Last night, sometime after two in the morning and before seven, it snowed. Everything is very pretty and bright outside, even though the trails are covered with footprints and there's not even enough snow to cover the grass. When I was (significantly) younger I read a poem that's stuck with me--or at least the last line has. The poem itself is somewhere below mediocre, and apparently from a greeting card collection or an anthology of Christmas card poetry? I'm not quite sure. (I found a reference and the full text here).
"Despite the forecast's promise,
It didn't snow that night;
But in the morning, flakes began
To glade all right.
Not enough to cover roads
Or even hide the grass;
But enough to change the light."
Say what you will (and I have plenty to say) about the use of "glade," but I just can't forget the very last line. But enough to change the light. That's what snow does: reflects light around, even when it's clouded over, until everything seems different--lighter, brighter, fresh, new. Even if there's only a little tiny bit of it.
The other thing I love about snow is the smell of it. On very cold nights, or when you go outside first thing in the morning after it's snowed, you can smell: bright and cold. Sometimes when it doesn't snow, and it's just cold outside, you can smell it, too. I guess it's my version of the smell of rain, which I don't have strong associations to: I'm from the Pacific Northwest, and we don't get torrential downpours. We get drizzle, and either the smell's not there or it's so prevalent that I don't even notice it. I think it's the former.
Either way, I didn't smell rain until a chemistry lab this fall: we were taking a spectrographic reading of ozone, which required making ozone and then bottling it. The teacher let us smell it: the smell of rain. Free oxygen radicals created by high energy breaking apart a stable O=O (O2) molecule into its components, and then the unstable free radicals joining a whole O2 molecule to create ozone, O3. The smell of rain is ozone, and it seemed incongruous in a classroom full of students trying to get spectrometers to analyze light absorbtion or whatever else. It was a little bit surreal.
Monday, December 7, 2009
Sunday, December 6, 2009
Faith
I just came back from singing at a gospel concert. It was a religious experience. I was moved--by the spirit, by God, by whatever you want to call it. I felt it, profoundly. Now I'm finishing an essay about allelopathy and the novel weapons hypothesis. It will incorporate critique about the effectiveness of bioassays in determining allelopathy, discussion of forms of allelopathy other than phytotoxicity, and community-specific allelopathy and how that relates to several specific theories about plant communities.
I get a certain number of questions about how faith and science can coexist in my life. There seems to be this idea that science is all cold rationality (and good science mostly is that) and that religion is inimical to realism and hard facts--and religion is, at its roots, about faith, which requires an absence of definitive proof.
But I think that limiting yourself to one or the other is a little sad. I can believe in God while I'm carefully investigating the role of arbuscular mychorrhizae fungus in the invasive potential of Centaurea diffusa, and it will affirm my faith in God.
To me, the fact that everything is is the greatest miracle. Nothing is more spectacular than everything--every living and non-living thing, outer space and all the stars including our own, the earth we live on. It's incredible. A God that can create that is something to believe in.
And it doesn't have to be that, a few thousand years ago, God appeared and, boom!, created the Earth, exactly as it is today, only maybe with less carbon dioxide. And it only took seven days.
A God that can create evolution is something greater to me. A God that is in every natural process, that is every natural process--in gravity, and in the scientific explanation for gravity, in natural selection and photosynthesis (photosynthesis is so incredible) and Hadley cells and everything else--that's what I believe in.
And God is in everyone. Everyone. One of the tenets of my religion (I'm a Unitarian Universalist, and we don't have much but I believe in it) is "the inherent worth and dignity of every human being." To me, that's because God is in all of us. Every day. When I'm driven to create, that's God speaking through me. When I'm working to unravel the mystery that is our every-day life, that's God, too. God is in art and music and teaching and everything else that inspires people, but it's in biology and chemistry and anthropology and particle physics. And every-day things--doing the dishes, being nice to people, waking up every day. Ever felt like you've touched something greater than yourself? Had a moment where you knew what to do, intrinsically, or a moment of divine inspiration? Just a time when you made a difference?
To me, that's God. That's religion. And that's how I can believe in science and all that airy-fairy supernatural stuff at the same time. I just don't differentiate.
I get a certain number of questions about how faith and science can coexist in my life. There seems to be this idea that science is all cold rationality (and good science mostly is that) and that religion is inimical to realism and hard facts--and religion is, at its roots, about faith, which requires an absence of definitive proof.
But I think that limiting yourself to one or the other is a little sad. I can believe in God while I'm carefully investigating the role of arbuscular mychorrhizae fungus in the invasive potential of Centaurea diffusa, and it will affirm my faith in God.
To me, the fact that everything is is the greatest miracle. Nothing is more spectacular than everything--every living and non-living thing, outer space and all the stars including our own, the earth we live on. It's incredible. A God that can create that is something to believe in.
And it doesn't have to be that, a few thousand years ago, God appeared and, boom!, created the Earth, exactly as it is today, only maybe with less carbon dioxide. And it only took seven days.
A God that can create evolution is something greater to me. A God that is in every natural process, that is every natural process--in gravity, and in the scientific explanation for gravity, in natural selection and photosynthesis (photosynthesis is so incredible) and Hadley cells and everything else--that's what I believe in.
And God is in everyone. Everyone. One of the tenets of my religion (I'm a Unitarian Universalist, and we don't have much but I believe in it) is "the inherent worth and dignity of every human being." To me, that's because God is in all of us. Every day. When I'm driven to create, that's God speaking through me. When I'm working to unravel the mystery that is our every-day life, that's God, too. God is in art and music and teaching and everything else that inspires people, but it's in biology and chemistry and anthropology and particle physics. And every-day things--doing the dishes, being nice to people, waking up every day. Ever felt like you've touched something greater than yourself? Had a moment where you knew what to do, intrinsically, or a moment of divine inspiration? Just a time when you made a difference?
To me, that's God. That's religion. And that's how I can believe in science and all that airy-fairy supernatural stuff at the same time. I just don't differentiate.
Wednesday, December 2, 2009
Allelopathy and Methodology
Sometimes you find what you look for. Sometimes it's accidental, or incidental: like measuring light, which is either a particle or a wave, depending on the test used, because the form of measurement defines it. Sometimes it's just bad science.
In the 70s, allelopathy gained a lot of attention. The science of chemical warfare between plants (the release of toxins into the soil by one plant that negatively affected another), it's a pretty fascinating topic--a lot of people like a little danger or excitement in their science, and the plants are essentially poisoning each other.
The field was started in 1925, when A. B. Massey published "Antagonism of the Walnuts (Juglans nigra and J. cinerea) in Certain Plant Associations." It demonstratively showed the phytotoxicity of chemicals contained in walnut leaves on other plants. There are definitely walnuts out there with no plants growing around their base--although shade could just as easily play a role in this as allelopathy.
But there's just as many walnuts who do have plants growing around their bases. Regardless, allelopathy as a theory peaked around the 70s, garnering a lot of attention and proving that many, many plant species were allelopathic in effect.
The problem was in the methods of the study. The most common (both then and now) test for allelopathy is a petri-dish bioassay: a solution of chemicals from the plant is attained by washing it in a solvent, usually water. The concentration of the potential phytotoxins can be very high. Then it's added to a medium--water or agar, not dirt--and seeds are added and sprouted. Usually, there's lowered germination rates and slowed growth--possibly deformities in the roots or browning. Or death. The solution is clearly not very good for the plants in question.
At the peak of things, just growth habits could be considered proof of allelopathy. One of the better-known studies in allelopathy is the experiments run by C. H. Muller in California on a shrubby species of Salvia* during the 1960s. There were obvious bare zones around the clumps of shrubs. Muller's experiments indicated allelopathy: after all, sages have some pretty strong chemicals in them--that's what makes them so aromatic (and therefore delicious.)
Further experiments were run by Bartholomew, Halligan, and Christensen and Muller during the 1970s. They discovered that the very shy rabbits of the region lived in the tangled shrubbery of the salvias, and that they didn't stray very far from the shrubs to eat, ever. When Bartholomew ran a study where rabbits, birds and other relatively large animals were excluded from the area surrounding the shrubs using cages, the grass grew just fine. The rabbits had been the ones eating the grass, causing the dead zone--they wouldn't go any further away from the shrubs, and so they ate all the tasty grass down to the ground in the areas they considered safe.
Bioassays aren't as dramatic an example. But there's strong evidence (see Stowe's 1979 paper "Allelopathy and its influence on the distribution of plants in an Illinois old-field") that almost any plant will show up as allelopathic if the secondary metabolites it contains--all the volatile chemicals, the flavenoids and sesquiterpene lactones**, the phenolics--are isolated and concentrated enough.
But a lot of these chemicals aren't going to enter the soil at all. A lot of them are highly volatile, evaporating or breaking down very quickly--before they can build up to levels that can damage plants. Even the soil itself will absorb some of the chemicals, making it inaccessible to the plants. The microorganisms in the soil can break down allelochemicals. A 1957 study by Le Tourneau and Heggeness ("Germination and growth inhibitors in leafy spurge foliage and quackgrass rhizomes") proved that leafy spurge (Euphorbia esula) is toxic in bioassays but neutral when the plants are grown in soil--especially if it was non-sterile soil still rich in microorganisms.
Things get exaggerated. And it's done nothing but disservice to the field of allelopathy. As methodology approves and allelopathy is re-approached as a potential component in the success of certain plants (especially specific invasives--more on this and the Novel Weapons Hypothesis at a later date) instead of a unified, universal theory, this history of exaggeration and poor experimental design continues to haunt the study of allelopathy.
Allelopathy really shouldn't be discredited entirely. Its role was overexaggerated in the past, but it can still be a significant factor. Two particular invasive plants, garlic mustard (Alliaria petiolata) and certain knapweed species (Centaurea species among others, especially C. maculosa), are almost definitely allelopathic--experiments have been done to study the effects of the allelochemicals in soil, not just in bioassays, and the behavior of the chemicals in field soils has been studied--they know that (+/-)-catechin persists at levels high enough to be phytotoxic.
Part of the problem lies in the struggle to design a good experiment to test allelopathy. You need to mimic, as closely as possible, the behavior of the allelochemical in the field. At the same time, you need to be sure that you're measuring true allelopathy instead of just competition--you can't plunk a bunch of garlic mustard into a planter box with some wheat in it and see what happens. Even if allelopathy plays a role in the success of invasives, it's also almost definitely because they are more fit an organism--they're highly evolved to take advantage (and control) of resources.
There are ways around it, but most people haven't taken the time. Bell and Koeppe's 1972 study "Noncompetitive effects of giant foxtail on the growth of corn" used a "stairstep apparatus" where a nutrient solution filtered through the roots of both the potential allelopath (giant foxtail or Setaria faberii) and those of the test subject (corn--Zea mays), but the plants themselves were in different containers, preventing competition from playing a role. The Steenhagen and Zimdahl study "Allelopathy of leafy spurge (Euphorbia esula)" (1979) took soil samples from areas with very high populations of quack grass (Agropyron repens) and incorporated it into the soil of potted tomatoes, where it had strong negative effects on their growth. In 1980 Stachon and Zimdahl's study "Allelopathic activity of Canada thistle (Cirsium arvense) in Colorado" used soil mulched with leaves in addition to bioassays--it showed allelopathy in both sets of experiments. More recently, Abhilasha, Quintana, Vivanco and Joshi's 2008 study "Do allelopathic compounds in invasive Solidago candensis restrain the native European flora?" used soil that had had allelopathic Solidago canadensis growing in it--for the controls, they added activated carbon, which absorbs/deactivates organic chemicals (like phytotoxins) without affecting important nutrients like nitrogen. (More on this method in Le Tourneau and Heggeness's "Germination and growth inhibitors in leafy spurge foliage and quackgrass rhizomes" (1957) paper.) Again, activated carbon significantly improved the growth of plants, indicating allelopathy.
So the poor science that's been the norm reflects badly on the field as a whole. Allelopathy isn't some sort of miracle answer for complex plant interactions, and it's certainly not that common, but at the same time it's not totally insignificant in every situation, and it's definitely a factor in certain plants. As methodology improves, no doubt there's more to discover about it.
*Before somebody brings up the drug reference: Salvia is the genus name for sage. The sage you use in cooking? It's a salvia. So are many common garden shrubs. None of them are psychoactive. Neither is the shrub we're talking about. Sorry.
**Whenever I try to spell "sesquiterpene lactones" I inevitably end up writing "lactates." Which would be something else entirely.
In the 70s, allelopathy gained a lot of attention. The science of chemical warfare between plants (the release of toxins into the soil by one plant that negatively affected another), it's a pretty fascinating topic--a lot of people like a little danger or excitement in their science, and the plants are essentially poisoning each other.
The field was started in 1925, when A. B. Massey published "Antagonism of the Walnuts (Juglans nigra and J. cinerea) in Certain Plant Associations." It demonstratively showed the phytotoxicity of chemicals contained in walnut leaves on other plants. There are definitely walnuts out there with no plants growing around their base--although shade could just as easily play a role in this as allelopathy.
But there's just as many walnuts who do have plants growing around their bases. Regardless, allelopathy as a theory peaked around the 70s, garnering a lot of attention and proving that many, many plant species were allelopathic in effect.
The problem was in the methods of the study. The most common (both then and now) test for allelopathy is a petri-dish bioassay: a solution of chemicals from the plant is attained by washing it in a solvent, usually water. The concentration of the potential phytotoxins can be very high. Then it's added to a medium--water or agar, not dirt--and seeds are added and sprouted. Usually, there's lowered germination rates and slowed growth--possibly deformities in the roots or browning. Or death. The solution is clearly not very good for the plants in question.
At the peak of things, just growth habits could be considered proof of allelopathy. One of the better-known studies in allelopathy is the experiments run by C. H. Muller in California on a shrubby species of Salvia* during the 1960s. There were obvious bare zones around the clumps of shrubs. Muller's experiments indicated allelopathy: after all, sages have some pretty strong chemicals in them--that's what makes them so aromatic (and therefore delicious.)
Further experiments were run by Bartholomew, Halligan, and Christensen and Muller during the 1970s. They discovered that the very shy rabbits of the region lived in the tangled shrubbery of the salvias, and that they didn't stray very far from the shrubs to eat, ever. When Bartholomew ran a study where rabbits, birds and other relatively large animals were excluded from the area surrounding the shrubs using cages, the grass grew just fine. The rabbits had been the ones eating the grass, causing the dead zone--they wouldn't go any further away from the shrubs, and so they ate all the tasty grass down to the ground in the areas they considered safe.
Bioassays aren't as dramatic an example. But there's strong evidence (see Stowe's 1979 paper "Allelopathy and its influence on the distribution of plants in an Illinois old-field") that almost any plant will show up as allelopathic if the secondary metabolites it contains--all the volatile chemicals, the flavenoids and sesquiterpene lactones**, the phenolics--are isolated and concentrated enough.
But a lot of these chemicals aren't going to enter the soil at all. A lot of them are highly volatile, evaporating or breaking down very quickly--before they can build up to levels that can damage plants. Even the soil itself will absorb some of the chemicals, making it inaccessible to the plants. The microorganisms in the soil can break down allelochemicals. A 1957 study by Le Tourneau and Heggeness ("Germination and growth inhibitors in leafy spurge foliage and quackgrass rhizomes") proved that leafy spurge (Euphorbia esula) is toxic in bioassays but neutral when the plants are grown in soil--especially if it was non-sterile soil still rich in microorganisms.
Things get exaggerated. And it's done nothing but disservice to the field of allelopathy. As methodology approves and allelopathy is re-approached as a potential component in the success of certain plants (especially specific invasives--more on this and the Novel Weapons Hypothesis at a later date) instead of a unified, universal theory, this history of exaggeration and poor experimental design continues to haunt the study of allelopathy.
Allelopathy really shouldn't be discredited entirely. Its role was overexaggerated in the past, but it can still be a significant factor. Two particular invasive plants, garlic mustard (Alliaria petiolata) and certain knapweed species (Centaurea species among others, especially C. maculosa), are almost definitely allelopathic--experiments have been done to study the effects of the allelochemicals in soil, not just in bioassays, and the behavior of the chemicals in field soils has been studied--they know that (+/-)-catechin persists at levels high enough to be phytotoxic.
Part of the problem lies in the struggle to design a good experiment to test allelopathy. You need to mimic, as closely as possible, the behavior of the allelochemical in the field. At the same time, you need to be sure that you're measuring true allelopathy instead of just competition--you can't plunk a bunch of garlic mustard into a planter box with some wheat in it and see what happens. Even if allelopathy plays a role in the success of invasives, it's also almost definitely because they are more fit an organism--they're highly evolved to take advantage (and control) of resources.
There are ways around it, but most people haven't taken the time. Bell and Koeppe's 1972 study "Noncompetitive effects of giant foxtail on the growth of corn" used a "stairstep apparatus" where a nutrient solution filtered through the roots of both the potential allelopath (giant foxtail or Setaria faberii) and those of the test subject (corn--Zea mays), but the plants themselves were in different containers, preventing competition from playing a role. The Steenhagen and Zimdahl study "Allelopathy of leafy spurge (Euphorbia esula)" (1979) took soil samples from areas with very high populations of quack grass (Agropyron repens) and incorporated it into the soil of potted tomatoes, where it had strong negative effects on their growth. In 1980 Stachon and Zimdahl's study "Allelopathic activity of Canada thistle (Cirsium arvense) in Colorado" used soil mulched with leaves in addition to bioassays--it showed allelopathy in both sets of experiments. More recently, Abhilasha, Quintana, Vivanco and Joshi's 2008 study "Do allelopathic compounds in invasive Solidago candensis restrain the native European flora?" used soil that had had allelopathic Solidago canadensis growing in it--for the controls, they added activated carbon, which absorbs/deactivates organic chemicals (like phytotoxins) without affecting important nutrients like nitrogen. (More on this method in Le Tourneau and Heggeness's "Germination and growth inhibitors in leafy spurge foliage and quackgrass rhizomes" (1957) paper.) Again, activated carbon significantly improved the growth of plants, indicating allelopathy.
So the poor science that's been the norm reflects badly on the field as a whole. Allelopathy isn't some sort of miracle answer for complex plant interactions, and it's certainly not that common, but at the same time it's not totally insignificant in every situation, and it's definitely a factor in certain plants. As methodology improves, no doubt there's more to discover about it.
*Before somebody brings up the drug reference: Salvia is the genus name for sage. The sage you use in cooking? It's a salvia. So are many common garden shrubs. None of them are psychoactive. Neither is the shrub we're talking about. Sorry.
**Whenever I try to spell "sesquiterpene lactones" I inevitably end up writing "lactates." Which would be something else entirely.
Subscribe to:
Posts (Atom)
Posts
