There is a scientific society dedicated to the study of almost anything. But until recently (2005) there was no society dedicated to the study of the behaviors of plants. Enter The Society of Plant Neurobiology. which states on its website:
"Plant Neurobiology describes a newly named, but also old and fascinating field in plant biology addressing the physiological basis of adaptive behavior in plants. Perhaps this field could be called "Sensory Biology in Plants" or something similar. However, these names don't quite cover topics like plant cytology and anatomy, adaptive plant behavior, signaling and communication in symbiosis and pathogenesis, or newly emerging topics like for instance plant immunity, plant memory and learning, plant-plant communication, as well as plant intelligence."
This is very convenient for me, as I am currently writing a paper on, among other things, taxonomic bias in definitions of the word 'behavior.' Having gotten input from member of the Animal Behavior Society and the International Society for Applied Ethology, I am thrilled to be able to get the viewpoints of botanists interested in behavior. I emailed the chair of their steering committee, asking her to forward a link to my "what is behavior?" survey to their membership. If she is sympathetic, this could be really cool.
I learned of the existence of SPNb through this article on NYTImes.com. Check out the video of the parasitic plant sniffing for prey and pouncing on the unsuspecting tomato vine.
Monday, June 09, 2008
Rotifer fluid mechanics
One of my best students, NN, has become fascinated with the ways in which rotifers use their cilia, and wants to do a senior honors thesis on the fluid mechanics of rotifer cilia. She is interested in issues of scaling, how they use their cilia in feeding and locomotion, and the differences in the cilia between males and females. Males use their cilia only for locomotion, while females use them for both locomotion and feeding, leading to some fascinating questions about the trade-offs females make to have their cilia serve these two very different, and very important roles.
I very much want to encourage her in this, but started by explaining to her that as an evolutionary demographer, I know squat, make that squat/2 about biomechanics. And of all the parts of biomechanics I don't understand, Low Reynolds Number Fluid Mechanics may just be the part I understand least. I understand it so little I don't even know what it means. The Reynolds number has something to do with the ratio of the size of the object to the viscosity of the fluid, or something like that. This helpful Wikipedia article describes it in terms I only vaguely understand. What I understand it to mean is that the smaller an organism or piece of an organisms is, the more viscous the fluid effectively is. A whale moving through water experiences an environment in which viscosity is much less important than a rotifer moving through the same, equally viscous water. The rotifer has a very low Reynolds number, and its cilia have even lower Reynolds numbers. The viscosity of the water they move is so high, it is like a human arm through tar. Or something like that.
But don't quote me on any of that because it is probably wrong.
So I told NN that I was glad to work with her on that, but she would need an adviser from a biomechanics lab, like that of Mimi Koehl. Luckily, one of my best friends in my department is one of Mimi's students, and is interested in ciliary feeding. And this morning we went to the grocery store together, and by the time the groceries were in the fridge, my friend had agreed to meet with my student and help her figure out how to frame and answer her question. My only claims on the project will be that I helped generate the questions, am brining the collaboration together, and am providing the study organisms. In other words, I may end up co-advising a senior thesis on a topic I know nothing about. Hopefully by the end I will at least know what a Reynold's number is.
I very much want to encourage her in this, but started by explaining to her that as an evolutionary demographer, I know squat, make that squat/2 about biomechanics. And of all the parts of biomechanics I don't understand, Low Reynolds Number Fluid Mechanics may just be the part I understand least. I understand it so little I don't even know what it means. The Reynolds number has something to do with the ratio of the size of the object to the viscosity of the fluid, or something like that. This helpful Wikipedia article describes it in terms I only vaguely understand. What I understand it to mean is that the smaller an organism or piece of an organisms is, the more viscous the fluid effectively is. A whale moving through water experiences an environment in which viscosity is much less important than a rotifer moving through the same, equally viscous water. The rotifer has a very low Reynolds number, and its cilia have even lower Reynolds numbers. The viscosity of the water they move is so high, it is like a human arm through tar. Or something like that.
But don't quote me on any of that because it is probably wrong.
So I told NN that I was glad to work with her on that, but she would need an adviser from a biomechanics lab, like that of Mimi Koehl. Luckily, one of my best friends in my department is one of Mimi's students, and is interested in ciliary feeding. And this morning we went to the grocery store together, and by the time the groceries were in the fridge, my friend had agreed to meet with my student and help her figure out how to frame and answer her question. My only claims on the project will be that I helped generate the questions, am brining the collaboration together, and am providing the study organisms. In other words, I may end up co-advising a senior thesis on a topic I know nothing about. Hopefully by the end I will at least know what a Reynold's number is.
Wednesday, June 04, 2008
Inching toward science
For as long as there have been science classes, creationists have wanted to teach creationism as science. And in many countries, including this one, they have often done so. In some countries, much more so than the US, they still do. But in the US they have suffered a long series of court defeats on the basis that creationism is religion, and not science, and therefore does not belong in science classes. And it often seems like a battle that can't really be won, because as soon as they lose one court battle they repackage and try again. But considering that history as outlined in this NYTimes article gives me a sense that while we will never convince them to give up entirely, in the long run they are gradually being forced to adopt positions with more and more resemblance to science.
At first, of course, they simply outlawed the teaching of evolution where they could. These laws didn't stand up in the courts, so they decided that creationism and evolution would be taught side by side. That didn't stand up either, so they came up with the bright idea of wrapping creationism in a thin film of scientific lingo and calling it 'creation science.' That didn't stand up to examination for very long either. Next they decided that rather than creationism painted science-color, they would have the nugget of creationism with many layers of scientific sounding text, language, calculations and books wrapped around it, and call it Intelligent Design Theory. No explicit mention of any particular intelligent designer, just a very selective use of scientific knowledge and concepts with the goal of concluding that evolution can't explain the universe, and therefore there must be a creator. Some of them even went so far as to acknowledge microevolution (the modification of existing forms) while still rejecting macroevolution (the accumulation of those modifications to the point that it seems to us to be a really different form). That, as you know, didn't stand up in court either. Partly their arguments made no sense, and partly there was plenty of documentation of the fact that they had started with a conclusion and worked backwards, making up results to support that conclusion, making up methods that would lead to those results and then trying to figure out what question they should pretend to have been trying to answer. In other words, they were demonstrably engaged not in science, but in fraud. But for all its repugnance, ID had the desirable property of getting the creationists to agree that they needed to make evidence based arguments, even if they then failed to do so. ID, exposed as the cynical lie that it is, is now dying from too much light. Thus always to imposters.
But creationists have too much faith in their own infallibility to give up and go home. So the Discovery Institute and its usual corral of quacks are designing a new and improved 'science curriculum' intended to highlight the 'strengths and weaknesses' of Darwinian evolutionary theory. I have absolutely no doubt that this is just the same spoiled sausage in a shiny new casing, but at least they have finally been forced to adopt a truly scientific casing. Examining the strengths and weaknesses of theories is what science is about. Now there are unscientific ways of going about it, and I have no doubt they will employ almost all of these, but the details of the curriculum can be challenged in court.
There are of course downsides to them having finally found a really scientific name to call their beliefs. They are adapting to the fact that their ideas are demonstrably not science by gradually phrasing them in a more and more scientific way. That may make it a little bit harder each time to prove that religion is still not science, and harder for the average person to understand exactly why it is not science. This time, instead of getting 'strengths and weaknesses' thrown out of the classroom entirely, we may have to fight item by item about what can be presented as a strength or a weakness, and how they can be presented.
But as long as we can continue to find judges willing to judge on the evidence (which I know is in some doubt), we will continue to win those fights. Religion really isn't science, and no matter how cleverly disguised will continue to not be science. We can explain the data without invoking non-scientific concepts like a benevolent omnipotent and omniscient creator, and they can't. So once the argument is on our turf, once they are arguing with us about what evidence and logic show, they can only lose. Not to say that it will be a sea-change. What we have accomplished to date is extremely incremental, and that will continue. But we are pushing them back, inch by inch, foot by foot, concept by concept. They will argue that the human eye is irreducibly complex, we will use data and logic to show that that is ignorant nonsense. The courts will be forced to rule in our favor. They will argue that the laws of thermodynamics make it impossible for order to arise from disorder. We will explain to the judges that this is true only in a closed system, with no input of order, and there will be a court ruling that says that their argument is not science. And on. And on. But as long as our country holds it together enough to continue having a judiciary that has to listen to evidence most of the time, and as long as the data and logic are all on our side, all they can do is stall, limit the rate at which they lose ground. And as that happens, they will be forced to incorporate more and more actual science into their arguments. Who knows, maybe some day they will be forced to admit to both microevolution and macroevolution, but continue arguing that their had to be a creator to get it all started. At that point, they will be in agreement with Darwin himself, who wrote in The Origin of Species, "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." This view is of course still not science, but if they can be driven back this far they will be rendered, in my view, mostly harmless.
At first, of course, they simply outlawed the teaching of evolution where they could. These laws didn't stand up in the courts, so they decided that creationism and evolution would be taught side by side. That didn't stand up either, so they came up with the bright idea of wrapping creationism in a thin film of scientific lingo and calling it 'creation science.' That didn't stand up to examination for very long either. Next they decided that rather than creationism painted science-color, they would have the nugget of creationism with many layers of scientific sounding text, language, calculations and books wrapped around it, and call it Intelligent Design Theory. No explicit mention of any particular intelligent designer, just a very selective use of scientific knowledge and concepts with the goal of concluding that evolution can't explain the universe, and therefore there must be a creator. Some of them even went so far as to acknowledge microevolution (the modification of existing forms) while still rejecting macroevolution (the accumulation of those modifications to the point that it seems to us to be a really different form). That, as you know, didn't stand up in court either. Partly their arguments made no sense, and partly there was plenty of documentation of the fact that they had started with a conclusion and worked backwards, making up results to support that conclusion, making up methods that would lead to those results and then trying to figure out what question they should pretend to have been trying to answer. In other words, they were demonstrably engaged not in science, but in fraud. But for all its repugnance, ID had the desirable property of getting the creationists to agree that they needed to make evidence based arguments, even if they then failed to do so. ID, exposed as the cynical lie that it is, is now dying from too much light. Thus always to imposters.
But creationists have too much faith in their own infallibility to give up and go home. So the Discovery Institute and its usual corral of quacks are designing a new and improved 'science curriculum' intended to highlight the 'strengths and weaknesses' of Darwinian evolutionary theory. I have absolutely no doubt that this is just the same spoiled sausage in a shiny new casing, but at least they have finally been forced to adopt a truly scientific casing. Examining the strengths and weaknesses of theories is what science is about. Now there are unscientific ways of going about it, and I have no doubt they will employ almost all of these, but the details of the curriculum can be challenged in court.
There are of course downsides to them having finally found a really scientific name to call their beliefs. They are adapting to the fact that their ideas are demonstrably not science by gradually phrasing them in a more and more scientific way. That may make it a little bit harder each time to prove that religion is still not science, and harder for the average person to understand exactly why it is not science. This time, instead of getting 'strengths and weaknesses' thrown out of the classroom entirely, we may have to fight item by item about what can be presented as a strength or a weakness, and how they can be presented.
But as long as we can continue to find judges willing to judge on the evidence (which I know is in some doubt), we will continue to win those fights. Religion really isn't science, and no matter how cleverly disguised will continue to not be science. We can explain the data without invoking non-scientific concepts like a benevolent omnipotent and omniscient creator, and they can't. So once the argument is on our turf, once they are arguing with us about what evidence and logic show, they can only lose. Not to say that it will be a sea-change. What we have accomplished to date is extremely incremental, and that will continue. But we are pushing them back, inch by inch, foot by foot, concept by concept. They will argue that the human eye is irreducibly complex, we will use data and logic to show that that is ignorant nonsense. The courts will be forced to rule in our favor. They will argue that the laws of thermodynamics make it impossible for order to arise from disorder. We will explain to the judges that this is true only in a closed system, with no input of order, and there will be a court ruling that says that their argument is not science. And on. And on. But as long as our country holds it together enough to continue having a judiciary that has to listen to evidence most of the time, and as long as the data and logic are all on our side, all they can do is stall, limit the rate at which they lose ground. And as that happens, they will be forced to incorporate more and more actual science into their arguments. Who knows, maybe some day they will be forced to admit to both microevolution and macroevolution, but continue arguing that their had to be a creator to get it all started. At that point, they will be in agreement with Darwin himself, who wrote in The Origin of Species, "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." This view is of course still not science, but if they can be driven back this far they will be rendered, in my view, mostly harmless.
Of listing and sex
Among many bird-watchers, there is an obsession with listing. Species one has seen anywhere, species one has seen in Ontario, species one has seen in Ontario in October, species one has seen through a particular window while sitting on the toilet and so on. I once had a colleague point his binoculars up at the sky for a few seconds, and say, "Awesome, I've never seen a Red-Throated Loon on the southward migration over Lake Eire before. Another tic for my list."
I keep a few place specific lists, "birds I've seen in the El Cerrito Hillside Natural Area," or, "birds of Mahopac, NY," and used to keep a life list (e.g. all the wild birds I've ever seen anywhere) but I've never really gotten into listing for listing's sake. Hard-core listers (commonly referred to as twitchers for their inability to hold still if someone suggests a bird they don't yet have on a particular list is nearby) are often far more interested in adding birds to lists than in actually looking at the birds, and will often travel long distances to find a bird, look at it for just long enough to confidently add it to their list, then begin the long journey home. Those of us who are not twitchers, but know people who are, enjoy the game of making up new types of lists and mentioning them to twitchers so that they will feel compelled to rush out and start building a bigger, longer more impressive list with more rare species. So, in that spirit, I have started to compile a copulation list, of all the bird species I have ever observed copulating. This list is necessarily incomplete, as I am only including those species which I know a particular time and place when I witnessed a copulation in the wild, but excluding all the other species that I forget where or when. This list was inspired by the activity of two house-sparrows this fine June morning.
In no particular order:
House Sparrow
California Condor
Turkey Vulture
Fairy Bluebird
Florida Scrub-Jay
Western Scrub-Jay
Steller's Jay
Common Raven
American Crow
Bald Eagle
House Finch
European Starling
Canada Goose
Mallard
Muskovi Duck
Great Egret
American Robin
Dark-Eyed Junco
California Towhee
Red-Tailed Hawk
Red-Shouldered Hawk
Willie Wagtail
I keep a few place specific lists, "birds I've seen in the El Cerrito Hillside Natural Area," or, "birds of Mahopac, NY," and used to keep a life list (e.g. all the wild birds I've ever seen anywhere) but I've never really gotten into listing for listing's sake. Hard-core listers (commonly referred to as twitchers for their inability to hold still if someone suggests a bird they don't yet have on a particular list is nearby) are often far more interested in adding birds to lists than in actually looking at the birds, and will often travel long distances to find a bird, look at it for just long enough to confidently add it to their list, then begin the long journey home. Those of us who are not twitchers, but know people who are, enjoy the game of making up new types of lists and mentioning them to twitchers so that they will feel compelled to rush out and start building a bigger, longer more impressive list with more rare species. So, in that spirit, I have started to compile a copulation list, of all the bird species I have ever observed copulating. This list is necessarily incomplete, as I am only including those species which I know a particular time and place when I witnessed a copulation in the wild, but excluding all the other species that I forget where or when. This list was inspired by the activity of two house-sparrows this fine June morning.
In no particular order:
House Sparrow
California Condor
Turkey Vulture
Fairy Bluebird
Florida Scrub-Jay
Western Scrub-Jay
Steller's Jay
Common Raven
American Crow
Bald Eagle
House Finch
European Starling
Canada Goose
Mallard
Muskovi Duck
Great Egret
American Robin
Dark-Eyed Junco
California Towhee
Red-Tailed Hawk
Red-Shouldered Hawk
Willie Wagtail
Tuesday, June 03, 2008
Rotifer Photos
I have a couple of students working with me this summer on an ethogram of my rotifers. An ethogram is a list of behaviors exhibited by a species, with a description of each one. One of the students, Laura is particularly interested in invertebrate behavior, and the other, Harmony, wants to get experience in scientific illustration. Harmony will make the illustrations of that go with the descriptions of each behavior.
In order to help her with this, I am figuring out how to get good photos of the rotifers through a compound scope. Here are some of the prototypes:
In order to help her with this, I am figuring out how to get good photos of the rotifers through a compound scope. Here are some of the prototypes:
A juvenile female rotifer feeding on bright green algal cells.
This very small female (on the right) dwarfs the normal sized male on the left. Male rotifers are tiny, fast and anatomically simple. He has no digestive system, a very rudimentary foot, and no defensive spines. The very dark area in the middle of the female is her trophi (aka teeth). The male has none. His penis is at the base (caudal end) of his foot, and he is attempting to inject sperm into the female.
This juvenile female has retracted her head and foot into her shell (lorica) in a defensive posture, because I poked her with my pipette.
This is a high magnification shot of a dried out male rotifer. The males never hold still and are very hard to get photographs of in life. I dried this male onto a microscope slide with a lamp. On the left you can see his shaggy 'mane' of cillia, which propel him through the water. The males are very small compared to their cillia, which may help to explain why they are so damn fast.
Sunday, June 01, 2008
Three Birds, Two Cats and a primate
It was an awful lot of croaking for a Friday afternoon. I went out on the patio to investigate. The Ravens were in an uproar about something. My first thought was that one of their nestlings had fledged and was hiding in our yard. They were flying back and forth, low over the top of the apple tree, scolding and creaking and booming. I decided their fledgling must be in the top of the tree, and they must be trying to tell it that this was not a safe place. My eyes scanning the trees for a fledgling, I was impressed and intimidated to see these two birds, each the size of a large hawk, diving and screaming just over my head. And just as I was starting to think they might really be screaming directly at me, I heard something moving only a couple of yards from my feet. Looking down, I saw this:
A turkey right in our garden, and clearly the focus of the Ravens' ire. They were responding to it as they would any large animal (except humans and deer, which they seem to be used to ) getting too close to their nest tree: by screaming and scolding, "you better git the hell off our land if you know what's good fer ya!" The turkey had apparently responded by hunkering down by Betty's compost bin.
I pulled out my cell phone and started to take pictures. After a couple of minutes the ravens went off to scream at something else and the turkey and I were left to talk amongst ourselves. I went for my better camera, but finding the batteries dead, knocked on Betty's door and said, "Hi Betty, sorry to bother you, but there is a turkey in the backyard. You should bring your camera please."
It was a very tame turkey. I taking photos with my cellphone and Betty with her big digital SLR each stood about 10 feet from it. "People have been feeding it." I said as it watched us hopefully and I resisted the urge to feed it. It rooted around in the garden.
FeLion wandered out onto the patio and saw the turkey. Her response seemed perfectly split between, "That is the biggest bird I have ever seen, I'm gonna eat it." and "that is the bigest bird I have ever seen, I hope it doesn't try to eat me." She was frozen with indecision.
Betty's cat Sophie, on the other hand, was not at all reluctant to charge a bird twice her weight. She burst out of the bushes and sprinted toward the turkey, who turned tail and ran up the step to the very top of our yard.
When I caught up, the turkey was defending a position on top of the garden gate arch, and Sophie was attempting to storm the battlements.
Eventually she succeeded, and the Turkey took to the air, at which point the Ravens resumed their harrying. The turkey, pursued from above an below. stopped in a tangle of low Eucalyptus branches. Betty and I snapped a few more shots and then took the cats inside.
A turkey right in our garden, and clearly the focus of the Ravens' ire. They were responding to it as they would any large animal (except humans and deer, which they seem to be used to ) getting too close to their nest tree: by screaming and scolding, "you better git the hell off our land if you know what's good fer ya!" The turkey had apparently responded by hunkering down by Betty's compost bin.
I pulled out my cell phone and started to take pictures. After a couple of minutes the ravens went off to scream at something else and the turkey and I were left to talk amongst ourselves. I went for my better camera, but finding the batteries dead, knocked on Betty's door and said, "Hi Betty, sorry to bother you, but there is a turkey in the backyard. You should bring your camera please."
It was a very tame turkey. I taking photos with my cellphone and Betty with her big digital SLR each stood about 10 feet from it. "People have been feeding it." I said as it watched us hopefully and I resisted the urge to feed it. It rooted around in the garden.
FeLion wandered out onto the patio and saw the turkey. Her response seemed perfectly split between, "That is the biggest bird I have ever seen, I'm gonna eat it." and "that is the bigest bird I have ever seen, I hope it doesn't try to eat me." She was frozen with indecision.
Betty's cat Sophie, on the other hand, was not at all reluctant to charge a bird twice her weight. She burst out of the bushes and sprinted toward the turkey, who turned tail and ran up the step to the very top of our yard.
When I caught up, the turkey was defending a position on top of the garden gate arch, and Sophie was attempting to storm the battlements.
Eventually she succeeded, and the Turkey took to the air, at which point the Ravens resumed their harrying. The turkey, pursued from above an below. stopped in a tangle of low Eucalyptus branches. Betty and I snapped a few more shots and then took the cats inside.
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