Monday, June 03, 2013

Hidden Lives - the Movie

As I announced over a year ago, I have a website featuring the protists (protozoans and algae) that one can find in freshwater (ponds, reservoirs, drains...) in Singapore. The pages are illustrated with pictures (photomicrographs) and videos, and are organized as a guidebook (inspired by the Singapore Science Centre nature guidebooks that I grew up with).

With my collection of videos, though, I wanted to put them together into a documentary-style film, and I finally found time to do it this summer.

Hidden Lives (SD) from brandon seah on Vimeo.

This was made with iMovie '08, with music sourced from ccMixter. Feel free to share, with credits! Read more about the motivation here.

Thursday, May 30, 2013

Don't let the nutrients fly away!

Pitcher plants are beautiful but disturbing. Their vase-shaped pitchers are so elegant to look at, yet violate our notion of plants as passive and peaceful, because they are death traps for unwary insects and other small animals that fall in and drown in the pitcher fluid. Pitcher plants (genus Nepenthes) are one of the few carnivorous plants, who also include the Venus Fly Trap and the Bladderwort, that invert the food chain by gaining some of their nutrients from animals.

Nepenthes bicalcarata (by David Sucianto, via Wikimedia Commons)

Why would a photosynthetic organism need to trap animals? After all, they still have green leaves and chlorophyll, like any other plant. But other nutrients, especially nitrogen, are important to plant growth as well. Pitcher plants can grow in nutrient poor soil because they can supplement their intake of nitrogen and other nutrients by trapping and digesting animals, which are especially nitrogen-rich.

Not all animals will die in pitchers, however. Some insects, including the larvae of several dipteran (fly) species, can live in the pitchers and feed on the organic matter found there. The pitcher species Nepenthes bicalcarata also plays host to an ant species, Camponotus schmitzi, that is found only with N. bicalcarata. The ants are somehow able to walk on the slippery inner surface of the pitcher, and predate upon the fly larvae and other organic material, and also feeds on nectar from the plant.

It would seem at first that this is a lousy deal for the plant. The flies and ants are stealing its food right from its mouth! A new research paper published in PLoS ONE shows how the ants and pitcher plants actually derive mutual benefit.

By looking at the nitrogen isotope ratios in the plant tissue, and using isotope labeling experiments, the researchers showed that nitrogen is being transferred from the ants to the nutrients. They also observed how the ants predate upon the fly larvae that live and mature inside the pitchers. Left to their own devices, these larvae would consume the pitcher's nutrient supply, and then literally fly away with the stolen nutrients when they metamorphose into adults. For this they are (harshly) called kleptoparasites, or "thief-parasites". By capturing and eating the flies while they are still larvae or pupae, the ants put a stop to this thievery. The plant itself then recovers these nutrients in the form of the ant colony's waste products.

The ants are hence not only improving the pitcher's prey-capture efficiency, by keeping the slippery pitcher walls clean, but also prevent the nutrients from escaping with the insects. A fascinating story of symbiosis, that reveals just how dynamic and interconnected all these nutritional and behavioral relationships are in Nature.

Sunday, May 26, 2013

Cockroach vs. human arms race

Blatella germanica (German cockroach)
German cockroach (via Wikimedia Commons)

The cockroach is a creature that universally elicits feelings of disgust, but anyone who has tried to catch or kill them would also concede a grudging admiration for their toughness. They thrive on the refuse of our human civilization, and it has been said that if the human race somehow managed to wipe itself out through nuclear war, it would be cockroaches that flourish in the ruins.

Much human ingenuity has also gone into designing new and improved ways to kill cockroaches. Sugar laced with poison is commonly used to bait and exterminate these pests. The large-scale deployment of such traps, however, also constitutes a huge inadvertent experiment on the effectiveness of natural selection. Some populations of the German cockroach, Blatella germanica, have become immune to such traps because they are no longer attracted by the glucose sugar used as bait.

Recent research by a team from North Carolina State University (article abstract) has uncovered the physiological basis for this glucose aversion. The sense of taste is mediated by gustatory sensory neurons (GRNs); different substances activate different neurons and trigger different behavioral responses. In normal, wild-type cockroaches, glucose stimulates sugar-GRNs. The researchers found that this is also the case in the glucose-averse cockroaches, but that glucose also additionally stimulates bitter-GRNs, which are usually simulated by substances such as caffeine to which cockroaches are averse. The activation of bitter-GRNs suppresses the usual response of sugar-GRNs and causes the glucose-averse behavior.

This is a nice and neat story that illustrates how quickly natural selection can act, especially considering how numerous the cockroaches must actually be. Whereas evolutionary arms races between most organisms are limited by the rate at which natural selection can act, our human battles against the organisms that we consider pests and weeds are accelerated greatly by the pace of technological change and innovation. This episode shows, however, that natural selection can sometimes keep up and catch us when we are not wary.

Wednesday, May 01, 2013

Hey there sailor...

... want to be a scientist? All you need is a bucket lid, a length of rope, and a smart phone app.

Scientist Richard Kirby at Plymouth investigates how climate change affects phytoplankton in the oceans. One of the oldest and yet simplest methods to measure the density of phytoplankton in surface waters is to use a device called the Secchi disk, invented by the Jesuit Pietro Angelo Secchi in 1865. This is simply a plain white disk, usually made of plastic, that's lowered into the water until it can no longer be seen; this depth is read off from the line. The denser the plankton, the more turbid the water and the faster the disk disappears from view.

Kirby's team has developed an app to gather data from "citizen-scientists". Because of its simplicity, the Secchi method is well-suited for crowd-sourcing, and can be made quickly from easily-available materials. The group's aim is to get data on plankton density from throughout the world's oceans, far more than any single scientific group would be able to accomplish on its own.

Download the app for iPhone or Android from the Secchi App website.

Wednesday, April 24, 2013

How periodic cicadas evolved their timing

Every few years, the periodic cicadas come into the news, when they simultaneously complete their life cycles and emerge from the ground as winged adults. They swarm over large parts of the eastern United States and attract both curiosity and alarm from residents and the media. After a few weeks, their mating and egg-laying over, they disappear just as quickly as they appeared. Of course, they are not completely gone: their juveniles live underground, having perhaps the longest maturation of any insect, to emerge as adults after a period of 13 or 17 years.

Brood XIX Cicada
13-year cicada from Brood XIX. Via Wikimedia Commons.

Why 13 or 17 years? These prime-numbered periods have puzzled more mathematically-minded biologists for ages, with one suggestion being that a prime-numbered life cycle would minimize the number of predator life cycles that could synchronize with it (because a prime number has no factors but itself). But how did this situation evolve?

A new paper published in PNAS (open access) from a group of Japanese scientists looks at the phylogeny and population genetics of the known species of periodic cicadas. The periodic cicadas fall within the genus Magicicada, within which are species partly defined by the length of their period. M. tredecim for example is a 13-year species, while M. septendecim is a 17-year species. Within each species there are also multiple "broods", representing different cohorts have the same emergence and mating cycles. One brood may encompass multiple species. Siva blogged here about one such brood in 2004, the ominously-named Brood X, which had an unusually large emergence (the "X" is actually just a roman numeral). The different species fall within three species groups, each with both 13- and 17-year species.

Contrary to expectations, the old species, defined by morphology and period, do not correspond to the evolutionary history as uncovered by molecular phylogeny and haplotyping. The three big species groups are still supported, representing two evolutionary splits at about 3.9 and 2.5 million years ago (Mya). The splits within the species groups, however, are relatively recent, mostly less than 0.5 Mya. Furthermore, the splits correspond more to geographical regions than to life cycle period. The split between 13- and 17-year periods have also evolved multiple times. To quote from the paper:
Our results are broadly consistent with the previous idea that an ancestor of all Magicicada diverged into three species allopatrically, and later, the three became sympatric and each species independently diverged into 13- and 17-y cicadas. Surprisingly, however, the divergence of 13- and 17-y cicadas was asynchronous among the species groups and occurred repeatedly even within a species group. This finding is all of the more interesting given that each species group shows similar eastern, middle, and western phylogeographic divisions similar to post-Pleistocene patterns observed in other North American taxa, suggesting that the three Magicicacda groups shared multiple refugia during the last glacial maximum.
This is a nice surprise, and as the authors point out, the repeated switching between 13- and 17-year forms suggests that there is a single genetic "switch" involved, because it is unlikely that a complex mechanism could be repeatedly gained and lost in such a manner.

Thursday, April 11, 2013

Germany's green energy revoluton

The terrain in North Germany is largely flat, and cycling in the countryside one can see it rolling on for miles. From almost any point one can also see the electricity-generating windmills keeping watch over the countryside. The building boom in windmills and solar panels is a result of the German government's plan to transition entirely towards renewable energy sources.

Soon after the Fukushima disaster in Japan, the announcement was made that the country would shut down its remaining nuclear power plants. In the short term, as this commentary in Nature points out, this means that the country is more reliant on fossil fuels like coal and gas. But it rightly says that the Energiewende, or Energy Transition, is an experiment. There is a risk, after all, that renewable energy is not enough, and that anticipated improvements in technologies for the production and distribution of energy will not pan out.

Another commentary article, this one from the Economist, is less optimistic and more cautious. Much of the initial boom in building renewable energy plants and decentralizing energy production has been fueled by government grants and subsidies. Eventually, however, consumers will see their electricity bills go up. Remodeling the energy infrastructure changes patterns of supply and demand. On top of the technological challenges are the economic ones, that ultimately depend on human factors: how much citizens and businesses are willing to pay, and what politicians have the will to push through.

Saturday, March 23, 2013

Pretty Protozoa

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.

Sunday, March 10, 2013

Environmentalist recants anti-GM position

Mark Lynas, an environmental activist and writer on subjects including climate change, publicly recanted his previous opposition to genetically-modified foods at a public lecture in the Oxford Farming Conference in January. People change their minds all the time, but his action surprised people because he was in the past deeply involved in activism against GM foods, even joining groups who attacked and uprooted GM crops in farms and research stations. In an interview, he describes how his former associates have reacted to his about-face:
Lynas's speech made the news internationally and, along with it, "all the hate started coming through". He found himself accused of being in the pay of Monsanto which, he says, "shows that people think I have no integrity and look at me with complete contempt".
It wasn't an impulsive decision, however, but one based on his immersion in science and the scientific literature when researching his books on climate change. As he learned more about the science behind climate, he found himself arguing with climate-change deniers, and saw that he was looking at himself in the mirror:
My second climate book, Six Degrees, was so sciency that it even won the Royal Society science books prize, and climate scientists I had become friendly with would joke that I knew more about the subject than them. And yet, incredibly, at this time in 2008 I was still penning screeds in the Guardian attacking the science of GM – even though I had done no academic research on the topic, and had a pretty limited personal understanding. I don’t think I’d ever read a peer-reviewed paper on biotechnology or plant science even at this late stage.
His speech is worth reading for people on either side of the fence, if only to have a peek into how people think on their other side....

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:
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.

Tuesday, January 29, 2013

United States of America vs. One Tyrannosaurus bataar Skeleton

Many countries have laws to prevent the export of fossils and other natural treasures, including Mongolia, which encompasses the Gobi Desert, a rich source of dramatic dinosaur fossils. However, "fossil poaching" is rife, given the vastness of the desert and the lucrative profits that can be made on the high-end fossil market. When a three-quarters-complete Tyrannosaurus bataar skeleton went on auction in New York in 2012, the Mongolian government asked US authorities to intercede, because it had likely been illegally smuggled out of Mongolia. The sale was halted, and the fossil put into storage as the legal challenge moved forward:
"Two weeks later, in downtown Manhattan, the U.S. attorney for the Southern District of New York sued for custody of the specimen, on behalf of the nation of Mongolia. Procedure required that an arrest warrant be issued against the dinosaur itself, so the action became known as United States of America v. One Tyrannosaurus Bataar Skeleton."
Read more on the story of this outrageously brazen auction attempt, and the legal battle that ensued.

Update (9 May 2013): The bones were handed over by the US to the Mongolian government on Monday, putting this legal saga to an end. According to the Mongolian culture and tourism minister, they intend to set up a dinosaur museum in Mongolia, as they do not currently have such a museum to display their fossils. It's surprising that they don't have one already, given the importance of the Gobi Desert as a source of important and dramatic vertebrate fossils.