The Biology Refugia

Hidden Lives - the Movie

2013-06-03T19:00:00.000+08:00

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.

Don't let the nutrients fly away!

2013-05-30T19:00:00.000+08:00

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.

Cockroach vs. human arms race

2013-05-26T19:00:00.000+08:00

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.

Hey there sailor...

2013-05-01T12:00:00.000+08:00

... 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.

How periodic cicadas evolved their timing

2013-04-24T11:22:00.001+08:00

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.

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.

Germany's green energy revoluton

2013-04-11T18:00:00.000+08:00

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.

Pretty Protozoa

2013-03-23T03:52:00.002+08:00

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.

Environmentalist recants anti-GM position

2013-03-10T18:00:00.000+08:00

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....

Backyard Naturalists

2013-02-17T07:00:00.000+08:00

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.

United States of America vs. One Tyrannosaurus bataar Skeleton

2013-01-29T07:00:00.000+08:00

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.

Taxonomists are not going extinct

2013-01-26T07:00:00.000+08:00

When talking to people studying biodiversity, one often hears that "taxonomists are a dying breed", an opinion that has been expressed on this blog before.

A newly-published meta-analysis looks at whether science can realistically finish cataloging all the world's biological species before they go extinct:

"Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity."

They found that it's not true that taxonomists are a dying breed, but that the profession is undergoing a geographical shift from Western countries where modern taxonomy and big museum collections were first developed, to South America and Asia-Pacific countries. They argue that this is a good development because those are the countries where much of the world's biodiversity actually lies.

The number of active taxonomists was estimated by looking at databases to find out who is publishing new species descriptions. It's also not true that the current generation of taxonomists are mostly "one-hit wonders" who only describe one or two new species in their careers; there is not much difference between the previous and current generations of taxonomists in their productivity.

If we want to catalog all the world's biodiversity, declining lack of expertise is then not the problem. What's problematic is that even as we are still in a state of ignorance about the world's biodiversity, species are going extinct at a steady rate due to human activity. We are also victims of our own success: as more and more species have been described, it becomes harder to find new ones among the existing known diversity. It's like being stuck at home for the weekend: after you've read most of the books and watched most of the movies in your house, it's harder to find something new to do (at least before the Internet...).

But what's the point of all this taxonomic toil? Why describe new species? The questions of "how many species on Earth?" and "what is the extinction rate?" are notoriously difficult to answer. Whereas we now have a fair guess at the answer to the first question, estimates of the extinction rate vary widely, reflecting the huge uncertainties involved. As the authors point out: "Taxonomists are not in danger of extinction. They are increasing in numbers and will become more in demand as more species mean more diagnostic challenges to discriminate species, whether they are pests, pathogens, food, ecological keystone, or endangered species." This highlights how knowledge of biodiversity is important, both for its own sake and for the sake of human interests.

Keystone species, Keystone teacher?

2013-01-20T07:00:00.000+08:00

Keystone species are members of ecological communities that have a disproportionate effect on the community if they are removed. They need not be the most abundant element, but may play an important role, e.g. in keeping down the population of some other species that would otherwise dominate.

The classic experiment was performed in the 1960s by ecologist Bob Paine, who removed a species of sea star Pisaster ochraeus from a rocky shore intertidal environment. In months, the community became dominated by mussels and decreased in diversity. Because of this, he coined the term "keystone species" for the role that this sea star was playing in this community.

Pisaster ochraeus (via Wikimedia)

Paine himself has had a disproportionate influence on the academic community in the field of ecology. This profile article describes his career and students, and illustrates well how a single teacher can not only be a good mentor to his or her students, but also go beyond that to build a scientific family.

Carl Woese, Discoverer of the Archaea, RIP

2013-01-05T22:00:00.000+08:00

One of the first things that students learn today about the diversity of life is the concept of the Three Domains of Bacteria, Archaea, and Eukarya. In the past, they would have learned about the Five Kingdoms — Prokaryotes, Animals, Plants, Fungi, and Protists —a concept popularized by the late Lynn Margulis, but we now know that the animals, plants, and fungi are relative newcomers on the evolutionary scene, and that the "prokaryotes" actually contain two ancient lineages, the Bacteria and Archaea, which split long before the eukaryotic kingdoms.

Carl Woese in 2006, via U Illinois

For this insight, we can thank Carl Woese, who passed away just before the New Year at the age of 84 (U Illinois press release, NY Times obituary). Woese made his discovery in the 1970s, when sequencing DNA and RNA was anything but routine. At that time, the prokaryotes were classified primarily by physiological characteristics and morphological appearance. There was little attention paid to microbial evolution, except in a speculative way, simply because there was no easy way to go about studying it.

Woese's insight was to recognize that ribosomal RNA could be used as a marker of evolution. Every living cell contains ribosomes, and both their structure and function are conserved, meaning that even distantly-related organisms could be compared using their rRNA. But rRNA sequences are not completely frozen in time: they evolve at a rate that's well-suited to reconstructing the evolutionary relationships between the major groups of life.

Ribosomal tree of life, showing the three domains, from Woese 1987.

Today, sequencing rRNA is routine work: we use PCR to amplify the sequences, and then sequence them using one of a variety of technologies. In Woese's day, this was not possible. What he used instead was a method called "oligonucleotide cataloguing". First the rRNA had to be physically isolated from the cells of an organism. They were then cut into fragments at every G residue by an enzyme derived from fungi, called ribonuclease T1. These fragments were then separated by electrophoresis on ~~a 2D gel~~ paper [thanks to George Fox for correction in comments. 31 May 2013]. Selected spots could be cut out and digested further. Each unique RNA sequence would produce its own characteristic pattern or "catalog". For each organism of interest, a catalog was compiled. Between each pair of organisms, an evolutionary distance could be calculated by counting how many fragments they had in common. For a group of organisms, these distances could be used to calculate a phylogenetic tree, showing who was more closely related to whom. It was arduous work, and Woese did much of it himself.

It was with oligonucleotide cataloging that he discovered the third domain of life, when he compared the catalogs from methanogens, a group of prokaryotes that produce methane as a by-product of their metabolism, to other organisms. He found that they were as distant from the bacteria as they were from the eukaryotes: despite looking to other microbiologists like bacteria, they were instead a totally new group of life! Other lines of evidence apart from rRNA have since confirmed the uniqueness of the Archaea, but when his results first came out, few people believed him or thought that it was important. Lynn Margulis, for example, still favored the term "prokaryote" because in her system, eukaryotes represented a wholly new grade of cellular organization over the prokaryotes. The comments by Joe Felsenstein in this post on the Panda's Thumb blog provide a good idea of the context in which Woese was proposing his new ideas.

It took a long time for Woese's views to win out over his detractors, a battle which reportedly left him a "scarred revolutionary", according to a 1997 profile in Science (also available here). Some of his skeptics could afford to hold out well into the 1990s, because they were already established names (such as Ernst Mayr). Today, the use of rRNA as a phylogenetic marker is pervasive. The small-subunit rRNA gene is the most widely-used phylogenetic marker, and there exist specialized databases devoted to rRNA data, such as CRW and SILVA. The three domains are textbook dogma, but current research is moving beyond using single molecules to reconstruct phylogeny. Using multiple genes is now the standard for serious phylogenetics, and phylogeny is being used as a guide for genome sequencing projects.

Microbiology was one of the last major fields in biology to thoroughly incorporate an evolutionary perspective, and Carl Woese was the individual who did the most to cause that shift. Indeed it may have even gone a bit too far: because sequencing is much easier than isolation and cultivation of new organisms, we now have a surfeit of genomic sequences from environmental organisms, but a limited set of cultivated microbes for performing experiments that help us make sense of these genomes. The future for environmental microbiology appears to lie in making the best use of new high-throughput sequencing technologies with targeted cultivation of selected strains, to both broaden and deepen our understanding.

Wallace's biogeographic map updated - and there are three new realms

2013-01-05T05:27:00.001+08:00

Three new realms have been added to an update of Wallace's biogeographic map: Panamia, Sino-Japanese and Oecania. The abstract says, "a global map of zoogeographic regions was generated by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. 20 distinct zoogeographic regions are grouped into 11 larger realms.

Phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world."

“Wallace’s map still makes a lot of sense,” said Jean-Philippe Lessard, an ecologist at McGill University in Montreal who was formerly at the University of Copenhagen. “We’re not inventing anything here, we’re just implementing Wallace’s vision at an age where we have tons of DNA and more information on where species are on the planet.”

- see the article in New York Times. Article: Holt et al., 2012. An update of Wallace’s zoogeographic regions of the world. Science, 339 (6115): 74-78. DOI: 10.1126/science.1228282. Published online 20 Dec 2012.

Google Earth resource available from: http://macroecology.ku.dk/resources/wallace.

Thanks to Leong Wai for the alert.

Children of the wilderness

2012-09-17T15:49:00.000+08:00

A young girl disappears in the forest while playing with a cousin. The cousin is found several days later, but no one can find the girl. Some time later, stories emerge from the forest about a girl seen walking alongside a tiger, about a wild woman walking around with long hair and nails, but she is never found and the search is eventually abandoned. Thirty-eight years later, she is finally rediscovered at the age of 42, after having wandered through the forests on the borders of three different countries.

This sounds like a chapter from a magical realist novel, or some fairy-tale fable, but it is the true story of Ng Chhaidy from the district of Mizoram in India, close to the border with Myanmar. Chhaidy’s story is astonishing for the length of time that she has been missing, long enough for her to lose the ability to use language, even though she was fluent in her native Mara when she disappeared as a four-year-old. It seems remarkable to those of us living in the developed and urbanized world, far removed from close contact with forest and wilderness, that such a thing could happen in modern times.

Chhaidy joins the annals of those termed “feral children” – humans who whether from deliberate neglect or accident have ended up living in the wild away from human contact. The article by Lhendup Bhutia (linked above) describes some well-known cases:

“One of the best known cases of a feral child was that of The Wild Boy of Aveyron, who was captured in a French forest back in 1797. He was around 10 years old, but could neither walk upright nor speak. A physician tried to rehabilitate him, but without much success. Then there is the case of the Ukrainian girl Oxana Malaya, who came to be known as ‘The Dog Girl’. She was found in 1991 living with several wild dogs in a shed. She was only eight, and had lived for over five years with canines. She walked on all fours, survived on raw meat and barked like a dog. She is currently believed to be living at a home for the mentally handicapped.”

The shock and horror that we feel when thinking about such cases stems from the very core of our concept of what it means to be human. Far from “mere biology”, humanity prides itself on culture, and what is culture but the accumulated fruits of society? Although a theoretical understanding of sociality, in the context of biology, was only possible after the acceptance of Darwin’s ideas on evolution, and their synthesis with modern genetics in the 20th century by William Hamilton and other pioneers of sociobiology, I think all humans have an intuitive understanding of the importance of social life both to our species and to other social animals that we observe in close quarters, such as our pets and livestock.

Feral children therefore appear impaired, being somehow incomplete people. The most striking characteristic is their loss of language. Unlike the popular saying, the true window to one’s soul is language, not the eyes. It’s the best way that we humans can communicate what’s going on inside our heads, with which no amount of mute eye-gazing can compare. A person without language remains a cypher, cryptic and unknowable.

Carolus Linnaeus, the “father of taxonomy”, must have recognized this, even if his conception of human nature (grounded in the classics and Christian religion) might be very different from ours. He circumscribed a boundary between feral people and the rest of humanity in the 1758 edition of his masterwork, the Systema Naturae (via Biodiversity Heritage Library). The Systema Naturae was an attempt to classify all known species—Animal, Vegetable, and Mineral—into systematic kingdoms, classes, orders, genera, and species. Holding pride of place were the humans, genus Homo in the order Primates, foremost among the mammals. In lieu of describing this special group of animals, he merely enjoined the reader “nosce te ipsum” – know thyself.

Description of "Homo sapiens ferus" from the Systema Naturae, 1758.

Within the species Homo sapiens were several races, reflecting the attitudes of his time towards human diversity: Americanus, Europaeus, Asiaticus, Afer, and Monstrosus (the monsters and “freaks” such as conjoined twins). But heading the list was Homo sapiens ferus: the feral people, of whom he cited the cases known to him from previous reports: the “Bear Boy of Lithuania”, the “Wolf Boy of Hesse”, the “Sheep Boy of Ireland”, and so on. What were their distinguishing characteristics? He confidently states that they go on all fours, are mute, and hairy, which perhaps matches our mental archetype of a “wild man”. The word “mute” stands out: it is the ability to use language that stands between normal life and the wilderness.

In an age when aristocrats collected purported “mermaids” for their curiosity cabinets, when two-headed calves were seen as inauspicious portents, and when people like the Hottentot Venus were exhibited for a paying public, maybe it is only to be expected that Linnaeus would want to put feral people in a box of their own, away from the rest of teeming humanity. But it is significant that he didn’t group them with the “monsters”, where one might find the one-testicled Hottentot and the pointy-headed macrocephalous Chinese. Linnaeus saw a difference between the results of abnormal nature and abnormal nurture; it was the lack of human society that made the feral children what they were, not something wrong with their biology, and this was an important distinction for him to maintain. They were still an anomaly, having no place in his neat stereotyped racial system, but an anomaly of culture not physiology. Unfortunately, for Linnaeus, this understanding of the power of culture to shape a person could not overcome the boundaries between the races. He could not see, as we now do, that our upbringing and education have a stronger effect on our dispositions and character than our ancestry.

Ng Chhaidy’s case is sad, but her story ends (and continues) optimistically. She is able to communicate with others in her village, non-verbally and also through a small idiosyncratic vocabulary. She can be sociable, and helps out with a number of tasks around the house. Although she has “received no medical or psychological attention”, she has the benefit of returning to a village where people are sympathetic and willing to interact with her. Perhaps the first four normal years of her life also help her readjustment, despite the thirty-eight intervening ones in the forest. The journalist’s turn of phrase, that “she has only just begun to experience childhood and adolescence”, is apt. These are stages of life which all of us have to go through, where we step beyond the immediate family and become socialized. It is being a part of wider society that makes us fully human.

Giving “junk DNA” the credit that it’s due

2012-09-10T17:57:00.001+08:00

When the Human Genome Project was completed over a decade ago, in 2001, many biologists were surprised that the human genome only contains about 20000 to 25000 genes, which occupy less than 1% of the total DNA sequence. This was surprising news: how could such a complex system as a human being be coded for by only 25000 instructions, when a microscopic worm (C. elegans) has 21000, and a bacterium (E. coli) has 5000? And what was the point of carrying all this other DNA around? The term “junk DNA” was coined to refer to these non-protein-coding sequences. Are they really junk — relics of past evolution, gene duplication, viral infection, and other hypothesized mechanisms of sequence accumulation — or do they have a function that we simply haven’t found out about yet?

The ENCODE (Encyclopedia of DNA Elements) project has recently released its first results in a series of publications in Nature and other scientific journals. There was plenty of news surrounding it; not surprising given the $180 million that have already been spent, and the over 400 scientists working on it. Articles appeared in major newspapers and news outlets, but then I got an email from a college friend, who’s not a biologist, asking me what all this fuss was about. He’d read the newspaper articles, which were full of quotes from scientists lavishing praise on the project and its promise, but couldn’t quite figure out exactly what it was about. The generic-sounding name of the project doesn’t give many clues, either. And so, even though I’m supposed to be a microbiologist and not a human geneticist, I thought I’d take a shot at explaining the significance of the ENCODE results.

The idea of the “gene” has been a long and problematic one. It has a peculiar history for a biological concept, because the existence of genes was predicted by theory (the experiments of Mendel and his successors) long before we had any clue of what the physical nature of genes were. Eventually biologists figured out that DNA was the hereditary material, and the Central Dogma took shape: that genetic information stored on DNA was first transcribed to RNA, which was then translated to proteins, and that proteins were the main functioning parts of the cell: the scaffolding, motors, and carriers that performed the business of life. A gene was just the information needed to make a protein, and if asked to define the physical manifestation of a gene, one would have said that it was the stretch of DNA that held the instructions for making that protein.

As we found out more about genes and how they were regulated, however, the story began to get complicated. It wasn’t necessarily true that one gene = one protein: some genes could be spliced in different ways to give different products. Nor was it true that proteins were the only functional pieces of the cell: sure, we’ve known about ribosomal RNAs (rRNA) and transfer RNAs (tRNA) for a long time, but other small RNAs, some with catalytic functions, have also been discovered. Gradually, we’ve also come to appreciate that the complexity of life is not just the result of proteins interacting with other proteins, with DNA sitting passively by; many proteins also interact with DNA, determining which genes are going to be expressed, and which should stay silent. In the classical textbook examples, regulatory elements lie close to the genes which they administer, but it is now known that this isn’t necessarily so. New mechanisms of silencing genes have been discovered, some which work by chemically modifying DNA (methylation), and others which involve a dizzying dance of RNA and protein molecules (RNA interference). Is it time to revise the concept of the “gene”, or should we simply acknowledge that protein-coding genes are not the only significant pieces of a genome?

The ENCODE project has shown this very clearly. Far from being “junk”, the non-protein-coding sequences in a genome are actually doing something and not just sitting there passively. At least 80% of the genome can be experimentally shown to have some kind of function (recall that less than 1% of the genome codes for proteins), or as the authors put it: a “demonstrable biochemical function”. They may be regulators or promoters, i.e. sequences which control the expression of genes by binding to proteins involved in the machinery of transcription. They could be regions that are controlled by DNA methylation, which silences expression. Or they could be regions which are exposed to transcription factors, instead of being coiled up in histones.

This was a large scale project with many participants. What they did to discover this was a process of systematic cataloging. They used almost 150 different human cell lines in culture (including the famous HeLa cells) and performed different experiments to spot different functions. For example, to see what portion of the DNA was actually being transcribed, they extracted and sequenced RNA en masse, an approach made possible by new methods of nucleic acid sequencing which can sequence huge numbers of small lengths very quickly. To see what sequences bind to known proteins, they performed a method called ChIP, chromatin immunoprecipitation. For a protein which is thought to bind to DNA, antibodies are raised against it. The protein is then exposed to genomic DNA; it seeks out and binds to the specific sequence that it interacts with. A chemical is added to cross-link the protein and DNA, and this complex is fished out using the antibodies developed earlier. The crosslinks are removed, and the DNA is sequenced, to find out what region of the genome this protein interacts with. Other types of experiments were performed to find out which parts of the genome are methylated, are accessible to transcription factors, and so on. They’ve also analyzed how the regulatory elements in a genome interact with each other, and how the three-dimensional folding of the DNA itself affects the interactions between different parts of the genome.

One of the surprising findings was that much of the genome (75%) is actually transcribed to RNA at some point or another, even though most of these don’t end up being translated to proteins. Textbooks usually mention the three classical types of RNA: messenger RNA (mRNA), rRNA, and tRNA (described above), but aside from these workhorses, RNA was usually thought of as a sort of “relic” molecule, doing only these few menial jobs. But recent research is accumulating evidence for the importance of various kinds of small RNAs in the eukaryotic cell, and the ENCODE project could help the task of cataloging them all.

There are a whole bunch of other sub-projects (or “threads”, as they call them on the ENCODE website) that have been carried out by the ENCODE consortium. As a way of doing science, I think it points the way to the future: big consortia collecting big data and crunching big numbers. For biology, the new sequencing technologies (collectively called “next-generation sequencing”, or NGS) are a tremendous advance over traditional Sanger-type sequencing, which was developed decades ago and still based on the same principles. NGS came into the market just in time for the ENCODE project, allowing them to sequence several times as much DNA for the same cost. We are now reaching the point when you could have your own personal genome sequence for a thousand dollars or even less. The limit on what we can do is imposed instead by our ability to store, transmit, and compute such massive quantities of data.

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The first batch of papers published by the ENCODE consortium are available via the website of Nature. They’ve also got some snazzy interactive graphics.

Stephen Asma on Body Worlds and the macabre

2012-08-20T22:36:00.000+08:00

Humans have always been fascinated by death and the macabre. Long before Body Worlds brought plastinated human bodies on display around the world, people were jostling to see mummies dug out of dusty crypts, or executed murderers freshly cut down from the gallows. Stephen Asma, whose interest in death, decay, and decrepitude has been marked by books on monsters (On Monsters) and natural history museums (Stuffed Animals and Pickled Heads), writes about our shared predilection to gawp at death. I cannot deny being one of the gawpers myself, either!

Google Earth and Science

2012-07-11T22:14:00.000+08:00

Google Earth and its cousin, Google Maps, are really useful. I don't think I've used a street directory or road map since I learned how convenient it was to just google it. Aside from just being a tool for finding out how to get from point A to point B, or for businesses to promote themselves, it's also a great tool for crowdsourcing, as memorably happened after the Haiti earthquake two years ago.

It's really useful for scientists too. I'm sure many of us have used Google Maps to check out field sites before going there, and also afterwards to plot localities and routes. The terms "virtual globe" or "Digital Earth" refers generally to such tools, which represent geographical features in digital form. A recent paper in PNAS looks at how current virtual globe tools have been used to help science and make it accessible to the public, and what the prospects are for the future.

One way to get more out of Google Maps is to use KML, a standard markup language for displaying geographical data in virtual globe software (tutorial). If you already use the "My Maps" feature, you can download your maps as KML to share with others. Alternatively, if you want to plot known coordinates and annotate them, you can mark up your data as KML and import into Google Earth to visualize it.

Scientific turnover and the fate of old theory

2012-05-20T14:01:00.000+08:00

The Arts and Sciences are often seen as non-overlapping complements, as naturally opposed as North and South, or the two sexes male and female. It's therefore surprising to find someone who can make a significant career in both, not just as an amateur but as a paid professional.

Vladimir Nabokov is best known as the author of the novel Lolita, but before becoming famous for his writing in English, he was a professional lepidopterist, an expert on a group of butterflies known as the Blues. An earlier blog post here highlighted some recent research on "his" group of butterflies.

His two careers were also the subject of an essay by Stephen Jay Gould. Gould used Nabokov's example to examine our attitudes to "genius". If Nabokov was a genius in literature, does it follow that his scientific work was also illuminated by the same genius? Was his scientific writing especially fluent or literary, as some literary critics claim? Gould found that, in the opinion of other professional lepidopterists, Nabokov's scientific work was competent and painstaking, but not especially pathbreaking or profound. Nor was his scientific writing unusually poetic or stylistically striking, in the way that his novels were.

In fact, Gould goes as far as to characterize Nabokov as being somewhat of a "stick in the mud." At the time when he was engaged in his butterfly work full-time at the Museum of Comparative Zoology at Harvard, from 1942 to 1948, a revolution was underway in taxonomy. Where previously the morphological characters, such as wing coloration or genital anatomy (a serious preoccupation of much of entomology!) were the means by which new species were defined, the budding science of cytology (the study of cells) had introduced chromosomes as yet another important character. "Cryptic" species with identical morphology were now being defined on the basis of their differing karyotypes (the number and appearance of the chromosomes). Nabokov rejected the use of chromosomes for defining new species, perhaps as a matter of practicality: pinned butterfly specimens in museums only preserve the morphology, so it would be impossible to distinguish karyotype variants in the museum cabinet.

His autobiography, however, seems to belie this depiction of Nabokov as a rigid conservative. Nabokov spoke about "great upheavals... taking place in the development of systematics." The year that Nabokov started working in the Museum was also the year that Ernst Mayr, by then also an emigre to the United States, published his Systematics and the Origin of Species, the book which established the biological species concept, that species (at least for sexual macroorganisms like birds and insects) are defined by their potential for breeding to produce viable offspring. The new emerging school of taxonomy represented by Mayr were strong champions of geographic variation. Species were not immutable, platonic ideals. The variation represented by geographic "races" or subspecies was just as important as the original "type" of a species. Conceptually, this so-called Neo-Darwinian revolution was when darwinism finally became orthodoxy in taxonomy, the field that had inspired it, nearly a century after the publication of the Origin of Species.

Nabokov was aware of this theoretical revolution - how could he have ignored it? This was a tremendous change from the lepidoptery of his youth, which could well be said to be truly "butterfly collecting". As he observed:

"Since the middle of the [19th] century, Continental lepidopterology had been, on the whole, a simple and stable affair, smoothly run by the Germans. Its high priest, Dr. Staudinger, was also the head of the largest firm of insect dealers. Even now, half a century after his death, German lepidopterists have not quite managed to shake off the hypnotic spell occasioned by his authority. He was still alive when his school began to lose ground as a scientific force in the world. While he and his followers stuck to specific and generic names sanctioned by long usage and were content to classify butterflies by characters visible to the naked eye, English-speaking authors were introducing nomenclaturial changes as a result of a strict application of the law of priority and taxonomic changes based on the microscopic study of organs. The Germans did their best to ignore the new trends and continued to cherish the philately-like side of entomology. Their solicitude for the "average collector who should not be made to dissect" is comparable to the way nervous publishers of popular novels pamper the "average reader"--who should not be made to think.

"There was another more general change, which coincided with my ardent adolescent interest in butterflies and moths. The Victorian and Staudingerian kind of species, hermetic and homogeneous, with sundry (alpine, polar, insular, etc.) "varieties" affixed to it from the outside, as it were, like incidental appendages, was replaced by a new multiform and fluid kind of species, organically consisting of geographical races or subspecies. The evolutionary aspects of the case were thus brought out more clearly, by means of more flexible methods of classification, and further links between butterflies and the central problems of nature were provided by biological investigations."

(Speak, Memory: An Autobiography Revisited, pp.122-123)

So it wasn't that Nabokov was a conservative who didn't like change. He had already spanned the era between "hobbyist" and scientific entomology. He was already witness to a revolution (in science, and also in his homeland of Russia). There's a quip I've heard attributed to the physicist Max Planck, that science doesn't progress because people come to accept new theories on the strength of their evidence; it progresses because old scientists who believe the old theories die out. It's certainly an exaggeration, but we are equally certainly products of our education. Every generation in science has its own revolution of understanding, and maybe it's unfair to expect someone to accommodate a second one, just as he or she was getting comfortable with the first!

How to foster good science in Singapore?

2012-05-16T22:06:00.000+08:00

The institute in Germany where I'm studying was recently subject to an external review. Our staff and students got to mingle with the reviewers at a dinner in-house one evening, and while waiting in line at the buffet I started talking to someone who turned out to be a senior official in our research organization and also a practicing biologist.

I mentioned that I was from Singapore, and there was a look of recognition in his face. He asked me "ah, A-Star?" Like many others around the world who work in science, he knew about Singapore's big investment in research and technology, and of course also knew about Philip Yeo ("a very smart man"). But he also felt that the Singapore model had a few serious shortcomings, and after our conversation I thought it would be useful to share some of these observations, especially because they are held by someone who is himself a senior scientist and is responsible for administering a large scientific organization.

Singapore has been very successful at setting up the physical infrastructure for research, mobilizing plenty of money and political will to build new institutes and stock them with equipment and supplies. In terms of talent, which is the perennial Singaporean question, we've gone for a top-down approach: recruiting the "big names" in various fields, giving them very good salaries (the few scientists in the US whom I've talked about this before have all mentioned the attractive remuneration) and more importantly the funding to continue their projects in Singapore.

The official said that he didn't think this was the best way to build up a scientific community. What about the students? As he put it, if you're a senior scientist wanting to set up a lab in another institution, the first question you're going to ask is whether you're going to have good students (who of course do all the actual lab work). Unfortunately, Singapore seems to do a very good job of exporting its best students. They're sent overseas on fully-funded, prestigious scholarships to foreign institutions. In the case of A-Star's PhD scholarships, the recipients only make their way back to Singapore after about a decade of study abroad, and maybe even longer if they do a post-doctoral fellowship or two to gain additional experience. While they are overseas, they're not just learning but actively contributing to science. I think that most graduate students would agree that graduate school is not about learning at the feet of your professors, but is instead about finding one's own way in science, while being guided to independence. As a research student, you are actively making science while learning it.

My own experiences appear to bear this out. When I was studying in the US, it was (and is) common for undergrads to do active scientific research, usually mentored by graduate students or post-docs; this was something that was actively encouraged. When asked about undergraduate research opportunities, many professors would comment on how fortunate they themselves were to be in an institution where bright and motivated young people would come and ask to work with them. The professors are undoubtedly good at what they do, but they need good students to keep the research going at a high level, and they recognize this fact.

I explained to him that such scholarships are not limited to the sciences, but are also the most culturally prestigious means for recruitment to careers in public service. At that point I saw the general relevance of what he had said to this entire system of talent recruitment. It's not just about the money that's being spent on having these students shipped abroad and tutored far away from home. Prestige matters too. If the best students do not stay in the country, then it is difficult to develop local institutions to higher levels. Worse still, we are not building confidence in our own institutions.

The foregoing isn't meant to say that the research and graduate students in Singapore are not up to par. Several of my friends are doing science in Singapore, and they certainly have motivation and ability. The matter is whether, for the amount of resources we have poured into the project, we can build up a human infrastructure to match the physical infrastructure.

It's not about how many citations or high-impact papers we can garner. It's about whether we can build a self-sustaining research community that will renew itself by training new scientists. Instead of importing "big names" (the top-down model), let's find a better way to nurture the talent we already have (the bottom-up model).

Some other comments:

I myself am a participant in the (I hope, temporary) brain-drain, although I'm not on a state-funded scholarship. As I want to return home to work in Singapore in the future, I feel that I have to keep an eye on how science and research are developing there. I've also decided not to name the official that I talked to because I don't want it to seem like these are the official views of our organization, neither did I think at the time to ask him for his permission to share them publicly.

Also, the model for scientific training that I've described -- senior scientists leading labs training graduate students who also generate the scientific results and publications -- is causing serious problems in other developed countries, especially the US. Supply of newly-minted PhDs seriously outstrips demand, in terms of the number of new faculty positions opening up for them in academia. This is a well-recognized problem (see the careers pages of many recent issues of Nature and Science), and according to this perspective article in Science, the seeds for the current situation were sown in the 1940s with the recommendations of Vannevar Bush that led to the establishment of the National Science Foundation in the US. That's another unpleasant outcome that we have to avoid.

Plant collectors are endangered species

2012-04-30T16:49:00.000+08:00

The days of the botanical adventurer, a relic of the western Age of Discovery, may be over:

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.

Visiting the Hunterian Museum

2012-04-13T19:26:00.000+08:00

I have always been enthralled by dissection and the appearance of well-dissected specimens. It's a strange kind of art form: the structure is already there, formed by the hand of Nature, so the artist's job is not to create something new, but to reveal something hidden. In school I participated in biology competitions where we trained on dissecting earthworms, cockroaches, flowers, and the like, while in college I had a memorable experience cutting open a gravid dogfish with a friend.

But the enthusiastic hacking of amateurs and students is one thing, while the preparation of display specimens is another. The Hunterian Museum is one of the most well-known collections of its kind. It's owned by the Royal College of Surgeons of England, and was originally put together by John Hunter, the famed 18th century anatomist and surgeon, some of whose exploits have been described before on this blog. I recently got to visit the museum because I was in London, and despite it being a relatively small collection (two thirds of the original collection was lost by bombing during World War II), I spent more than 2 hours wandering around. Unfortunately photography is forbidden, so no photos this time.

Used for both teaching and research, it is notable for its bringing together of both human and non-human (including plants!) specimens in a systematic arrangement. Unlike most museums of the time, which arranged things in a taxonomic layout (according to classification), Hunter arranged his museum to demonstrate his ideas of comparative physiology and anatomy. For example: flowers, eggs, uteruses would be brought together in one case under the heading "organs of reproduction". What struck me was the range of non-human material that was present. I had read about this before, but actually seeing the collection led me to appreciate how deeply Hunter was trying to draw analogies between the different classes of life (before the advent of evolution theory), which is a project that biologists today are still working on.

There were lots of children with their parents, when I was visiting. One would think that a young child would be terrified of seeing recognizable pieces of people (some of the specimens were stained and looked quite lifelike), but I don't think most of them were too put off by it. Perhaps the sheer quantity of stuff to see distracted them from the particularly morbid examples. One case that did give many visitors some pause was the display of human fetuses at various stages of development. I heard one parent mutter "that can't be right...."

Halfway through my visit, the children trooped off to hear a presentation in period costume about 18th century surgeons, and I was left in near-silence again, with a few other people who were sitting on stools and making drawings. In the upper floor of the gallery are the pathological specimens, collected to demonstrate the different diseases and abnormalities that a practicing surgeon might encounter. Some of these show how "nasty, brutish, and short" life was like before antibiotics and modern medicine: skulls devastated by syphilis, spines bent over by tuberculosis. The smallpox exhibit was especially heartbreaking, because it contained half the face of a child victim of smallpox, to illustrate the scarring. It was injected with red dye to stain the arteries, but that also gave a rosy glow to the cheeks.

Another disconcerting thing is seeing specimens that come from named persons: a cancerous tumor from Miss Somebody, a diseased body-part from Lord Someplace. Hunter was a surgical innovator, but that also meant that many patients died anyway, and their body parts would end up in his collection.

Hunter's skill in anatomical preparation, and the care taken by conservators in the years since, have kept much of the collection in very good shape. I marveled especially at the dissections of invertebrates to demonstrate the nervous system: one of the most challenging things to display in a tiny animal. Sadly, the anatomist's art is in defiance of nature: to unveil the concealed, to prevent decay, and to simulate the appearance of life. Even if specimens are well conserved and do not decay, plenty of work is involved, and they are ever prone to destruction because most are highly flammable and fragile. One photograph on display from 1941 shows the aged retired curator Arthur Keith helping to salvage from the wreckage after the bombing, beside a bust of Richard Owen, the 19th century anatomist, poking out from the rubble. An anatomist's lifetime's work could be easily reduced to ashes within minutes, but on reflection, it is the knowledge gained that is most precious. The medical anatomists are fortunate in that their hard-won learning is valuable to society and is therefore carefully passed on. The comparative biology of other organisms, however, suffers from a lack of qualified taxonomists and specialists in many groups. Even today we need more people like John Hunter, who are driven to seek out the connections between the familiar and the unfamiliar, the immediately relevant and the merely philosophical.

(For those who are visiting London: The museum is free, and is open Tuesdays to Saturdays, 10 am to 5 pm. It is located beside Lincoln's Inn Fields; the nearest Tube stop is Holborn.)

Plankton Chronicles

2012-04-09T17:22:00.000+08:00

The word "plankton" literally means "wanderer", and these floating wanderers of the ocean have a strange and alien beauty that has fascinated generations of biologists.

The Plankton Chronicles project uses modern microscopy and videography to make this world accessible to the average armchair explorer. They've produced a series of videos highlighting different planktonic organisms, using a technique called dark field optics, where objects are made visible by the light that they scatter, appearing light against a dark background.

The project is a collaboration between the Tara Oceans Expedition and the Oceanographical Observatory at Villefranche-sur-Mer.

One of the episodes, on planktonic protists (of course!), is embedded below:

I came by the site by way of this TED Talk by Tierney Thys:

Out of proportion: Carbon infographic from the Guardian

2012-03-30T01:22:00.001+08:00

The Guardian newspaper has an infographic on the carbon footprint of countries around the world. It's a world map which distorts the size of different countries to represent relative population size, energy consumption, carbon emissions, and so on.

It's cool to see the familiar world map blobber and change as you click on the different buttons, but chilling to think about what it represents: how unequal is the human condition around the planet. It also shows very clearly how the affluent world hogs most of its resources and produces most of its pollution.

On most world maps you can't even see Singapore, but play around with this interactive graphic for a while and see when our little dot starts to pop.

Light and deep-sea organisms

2012-03-10T12:00:00.000+08:00

Did you know that...

... the US Navy funded research into bioluminescence because they were worried that glowing plankton would give away the position of their submarines?
... the "green-eyed fish" Chlorophthalmus converts the light it receives in its lens to green light by fluorescence because that's what its retina is most sensitive to?
... that mackerel and other shiny fish reflect light off their undersides to confuse predators looking up at them from below, and also manage to match the polarization of the reflected light?

Read more about these cool ways in which biology uses light in this magazine article in Science summarizing recent results that were presented at the SICB meeting in January.