrophs and of non-phototrophs that can scatter the light. Thus almost all photosynthetic microorganisms have evolved mechanisms to "hog" the light. (This is referred to as a "large light-harvesting chlorophyll antenna size", or simply "antenna"). An individual cell harvests more light than it really needs to do photochemistry, then quenches the excess excitation energy that it does not need. In a pure culture of a microalga (as envisioned for algal-aquaculture), cells increase their antenna size to try and capture as much light as possible; thus, light rarely penetrates the surface layers of the reactor. This is "self-shading". This can be circumvented by either using shallow path-length reactors (arrays of tubes is one idea, or flat panel reactors) or by employing strains of algae that have decreased antenna sizes. A decreased antenna size sounds counterintuitive; less chlorophyll means less photosynthesis capable of being performed! But no, this only goes for lower light intensities. Antenna mutants saturate at higher light intensities than cells with normal (large) antennae. Efficiency PER CULTURE goes up (although efficiency per cell is probably lower).
Check out www.geni.org
Global Energy Network Institute, a Bucky Fuller-inspired nonprofit that studies the efficacy of hooking up and decentralizing the world's energy grids.
One large advantage is to offset peak loading (say, a dam in India at night can help supply energy to American daytime activities) or between hemispheres to offset seasonal variations. They have collected tons of facts about the energy available, but I was never one for remembering facts so check out the website.
This article's topic would support this idea even more.
Peace.
What did you think of Richard Dawkins? I am almost done with his "Unweaving the Rainbow" where he attempts to distinguish good poetic science from bad poetic science. It is often interesting, but it jumped from fluffy and easy-to-understand (for an aspiring scientist, myself) to a mode that needs much more thinking. I often found myself disagreeing with him, and even feeling he was arrogant. But that's what popular science writers are, thinking that the pride of being a poet is even more enhanced by possessing "objective" scientific knowledge. it's all subjective, no matter which way you look at it.