While browsing the web I came across a tumblog called "Pretty Protozoa", which regularly posts scientifically interesting or visually attractive images of protists. Most of them seem to be from scientific publications or scientists' websites, but are properly credited to the original authors, as far as I can tell.
Another great protist blog worth mentioning is The Ocelloid, and its predecessor Skeptic Wonder, both maintained by a grad student at Indiana University. She writes with plenty of enthusiasm, she definitely knows a lot about all sorts of protists, and the blog is often illustrated by her own micrographs.
Showing posts with label biophilia. Show all posts
Showing posts with label biophilia. Show all posts
Saturday, March 23, 2013
Sunday, February 17, 2013
Backyard Naturalists
There's a great article on the BBC website about amateur naturalists who discover new species in their spare time. One would think that the flora and fauna of Europe has been largely cataloged, but new species are still being discovered there, mostly by people who pursue natural history as a hobby.
Much of this new biodiversity is small, especially insects and other invertebrates:
Much of this new biodiversity is small, especially insects and other invertebrates:
New species are sometimes hiding in plain sight - a new species of wasp was recently discovered by a technician in a car park by his office in Spain. And not long ago, a retired man in Wales came across a new type of slug in his back garden.The article links to a recent (2012) study published in PLoS ONE, which found that 60% of new species from Europe were described by non-professional taxonomists. As professional expertise in taxonomy moves from the West to emerging economies like those of Latin America and Asia, perhaps this could be a new model for how the study of biodiversity could be kept alive in those regions.
Monday, April 30, 2012
Plant collectors are endangered species
The days of the botanical adventurer, a relic of the western Age of Discovery, may be over:
The lifestyle can be punishing. Among the explorers mentioned in the article are Alwyn Gentry of the Missouri Botanical Garden, who died in a plane crash in 1993, and Leonard Co of the Philippines, who was accidentally killed in a military operation while collecting in the field.
For science, the decline of general taxonomic knowledge is worrisome. Specialization is a natural consequence of the growth of knowledge, because as the amount of information grows, the proportion that one can master is correspondingly smaller. No one today would dare like Linnaeus to claim that he or she has constructed a complete System of Nature. But this doesn't mean that being able to name the plants and animals around one's home is irrelevant. As the article points out, one has to start early, when the mind is still impressionable and soaks up information readily. Humans are natural pattern-recognizers, and we have an innate urge to put names to things and classify them.
As a scientist I also value this sort of general knowledge. Science seeks to test hypotheses and answer questions, but these hypotheses and questions have to come from somewhere. In biology, the interesting questions tend to come from observing nature and pondering why something is the way it is: natural history in its most basic sense. Our world would be much poorer without it, and without the people who keep this knowledge alive.
The modern botanist tends to focus on one plant group and uses DNA sequences to decode evolutionary history and relationships. “We'll see fewer collections per individual because people are becoming so specialized. Just collecting a lot of specimens isn't something people have much respect for,” says Robbin Moran, who studies ferns at the New York Botanical Garden. The shifts in botany have had costs, he says. “The really big collectors have been tremendous generalists, and that's something that's being lost.”This news feature in Nature discusses the work of some of the last botanical generalists - plant collectors who venture into the field to collect widely, rather than just particular groups that they specialize in. Why is their number dwindling? Among the reasons: fewer opportunities for botanical fieldwork, the increasing specialization of academic botany, and tighter controls on collection and export of plant specimens by countries which have the forests.
The lifestyle can be punishing. Among the explorers mentioned in the article are Alwyn Gentry of the Missouri Botanical Garden, who died in a plane crash in 1993, and Leonard Co of the Philippines, who was accidentally killed in a military operation while collecting in the field.
For science, the decline of general taxonomic knowledge is worrisome. Specialization is a natural consequence of the growth of knowledge, because as the amount of information grows, the proportion that one can master is correspondingly smaller. No one today would dare like Linnaeus to claim that he or she has constructed a complete System of Nature. But this doesn't mean that being able to name the plants and animals around one's home is irrelevant. As the article points out, one has to start early, when the mind is still impressionable and soaks up information readily. Humans are natural pattern-recognizers, and we have an innate urge to put names to things and classify them.
As a scientist I also value this sort of general knowledge. Science seeks to test hypotheses and answer questions, but these hypotheses and questions have to come from somewhere. In biology, the interesting questions tend to come from observing nature and pondering why something is the way it is: natural history in its most basic sense. Our world would be much poorer without it, and without the people who keep this knowledge alive.
Friday, October 14, 2011
Riding ants all the way
EO Wilson has had a storied career in evolutionary biology: the originator of island biogeography and sociobiology, one of the world's leading experts on ants, and two-time Pulitzer Prize winner. Recently, he plunged into scientific controversy again with the publication of a paper authored with two Harvard mathematician colleagues, Corina Tarnita and Martin Nowak, claiming that kin selection is unnecessary to explain the origin of eusociality (Nature paper, Biology Refugia blog post).
A new profile of Wilson in the Atlantic magazine tells us what he has been up to lately: participating in a conservation project at Gorongosa Park in Mozambique, traveling, and still reveling in collecting and identifying ants and other insects.
A new profile of Wilson in the Atlantic magazine tells us what he has been up to lately: participating in a conservation project at Gorongosa Park in Mozambique, traveling, and still reveling in collecting and identifying ants and other insects.
...For minutes at a time, the white-haired scientist resembled nothing so much as a grandmaster smiting a score of enthusiastic challengers at a speed-chess exhibition, as he quickly named each animal brought to him:I can only hope to be half as energetic and productive when I am 82!
“And here we have—very good—a lycaenid butterfly. Probably that’s a new species, but I’m not going to keep it. Who got that butterfly? … What is this? Wait a minute, where is my magnifying glass, I’ll tell you. Oh yeah, that one I know. I know the genus. That one is a Tetragnatha. … Now the ants … This is an important one. Can you be sure to get that one? All right, wait a minute. I want that one. It’s different. That’s a reduviid, an assassin bug … That’s a—wait a minute, it’ll come to me. This is a coccinellid.”
This medley, one of many, concluded with Wilson saying: “Wow, this is the way to make a real collection, if you are an entomologist. Get a bunch of kids around. No, seriously.”
Later, in a quieter moment, I asked Wilson how he managed to name so many of the creatures, particularly ones far outside his specialty, and on a continent he’s never visited before. He told me that he’d prepped intensively for the experience for two months, consulting both reference books and experts, committing the descriptions of thousands of species to memory. Silently, I recalled a critic’s recent characterization of him as senescent.
Wednesday, October 12, 2011
Björk and the Zombie Snails
No, it's not a tribute band. The quirky Icelandic musician Björk has a new album out, called Biophilia. Appropriately enough, the tracks are inspired by themes of nature and biology.
One of the songs in particular, "Virus", was written after Björk learned about "zombie snails" on YouTube. It has nothing to do with real viruses, though (Disclaimer: I haven't heard the album yet so I can't say if the music is any good). These snails are parasitized by a trematode worm called Leucochloridium paradoxum, which you can see in the photo below.
Look closely at the eyestalk on the right. Yup, that's filled with worm. But it's not just one worm. It's a structure called the brood-sac, which contains hundreds of cercariae – little larval worms ("trematode life cycle" on Wikipedia. The sac is banded and green and pulsates. This attracts the attention of birds, which think that it's actually their favorite food, maggots or caterpillars. They swoop in and peck off an eyestalk with all the worms in them. The worms end up in the gut of the bird, and are carried in there to be pooped out somewhere else. Free transportation! Snails grazing along eat some bird poop with the parasites in them, and get infected, completing the cycle.
Find out more about the sneaky life cycle of this worm from this article on Wired magazine, or read the Wikipedia article, or just watch the video that inspired Björk:
One of the songs in particular, "Virus", was written after Björk learned about "zombie snails" on YouTube. It has nothing to do with real viruses, though (Disclaimer: I haven't heard the album yet so I can't say if the music is any good). These snails are parasitized by a trematode worm called Leucochloridium paradoxum, which you can see in the photo below.
 |
| Snail infected with Leucochloridium paradoxum in its eyestalk. |
Find out more about the sneaky life cycle of this worm from this article on Wired magazine, or read the Wikipedia article, or just watch the video that inspired Björk:
Saturday, October 08, 2011
Slime is going places
In college I kept a pet in my dorm room, possibly against regulations. However, it didn't make any noise, didn't poop all over the place, and didn't need to be fed every single day. When it got too troublesome to take care of it, I simply cut off a piece of it to keep, and killed the rest. Before you think I'm some kind of cruel monster, here's a photo of my pet.
Slime molds are amazing creatures. They're neither plant nor fungus nor animal, but are protists, the "eukaryotic leftovers". The one I had is called Physarum polycephalum, and is a common organism used for demonstrations in schools and biology classes. It's bright yellow, big, grows fast, and is easy to revive from a dormant culture. Slime molds come in two "flavors": the plasmodial molds like Physarum which are essentially giant single cells, and the cellular ones which are an aggregate of numerous individual amoeboid cells.
The New York Times science section, which has possibly the best science reporting of any mainstream newspaper, recently featured an article by Carl Zimmer on slime molds and why they're exciting to current biology research (via Twitter).
He highlights Physarum and its ability to solve "mazes" where the objective is to connect up different particles of food scattered on a substrate. This research won a team of Japanese researchers the prize in Transportation Planning for the tongue-in-cheek Ig Nobels in 2010 (and before in 2008). What the organism does is to spread its plasmodium outwards (much like the photo above) until it encounters these food particles, and then retract those parts of the plasmodium which are on barren areas leaving behind thicker "veins", connecting the food particles with each other and with the exploring front of the plasmodium. The link to transportation? When the particles are scattered in an arrangement resembling the major centers of the Tokyo metropolitan area, the resulting plasmodial vein network is quite similar to a map of the Tokyo rail network!
It sounds relatively easy to design an optimal transport network but such design actually requires a whole lot of trade-offs and is not straightforward. However I wouldn't go quite as far as hire them as transport engineers. The Japanese team used the mold's behavior as a template to come up with an algorithm for making such networks. The computational model is more easily controlled!
In addition to Physarum the other molds mentioned include the cellular slime mold Dictyostelium, which has a long and distinguished history of use as a lab organism for studying simple multicellularity. It's interesting to evolutionary science because to make its fruiting bodies (which release spores for dispersal), some of the slime mold cells in the colony have to sacrifice themselves to form the stalk, which leaves no descendants. This is an example of a cooperative behavior, which is puzzling from an evolutionary standpoint because it should theoretically collapse in a maelstrom of cheating for individual benefit.
In the wild the diversity of slime molds has not been given as much attention as other organisms, but they have their own distinctive beauty. They come in many colors and shapes, but require some patience to find, by peering closely at decaying wood and leaf litter. There are slime molds in Singapore too, and I've posted a gallery of beautiful images taken by Serena Lee of the Botanic Gardens to the Protists in Singapore webpage. One particularly striking one is Diachea leucopodia, which has an iridescent black fruiting body borne on a white stalk (above). The diversity of slime molds from the tropics is poorly understood, with many species that look like temperate ones but may or may not be the same thing.
These creatures are often sidelined because of their taxonomic obscurity, and maligned because of their unfortunate name. Let's help to spread a better appreciation for them among the nature-loving public!
 |
| Slime mold Physarum polycephalum growing outwards to feed on oat flakes. |
Slime molds are amazing creatures. They're neither plant nor fungus nor animal, but are protists, the "eukaryotic leftovers". The one I had is called Physarum polycephalum, and is a common organism used for demonstrations in schools and biology classes. It's bright yellow, big, grows fast, and is easy to revive from a dormant culture. Slime molds come in two "flavors": the plasmodial molds like Physarum which are essentially giant single cells, and the cellular ones which are an aggregate of numerous individual amoeboid cells.
The New York Times science section, which has possibly the best science reporting of any mainstream newspaper, recently featured an article by Carl Zimmer on slime molds and why they're exciting to current biology research (via Twitter).
He highlights Physarum and its ability to solve "mazes" where the objective is to connect up different particles of food scattered on a substrate. This research won a team of Japanese researchers the prize in Transportation Planning for the tongue-in-cheek Ig Nobels in 2010 (and before in 2008). What the organism does is to spread its plasmodium outwards (much like the photo above) until it encounters these food particles, and then retract those parts of the plasmodium which are on barren areas leaving behind thicker "veins", connecting the food particles with each other and with the exploring front of the plasmodium. The link to transportation? When the particles are scattered in an arrangement resembling the major centers of the Tokyo metropolitan area, the resulting plasmodial vein network is quite similar to a map of the Tokyo rail network!
It sounds relatively easy to design an optimal transport network but such design actually requires a whole lot of trade-offs and is not straightforward. However I wouldn't go quite as far as hire them as transport engineers. The Japanese team used the mold's behavior as a template to come up with an algorithm for making such networks. The computational model is more easily controlled!
In addition to Physarum the other molds mentioned include the cellular slime mold Dictyostelium, which has a long and distinguished history of use as a lab organism for studying simple multicellularity. It's interesting to evolutionary science because to make its fruiting bodies (which release spores for dispersal), some of the slime mold cells in the colony have to sacrifice themselves to form the stalk, which leaves no descendants. This is an example of a cooperative behavior, which is puzzling from an evolutionary standpoint because it should theoretically collapse in a maelstrom of cheating for individual benefit.
 |
| Diachea leucopodia fruiting bodies, from MacRitchie Reservoir area in Singapore. |
These creatures are often sidelined because of their taxonomic obscurity, and maligned because of their unfortunate name. Let's help to spread a better appreciation for them among the nature-loving public!
Wednesday, May 13, 2009
Cenchrus brownii
Cenchrus brownii - before I forget again and have to hunt the web for the scientific name!
Its quite common along the beach forest and it was first recorded in Singapore in 1950. I browsed the www and realised that the plant is in some flickr sets in Singapore without the name (I commented on them).. so here's the name so that the next time someone gets poked by it, at least can curse it properly.
Here's a nice picture of it courtesy of Ria from wildsingapore
It belongs to the grass family and not the sedge family.
Cenchrus brownii -!
As you can see, I am pretty invigorated by the fieldtrip I had this morning...
Its quite common along the beach forest and it was first recorded in Singapore in 1950. I browsed the www and realised that the plant is in some flickr sets in Singapore without the name (I commented on them).. so here's the name so that the next time someone gets poked by it, at least can curse it properly.
Here's a nice picture of it courtesy of Ria from wildsingapore
It belongs to the grass family and not the sedge family.
Cenchrus brownii -!
As you can see, I am pretty invigorated by the fieldtrip I had this morning...
Nudibranchs and the power of the sun in their tentacles
Saw this cutie at Sentosa today - Polka-dot nudibranch (Jorunna funebris)
Besides nudibranchs, there were a few other people from the seashore groups that were there brought in by the low tide today.
Then I happened to see this slug or is it a nudibranch (could it be Phyllodesmium briareum? asks Ria from the blur photo I sent her) and this dude who happened to be there mentioned that it was a slug that could photosynthesize. I can't verify the species but the nugget about slugs photosynthesizing brought to mind an article I read. But first the pictures of this fair creature... I hope this is really a slug of some sort! I thought they were a cluster of mollusc eggs. I am not sure if this slug really photosynthesizes though.
But anyway, more about photosynthesizing slugs! Well they don't really but they do collect the plastids (chloroplasts basically) by feeding on the algae (they one that this slug is feeding on is presumably Bryopsis). Collecting the plastids is already quite amazing since the slugs selectively do not digest this organelle. Another most profound aspect of this ability to harness photosynthetic machinery is a gene that is co-opted by the slug in its co-evolutionary history... so baby slugs are born with one photosynthetic gene that helps maintain the ingested plastids for at least 9 months... cool.
Besides nudibranchs, there were a few other people from the seashore groups that were there brought in by the low tide today.
Then I happened to see this slug or is it a nudibranch (could it be Phyllodesmium briareum? asks Ria from the blur photo I sent her) and this dude who happened to be there mentioned that it was a slug that could photosynthesize. I can't verify the species but the nugget about slugs photosynthesizing brought to mind an article I read. But first the pictures of this fair creature... I hope this is really a slug of some sort! I thought they were a cluster of mollusc eggs. I am not sure if this slug really photosynthesizes though.
But anyway, more about photosynthesizing slugs! Well they don't really but they do collect the plastids (chloroplasts basically) by feeding on the algae (they one that this slug is feeding on is presumably Bryopsis). Collecting the plastids is already quite amazing since the slugs selectively do not digest this organelle. Another most profound aspect of this ability to harness photosynthetic machinery is a gene that is co-opted by the slug in its co-evolutionary history... so baby slugs are born with one photosynthetic gene that helps maintain the ingested plastids for at least 9 months... cool.
Solar-powered Sea-slugs Live Like Plants
ScienceDaily (Dec. 3, 2008) — The lowly sea slug, “Elysia chlorotica,” may not seem like the most exciting of creatures, but don’t be fooled
“Photosynthesis needs around 2,000 to 3,000 genes, and animals do not have many of the critical genes,” says Manhart. So Manhart and his co-workers looked into how the plastids consumed by the slug can continue photosynthesizing.
“We found that the slug has at least one gene required for photosynthesis in its nuclear genome, which has never been found in any animal,” says Manhart. “The critical thing is the plastids come from the alga, but the slug nucleus contains at least one, and probably more of the genes required for plastid functioning,” he adds.
Wednesday, June 04, 2008
Final fieldtrip for the 2008 Biophilia programme
Here's a little summary from the final fieldtrip to sentosa for the biophilia programme (24th May 2008). The students have been great to work with thanks to their initiative and level of enthusiasm. (hmmm but why haven't they contributed to this blog?!?). Fellow colleagues that came for the fieldtrips made the programme successful in its own way.
We've been lucky with the tides this year and all the saturdays low tides were around 9 am so we could schedule those saturday fieldtrips.
For me again, there were new things to see (as with every fieldtrip to this spot) and this school of catfish was one. It was a tight ball and they were swimming around each other and moving as a school.
[youtube=http://www.youtube.com/v/haKV3YYZ89s]
I chanced upon another school of smaller catfish later and demonstrated to the students the fountain effect of how a school of fish move away from an incoming predator. See embedded video. Here, I wade towards the school of fish and through the school. Note how the school doesn't swim away but split into 2 and swim around me by first swimming away and doing a flanking turn to the outside and around me and regrouping behind me. That's apparently optimal evasion tactics from a predator... cool. I got the chance to gather the students to demonstrate this in situ, something I had learnt from Prof Munroe in Animal Behaviour class when I was in year 2 or 3 when I was an undergraduate. Those are just some of the biodiversity lessons that I never forgot. It was nice to demonstrate this to a bunch of students who may not take any Biodiversity modules as undergraduates. In fact its hard to imagine that with the ever changing syllabus to molecular biology that students will ever learn this.
Here's a mermaid's purse or more informatively, the egg that is laid by a shark, stingray and attached to seawead. The eggcase is usually washed to shore after the baby shark emerges. There are plenty of this around at the sentosa beach.
And finally, a picture of students working at the site. Its nice to see that they have learnt much from this experience. It has been a fulfilling programme and one that the teachers and I have found exciting, refreshing and something we looked forward to. Its definitely a different pedagogy, the open classroom. Some students have remarked that they enjoyed the freedom to explore and craft their own projects. Will post some reflections below as they are nice (I have omitted some parts)
~"The most memorable part of Biophilia will definitely be the day on the beach when for the first time in my life I watched 2 ‘blue-blooded’ horseshoe crabs mate. I was really surprised to be able to find such amazing creatures in Singapore, because all along I saw Singapore as a place with minimal biodiversity. This programme has thus taught me not to underestimate the biodiversity of creatures in Singapore."~
~I really enjoyed every single session of the Biophilia programme as I was working with what I enjoy and am interested in most. The fieldtrips really heightened my interest towards marine organisms and I really learnt a lot about Singapore’s shores during the trips. I have also started to fully appreciate Singapore’s biodiversity after seeing such a huge variety of organisms living on such a small stretch of beach. I used to think that Singapore does not have any sea anemones or coral reefs but I realized was very much mistaken after seeing the beautiful sea anemones on the Sentosa beach. I’m glad to know that there are such programmes to let me learn more about Singapore’s biodiversity as I feel that our biodiversity is just as important as the developments in our country. Our biodiversity is part of our environment as well as our heritage so we should treasure it as well and not cast it aside as something less important. If I have a chance I would want to go for this programme again and I hope that it will be for a longer period of time as I feel that the time period this time is too short.~
~From the fieldtrip I attended, the experience and new discoveries I made gave me a great sense of achievement. I think it is wonderful that I have had this opportunity to observe and even touch some of the organisms we found. Wading in the water and sometimes mud in search of fish, crab and whatever else we could find was truly a great experience. I am glad to have been selected to participate in this program. I never realized that the area behind underwater world had so many cool organisms despite all the times I have been to Sentosa. The thought that that little ecosystem will most likely be destroyed in the future with the ongoing construction around that area is rather depressing. As unlikely as it is, I hope that the short video that my group has produced throughout this program will achieve its purpose in increasing the awareness about the ecological value of that area, and perhaps more might learn to value this more than the monetary profits it could bring. ~
We've been lucky with the tides this year and all the saturdays low tides were around 9 am so we could schedule those saturday fieldtrips.
For me again, there were new things to see (as with every fieldtrip to this spot) and this school of catfish was one. It was a tight ball and they were swimming around each other and moving as a school.
[youtube=http://www.youtube.com/v/haKV3YYZ89s]
I chanced upon another school of smaller catfish later and demonstrated to the students the fountain effect of how a school of fish move away from an incoming predator. See embedded video. Here, I wade towards the school of fish and through the school. Note how the school doesn't swim away but split into 2 and swim around me by first swimming away and doing a flanking turn to the outside and around me and regrouping behind me. That's apparently optimal evasion tactics from a predator... cool. I got the chance to gather the students to demonstrate this in situ, something I had learnt from Prof Munroe in Animal Behaviour class when I was in year 2 or 3 when I was an undergraduate. Those are just some of the biodiversity lessons that I never forgot. It was nice to demonstrate this to a bunch of students who may not take any Biodiversity modules as undergraduates. In fact its hard to imagine that with the ever changing syllabus to molecular biology that students will ever learn this.
Here's a mermaid's purse or more informatively, the egg that is laid by a shark, stingray and attached to seawead. The eggcase is usually washed to shore after the baby shark emerges. There are plenty of this around at the sentosa beach.
And finally, a picture of students working at the site. Its nice to see that they have learnt much from this experience. It has been a fulfilling programme and one that the teachers and I have found exciting, refreshing and something we looked forward to. Its definitely a different pedagogy, the open classroom. Some students have remarked that they enjoyed the freedom to explore and craft their own projects. Will post some reflections below as they are nice (I have omitted some parts)
~"The most memorable part of Biophilia will definitely be the day on the beach when for the first time in my life I watched 2 ‘blue-blooded’ horseshoe crabs mate. I was really surprised to be able to find such amazing creatures in Singapore, because all along I saw Singapore as a place with minimal biodiversity. This programme has thus taught me not to underestimate the biodiversity of creatures in Singapore."~
~I really enjoyed every single session of the Biophilia programme as I was working with what I enjoy and am interested in most. The fieldtrips really heightened my interest towards marine organisms and I really learnt a lot about Singapore’s shores during the trips. I have also started to fully appreciate Singapore’s biodiversity after seeing such a huge variety of organisms living on such a small stretch of beach. I used to think that Singapore does not have any sea anemones or coral reefs but I realized was very much mistaken after seeing the beautiful sea anemones on the Sentosa beach. I’m glad to know that there are such programmes to let me learn more about Singapore’s biodiversity as I feel that our biodiversity is just as important as the developments in our country. Our biodiversity is part of our environment as well as our heritage so we should treasure it as well and not cast it aside as something less important. If I have a chance I would want to go for this programme again and I hope that it will be for a longer period of time as I feel that the time period this time is too short.~
~From the fieldtrip I attended, the experience and new discoveries I made gave me a great sense of achievement. I think it is wonderful that I have had this opportunity to observe and even touch some of the organisms we found. Wading in the water and sometimes mud in search of fish, crab and whatever else we could find was truly a great experience. I am glad to have been selected to participate in this program. I never realized that the area behind underwater world had so many cool organisms despite all the times I have been to Sentosa. The thought that that little ecosystem will most likely be destroyed in the future with the ongoing construction around that area is rather depressing. As unlikely as it is, I hope that the short video that my group has produced throughout this program will achieve its purpose in increasing the awareness about the ecological value of that area, and perhaps more might learn to value this more than the monetary profits it could bring. ~
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