Free flow essay time
I'm stuck. Let's try to unstuck.
Ok, I got this paper: "where's the ecology in molecular ecology?" It's very recent, may 2009. I gotta jump into their debate and write "a thoughtful fact-rich critique, rebuttal, addendum" whatev.
In the above paper, these 3 guys, two fairly young faculty and a grad student, do a gross review of three journals:
1. Ecology
2. Evolutionary Biology
3. Molecular Ecology
They classify the papers as either evolutionary or ecological (by assigning it to various subdivisions of each) and note whether they use molecular tools or not. So what's a molecular tool you say? Good motherfucking question. Damn, I really don't think they defined it. So I will. It's any use of nucleic acid or protein sequence data.
In the paper they mention X basic methods:
1.
2.
3.
Other methods may include:
1.
2.
3.
Now they make this big stink about how:
- evolutionary biology studies molecular methods much more often than ecology studies
- molecular ecology is publishing quite a bit more evolutionary studies than ecological studies
- they're surprised, but I'm not
I think that the use of DNA, which is generally inherited from one's predcessors is OBVIOUSLY gonna be easier to apply to problems of decent and modification through time. BUT I don't want to go into this. I don't think it's interesting or useful to debate whether Ecologists are slackers when it comes to molecular methods. (I'm noticing there's a bit of a competition(?) between ecology and evolutionary biology (which I think is best seen as a daughter discipline to ecology which exploded a bit after we decoded proteins).) What do I want to go into?
Well, how about the growth of ecology? New tools, new directions, what have molecular tools given us, what are the new ways in which they may be applied to old questions? New questions? The dudes above advocate a basic working knowledge of molecular tools for all ecologists, what would those look like? What about interdiscimplinary work?
Do I have to justify whether we need it or not? How about it’s the prudent course of action? After all, we may be seriously fucking the planet by disturbing basic geological processes including the living bacterial and archeal components. Molecular methods are those of choice/availability in microbial systems, for speed as well as to get around the nonculturable issue. When it comes right down to it, molecular methods will be developed for the study of microorganisms.
Do I want to be a dick and say that microorganismal diversity is so much fucking bigger than that of the tiny tippy tip of the eukaryotic branch that has been the focus of ecology and evolutionary biology for all but the last decade or so? And that animals, plants and fungi probably have no effect on the aforementioned biogeochemical cycles we might be destroying as we speak. Heck, we might not, but we have only a frighteningly rudimentary understanding of the interactions of microorganisms with the biotic environment. Nah, I don’t really want to argue this. Again, it doesn’t move us forward.
What would move us forward?
1. Promoting interdisciplinary work, (I could cite my interdisciplinary training grant, my interdisciplinary research institute, my interdisciplinary program as examples)
2. Education, continuing and otherwise on the use of molecular tools in ecology. Could I propose the organization behind the molecular biology journal organize a training session? How about someone actually do a good comprehensive review of molecular methods in ecology? -maybe I can find a few and criticize them.
I can talk about what’s holding us back. “where’s the ecology” says some ecologists feel molecules are at odds with natural history, perhaps there’s no teaching some old dogs new tricks. (but god I don’t want to put it that way). How about we admit there is a natural rate of obscelescene in any scientist and we be okay with that while we prepare for that future anyway? Some stuff really is holding us back, and it’s not intellectual laziness.
I think that it’s not all that hard to make a decent phylogenetic tree, but it’s hard to do a microarray. It’s also not too difficult to use markers to track individuals or estimate genetic diversity, but that doesn’t need you to know what the genome means. Function is hard to grok. First of all, there’s all the genes we got no functional data for. Even the well characterized ones are difficult to link to function/phenotype because we’re still figuring out how to link them up into networks. Even the “where’s the ecology” article mentions several bottlenecks [list here].
So what’s the basic outline?
1. where’s ecology going (maybe put/explain a few important people’s visions here)
2. what about molecular methods in ecology, is there enough? Is the focus narrow?
3. current bottlenecks in use of molecular tools
4. preparing for the future in ecology (interdisciplinary focus, education)
Ok, I got this paper: "where's the ecology in molecular ecology?" It's very recent, may 2009. I gotta jump into their debate and write "a thoughtful fact-rich critique, rebuttal, addendum" whatev.
In the above paper, these 3 guys, two fairly young faculty and a grad student, do a gross review of three journals:
1. Ecology
2. Evolutionary Biology
3. Molecular Ecology
They classify the papers as either evolutionary or ecological (by assigning it to various subdivisions of each) and note whether they use molecular tools or not. So what's a molecular tool you say? Good motherfucking question. Damn, I really don't think they defined it. So I will. It's any use of nucleic acid or protein sequence data.
In the paper they mention X basic methods:
1.
2.
3.
Other methods may include:
1.
2.
3.
Now they make this big stink about how:
- evolutionary biology studies molecular methods much more often than ecology studies
- molecular ecology is publishing quite a bit more evolutionary studies than ecological studies
- they're surprised, but I'm not
I think that the use of DNA, which is generally inherited from one's predcessors is OBVIOUSLY gonna be easier to apply to problems of decent and modification through time. BUT I don't want to go into this. I don't think it's interesting or useful to debate whether Ecologists are slackers when it comes to molecular methods. (I'm noticing there's a bit of a competition(?) between ecology and evolutionary biology (which I think is best seen as a daughter discipline to ecology which exploded a bit after we decoded proteins).) What do I want to go into?
Well, how about the growth of ecology? New tools, new directions, what have molecular tools given us, what are the new ways in which they may be applied to old questions? New questions? The dudes above advocate a basic working knowledge of molecular tools for all ecologists, what would those look like? What about interdiscimplinary work?
Do I have to justify whether we need it or not? How about it’s the prudent course of action? After all, we may be seriously fucking the planet by disturbing basic geological processes including the living bacterial and archeal components. Molecular methods are those of choice/availability in microbial systems, for speed as well as to get around the nonculturable issue. When it comes right down to it, molecular methods will be developed for the study of microorganisms.
Do I want to be a dick and say that microorganismal diversity is so much fucking bigger than that of the tiny tippy tip of the eukaryotic branch that has been the focus of ecology and evolutionary biology for all but the last decade or so? And that animals, plants and fungi probably have no effect on the aforementioned biogeochemical cycles we might be destroying as we speak. Heck, we might not, but we have only a frighteningly rudimentary understanding of the interactions of microorganisms with the biotic environment. Nah, I don’t really want to argue this. Again, it doesn’t move us forward.
What would move us forward?
1. Promoting interdisciplinary work, (I could cite my interdisciplinary training grant, my interdisciplinary research institute, my interdisciplinary program as examples)
2. Education, continuing and otherwise on the use of molecular tools in ecology. Could I propose the organization behind the molecular biology journal organize a training session? How about someone actually do a good comprehensive review of molecular methods in ecology? -maybe I can find a few and criticize them.
I can talk about what’s holding us back. “where’s the ecology” says some ecologists feel molecules are at odds with natural history, perhaps there’s no teaching some old dogs new tricks. (but god I don’t want to put it that way). How about we admit there is a natural rate of obscelescene in any scientist and we be okay with that while we prepare for that future anyway? Some stuff really is holding us back, and it’s not intellectual laziness.
I think that it’s not all that hard to make a decent phylogenetic tree, but it’s hard to do a microarray. It’s also not too difficult to use markers to track individuals or estimate genetic diversity, but that doesn’t need you to know what the genome means. Function is hard to grok. First of all, there’s all the genes we got no functional data for. Even the well characterized ones are difficult to link to function/phenotype because we’re still figuring out how to link them up into networks. Even the “where’s the ecology” article mentions several bottlenecks [list here].
So what’s the basic outline?
1. where’s ecology going (maybe put/explain a few important people’s visions here)
2. what about molecular methods in ecology, is there enough? Is the focus narrow?
3. current bottlenecks in use of molecular tools
4. preparing for the future in ecology (interdisciplinary focus, education)