The Dead Grandmother/Exam Syndrome and the Potential Downfall Of American Society
Enjoy!
Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development1 week ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.1 week ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Thought of the day
I wish I worked on Zea mays (corn)... so that upon saying "I'd rather watch grass grow", I would actually be serious...
That's it. Did you expect something profound?
(Busy days yet again...)
Addendum: Now if I were a chemist in the paint industry... ah, possibilities... =P
That's it. Did you expect something profound?
(Busy days yet again...)
Addendum: Now if I were a chemist in the paint industry... ah, possibilities... =P
Millions of little plant mouths
Now for something a bit different.
You may have heard of stomatal guard cells back in highschool. Something about shrivelling up to close when hot, potassium ion channels and carbon dioxide? Yeah, for most people they fade forever into the vague memories of cramming for a science test. The only lasting effect of this exercise tends to be an aversion to anything botany.
That's how it worked for me anyway. I recall finding plants to be the most boring unit in highschool biology, despite having a good teacher. They fail to convey the wonders of land plants, instead falling back on dry diagrams and that wretched photosynthesis 'equation'.
Of course, one can't really blame them -- the teachers themselves have learned it the same way. And you simply cannot even begin to share the amazing world of stomatal development in a highschool classroom. After all, I've worked hard over a year in the field, and I'm still just a novice. But I do believe the approach could be altered to make the time used in a more constructive, and enjoyable, manner for both students and teachers.
I think part of highschool education should promote asking good questions. There is almost no aid in that aspect of learning -- information is just presented, and some students never realise the diversity of questions they could ask about it.
First of all, why do plants even bother? A stoma is a fairly complex structure:
(Fred Sack)
Bilateral symmetry requires a coordinated process of development; special care must be taken to ensure spacing between stomata; the guard cells must maintain a kidney shape for optimal functioning. Such structures must be really worth the trouble to evolve!
Plants, like most terrestrial life, have their origins in water. Their ancestors looked something like this:
(source)
This Charophyte lacks stomata. Living in water, your cells are already in the aquatic environment they are specialised for. There are some special adaptations for dealing with freshwater due to differences in osmotic pressure, but we'll overlook those.
The problem with migrating onto land is that cells require an aquatic environment to function. When our ancestors left water, they had to figure out a way to carry the aquatic environment with them. Fungi generally live inside their food, or in soil; still, they have a chitinous wall for protection and structural support. Our lineage came up with skins and an intricate system of vessels.
Some plants do quite fine sticking to damp areas and not dying upon dessication. Surviving drying up was probably already advantagous enough for aquatic plants, since ponds are prone to drought. Liverworts are only a few cell layers thick, lack a vascular system, and have a very thin coat of wax on the surface:
(source)
(I think I'll just have to introduce thallose liverworts someday -- they're awesome!)
A good bryophyte reference here
Being thin enough and living in damp places allows you to skip stomatal development:
(Psi)
However, as plants move into dryer places and gained size, dessication becomes a problem. The solution? A think layer of cuticular wax to stop water evaporation:
(Lacey Samuels)
Now we have a problem. Wax doesn't breathe very well. You need to inhale CO2 for photosynthesis; you need to exhale O2. Having open holes in the waxy cuticle defeats the very purpose of having one, as well as exposing the organism to invaders. That's where stomata come in. Stoma is Greek for 'mouth', and that's pretty much exactly what these structures are: millions of mouths covering the leaf surface, enabling the plant to breath while regulating water loss.
There are also specialised uses for stomata as a result of structural neofunctionalisation, such as nectar secretion. Some plants even have stomata on their roots -- apparently the mycorrhizal associations (fungal-plant symbiosis) began by hyphae penetrating open root stomata!
Early stomata consisted of a single cell with an opening in the middle, much like this fern stoma:
(source PJ Franks, Plant Physiol)
In flowering plants, stomata contain two cells instead, perhaps resulting from an extra (symmetrical) division somewhere in the evolutionary past. Aren't they cute?
Next question: How do they 'happen'?
Next time~
You may have heard of stomatal guard cells back in highschool. Something about shrivelling up to close when hot, potassium ion channels and carbon dioxide? Yeah, for most people they fade forever into the vague memories of cramming for a science test. The only lasting effect of this exercise tends to be an aversion to anything botany.
That's how it worked for me anyway. I recall finding plants to be the most boring unit in highschool biology, despite having a good teacher. They fail to convey the wonders of land plants, instead falling back on dry diagrams and that wretched photosynthesis 'equation'.
Of course, one can't really blame them -- the teachers themselves have learned it the same way. And you simply cannot even begin to share the amazing world of stomatal development in a highschool classroom. After all, I've worked hard over a year in the field, and I'm still just a novice. But I do believe the approach could be altered to make the time used in a more constructive, and enjoyable, manner for both students and teachers.
I think part of highschool education should promote asking good questions. There is almost no aid in that aspect of learning -- information is just presented, and some students never realise the diversity of questions they could ask about it.
First of all, why do plants even bother? A stoma is a fairly complex structure:
(Fred Sack)
Bilateral symmetry requires a coordinated process of development; special care must be taken to ensure spacing between stomata; the guard cells must maintain a kidney shape for optimal functioning. Such structures must be really worth the trouble to evolve!
Plants, like most terrestrial life, have their origins in water. Their ancestors looked something like this:
(source)
This Charophyte lacks stomata. Living in water, your cells are already in the aquatic environment they are specialised for. There are some special adaptations for dealing with freshwater due to differences in osmotic pressure, but we'll overlook those.
The problem with migrating onto land is that cells require an aquatic environment to function. When our ancestors left water, they had to figure out a way to carry the aquatic environment with them. Fungi generally live inside their food, or in soil; still, they have a chitinous wall for protection and structural support. Our lineage came up with skins and an intricate system of vessels.
Some plants do quite fine sticking to damp areas and not dying upon dessication. Surviving drying up was probably already advantagous enough for aquatic plants, since ponds are prone to drought. Liverworts are only a few cell layers thick, lack a vascular system, and have a very thin coat of wax on the surface:
(source)
(I think I'll just have to introduce thallose liverworts someday -- they're awesome!)
A good bryophyte reference here
Being thin enough and living in damp places allows you to skip stomatal development:
(Psi)
However, as plants move into dryer places and gained size, dessication becomes a problem. The solution? A think layer of cuticular wax to stop water evaporation:
(Lacey Samuels)
Now we have a problem. Wax doesn't breathe very well. You need to inhale CO2 for photosynthesis; you need to exhale O2. Having open holes in the waxy cuticle defeats the very purpose of having one, as well as exposing the organism to invaders. That's where stomata come in. Stoma is Greek for 'mouth', and that's pretty much exactly what these structures are: millions of mouths covering the leaf surface, enabling the plant to breath while regulating water loss.
There are also specialised uses for stomata as a result of structural neofunctionalisation, such as nectar secretion. Some plants even have stomata on their roots -- apparently the mycorrhizal associations (fungal-plant symbiosis) began by hyphae penetrating open root stomata!
Early stomata consisted of a single cell with an opening in the middle, much like this fern stoma:
(source PJ Franks, Plant Physiol)
In flowering plants, stomata contain two cells instead, perhaps resulting from an extra (symmetrical) division somewhere in the evolutionary past. Aren't they cute?
Next question: How do they 'happen'?
Next time~
Eukaryote Biodiversity Series
01: Looking at Life
(Just pretend I posted this on Thursday, ok? Thanks! <_<)
Protista is a vast kingdom surrounding the three miniscule enclaves of Fungi, Animalia and Plantae. Together, they form the domain Eukarya, a humble accident on the shores of vastly prokaryotic life. In the Eukarya, Protista is the most diverse and fascinating place: a realm seldom touched by human exploration; a realm with many secrets beckoning our attention; a realm of strange mystery and eerie familiarity.
To celebrate Darwin Year, evolution and biodiversity, join me on a journey along this land -- so we can wander lost together!
(Hopefully) Resolving some confusion
I've touched on this before, but since this is an introductory post: There is some confusion with respect to what Protista includes, and doesn't include. This confusion permeates the majority of reputable government and educational publications by non-specialists. For example, the government of Nova Scotia thinks: (emphasis mine)
2. Most protozoans have absolutely nothing to do with animals. They are fundamentally different lineage. Same with the algae. More importantly, no modern organism (alive today) is a first anything. Fish are not our ancestors. Our ancestors likely looked fish-like at some stage. Modern fish are a distinct lineage with their own long and ardurous evolutionary journey. It makes as much sense to say modern fish are early man as it is to say modern man is early fish...
3. Kelps can grow up to 60m. They have distinct tissue types -- a holdfast (root), stipe (stem), and blades (leaves). Red and green algae are multicellular as well, with distinct tissue types. Multicellularity is more common that one would think, and has occurred at least 8 times independently even if you take a conservative approach.
4. Amoebae, Toxoplasma, diatoms and Saccinobaculus disagree.
But don't take this as an attack on whoever painstakingly put that page together. As you see, Protista is a rather diverse and poorly-unified kingdom. Part of the reason is the 'racist' arrogance of the residents of one of the isolated enclaves -- Animalia. Fungi, Animals, Nucleariids, Ichthyosporeans and Choanoflagellates could coexist peacefully in Kingdom Opisthokonta, unified by proudly wearing a tail on their asses, instead of waving it before them like all normal Eukaryotes. Unfortunately, some clans of the Animal tribe can barely accept sharing an association with fellow Animals, let alone little moldy unicellular things that give us beer. Instead, we prefer to spend our lives entangled in a taxonomical nightmare.
Brief History of Protistology
The main reason for the taxonomical mess is historical. Before the 1600's, there was no way to see microscopic organisms, so no one had a reason to suspect their existence. Life was sorted into plants (green, static) and animals (motile). This may even be an innate categorisation! Fungi were categorised as plants, for they didn't seem to move. Signs of microbial presence were just seen as rot, which was a manifestation of 'foulness', etc.
Then came the 17th century with Robert Hooke and Antonie van Leeuwenhoek, who created the first microscope and discovered the first unicellular organism, respectively. Hooke looked at a section through cork and discovered cells, apparently named for their resemblence of the monastic ones, or so says Wikipedia:
(Hooke 1665 Micrographia)
Leeuwenhoek was a Dutch cloth merchant who had never gone to university,thereby retaining some creativity and intelligence. He invented a special technique for making microscope lenses which was later found to involve melting glass into spheres, as opposed to grinding it. In fact, we got to try out the technique in class once. Never thought a protistology lab could involve propane torches and glass melting. The scope mimics something like Leeuwenhoek's:
but simpler, of course. Amazingly enough, it actually works! It's quite astonishing that you can actually see microorganisms in pond water through that thing! Microbiology was no longer some distant world kept apart from us by rediculously expensive and complicated optical instruments. A glass sphere is enough to observe it! (we had to make one of those for a lab exam afterwards -- this guy managed to involve a propane torch in a freaking protistology lab exam, somehow...truly memorable!)
So using such a simple tool, Leeuwenhoek discovered the first unicellular organism, likely some sort of ciliate. Apparently there aren't any drawings of it out there; if anyone knows whether Leeuwenhoek ever made a drawing, could you let me know where to find one? I'm utterly curious! He does have some bacteria though:
Afterwards, there was an explosion of people playing with scopes and painstakingly recording their findings. Some examples from Haeckel here and more scans here.
Now life no longer made much sense. Of course there were still things that looked like plants (sessile algae, eg. spirulina) and things that looked like animals (eg. ciliates) -- those were called protozoa, since they were considered to be ancestors of animals (most aren't, as we shall see later). There were some hyphal non-green forms, but those were fungi... which were considered to be plants for a long time. Mycology is still often considered part of botany, and is done in botany departments to this very day.
Over time, people got more and more confused as discoveries piled up. You had motile algae, which didn't quite fit the 'plant' category very well. Fungi also resisted the plant kingdom as more and more was learned of them. Eventually, fungi gained independence. Protists were classified into 'algae' (Plantae), 'protozoa' (Animalia), 'sporozoa' (Fungi). Since those organisms shared a lot in common, at first glance, they were granted their own kingdom in 1866 by Haeckel -- he named the them Protista.
A more recent rendition of this idea:
(source)
This thing honestly makes my eyes hurt. There's just so much WRONG with that tree I barely know where to start. I mean, back in 1969 when this was made, molecular biology was barely starting so they didn't know any better. The tree was constructed mostly on morphological data, which can be extremely elusive due to evolutionary convergence. I'll discuss that in more detail later: there are some wonderful examples of this. The entire non-photosynthetic heterokont group had to be assembled from bit and pieces all over the tree once molecular data came out!
Another, more fundamental, issue with this tree... is this stupid notion of some forms of life being 'beyond' others, more 'complex', more 'advanced', more 'evolved'... this idea that evolution pursues progress, and we're at its apex. Evolutionary Creationism, nothing less. "Fine, if there's no loving god... then there must be loving evolution that worked 3.8 billion years to create us in the end!"
(moreover, in terms of 'evolvedness', we lag far behind the bacteria, due to our retardedly long generation spans...)
You'd laugh, but some professionals hold this kind of view, without realising it. Oh how many times I've mentioned my interest in protists, only to be subject to "Protists? Oh, the primitive eukaryotes!" I'm talking about professors here. I argue they're not actually all that 'primitive', that term is fundamentally flawed in this application. They look at me funny and avoid the topic altogether...!
Moving on, after many long arduous years of poor grad students (and undergrads! =P) slaving away at the bench, thus far we have something like this:
(
(Taken from here; originally from The Tree of Life: An Overview. S. L. Baldauf, D. Bhattacharya, J. Cockrill, P. Hugenholtz, J. Pawlowski, A. G. B. Simpson. Chapter 4 in Assembling the Tree of Life (Eds. Cracraft and Donoghue, Oxford University Press, 2004)
There is still much uncertainty about the root of eukaryotes; that's a topic for a later post.
Along the way, there was an interesting hypothesis based on some organisms appearing to lack mitochondria. It has been disproven upon further investigation, but modern textbooks still parade it around as fact... almost a whole decade out of date! More on that later...
Hopefully now we may have a clearer idea of what a protist is, as well as a bit of history of the field. Over the course of the year, I'd like to journey around the Keeling 2005 tree and also discuss some themes like multicellularity, endosymbiosis and the dangers of morphology. I hope to share some of the wonders of this alien kingdom as I just begin to explore it myself. Carl Sagan dreamed of alien life beyond -- I believe I've found his aliens. All he had to do was look closer here on the Pale Blue Dot!
Some resources:
The smallest page on the web - basic intro stuff, nice pictures
Tree of Life - put together by experts in various fields
Protista is a vast kingdom surrounding the three miniscule enclaves of Fungi, Animalia and Plantae. Together, they form the domain Eukarya, a humble accident on the shores of vastly prokaryotic life. In the Eukarya, Protista is the most diverse and fascinating place: a realm seldom touched by human exploration; a realm with many secrets beckoning our attention; a realm of strange mystery and eerie familiarity.
To celebrate Darwin Year, evolution and biodiversity, join me on a journey along this land -- so we can wander lost together!
(Hopefully) Resolving some confusion
I've touched on this before, but since this is an introductory post: There is some confusion with respect to what Protista includes, and doesn't include. This confusion permeates the majority of reputable government and educational publications by non-specialists. For example, the government of Nova Scotia thinks: (emphasis mine)
The kingdom Protista is used to group most single-celled organisms, except bacteria and blue-green algae. Protista is a large and variable group containing both plant and animal characteristics. This group includes about 50,000 species of protozoans (first animals) and between 8,000 and 12,000 species of algae (simple plants).1. Blue-green algae are bacteria. Also, Protista does not include myxosporidia (animals) and yeasts (fungi).
Protists are mostly microscopic and have no organs or tissues. They are single-celled but may occur in colonies. They may be free-living on land or in water, or live in association with other plants and animals. Locomotion is achieved by waving tiny hair-like threads.
2. Most protozoans have absolutely nothing to do with animals. They are fundamentally different lineage. Same with the algae. More importantly, no modern organism (alive today) is a first anything. Fish are not our ancestors. Our ancestors likely looked fish-like at some stage. Modern fish are a distinct lineage with their own long and ardurous evolutionary journey. It makes as much sense to say modern fish are early man as it is to say modern man is early fish...
3. Kelps can grow up to 60m. They have distinct tissue types -- a holdfast (root), stipe (stem), and blades (leaves). Red and green algae are multicellular as well, with distinct tissue types. Multicellularity is more common that one would think, and has occurred at least 8 times independently even if you take a conservative approach.
4. Amoebae, Toxoplasma, diatoms and Saccinobaculus disagree.
But don't take this as an attack on whoever painstakingly put that page together. As you see, Protista is a rather diverse and poorly-unified kingdom. Part of the reason is the 'racist' arrogance of the residents of one of the isolated enclaves -- Animalia. Fungi, Animals, Nucleariids, Ichthyosporeans and Choanoflagellates could coexist peacefully in Kingdom Opisthokonta, unified by proudly wearing a tail on their asses, instead of waving it before them like all normal Eukaryotes. Unfortunately, some clans of the Animal tribe can barely accept sharing an association with fellow Animals, let alone little moldy unicellular things that give us beer. Instead, we prefer to spend our lives entangled in a taxonomical nightmare.
Brief History of Protistology
The main reason for the taxonomical mess is historical. Before the 1600's, there was no way to see microscopic organisms, so no one had a reason to suspect their existence. Life was sorted into plants (green, static) and animals (motile). This may even be an innate categorisation! Fungi were categorised as plants, for they didn't seem to move. Signs of microbial presence were just seen as rot, which was a manifestation of 'foulness', etc.
Then came the 17th century with Robert Hooke and Antonie van Leeuwenhoek, who created the first microscope and discovered the first unicellular organism, respectively. Hooke looked at a section through cork and discovered cells, apparently named for their resemblence of the monastic ones, or so says Wikipedia:
(Hooke 1665 Micrographia)
Leeuwenhoek was a Dutch cloth merchant who had never gone to university,
but simpler, of course. Amazingly enough, it actually works! It's quite astonishing that you can actually see microorganisms in pond water through that thing! Microbiology was no longer some distant world kept apart from us by rediculously expensive and complicated optical instruments. A glass sphere is enough to observe it! (we had to make one of those for a lab exam afterwards -- this guy managed to involve a propane torch in a freaking protistology lab exam, somehow...truly memorable!)
So using such a simple tool, Leeuwenhoek discovered the first unicellular organism, likely some sort of ciliate. Apparently there aren't any drawings of it out there; if anyone knows whether Leeuwenhoek ever made a drawing, could you let me know where to find one? I'm utterly curious! He does have some bacteria though:
Afterwards, there was an explosion of people playing with scopes and painstakingly recording their findings. Some examples from Haeckel here and more scans here.
Now life no longer made much sense. Of course there were still things that looked like plants (sessile algae, eg. spirulina) and things that looked like animals (eg. ciliates) -- those were called protozoa, since they were considered to be ancestors of animals (most aren't, as we shall see later). There were some hyphal non-green forms, but those were fungi... which were considered to be plants for a long time. Mycology is still often considered part of botany, and is done in botany departments to this very day.
Over time, people got more and more confused as discoveries piled up. You had motile algae, which didn't quite fit the 'plant' category very well. Fungi also resisted the plant kingdom as more and more was learned of them. Eventually, fungi gained independence. Protists were classified into 'algae' (Plantae), 'protozoa' (Animalia), 'sporozoa' (Fungi). Since those organisms shared a lot in common, at first glance, they were granted their own kingdom in 1866 by Haeckel -- he named the them Protista.
A more recent rendition of this idea:
(source)
This thing honestly makes my eyes hurt. There's just so much WRONG with that tree I barely know where to start. I mean, back in 1969 when this was made, molecular biology was barely starting so they didn't know any better. The tree was constructed mostly on morphological data, which can be extremely elusive due to evolutionary convergence. I'll discuss that in more detail later: there are some wonderful examples of this. The entire non-photosynthetic heterokont group had to be assembled from bit and pieces all over the tree once molecular data came out!
Another, more fundamental, issue with this tree... is this stupid notion of some forms of life being 'beyond' others, more 'complex', more 'advanced', more 'evolved'... this idea that evolution pursues progress, and we're at its apex. Evolutionary Creationism, nothing less. "Fine, if there's no loving god... then there must be loving evolution that worked 3.8 billion years to create us in the end!"
(moreover, in terms of 'evolvedness', we lag far behind the bacteria, due to our retardedly long generation spans...)
You'd laugh, but some professionals hold this kind of view, without realising it. Oh how many times I've mentioned my interest in protists, only to be subject to "Protists? Oh, the primitive eukaryotes!" I'm talking about professors here. I argue they're not actually all that 'primitive', that term is fundamentally flawed in this application. They look at me funny and avoid the topic altogether...!
Moving on, after many long arduous years of poor grad students (and undergrads! =P) slaving away at the bench, thus far we have something like this:
(
(Taken from here; originally from The Tree of Life: An Overview. S. L. Baldauf, D. Bhattacharya, J. Cockrill, P. Hugenholtz, J. Pawlowski, A. G. B. Simpson. Chapter 4 in Assembling the Tree of Life (Eds. Cracraft and Donoghue, Oxford University Press, 2004)
There is still much uncertainty about the root of eukaryotes; that's a topic for a later post.
Along the way, there was an interesting hypothesis based on some organisms appearing to lack mitochondria. It has been disproven upon further investigation, but modern textbooks still parade it around as fact... almost a whole decade out of date! More on that later...
Hopefully now we may have a clearer idea of what a protist is, as well as a bit of history of the field. Over the course of the year, I'd like to journey around the Keeling 2005 tree and also discuss some themes like multicellularity, endosymbiosis and the dangers of morphology. I hope to share some of the wonders of this alien kingdom as I just begin to explore it myself. Carl Sagan dreamed of alien life beyond -- I believe I've found his aliens. All he had to do was look closer here on the Pale Blue Dot!
Some resources:
The smallest page on the web - basic intro stuff, nice pictures
Tree of Life - put together by experts in various fields
Half-assed excuses for half-assed posting...
Man, I fail. Got caught up in a whirlwind of school and research related crap again. I blame the plant cell cycle -- the more you read on that stuff, the more and more confused you get. There's no way out, all paths spiral downwards into an abyss of darkness and sheer utter befuddlement and stupefaction.
Why, oh why, did my research lead there? What have I done to come across such inconvienent yet awesome data?
It's kinda fun though. I'm, intellectually-speaking, a sadomasochist, apparently...
And then I have three exams next week. No, that I will NOT enjoy... I'm especially looking forward to Thursday: Exam monday morning, then o-chem lab with plenty of ether, then evening exam. Ether + evening exam is destined to be a rather lethal combination. Ow.
So I hope this is sufficient explanation for my half-assed internet presence lately. I tend to disappear for extended periods of time...
Week after next is reading break, however; I have no excuse then! Yet... <_<
Oh, and the protist series... is like, coming, soon, methinks...
Why, oh why, did my research lead there? What have I done to come across such inconvienent yet awesome data?
It's kinda fun though. I'm, intellectually-speaking, a sadomasochist, apparently...
And then I have three exams next week. No, that I will NOT enjoy... I'm especially looking forward to Thursday: Exam monday morning, then o-chem lab with plenty of ether, then evening exam. Ether + evening exam is destined to be a rather lethal combination. Ow.
So I hope this is sufficient explanation for my half-assed internet presence lately. I tend to disappear for extended periods of time...
Week after next is reading break, however; I have no excuse then! Yet... <_<
Oh, and the protist series... is like, coming, soon, methinks...
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