The Biology Refugia

Are they embryos or not?

2012-01-01T04:00:00.000+08:00

Once again, news about fossils (I promise that I'm not turning this into a paleontology blog).

The Doushantuo Formation in China is one of the most important sites for pre-Cambrian microfossils. These date back to before the Cambrian Explosion of animal life in prehistoric seas, exactly where you'd want to go looking if you were interested in the origins of animal diversity. What's important about Doushantuo is that the fossils recovered are microscopic and preserve fine structural detail, the original cells having been replaced by phosphate minerals.

Many of the Doushantuo microfossils were interpreted as fossilized animal embryos encased within ornamented walls (see image below, via Ministry of Science and Technology, China). If so, they would represent some of the earliest evidence for metazoan (i.e. multicellular animal) life. It is a particularly appealing idea, because they would then pre-date the known adult animal fossils.

But as always, fossilized forms are notoriously difficult to interpret, especially globs of microscopic spheres. Some others have suggested that they could be giant bacteria, analogous to the modern Thiomargarita namibiensis, which achieves its great size by accumulating nitrate in a big vacuole in the cell, which it uses as a source of energy.

To investigate this hypothesis, one group of scientists decided to go with the approach of experimental taphonomy. Taphonomy is the science that studies the process of fossilization, so essentially what they did was to kill the giant bacteria Thiomargarita and also some sea urchin embryos, and then see what they looked like as they decayed.

Well, that was the plan, anyway. According to their paper (recently published in the Proceedings of the Royal Society, B):

Attempts to kill the bacteria in a consistent manner using strongly reducing conditions induced with beta-mercaptoethanol (BME) were ineffective. ... Consequently, we relied on a decay pathway from the natural taphonomic spectrum in the population.

I.e. "we couldn't kill the bugs, so we fished out the dead ones from the mud instead."

They found that dead Thiomargarita look nothing like the Doushantuo fossils: because of their internal vacuole, they collapse readily. And so it seems that the "giant bacterium" theory is quite unlikely.

But does that mean that they're embryos? Another research group (sharing at least one team member as the previous group), this time publishing in Science, claims that they aren't, based on the patterns of cell division that they found by peering into the fossils using X-ray tomographic microscopy. (Blog post on Scientific American)

Reassuringly, they found structures that they interpret to be eukaryotic cell nuclei within the compartments. It's worth quoting their "criteria for biogenicity" to appreciate the reasoning that goes on "under the hood":

The nucleus-like bodies fulfill relevant criteria for biogenicity: Their occurrence is consistent and repeated (12 of the 14 specimens have one such body in each cell); they are regularly positioned in the cells within any single individual (central to the cells in four of the specimens, peripherally in the others); they have a consistently globular shape; and the volumetric ratio between bodies and cells corresponds to that of nuclei and cells in eukaryotes (fig. S6 and table S1). Furthermore, one specimen (Fig. 2 and fig. S1, D to H) has two elongated and one dumbbell-shaped nucleus-like body, suggesting that they are in the process of division.

In an observational science, as opposed to an experimental science, like paleontology, the standard of proof (to borrow the legal term) is more akin to "preponderance of evidence" (used in civil cases) than "beyond a reasonable doubt" (used in criminal cases). This is not to criticize the validity of their work, but just a comment on the practical limits of knowledge.

But the pattern of cell division that they observed wasn't like metazoan embryos. Embryos undergo a period of "palintomic division", where the overall size of the cell mass doesn't change but is simply subdivided into more and more cells. At some point, however, morphogenesis takes over and higher-order structures such as epithelial sheets start to form. In these fossils, they found no such differentiation. The pattern they found was instead of further and further undifferentiated cell division, and in some cases protrusions containing lots of small cells. Perhaps these might be propagules waiting to be released into the environment, they hypothesize.

In the title of their paper, the researchers interpret the Doushantuo microfossils to be a kind of "protist". The term is used as a grab-bag for all eukaryotes that are not plants, animals, or fungi. That is to say, they think it's an eukaryote, but don't quite know what kind. More observations will probably be necessary, and perhaps we may never know what it is.

Yet they're still valuable, because you don't always need to be able to slap a name on something to learn interesting things about it. These microfossils still represent an interesting example of multicellularity. It may or may not be the complex multicellularity exhibited by animals and plants, but it still gives a glimpse into the morphological organization that can be achieved by "simpler" living organisms.

Sources

JA Cunningham et al. Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils. Proceedings of the Royal Society, B. Online before print, 7 Dec 2011. doi: 10.1098/rspb.2011.2064
T Huldtgren, JA Cunningham et al. Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists. Science 334 (6063): 1696-1699. 23 Dec 2011. doi: 10.1126/science.1209537

Fossil instrument plays "Flintstones" theme

2011-12-30T23:53:00.001+08:00

No, it's not a fossilized musical instrument (though a carved animal bone thought be some to be a Neaderthal flute was found in 1995 in Slovenia). This is a xylophone made from fossils, in this case fossilized corals called Hexagonaria (Paleobiology Database, Wikipedia). Artist Tom Kaufmann carved an instrument from this stone, and plays (appropriately enough) the "Flintstones" theme song on it in this video:

He has made other instruments out of stone, which he calls "lithophones". Read more about his work on the Mental Floss blog.

These fossil corals are known as Petoskey Stone in the state of Michigan in the USA, where they are the official "state stone". The corals get their name from the six-sided appearance of the walls separating the individual corallites, which can be seen in the close-up at the beginning of the video, as well as in this brochure (pdf) from the Michigan state government.

As far as musical instruments made from living (or formerly living) organisms go, it's at least not as terrifying as the possibly apocryphal "cat piano".

How the 'brinicle' was filmed

2011-12-28T22:02:00.000+08:00

If you haven't seen this video by now, you should watch it!

As sea ice freezes in the Antarctic, it leaves behind a concentrated brine which is trapped in channels within the ice. When this cold, dense brine, which is colder than the freezing point of water, seeps to the underside of the ice layer and sinks into the water beneath, it forms a sheath of frozen water around it, which eventually extends to the sea floor as a 'brinicle'.

For the BBC Nature series Frozen Planet, these brinicles were filmed for the very first time. The film's producer, Kathryn Jeffs, said that when she was preparing to film them, she couldn't find any information about them, even on the Internet.

Now, this video is among the most popular nature video clips online.

Jeff describes the technically demanding and physically difficult process of filming under thick ice in 2ºC water. As she put it, they were tremendously satisfied when they

... knew [they] had captured, for the first time ever, the creation of a rather sinister wonder of nature.

Lynn Margulis - an appreciation

2011-11-26T01:32:00.001+08:00

Lynn Margulis passed away recently at the age of 73 (NY Times obituary). She was responsible for one of the great ideas of modern biology -- the endosymbiotic theory for the origin of organelles. This is the idea that chloroplasts and mitochondria of eukaryotic cells originated as independent prokaryotes that became associated symbiotically with host cells, and eventually became indispensable organelles. The whole process she called "symbiogenesis". Siva blogged about this here two days ago, and suggested that I share something to.

The story of the theory itself is also quite well known. Margulis put forward the hypothesis in a paper titled "On the origin of mitosing cells" (Journal of Theoretical Biology 14: 225, under her married name L. Sagan - PubMed, ScienceDirect) in 1967, but before it was accepted for publication there, it had been rejected 15 times by other journals. It was initially controversial--to think that an essential part of our own cells are actually bacteria in disguise!--but today it is textbook knowledge. Much like the theory of plate tectonics, this is one of the great Cinderella stories of modern science.

I was fortunate enough to hear Margulis speak a few years ago when I was in college. I don't remember the details now, but I do remember a few things she said. She recalled that the last time she was at Harvard, it was at a seminar where Ernst Mayr (one of the pioneers of the Neo-Darwinian Synthesis) was in the audience, sitting right there; she pointed at the seat in front of my friend Noor and me and we got a little thrill from it. "Although he was almost a hundred years old, he was still the sharpest mind in the room!"

(She wrote a reminiscence of Mayr when he passed away in 2005, which gives some flavor of their personalities. Mayr: "You don't have to tell me what 'symbiosis' is! I studied symbiosis with Paul Buchner in Griefswald [in the 1920s]." Buchner later wrote one of the classic books on symbiosis, Endosymbiose der Tier mit pflanzlichen Mikroorganismen.)

She also showed a video of protists from termite guts, some of which have symbiotic bacteria living on their surface, which act more or less as surrogate flagella. One could tell that she was really captivated by the beauty of these organisms, and I heard later from someone that she often showed this video at her talks.

Margulis's 1967 paper is best known for its hypotheses about chloroplasts and mitochondria, which have been validated by lines of evidence, such as DNA sequencing, that were not available to her at the time. Her remaining hypothesis was that eukaryotic flagella evolved from symbiotic spirochaetes, which are corkscrew-shaped bacteria that swim helically. This idea hasn't done so well, and hasn't been supported by evidence in the way which the chloroplast and mitochondrial hypotheses have, but as her fascination with the video shows, she was still thinking about it. One of her last papers, published in 2010, was on the microscopical structure of one kind of these bacteria on a termite-gut protozoan.

On rereading her 1967 paper, a few things stood out to me. She managed to synthesize a tremendous amount of information (the paper is 49 pages long) from very different fields, including microbiology, palaeontology, geology, cytology, and evolution.

This was where she first put forward many of the concepts and themes which she would continue to think about and work on for long afterwards. For example, the scenario for eukaryote evolution that appears as a figure is re-presented in modified form in her popular book, Five Kingdoms.

The book, which she coauthored with Karlene Schwartz, was one of my favorite books as a student. The latest edition is from 1998, but it's still a good read, giving a brief overview of all the major phyla of living organisms in the classical five kingdoms: Prokaryotes, Protoctists (i.e. protists), Plants, Fungi, and Animals. It was my first introduction to the weird and wonderful world of protist and microbe diversity, which otherwise get such short shrift in introductory biology. It also shows how effective she was as an encyclopedic collator and system-builder.

In her thoroughness she also delved into the older literature. She had an interest in the history of biology, and what might be called her intellectual predecessors. She was involved in a recent project to translate a 1924 Russian book titled Symbiogenesis: A New Principle of Evolution by Boris Kozo-Polyansky. She did not shy from acknowledging these "forbears" and other early insights and ideas that were "before their time".

I think that she represented a very "classical" sort of biology, informed by visual thinking and reasoning by analogy. Looking at older books of zoology, botany, or cytology, one finds a similar frame of mind and emphasis on pattern-recognition. Modern biology is definitely still about pattern-recognition, but much of it is now impossible to "eyeball", such as searching for gene homology.

Unfortunately, reasoning by analogy can sometimes lead us down the wrong track, and an over-enthusiasm for it seems to have been responsible for a controversy that involved her in 2009. As a member of the National Academy of Science in the USA, she sponsored a paper for publication in its Proceedings, which hypothesized that "caterpillars evolved from onychophorans [velvet worms] by hybridogenesis" with insects. The paper never made it into print, but attracted a storm of protest and the imputation that she misused the submission process to push through a paper which would never have been published elsewhere.

That episode didn't help her reputation for "eccentricity", which is a word which seems to crop up in describing her, alongside "maverick" or "rebel". Nonetheless, her place in biology is secured, and I think it's important to acknowledge why. She gave us a whole new way of thinking about evolution, spurred scientific interest in endosymbiosis and early evolution, brought protists and other formerly obscure organisms to the attention of scientists and public, and defended the importance of symbiosis to the evolutionary process.

In doing so, Lynn Margulis gave us a glimpse into the biological world as it could have been at its origin, and also into the present, where we still make regular use of the concepts that she pioneered. RIP.

Lynn Margulis, RIP

2011-11-24T09:13:00.001+08:00

In my first year at university, my cell biology text book stopped me right in my tracks. It was my first encounter with endosymbiosis.

See UCMP's Understanding Evolution

More than twenty years later, advances in several fields have seen the protists finally break out of their artificial confinement and endosymbiosis is now firmly at the cornerstone of the relationships between major eukaryotic groups. A work in progress (which heightens attention), it's providing a fascinating insight into the evolutionary process.

That endosymbiosis was in my textbook in the first place, was due to the efforts of Lynn Margulis. While we associate her with the "Five Kingdoms", it was endosymbiosis which stunned me, a most enjoyable and lasting phenomenon.

Last night I heard (via the Twitterverse reporting her son's facebook post) that Lynn Margulis had passed on peacefully - and by this morning, UMass Amherst had issued a news release: "Lynn Margulis, Renowned Evolutionary Biologist and Author at UMass Amherst, Dead at 73."

Photo courtesy of U Mass Amherst

Quite beautifully, grad student Leila Battison pens this heartfelt note on "Life in pen and ink" - "Lynn Margulis: An Unforgettable Woman.

Should conservationists give up?

2011-11-17T03:38:00.001+08:00

According to the latest IUCN Red List, the Western Black Rhinoceros (Diceros bicornis longipes), a subspecies of the African Black Rhinoceros, is now extinct in the wild (IUCN website, NPR News). Closer to home, the Javan Rhinoceros is "making its last stand", being extinct outside of the island of Java. Although captive populations exist in zoos around the world, it is unlikely that they'll ever be reintroduced into the wild in a viable way.

This has made some conservationists wonder: is it even worth the trouble to try and save all these species? They're not saying that we should give up entirely, but that we should set up a kind of conservation triage. "Triage" is a term which might be familiar to viewers of medical dramas on TV. It refers to sorting incoming patients according to their need for treatment and their possibility of survival. If resources are limited, care has to be parceled out, and we don't want to spend everything trying to save the ultimately unsavable. In this BBC News viewpoints article, we hear from the two sides of the triage debate.

I think that when the issue of conservation is framed in these terms, it really accentuates the different approaches to conservation, which in turn say something about why people want to save wildlife in the first place. Some people want to save landscapes in a holistic way, while others champion particular charismatic species.

If we had to choose which species to save, to "bring on the ark", so to speak, which ones would you bring? The most charismatic and aesthetically beautiful species may appeal to our human senses, but they need not be the keystone species that really hold the ecosystem together. In most cases, we don't even know enough about the ecology of a particular landscape to make that call.

In my opinion, ex situ conservation offers less return on investment than putting money into establishing reserves or policing existing ones. The Western Black Rhino did not go extinct because there weren't enough people who wanted to see it in zoos, but because of poaching in the wild. We can pull species out from the environment and keep them alive for a while, or maybe even a long time, but can we possibly hope to reassemble that ecosystem after everything has been wiped clean?

Take the unfortunate case of the land snail Powelliphanta augusta from New Zealand. It was discovered only in 1996 on a mountain ridge that was about to be cleared to make way for an open cast coal mine, and so 4000 individuals were caught and painstakingly relocated, 1600 being kept in refrigerated containers in a government conservation facility. What happened next is one of those things that really make you want to laugh even though it's sad, because of the sheer silliness of it:

Unfortunately, a fault in a sensor plunged the temperature in one of the units to zero, and 800 of the snails — a sizeable fraction of the entire species — froze to death. The fault was not noticed immediately because it happened over a public holiday.

The editorial in Nature that cites this episode calls for more "political will" to back conservation, but I think that this will has to be directed carefully.

I can't help but be reminded of tortoises when I think about captive breeding programs. The ethologist Konrad Lorenz, in one of his popular books, wrote that he wouldn't recommend turtles or tortoises as pets to the novice pet-keeper. Although they can survive for a long time under indifferent care, they're not really thriving. They just "slowly dying".

Things are not going to get better for captive-bred species. There probably won't be a happily-ever-after where they can be released to run free once again in their native habitats, because those habitats are on their way to being wiped out completely. Perhaps it's time to put our efforts into saving habitats instead of collecting tortoises.

Living fossil stromatolites found in Northern Ireland

2011-10-19T04:45:00.000+08:00

Stromatolites don't look like very much when you actually see them, but they are among the oldest evidence for life on Earth. They are interpreted as layers of sediment aggregated by mats of microbial organisms, which lived in shallow waters receiving lots of sunlight. Although traces of the microorganisms themselves are very rarely preserved, the characteristic cushion-shaped mats remain. Such structures are called "microbialites".

They appear in the fossil record in the late Archaean, about 3.5 billion years ago, and in the Proterozoic, from 2.5 billion years ago, they are believed to have been mostly made by cyanobacteria. The University of California Museum of Paleontology has a great introduction to cyanobacterial fossils and Proterozoic life on its history of life website.

Stromatolites are rare today, and one of the main hypotheses for this is that herbivore grazers would readily attack such a concentrated source of food. The best known examples of modern stromatolites are those in Shark Bay, Western Australia, where they live in highly saline water, which is not conducive to such herbivore grazers.

So it's a surprise to hear that a small stromatolite colony has been found among the rocks of the famous Giant's Causeway in Northern Ireland. The colony is in brackish water that is exposed to waves and potential grazers. It was found by environmental scientists from the University of Ulster who were out looking for other some geological features.

The basaltic columns of the Giant's Causeway, where the stromatolite was found.

The Causeway itself is an extraordinary geological structure, composed of interlocking "pillars" of basalt formed by volcanic activity. These pillars are more or less hexagonal in cross-section, making it look like a set of giant stepping stones.

A little more browsing on Wikipedia throws up a list of other modern stromatolites around the world, some of which are in fresh water. It's amazing how quickly the news report on the new stromatolite find was picked up and incorporated into Wikipedia.

I'm quite a fan of stromatolites. I had the opportunity to see some fossilized stromatolites in the field when my palaeontology class in college went out to upstate New York, to the fossil-rich area around Utica. Unfortunately most fossils look much better in the full glare of the sun (and the excitement of the moment!) than when they are photographed:

Stromatolite fossils in the ground. There's really something there, I swear!

The scientist who found them suggested that they could be much more common than we think they are. It would be really intriguing to see them live in the field, and even more informative to compare the cyanobacteria from different stromatolite colonies around the world: are they always the same kind of bacteria? What else is in these mats? How fast do they grow? What triggers the formation of these microbial mats? How curious, that slimy mats of microbes are the ones to tell us about the early origins of life on our planet!

The world's largest virus

2011-10-16T06:31:00.000+08:00

Back in January I blogged about how the physical constraint of capsid size may be forcing some viruses to squeeze their genomes into such a compact state that their genes overlap. Now we visit the other end of the scale to the largest virus yet discovered, appropriately called Megavirus chilensis, found in ocean waters off the coast of Chile.

As one of the paper's coauthors told BBC News, "You don't need an electron microscope to see it; you can see it with an ordinary light microscope." Each virus particle is about 680 nm across, or just under a micrometer, making it just barely visible as specks by light microscopy. They're structurally interesting, bearing a covering of fibers ("hair") all over the surface, and a five-pronged star-shaped structure on one vertex that the authors have called a "stargate", which the virus uses to release its nuclear material into the host cytoplasm.

They live in the cytoplasm of amoeboid protists called Acanthamoeba, which is a relatively widespread genus of amoeba. Previous studies on protozoan symbionts have revealed numerous types of intracellular bacteria in various Acanthamoeba species. The relatives of Megavirus are also hosted by Acanthamoeba, and are called Mimiviruses. The authors propose a family called Megaviridae that includes Megavirus, Mimivirus, and their relatives.

What more, it isn't just the largest known virus in terms of physical size. The information that it carries around in its genome is also large, weighing in at 1 259 197 base pairs. This is actually bigger than 8.4% of known bacterial genomes (according to the figures available on the NCBI website).

As an exercise I looked up information on bacterial and viral genome sizes from the NCBI Genome website. Go to "browse by organism groups" and you can download tables of genome information there. Fellow microbiologist blogger Guus Roeselers in the Netherlands points out that it is "remarkably easy to make some highly illustrative graphs."

I plotted a histogram of bacterial genome sizes (below) and as you can see, Megavirus has a genome size that would put some bacteria to shame (red triangle)!

Histogram of bacterial genome sizes, with red triangle marking the genome size of Megavirus chilensis.

What about other viruses? The distribution of viral genome sizes is more complicated than the bacterial case. There's a sharp peak at less than 50 kilobases (1 kilobase = 1000 nucleotides); the mean genome size is just over 31 kb. (NB: I calculated this based on total genome size, adding together all the segments for viruses with multiple nucleic acid segments). The previous record holder for largest viral genome is a mimivirus, also hosted by an acanthamoeba, that is 77 kb smaller.

Histogram of viral genome sizes, with red triangle marking genome size of Megavirus chilensis.

The very smallest genomes belong to the viral satellites. These are nucleic acid particles that can only replicate when the host cell is co-infected with a "helper virus". Entering the world of viruses is like walking into the verse by Jonathan Swift:

"So nat'ralists observe, a flea
Hath smaller fleas that on him prey,
And these have smaller fleas that bite 'em,
And so proceed ad infinitum."

At some point the boundary between "virus" and "selfish genetic element" blurs, and indeed some have even speculated that viruses are themselves selfish genes that have literally gone wild. (Digression: We know that some cancerous tumors can "break free" in such a manner too.)

Returning to Megavirus, this discussion has some relevance to the question of its origins: where do Megavirus and the other Megaviridae come from? When the scientists looked at the genome of Megavirus and mimiviruses, they found many genes that haven't been found in viruses before, but only in cellular organisms.

Several of these genes are involved protein translation. When we learn about viruses, we're usually told that they rely solely on the host translational machinery to produce their proteins, but Megavirus here may not be as dependent as other viruses. Megavirus has genes coding for aminoacyl-tRNA synthetases, which make the complexes of tRNA and amino acid that are brought together to string a new polypeptide chain during translation. Genes in this family have previously been found in mimiviruses. Megavirus not only has relatives to some of these genes, but also other genes in this family that have not been found in mimiviruses.

Could they have been acquired by horizontal gene transfer? Perhaps. But because the genes have relatives in mimiviruses, they were likely to have been present in the common ancestor of mimiviruses and Megavirus.

Megavirus also has DNA repair genes related to those in mimiviruses. These genes are unusually abundant in both these viruses, and Megavirus seems to be even more resistant to DNA damage by UV radiation than mimivirus!

The presence of yet more protein-translation genes in Megavirus, and the nature of the genes that it shares with other related large viruses leads the authors of this study to favor one hypothesis of giant virus origins: reduction from a cellular ancestor. They believe that it's more likely in this case that a cell somehow lost enough of its genome while turning viral, than it is that a virus accreted lots of cellular genes from its hosts or other sources to result in an enlarged genome.

The origins of viruses in general will still be debated for some time to come. But it is likely that any discussion will now have to factor in the example of this "dwarf among cells, but giant among viruses!"

Source
Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proceedings of the National Academy of Sciences USA, published online before print, 10 Oct 2011, doi: 10.1073/pnas.1110889108.

Riding ants all the way

2011-10-14T04:26:00.002+08:00

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.

...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:

“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.

I can only hope to be half as energetic and productive when I am 82!

Björk and the Zombie Snails

2011-10-12T01:59:00.000+08:00

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.

Snail infected with Leucochloridium paradoxum in its eyestalk.

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:

Do plants quiver in fear?

2011-10-11T01:44:00.001+08:00

Many trees have leaves that quiver in the wind. This property lends its name to the quaking aspen (below left), whose scientific name Populus tremuloides literally means "trembling poplar". In tropical Asia, the banyan tree (below right) is a commonly-encountered species with quivering leaves. They tend to have fairly broad, thin leaves and narrow, elongated petioles.

Quaking aspen (Populus tremuloides, left) and banyan (Ficus religiosa, right)

But what exactly is quivering good for? Biophysicists have looked at the way that leaves deform in strong winds, and some have hypothesized that this helps them avoid mechanical damage. On the other hand, it may simply be an unintended consequence of adaptation for other reasons, such as having an appropriate shape and orientation for the efficient capture of sunlight.

A new paper recently available online has suggested that quivering may be a means of avoiding herbivores. The author cites other examples of plant "behavior", such as the Sensitive Plant Mimosa pudica, whose leaflets fold up when touched, startling herbivores while simultaneously exposing the thorns on its twigs. Could quivering serve a similar function?

The author suggests that shaking leaves not only make it harder for small herbivores like insects to land on leaves, they may also cause pests and parasite propagules to be literally shaken off. He also hypothesizes that cryptic herbivores, like leaf and stick insects, would stand out from a background of quivering leaves and be made more vulnerable to their own predators.

At the moment this stands as only an interesting hypothesis. Most biologists would acknowledge that "theory is cheap, data is expensive". It's fun to think about, but it would be lovely if someone could do some experimental work on it. As a topic in sensory ecology, it reminds me of the hypothesis on why autumn leaves turn red, which was covered in this blog a few years ago. Yet I cannot help thinking that maybe this is reading too much adaptationist significance into what may turn out to be a "spandrel", a trait which is merely a by-product of other traits (a term coined by Steve Gould).

In the meanwhile, we can look at the leaves that flutter in the breeze and wonder: are they nervously trying to shake off their enemies?

Source:

Kazuo Yamazaki (2011) Gone with the wind: Trembling leaves may deter herbivory. Biological Journal of the Linnean Society, published online before print 3 Oct 2011, doi:10.1111/j.1095-8312.2011.01776.x

Slime is going places

2011-10-08T19:01:00.000+08:00

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 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.

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!

World's largest shark sanctuary around Marshall Islands

2011-10-07T06:45:00.000+08:00

The Marshall Islands (Wikipedia) are a remote country in the middle of the South Pacific, comprising a collection of islands and atolls and having a population of less than seventy thousand people. It's clear from the map below that its territory is mostly ocean.

View Larger Map

That's what makes the recent announcement all the more significant. All 1,990,530 sq. km of its territorial waters will now become the world's largest shark sanctuary. This comes after the country enacted a moratorium on the shark trade in March of this year. According to the Pew Environment Group:

Key provisions of the comprehensive Marshall Islands' law include:

A complete prohibition on the commercial fishing of sharks as well as the sale of any sharks or shark products. Its zero retention stipulation requires that any shark caught accidentally by fishing vessels must be set free.
Large monetary fines, anywhere between US$25,000 to US$200,000, for anyone who is found to be fishing sharks or in possession of shark fins. In addition, violators would be fined the market value of the product in their possession.
A ban on the use of wire leaders, a longline fishing gear which is among the most lethal to sharks.
A monitoring and enforcement provision which requires all fishing vessels to land their catch at one of the country's ports and bans at sea transfers.

Read more at the Pew Environment website. Via Science and National Geographic.

In related news from last month, Yao Ming, the famous Chinese basketball star, endorsed a renewed campaign against shark's fin soup in China (BBC News). This campaign is run by WildAid, an environmental NGO (press release). He's been associated with WildAid for at least the past five years (NY Times). As China becomes more affluent, demand for shark's fin is rising, but this raised awareness will hopefully help to counteract that.

Poster of Yao Ming by WildAid. From Bush Warriors blog

An indication of how things could be going is in Hong Kong, where recent surveys have shown that attitudes towards serving and consuming shark's fin are changing. The Malaysian newspaper The Star has recently published a good article on the shark trade, including perspectives from those who are in the shark-processing industry.

Afterword on "arsenic-life" affair

2011-10-06T00:48:00.000+08:00

Popular Science magazine has recently published a profile by Tom Clynes on the scientist in the middle of the "arsenic life" controversy, Felisa Wolfe-Simon (see previous Biology Refugia post). This comes after the Science finally published her paper in its 3 June 2011 print issue, along with a selection of responses from her critics (see the editor's note for links).

The magazine feature is sympathetic to her, and notes how much of the initial criticism started by criticizing the science then moved into questioning the scientists' motivations. Many accusations were made at the time, including that they were motivated by fame as a result doing "bad science". But Science didn't publish her paper without peer-review. In fact, additional evidence was gathered as a result of peer review. Were the results inadequate for the claims which were made in the media ("new form of life", "proof that extraterrestrial life is possible", etc.)? Yes, certainly.

My opinion is that this was a "perfect storm" caused by the confluence of mass media and science. Without making any assumptions about anyone's motivations, Wolfe-Simon's team or their critics, we can say that (i) the hyped-up press conference organized by NASA was a mistake, and the oversimplified media kit only led to a proliferation of misinformed headlines, (ii) the quick criticisms by scientists posted to their blogs and websites appeared much faster than any research team could possibly respond to carefully, (iii) the media attention on Wolfe-Simon made it difficult to respond to technical criticisms and also increased their defensive posture (reading the Pop Sci article, I'm struck by how overwhelming it must have been for her) – simply finding the time to do it would have been difficult. I quote Clynes's article:

I find it hard not to feel sympathy for her. In a matter of weeks she was catapulted to fame, then singled out and assaulted with professional and personal criticism, some of which resulted from missteps beyond her control. Wolfe-Simon is an early-career researcher in a field dominated by older men. Few scientists, no matter how established, would have the skills to navigate the situation that she found herself in. What made the level of criticism so extraordinary is that the paper, in itself, is not so flawed that it should not have been published. The argument was compelling, the conclusions were measured, the data was thorough, and the paper made it through the same peer-review process as other articles in Science.

Some who initially blasted Wolfe-Simon have since changed their mind. Blogger Alan Townsend, who directs the environmental studies program at the University of Colorado, says he was guilty of rash judgment, and that his preliminary opinions—expressed in writing and conversations with his colleagues—contributed to a response from the scientific community that was “often unprofessional, and at times became downright shameful.” He says, “Absent major ethical violations, no junior scientist full of passion for an idea deserves crucifixion for a professional failure or two. If a paper is flawed, it should be dismissed. The scientist should not.”

Learning to deal with the media is not typically part of a scientist's education. After all, most could only wish they were so lucky. If the need should arise at all, it's probably handled by PR departments of their institutions or employers, or from the agencies that fund them, like NASA in this case. Perhaps it's time for scientists to come together and figure out what a code of conduct for publicizing their work should be like. For example, is it a conflict of interest to write a newspaper column that trumpets your own work while raising criticism of your competitors, especially if this is unpublished research? How far should we go in "jazzing up" the science in order to sell it to the public? Some degree of spin and oversimplification is unavoidable, but a technical audience would know where to look when reading a scientific paper to judge for themselves whether a specific claim is justifiable (typically buried somewhere in the Materials and Methods). Should we always be cautious and measured in our pronouncements? What if the issue is something politically-charged like climate change, where climate change "deniers" seize upon caution and use it as supposed evidence of falsehood? Difficult questions for difficult times, and scientists should take the lead in trying to figure them out.

Planet Earths' debt ceiling

2011-10-01T23:18:00.000+08:00

You may have not noticed it amid all the news on the economy, but on Tuesday we've gone into ecological debt for the year. 27 September was this year's Earth Overshoot Day (via Discover), the day when human consumption and waste emission for the year has exceeded the Earth's annual productivity and ability to absorb waste. The organization responsible for this announcement is the NGO Global Footprint Network, which seeks to raise awareness of environmental sustainability. They've issued a media packet explaining the concept here (pdf). The idea was originally mooted by the UK-based new economics foundation (they do their name in lowercase) in the 1980s as Ecological Debt Day.

From Global Footprint Network website

It sounds like a straightforward calculation of income minus expenditure, but the reality of course is quite complicated. Most of the parameters, such as crop productivity and human greenhouse gas emissions, have to be estimated, so the date is not an exact one. Despite the uncertainties, the calculated date is actually be on the more generous (to humans) end of the scale.

What's scarier is that the date has been moving forward every year: from sometime in early November in 2001, to late September now, about 3 days a year. Even scarier, this ignores the cumulative effect of previous times when we've gone into debt. This crisis mirrors the financial one: in some heavily indebted countries, politicians are happy to report when they've simply slowed down the rate of debt increase.

This is a good way of getting people's attention, because of all the headlines that the poor economy has been grabbing lately. Even non-economists, like myself, have become acquainted with concepts like debt ceilings, defaults, and bailouts (though what a "tranche" is still remains opaque to me). Environmentalists and sustainability scientists are also working on figuring out how to put an economic price on ecosystems and the environment, to make the importance of preserving the environment more "real" to those who think in dollars and cents, such as policymakers and industry. Examples include factoring in the cost of ecosystem services into environmental impact assessments, or selling carbon credits, or swapping habitat protection for debt forgiveness. All of these schemes have their critics, but I like to think of them as experiments in progress, as people try to figure out what's a workable way to account for the environmental impact of our economic decisions.

Frogs can "drink" water from air

2011-09-29T02:29:00.000+08:00

Thirsty on a hot day? Most of us would reach for a glass of water to gulp down. But what if you could drink through your skin? And what if there isn't any water lying around because it's the dry season in the North Australian tropical savannah?

The green tree frog Litoria caerulea has figured out a clever way to virtually squeeze water out of thin air. Researchers from Australia's Charles Darwin University led by Christopher Tracy were intrigued by how frogs could still remain active even on cool nights, when their body temperatures (being cold-blooded animals, or poikilotherms) could plummet to as low as 12.5ºC. At those temperatures they are sluggish and so are unlikely to be hunting for food. Instead, the scientists thought they might be seeking out water instead.

Pockets of warm air remain in places like tree trunk hollows. Cool objects placed in warm air will tend to condense the water vapour that remains in the air, which is precisely why glasses of cold drinks "sweat" on the outside. They placed some of these chilled frogs into hollows where they also measured the temperature and humidity. Just to be sure, they also used artificial hollows, essentially chambers filled with humidified air.

By weighing the frogs before and after, they found a small (on the order of several tenths or hundredths of a gram) but perceptible gain in mass, which was on average about half a percent of the frog's mass. It doesn't sound like much, but a cup of water is about a quarter of a percent of my total body mass. Droplets of condensed water could also be observed on the frogs after some time.

For more information (and pictures of the frogs), have a look at the press release that went with the paper.

Source

CR Tracy, N Laurence, KA Christian. 2011. Condensation onto the skin as a means for water gain by tree frogs in tropical Australia. The American Naturalist 178 (4): 553-558.

Great TED Talks for biologists!

2011-09-28T20:05:00.000+08:00

Tim Handorf from the website Bestcollegesonline.com has compiled a list of "20 Unbelievable TED Talks for Biology Majors". These are very much worth watching! Among the highlights: Bonnie Bassler on how bacteria "talk" to each other, and John Kasaona on how poachers can become caretakers of wildlife.

The TED Talks are the cornerstone of the TED organization, a non-profit whose name stands for "Technology, Entertainment, and Design". They bring together people who have, as they put it, "Ideas Worth Spreading" and put their talks online. These ideas range from social causes to science and technology.

They're definitely good to watch and attention-grabbing, as you might expect from hearing people who're talking about what they are most passionate about.

One of my favourite videos which isn't on the list is David Gallo's show-and-tell of "Underwater Astonishments", ranging from deep-sea bioluminescent patterns (Edith Widder, who took the these videos, has a talk of her own) to the clever and changeable world of cephalopods (squid and octopods):

The TED concept has also spread to different countries and cities with the TEDx series, which are TED events organized by independent organizations. In Singapore there's TEDxSingapore, TEDxNTU, and TEDxNUS. The Biology Refugia's own Sivasothi gave a talk about protecting biodiversity in Singapore for TEDxNUS:

In another video, graduate student Ang Yuchen explains his research on insect sexual selection:

Plenty more videos on all manner of subjects are available on the TED website. So instead of listening to yet another music video or watching cute kittens play with string on YouTube, why not check some of them out instead? You'll definitely learn something new!

How the bean got its twist

2011-09-27T06:19:00.005+08:00

Legumes are among the most diverse and successful families of plants in the world. In the Neotropical rainforests, the dominant tree species are mostly legumes (unlike in Southeast Asia, where dipterocarps predominate).

Their defining feature are their eponymous fruits, which appear to have a myriad ways of breaking up to release the seeds within. Some drop to the ground and shatter, like the tubular pods of Cassia:

Broken Cassia fistula pod exposing seeds

... while others twist and contort as they dry out to present seeds to dispersers, like Acacia:

Dried up and twisted Acacia auriculiformis seed pods

Legumes are certainly not the only plants with structures that change their shapes as they desiccate. They're not the only organisms to do so, either (think of mushrooms with caps that curl upwards as they mature to release their spores). However, their ubiquity and convenient size makes them a good subject for study and experimentation.

A team of physicists and mathematicians from Israel have recently figured out the rules behind the seed pod's twist, using a legume Bauhinia variegata as the model (paper in Science behind paywall). The basic idea is that the pod wall is made of an anisotropic material, that is, its material properties are not uniform but depend on the direction that it's being manipulated in. In this case, the anisotropy results from the orientation of fibres in the wall. Expansion or shrinkage tend to happen transversely to the aligned fibres. It's also a composite material, being made from at least two layers of wall sandwiched together. These two layers, however, have their fibres aligned in different orientations. As a result, when they dry out, they want to shrink in different directions. This conflict results in a deformation of the wall that produces a helical pattern.

This understanding is not new. It's at least a hundred years old, as pointed out in the commentary article that went along with this new paper. One of the early papers cited there has been digitized by the Biodiversity Heritage Library, a very useful scholarly resource that I've used time and again to find old or obscure articles not otherwise available to the public. Unfortunately, it's written in German, so some effort was required to read it.

That old paper described a very simple experiment. Strips of paper were cut out, with the long axis of the strip either parallel, or perpendicular to the grain of the paper (its anisotropy). Wetting the paper on one side, by floating it on water, causes a curling that is directed perpendicular to the grain:

"Piece of letter-paper laid on top of water, to show its uneven expansion through imbibition. The lines on the rectangular surfaces give the direction of the original grain of the paper."

"Fig. 2. a and b are two pairs of rectangles of letter-paper, that are glued together wet. Alignment asymmetrical. The bold lines show, consistently in the later figures, the grain-lines that are closest to the observer. c such a pair twisted after drying. Fig. 3. a Two glued-together sheets of paper with symmetrical alignment. b The sheet contorted after drying."

He then went on to glue together two such strips of paper, with their grains aligned in different directions. The glue was wet, and when it dried out, the resulting strips were twisted in helical or more complicated shapes (above).

The latest research takes this much further, with an array of analytical tools. They stretched two latex sheets in perpendicular directions, and then glued them together while stretched. As a result, there is "residual stress" in the sheet.

Note that unlike the old experiments with the paper strips, these latex sheets are consistently at an angle of 90º to each other. What they varied, then, was the direction in which they cut strips from this double-sheet. They found that by varying just two parameters: the angle between the long-axis of the strip and the stress directions of the latex, and the relative width of the strip, they could reproduce a whole array of shapes (we might call this a "morphospace") that resemble what we see in nature. Additionally, by using a mathematical theory of incompatible elasticity, they were able to predict the appearances of the latex strips using just these two parameters.

These shapes fall into two major categories: "cylindrical helices" and "twisted helices". The former are like tightly-wound party streamers; they seem like they can be sewn back up to form a cylinder. The latter have a straight centre-line. This is best explained by the diagram below: "helix A" is a cylindrical helix, while "B" is a twisted helix. (The other headings relate to the original context of this image, a paper on chirality in molecular bilayers, which suggests the commonality of physical principles throughout nature. I found it while looking in Google for suitable images of ribbons.)

This is a remarkable finding that suggests a unity of cause underlying a big slice of the morphological richness we see in the natural world. It's also something that humans may be able to exploit, to develop materials that can adopt specific shapes under particular circumstances.

Biomechanics seems to promise that the dazzling multitude of form in biology can eventually be brought to our human understanding, a promise that goes back at least as far as the "first biophysicist", D'Arcy Thompson. While it reminds us that biology is subservient to the rule of physics, the ingenuity of biological solutions to physical problems never ceases to amaze me.

Sources

S Armon, E Efrati, R Kupferman, E Sharon (2011) Geometry and mechanics in the opening of chiral seed pods. Science 333 (23 Sep 2011): 1726-1730.
Y Forterre, J Dumais (2011) Commentary: Generating helices in nature. Science 333 (23 Sep 2011): 1715-1716.
C Steinbrinck (1906) Über Schrumpfungs- und Kohäsionsmechanismen von Pflanzen [On the shrinkage and cohesion mechanisms of plants]. Biologisches Centralblatt 26 (20): 657-677.

Plant collecting and ex-situ conservation

2011-09-25T15:19:00.000+08:00

Earlier this month I blogged about how beautiful wild orchids are under threat from indiscriminate plant collecting to satisfy the itch of orchid-fanciers to own the rarest and most delicate species in their gardens.

However, plant collecting does not always have a sad ending. The Victorian plant collectors who harvested rhododendrons and orchids in obscene quantity from the Himalayan uplands also ventured to other countries. In Japan, they came after the country ended its isolation from the West in 1854, and collected many species which found their way into British gardens and parks. Now, these same species are endangered in their native habitat, but relatively common in cultivation.

Preserving an endangered species outside its native environment is called ex-situ conservation. It's not ideal: they're largely removed from their natural interactions, the context is lost, and reintroducing them could be problematic, especially for animals with complex behaviors. Furthermore, only a few individuals can typically be preserved, so much of the genetic diversity is inevitably lost. However, with careful curation, like with the captive breeding programmes carried out in zoos, it is possible to minimize loss of genetic diversity in the existing captive gene pools and avoid inbreeding.

The article I linked to ends on a pessimistic note: all countries are having to deal with extinction of their native flora and fauna, to a greater or lesser extent. Ex-situ conservation can only help to a small extent, though anything is better than nothing at all.

In our anthropogenic age (what some people are calling the Anthropocene), with species being shuffled all over the globe and having their ways of life permanently changed, maybe it won't make sense to talk about native or non-native any more, except as a sort of historical documentation of what we have lost.

I'm not saying that tracts of the remaining "wild" nature are not worth preserving: the rain forests, taiga, and coral reefs are valuable for being as close to "native" as we can get. What I'm thinking of are the extreme cases of domesticated landscapes–much of old Europe, East Asia, and Mesopotamia–where any hope of reviving a pre-human species palette is impossible. Barring any great human cataclysm, the rest of the world will inevitably become more and more like these places over time.

"Moving Planet" event in Singapore, 24-25 Sep

2011-09-24T05:54:00.000+08:00

Keen on cycling? "Moving Planet" is a "world-wide rally to demand solutions to the climate crisis". The campaign is coming to Singapore, where organizers aim to encourage cycling to reduce the use of fossil fuels. It's on this weekend in Singapore (24th and 25th September), from 10 am to 10 pm at Youth Park in Orchard, and includes music performances and film screenings. The event is organized by local NGOs ECO Singapore and Xpose.

The agave's big bang

2011-09-13T02:16:00.000+08:00

One of the condominiums near my home has a bit of fancy horticulture at the entrance. Lined up along the road is a row of big agave plants, and lately four of them have been at various stages of flowering. If you haven't seen an agave plant (also called "century-plants") flowering, it's a sight to behold: the succulent leaves are thick and waxy, forming a rosette close to the ground, and from the middle emerges a spike-shaped stalked reaching taller than a person, from which the flowers will eventually unfurl.

Agave plants flowering in Portugal (Wikimedia)

The agave plants (see the Agavaceae webpage for more photographs) are also known as century plants because of a misconception that they only flower once a century. It is true however that it can take up to several years or even decades before an individual plant flowers. Once it does so, it apparently withers away and dies. For this reason, probably, in some of the plants that I saw, the flower stalks were cut away soon afterwards.

Why would any organism only flower once in its lifetime? Doesn't natural selection reward those who have more offspring? Isn't having only one crop of offspring akin to putting all your eggs in one basket?

This phenomenon has many names. Colloquially it's called "big bang reproduction", because organisms that do this tend to produce a huge number of offspring (after all, if you only have this one chance...). Zoologists tend to use the term semelparity (adjective "semelparous"), while the botanists have used monocarpy ("monocarpous") or hapaxanthy ("hapaxanthous"). The antonyms are similarly polysyllabic: iteroparity, polycarpy, and pleonanthy respectively.

Trying to find out more about monocarpy in plants, I found an article in the Kew Bulletin of 1980 (vol. 35, no. 2, pp. 235-245) by NW Simmonds that helped to clear up some of the terminology. It turns out that the agave is, strictly speaking, not monocarpous after all!

Agave plants typically have multiple stems. After a flowering event, the stem bearing the inflorescence dies, but the rest can survive. Therefore, it's not the entire plant that dies! The same situation applies to palms that produce suckers, which are new stems that emerge from the roots or base of a plant. The sago palm Metroxylon, for instance, does precisely this. It's the plant that we get the starchy food sago from. The stem which flowers and fruits will die, but the rest of them live on. The banana is yet another suckering food plant that behaves in this manner.

A stand of sago palms (Metroxylon sagu) in Java, photographed in 1904 (Wikimedia)

So which plants are truly semelparous/monocarpous/hapaxanthous? Which ones actually flower and fruit exactly once and then die? By definition this will include the annuals and biennials of seasonal climates. There are also the plants which have a single growing axis which eventually terminate in an inflorescence. Most plants grow vertically at their tips, with cell division taking place in a zone called the apical meristem, for those in the know. Some plants reach the end of their lives when the apex, instead of producing yet more stem and leaves, switches gears to produce flowers instead. Once these flowers bloom and fruit, there's no more apical meristem to grow further, and so the plant dies. Some palms, like the talipot palm Corypha have such a lifestyle, as do the false bananas Ensete. Finally, there are also those plants which don't have such a limit to their growth–their flowers don't sprout from the apical meristem–and yet they somehow just die after flowering and fruiting anyway, such as with many species of bamboo.

This field of study has a connection to Singapore, too. Much of the early research and theoretical speculation on plant flowering cycles (phenology) was done by RE Holttum and EJH Corner. They were botanists at the Singapore Botanic Gardens (Holttum was one of the Directors, and Corner was his Assistant Director), including the period of the Japanese Occupation.

What explains the phenomenon of monocarpy? The existing explanations draw heavily from a field called life history theory, which studies the trade-offs between different life-history traits, such as lifespan, the number of offspring, and the timing of reproduction. These are considered within the framework of natural selection: which combination of traits will maximize the number of viable offspring produced by a certain species under its conditions of existence?

Theoretically, it appears that there is a trade-off between allocating resources for survival vs. for reproduction. Put another way, the choice is between reproducing right now, or holding off to reproduce later. If the chances of survival for an individual are low, then it makes sense to pump energy into reproduction (i.e. developing the gonads quickly and reaching sexual maturity earlier) as soon as possible. If an individual has higher chances of survival, then it might produce more offspring over its expected lifespan by producing fewer offspring each time, but spread out over a long lifespan. The contrast between these two modes of reproduction has been called r vs. K selection. These terms are taken from the equations of population dynamics. r refers to the maximum growth rate of a population: species which live under r-selective conditions mature early and reproduce quickly. K is the carrying capacity of an environment. K-selected species have more stable populations, and tend to invest more in longer lifespans and have fewer offspring each time.

But how does this distinction help us understand the phenomenon of long-lived plants that reproduce only once, but with loads of offspring? I.e. the big-bangers.

A species of false banana, Ensete ventricosum, which flowers once then dies (Wikimedia)

We then have to introduce another consideration: the amount of resources invested per offspring. If more investment per offspring (e.g. food stored in the seed for future germination, diverted to making fleshy fruit to aid dispersal) then by corralling resources for as long as possible, before pumping everything into the production of flowers, fruit and seeds, they might do better than if they had to split resources between provisioning offspring and keeping themselves alive for the next round of reproduction.

There is also an ecological argument, first formulated by Dan Janzen. Having plenty of offspring each time, especially when this is coordinated between entire populations of the same species, is a means of overwhelming potential predators. If a plant flowers and fruits constantly at a low rate throughout the year, it can conceivably support a stable population of fruit- or seed-eaters that end up destroying much of the potential offspring, reducing the plant's fitness. If, however, it waits for ages and ages before fruiting, then potential predators are starved and their populations are kept low. When they finally do bloom, there is an excess of riches, and the hitherto starved fruit- or seed-eaters are stuffed, but their populations have been depressed for so long that they don't do much damage because there are few of them, and enough seeds escape to propagate the species. By producing so many seeds at such widely-spaced intervals, seed predators have to alternate between long periods of starvation with sudden gluts - that's no way to raise a stable family. The same argument applies to diseases and potential parasites, too. It is also one of the explanations for the phenomenon of mast-fruiting in the Old World tropics, where hundreds of unrelated tree species flower and fruit together at irregular intervals, possibly triggered by some sort of climatic event. The forest is boring and green for months and years on end, until suddenly there is a windfall: fruits and seeds everywhere.

There are several explanations, and quite possibly there is no single "answer" - each of these probably has some part to play, each is "true" to some extent. That's one problem with theory in biology: it's always an incomplete model of reality, and one can never hope to have a full knowledge of all the possible factors. As I look at the agaves and wait for them to come to full bloom, though, I'm happy to think that at least some sense can be made out of their curious suicidal tendencies, and that these mysteries are not beyond all hope of understanding!

[For the next two weeks I'll be traveling so updates will be much more infrequent.]

Plant gives birds a place to stand

2011-09-06T20:57:00.000+08:00

The Cape of Good Hope on the Southern tip of Africa is one of the world's great floristic zones: mega-centers of plant biodiversity where the weird and wonderful have made their home. One of these residents, a member of the Iris family called Rat's Tail, Babiana ringens, has an unusual structure that sticks out vertically, looking much like a rodent's nether appendage.

Botanists from the University of Stellenbosch in South Africa have lately suggested that this structure has evolved as a built-in perch for birds that pollinate the plant's flowers (BBC News, Univ. Stellenbosch). They observed that sunbirds were the only pollinators of these plants, and that the birds perched on the stalk while reaching down towards the flowers. Even more compellingly, in regions where the birds had access to other plant species for nectar, the perches were smaller, an instance of "relaxed selection", where a trait is less pronounced when natural selection is acting less strongly.

All this only serves to confirm my prejudice that animals are merely vehicles for plants to move around in.

Swifts in the city

2011-09-04T01:57:00.000+08:00

I live on the 18th floor and have a great view of the Eastern half of Singapore. It's also a great opportunity for bird-watching. What I can see from my window are not pigeons and crows, but those fascinating birds the swifts. Here's a video of one twirling in circles at the same height as my building.

Swifts circling outside my window from brandon seah on Vimeo.

The main problems with swift-watching are apparent from the video: they fly very fast and they're up very high. Living on the top floor solves the second problem but not the first, though sometimes I can get a fleeting close-up glimpse when they return to perch or nest in the roof above me.

When trying to look up more information about them, I found an entry on Ria Tan's website on Sungei Buloh flora and fauna. Swifts belong to a family of birds called the Apodidae, and the common swifts are in the genus Apus, which means "no feet". Swifts actually do have feet, but they're small and used mostly for perching rather than walking.

Here's some interesting facts I learned:

They live most of their life "on the wing" - eating, drinking, mating, and even sleeping
Their name is apt: they're among the fastest fliers in the world, achieving up to 110 km/h
Flying insects make up most of their diet
Swifts are common, although the edible-nest swifts are threatened by indiscriminate nest-harvesting
They're well-adapted to live in anthropogenic environments

Swifts can be confused with swallows, because both have the crescent-shaped wing profile characteristic of fast fliers. The two groups of birds are actually not very closely related. Swifts generally forage at higher altitudes than swallows, fly with a rapid flicking motion, and have shorter tails that are not notched at the ends.

Lately the LTA has been doing some works close to my home for the upcoming Downtown Line of the MRT. Part of Bedok Town Park close to the road has been flattened: the trees cut down and the ground dug into. Quite a number of swifts (among other birds) were circling over that area, fairly close to the ground, and I think they might have been hunting down the insects and other critters churned up by the works.

Perils of beauty - Attack of the "Orchid snatchers"

2011-09-02T00:42:00.000+08:00

Collectors of rare orchids are stripping them from the rainforest, driving the most beautiful and unique species to rapid extinction. Is beauty a curse? Perhaps so, if you're an orchid!

This is nothing new, of course. Even the Victorian Britons suffered the same collecting-mania, which they called "orchidelirium". The period saw a fashion for hothouses among the wealthy, and professional plant-collectors were despatched to far-flung parts of the world to procure new and interesting plants for horticulture. This is the subject of a book, The Plant Hunters, by Tyler Whittle.

Eminent botanists were not innocent parties either:

"Sir Joseph Hooker, traveling in India, remarks that Vanda caerulea is 'The rarest and most beautiful of Indian orchids'. Yet in a footnote he mentions that he collected 'seven men's loads' of this plant (few of which reached England alive); he goes on to suggest that collectors with better facilities for getting the plants home 'might easily clear from £2,000 to £3,000 in one season, by the sale of Khasia orchids' - and this is just what happened. ... Few orchids now remain in the Himalayan foothills."

This is quoted from Anthony Huxley's very readable book Green Inheritance: The WWF Book of Plants, originally published in 1984 but still a good source of information about the ways people make use of plants and relate to our green environment.

The BBC article cites the case of a new orchid species, Bulbophyllum kubahense, that was introduced into the black market even before its discoverer, the orchidologist Jaap Vermeulen, had even published the formal description in a botanical journal.

All orchids are in Appendix II of the CITES treaty (see list - scroll down), which means that permits are required for them to be exported. A number of rare species, including all the slipper-orchids (Paphiopedilium) are Appendix I species, where trade in wild-caught individuals is illegal except with special permits.

Monitoring the trade and policing the rainforest is a mammoth task, which perhaps can never be fully accomplished. The only hope may lie in cutting back demand. Most orchids on sale in garden shops are artificially propagated, with Singapore having played a major role in the development of orchid propagation techniques. Nonetheless, for the conscientious shopper, it is probably worth paying more attention to the provenance of your garden plants before buying them, just as people are paying attention to the provenance of the fish they eat and the coffee they drink.

Biodiversity of Singapore Symposium - 24 Sep 2011

2011-08-31T16:27:00.000+08:00

The Biodiversity of Singapore Symposium will be held on 24 September 2011 at the National University of Singapore. This is the third year that this event, jointly organized by NUS and NParks, is taking place. Three of our Biorefugia bloggers will be there either as speakers or moderators!

I remember attending the very first symposium way back in 2003 - I got to miss a day of classes in school, too. As a neophyte, it was my first introduction both to the wide array of research and activism that was going on in the Singapore environmental scene, and to the people who were involved. I even got a free copy of the Chek Jawa guidebook, which had just been launched, and which now occupies a proud position on my bookshelf.

There are three sessions on the three major habitat types: terrestrial, freshwater, and marine, which should satisfy most tastes. The speakers are a good mix of established names and younger people. If that's not enough to entice you, early birds get free coffee!

Remember to register by the 18th ($10 regular, $5 student). The deadline for poster submissions is also on the same day.

Protists in Singapore - New Website!

2011-08-29T22:29:00.000+08:00

Last month I featured photos of some protozoans that I found in a pond on the NUS campus (part 1, part 2). Even though it's somewhere right in the middle of the city, there's plenty of wild life to see if you're lucky enough to have a microscope to see it with.

Those images and plenty more are now on a new website that I've put together, Protists in Singapore, hosted at Wordpress. My aim is to highlight these under-appreciated organisms, which most nature enthusiasts have overlooked.

The guide itself is organized by the different groups of protists that one might commonly encounter. Navigate using the menu bar underneath the banner at the top of the page.

In addition to the named groups of protists, there are two other pages: Interactions, which highlights examples of interactions between different organisms, and By-catch, which features organisms other than protists, such bacteria and animals, that can also be observed in the same habitats.

A typical page will have both photographs and videos (hosted at Vimeo), as well as a short description.

Write in at the Contact page to let me know whether you found it useful!

How many species - why do we care?

2011-08-25T23:33:00.000+08:00

How many species are there on Earth? This is one of those simple questions that rapidly unravel when you try to pin down an answer. Despite over 250 years of the Linnaean system being available as a "filing cabinet" for humanity's systematic exploration of life on Earth, the answer is still not clear.

That we lack an answer is far from astonishing - there's plenty of Earth (and plenty of Ocean) to explore. Taxonomists still argue about what exactly is a species and how to recognize one when you see it.

A paper just published in PLoS Biology by Camilo Mora and colleagues has put forward the figure of 8.7 million species. This has been widely reported in the mainstream press (BBC, The Guardian, Today Online), though most omit mentioning that this figure has a generous margin, a standard error of +/- 1.3 million.

What I'm intrigued by is why there is so much attention being paid to this piece of news. After all, estimating the total species count of the planet is not a new endeavour.

The ecologist Robert May, known for his contributions to ecological theory, already asked this question in a classic 1988 paper titled "How Many Species are there on Earth?" (Science, 16 Sep 1988, p. 1441). Fittingly, he has contributed a commentary article to the recent paper, which builds on his earlier contribution.

There have been numerous tries before to get an estimate. One famous attempt (cited by both May and the recent paper) was by Terry Erwin, an entomologist with the Smithsonian Institution in Washington DC who specialized in beetles. He traveled to Panama and fogged trees with biodegradable insecticide, while assistants held out sheets below to catch the "rain" of dying insects. By laboriously identifying all these bugs, and making a few educated guesses, he surmised that each tree species in the tropical forest had 160 species of beetle that were specific to the canopy of that host species alone. He then multiplied this by the number of tree species, the proportion of beetles to the rest of the arthropods, and the ratio of canopy-dwelling to ground-dwelling species, he arrived at the figure of 30 million arthropod species in total.

It's easy to question his figures and assumptions. What's difficult is to come up with a better guess, and that's what the current authors claim to have done (view their table of other estimates and methods).

Like all previous estimates, Mora and colleagues extrapolated from what we know to guesstimate what we don't. They began with the observation that higher taxa - that is to say, families, orders, and phyla, are much better "sampled" than species. That's straightforward enough - it's harder to discover a new phylum of animals than to discover a new species (and new phyla are often "discovered" by shuffling already-known species around).

By modeling the accumulation curve for each taxonomic rank (the number of taxa of a certain rank, e.g. families, that have been discovered by a certain date), they extrapolated the asymptotic value, i.e. the projected number of taxa that would be discovered if the existing processes of discovery extend onward to completion.

At the level of species, however, the accumulation curve is nowhere near an asymptote. There, a different sort of extrapolation was necessary. They observed that taxa at different levels in the Linnaean hierarchy tended to have consistent ratios between them. If the higher levels are relatively well-sampled, then we can extrapolate downwards to the species level to estimate how many species there are in total. That is how they obtained their estimate of 8.7 million. By comparing species counts estimated by this method with other estimates in well-studied groups (like birds and mammals), they showed that their estimates were not too far off.

As Robert May stated: "This is higher than my earlier “best guess”, but I like the simplicity of this new method."

There are limitations, of course, and the authors are quick to point them out. For example, some taxonomic groups like the protozoa are still poorly known at the species level, and the scattered literature is not well aggregated. For the prokaryotes (Bacteria and Archaea), even the validity of having "species" is in doubt, because they do not practice sexual reproduction. There are remarkably few (only a few thousand) formally-described species of bacteria, despite their small size and ubiquity. This is almost certainly because the requirements for naming a new species (isolating the strain, establishing a pure culture, storing the culture in a depository) are much more arduous per species than the comparable procedures for plants and animals, and the proportion of microbiologists who are interested in taxonomy alone has always been much smaller than among other biologists.

Which brings us back to the original question: why has the media picked up on this paper and reported it so widely? After all, it's only a number. Although it's good to know, it doesn't have much of a direct impact on conservation (which would require more detailed and locality-specific data). Perhaps it might be an important parameter in some theoretical ecological models.

I think its appeal and wide reportage owes much to the desire for hard numbers. The natural world has always seemed infinite in its diversity and extent. Being able to pin down how many species exist could act as an anchor, a point of reference for thinking about nature. 8.7 million, after all, seems like a big number but isn't really so. If we accept the figure, then there are almost a thousand people for each species of life on the planet.

It also acts as a springboard for discussions about diversity and the on-going extinction of species because of human activity. Species discovery has not yet reached an asymptote, this line of commentary goes, but we humans are moving that asymptote downwards as we speak.

Reporters are happy when they have figures to cite. This species count is a sort of talisman. Complex ecological or climate models are hard to explain, and even their creators may not be fully conversant in the details or behavior. Counting the animals as they board the ark: now that's something that people can easily understand and that a journalist can write about in 500 words or less.

This suggests that scientists who are looking for more publicity for their work should try to encapsulate it in a telling figure or result. The obvious criticism is that this is merely trafficking in soundbites, but I think it can be done wisely. If out of a hundred people who read about this paper in the news, only one went to look up more details online, a significant contribution is still being made to public knowledge of science. Science reporting is most valuable when it serves as an invitation to learn more, than when it just goes "gee-whiz isn't that amazing?" without further comment.

Save the Dolphins concert on 28 Aug 2011

2011-08-22T09:54:00.000+08:00

Blogger Alex Au, best known for his political blogging, has also highlighted the work of the animal welfare group Acres on his blog Yawning Bread.

He describes their success in alerting the Agri-Food and Veterinary Authority (AVA), Singapore's regulatory authority for the wildlife products trade, to the sale of tiger parts and products in over 50 shops around the island.

Acres is now working to gather more support in its campaign, The World's Saddest Dolphins, to release the dolphins that have been captured for Resorts World Sentosa. 27 bottlenose dolphins were captured from the wild around the Solomon Islands, of which two have since died, which I previously blogged about here. Acres states that:

"Their world has already shrunk to a square sea pen, devoid of variety, bereft of sea life. They can’t hunt anymore. They beg and jump for handouts of dead fish, which arrive in buckets. There’s nowhere for them to roam, except back and forth. And nothing to do except turn round and round and go slowly mad."

These sentiments echo that of the Nobel-prize-winning student of animal behavior, Konrad Lorenz, who wrote in his book King Solomon's Ring:

"Now which are the animals really to be pitied in captivity? ... In the first place, those clever and highly developed beings whose lively mentality and urge for activity can find no outlet behind the bars of the cage.

...

"[O]f all the animals that suffer under the inefficient methods of many zoological gardens, by far the most unfortunate are those mentally alert creatures of whom we have spoken above. These, however, rarely awaken the pity of the zoo visitor, least of all when such an originally highly intelligent animal has deteriorated, under the influence of close confinement, into a crazy idiot, a very caricature of its former self."

Acres in collaboration with Young NTUC is hosting a free concert at Hong Lim Park in support of its Saddest Dolphins campaign, from 4:30 to 7:30 pm on the 28th of August (Sunday). Find out more on its Facebook event page

Do chimps have culture?

2011-08-18T09:59:00.000+08:00

It's hard being human, or at least, to define what exactly makes us human. It used to be tool-making, but our close cousins the chimpanzees have been found to use tools, such as sticks to gather insects for food. Could culture, the inheritance of behaviors by learning, be the next "exclusively human" trait to fall?

Evolutionary anthropologists are studying chimpanzee communities throughout the West coast of Africa to determine if different groups indeed have different cultures and traditions. There is geographical variation in what specific behaviors chimps exhibit, but this alone does not confirm that there are different traditions:

Deciphering culture in the wild is difficult because researchers must ensure that behavioural differences between groups do not have other causes, such as variation in genetics or environmental conditions. "Why is it all chimps don't do everything? One solution is that there are hidden ecological differences between populations," says primatologist Richard Wrangham at Harvard University in Cambridge, Massachusetts. A behaviour could be linked to any number of variables such as amount of rainfall, the types of tree available, or the kinds of predator in the area, he says.

Semakau landfill "no dump"

2011-08-16T23:01:00.000+08:00

Pulau Semakau has drawn international attention as the world's only landfill with a waiting list for visitors, as well as for its environmental credentials:

"... Semakau Landfill is the only active landfill that receives incinerated and industrial waste while supporting a thriving ecosystem, which includes more than 700 types of plants and animals and several endangered species."

Read more at the New York Times. The article also highlights some criticisms of the landfill, including the risk that waste might leak through to the sea, and the pollution caused by incinerators.

Ray the Rotifer!

2011-08-11T00:57:00.000+08:00

While gazing through the microscope at yet more pond water, I was surprised to see this swim past my field of view (click for larger versions)....

It is evidently some kind of rotifer (according to Maxine Mowe) with part of its cuticle expanded into lateral 'wings'. The animal is able to open and close these wings, and even flap them somewhat.

Do you think that there's some resemblance to the chaps below?

The resemblance may be misleading, though. The rotifer is about a quarter of a millimeter across, whereas these skates and rays can measure about a meter or more. The way that water behaves at microscopic scales is very different from the macroscopic scale that we (and these fishes) live in. For zooplankton, the dominant property of water is its viscosity, as opposed to its inertia. Where a manta ray would coast along for several meters after a flap of its mighty wings, this winged rotifer would instead come to an immediate halt. So what are those wings for, on the tiny rotifer? Looks like it's something for an enterprising student to find out.

Immigration and invasion - biological xenophobia?

2011-08-04T17:33:00.000+08:00

One of the hottest political topics in Singapore today is the issue of immigration: your 'foreign talent' may be my 'job-stealer', as the debate continues on just how much immigration is desirable for a small country like ours.

In the field of biological conservation, a similar conflict has popped up, as reported recently in the Boston Globe. Conservationists have traditionally spoken of 'introduced' vs. 'native' species, with the least desirable introduced species being termed 'invasive'. But a number of vocal critics have spoken up to say that this is simply nativism - an unthinking bias in favour of the supposedly native. They contend that the division between native and non-native is arbitrary and unscientific, in part because many familiar species were originally imports from elsewhere, and also because the environment is constantly changing, and species are continually migrating, and to try to freeze a community in time is akin to gardening nature. The author Michael Pollan went as far as to say that species-nativism was "xenophobic".

Classical examples of species invasions include the rabbit and cane toad in Australia, and the European starling in the USA (for which Shakespeare, bizarrely enough, is to blame). In Singapore, Clidemia hirta or Koster's Curse (a native of the Americas) has a tenacious foothold on forest fringes and clearings, preventing the re-establishment of native vegetation.

However, much of our modern landscape is precisely the product of introduced species. The grand arching wayside tree canopies that provide shade and shelter are often rain trees, Samanea saman, which are native to Brazil. These are perhaps the 'foreign talent' side of the argument.

We justifiably take pride in our native species, and among the popular Science Centre guidebook series is a volume on cultivating native plant species. But for an island as small as Singapore, does it make sense to speak of 'native' species? What hope is there of eradicating non-native species, anyway?

Ultimately, it may simply be a matter of rhetoric. The disagreement is not over the substance of the matter but the language that we use to talk about it. As the Globe article says:

Just as most ecologists accept that only a fraction of non-native species are harmful, the anti-nativists, when pressed, will admit that unequivocally destructive species like the Asian longhorned beetle should be reined in. Their disagreement lies more in how we should talk about the issue, how we justify our interventions and how we label the species we want to eradicate.

That is to say: when we call a species an 'invasive species', it's not enough simply to say that it's non-native and hence must be eradicated for that reason alone. We must be clearer about what 'invasiveness' means, and be able to justify our assertions about their harmfulness and undesirability.

Genetically engineered algae for biofuel?

2011-08-03T00:17:00.001+08:00

Scientists in the US are developing genetically engineered strains of algae, mostly cyanobacteria ("blue green algae") to produce alkane fuels in quantity. They are confident that algal biofuel avoids many of the drawbacks of corn- or grass-biofuels, such as competition with food supply, low yields per hectare, and need for extensive processing.

However, they're running into problems of their own: need for large volumes of water, difficult in scaling up the process from the lab to the field, and the high volume of carbon dioxide consumption that these algae have. Some of the problems were unexpected, however:

"Shrimp think algae are good food," says CEO Pyle [of the company Sapphire Energy]. "If you don't pay attention, you will ultimately have a shrimp farm."

The returns on such an investment might not be too bad either!

World's largest fungus fruiting body discovered

2011-08-02T00:43:00.000+08:00

Mycologists in China have discovered what may be the world's largest fungal fruiting body. It is a kind of bracket fungus, of the species Fomitiporia ellipsoidea, and forms a structure of about 10 meters in the longest dimension, and weighs up to half a metric ton. (Photos at BBC News website)

Bracket fungi thrive on dead wood, forming shelves or 'brackets' projecting perpendicular from the wood surface, instead of standing on stalks like classic mushrooms. They also have pores rather than gills, as openings for the dispersal of spores.

The size of this fruiting body is however dwarfed by the immensity of the world's (potentially) largest organism, also a fungus, called Armillaria ostoyae, whose underground mycelium covers an area of 965 hectares! Fruiting bodies like brackets and mushrooms are only the visible part that has emerged from the ramifying network of nutrient-gathering hyphae in order to accomplish sexual reproduction and spore dispersal. In the case of this newly discovered individual of Fomitiporia, scientists attribute its large size to the perennial nature of its growth, and the long time that it has been allowed to grow undisturbed.

Sources

BBC News article by Matt Walker
Dai YC, Cui BK (2011) Fomitiporia ellipsoidea has the largest fruiting body among the fungi. Fungal Biology, in press, doi:10.1016/j.funbio.2011.06.008

End of a botanical tradition

2011-08-02T00:13:00.000+08:00

Botanical Latin is a curious creature, with a grammar and vocabulary very different from classical or medieval Latin. It dates back to the traditional use of Latin in scientific and scholarly works as the common language of learning in multi-lingual Europe. In modern times, it has been restricted to the formal description, called a 'diagnosis', of a newly-published plant species.

As Latin grew less important to general education, however, botanists have had to seek help from other quarters in writing these diagnoses, but because of the independent evolution of botanical Latin for its special purposes:

... when a botanical author thanks a professor of classics for providing a Latin description, this is usually in bad or at any rate unconventional botanical Latin... (W.T. Stearn, Botanical Latin, viii.)

The use of Latin was codified in the International Code of Botanical Nomenclature - a set of rules for keeping the profusion of scientific names in order. It was preserved for both tradition's sake and also because taxonomists have usually argued that a common language is needed to keep communication possible amidst a profusion of vernacular languages. The parallel Zoological Code, however, did away with Latin descriptions a long time ago.

New editions of the Code are voted upon at meetings of the International Botanical Congress, and at the latest meeting in Melbourne, Australia, this tradition of botanical Latin may have met its demise (Nature news and editorial). Attendees have voted for several amendments to the code (full list of proposals here), including dropping the requirement for botanical Latin in new descriptions, and allowing the publication of new species names in electronic journals. The full congress will have to ratify these amendments before they become permanent.

The demise of botanical Latin might have been just a matter of time, but the issue of electronic publication is a relatively new one. Electronic-only journals have been proliferating, but for taxonomy, which is concerned with permanence and record-keeping rather than rapid communication of information, they have distinct disadvantages. There is no guarantee that a server crash or corrupted computer file may not wipe out a species description forever, resulting in a book-keeping nightmare when species names have to be revised or updated. The zoological Code, for example, still requires that a number of hard paper copies be sent to libraries around the world as an insurance against that possibility. This is what the Raffles Bulletin of Zoology, which is published in Singapore as an online journal, does to fulfill the requirements of the code.

So does this mean that William T Stearn's classic reference book, Botanical Latin, will become obsolete immediately? Not necessarily. A big fraction of the historical botanical literature, especially the earliest works from the time of Linnaeus onwards, are written exclusively in Latin and no translations exist for them. We also owe much of our technical nomenclature to Latin and Greek. Botanical Latin may be newly dead, but it still lives on.

Work on Bukit Timah Eco-Link begins

2011-07-31T15:45:00.000+08:00

Two years ago, Cheng Puay blogged about the announcement of an ecological 'bridge' to be built across the Bukit Timah Expressway (BKE) to connect Bukit Timah Nature Reserve and the Central Catchment area. Construction of the BKE 25 years ago had caused the two forested areas to be separated from each other, preventing animals from moving freely and making them run the risk of becoming roadkill.

Today the Straits Times reported that work on the Eco-Link@BKE has finally begun, at a projected cost of $17 million, to be completed around December 2013. It will certainly be an exciting experiment to see whether man-made forest corridors of this sort can be effective at allowing migration and genetic exchange between two forest fragments.

Incidentally, the previous blog post is the most often-visited post on this blog. Those who have read that article may hence be glad to have this update.

In other news, the ST today also reported on a growing poaching problem in forested areas around Singapore, including wild boar traps which have inadvertently maimed stray dogs. Nature aficionados who habitually walk through the undergrowth should watch out!

Singapore Protozoans Part 2 - A Murky Pond

2011-07-26T23:52:00.001+08:00

After looking at today's sample (from a small pond in the botany garden at NUS) under the microscope I think I might hesitate to stick my hands into warm murky pond water again. It's absolutely crawling with bacteria, and to illustrate what I mean by crawling I've even got a video:

Bacteria moving from brandon seah on Vimeo.

On the bright side, that means there's plenty of protists grazing on all these bacteria, including lots of small bacterivorous ciliates, and gliding euglenids (photo below). I really think that they look like twisted potato chips, don't you too? Diatom and dinoflagellates were common, but I saw more empty tests and frustules than living cells.

"Potato chip" euglenids with flagellum that points in the direction of motion.

One of the highlights was a big amoeba which had really awesome cytoplasmic streaming and which moved by blebbing outwards in a way which is easier to show than to describe in words.

Large Amoeba from brandon seah on Vimeo.

See the full set of photographs on Flickr. [Update 6/9/11 - I've moved all the photos to my new protist website and the Flickr album is no longer available.]

Singapore Protozoans Part 1

2011-07-26T01:11:00.001+08:00

Heliozoan from Kranji Reservoir. Each unit on the graticule scale is 2.5 microns.

Microscope, murky water, a camera, and free time.

Lately I've been volunteering at Darren Yeo's new freshwater biology lab, but Maxine, the graduate student whose project I'm supposed to help with, has been busy with the Honours fieldtrip to Pulau Tioman and with getting sick (get well soon!) In the meantime, I've found that her plankton net samples from Kranji Reservoir are teeming with interesting and picturesque protozoa!

Today I captured some shots of microscopic aquatic life to share online, and you can browse the full set on Flickr [update 6/9/11 - I've moved all the media to my new protist website and the album is no longer available]. The picture above shows an organism called a heliozoan. The long radiating arms, called axopods, appear to be beaded with dew drops, which are actually organelles involved in prey capture called extrusomes. The spherical cell body itself is covered in a layer of spicules, which seem like a fuzzy layer of hair, but reveal finely ornamented detail under electron microscopy.

These pictures were taken in a fairly primitive way: by balancing a camera in front of the eyepiece of the microscope. The microscope was set up for brightfield illumination, but I closed down the condenser aperture to improve contrast, in the absence of any better option. Still, there's enough detail to recognize lots of protozoans and to tell a good story.

When I've got a decent bunch of these pictures and descriptions, I'd like to eventually put up a photographic guide to common protozoans in Singapore. That might help to address some of the 'macrobe' bias in the natural history scene here, by showing the beauty hidden in the very small.

As a bonus here's a video of ciliates squirming in the carcass of a dead planktonic crustacean. The bright droplets are oil globules, which the ciliates are feeding on (ingested oil globules are also visible within their cytoplasm). Outside the animal carcass you can see another ciliate which has been left out of the feeding frenzy, and is trying to find its way in....

Squirming ciliates from brandon seah on Vimeo.

"Southeast Asian Sea Life" according to xkcd

2011-07-25T23:51:00.002+08:00

From xkcd.com by Randall Munroe

The latest comic from this popular geeky web-comic pays tribute to the mimic octopus, whose camouflage powers have gained it minor celebrity status on YouTube...

No more bananas by mid-century?

2011-07-24T23:45:00.000+08:00

Four varieties of banana (Wikimedia Commons)

They can see it coming. Most bananas sold today belong to the Cavendish variety, which is grown in extensive monoculture plantations around the world. The plants are virtually sterile, and are propagated by transplanting suckers or cuttings. The cultivar Gros Michel, which was the predecessor to the Cavendish, was wiped out in the early 20th century by a fungus called the Panama disease, Fusarium oxysporum f. sp. Cubense, which as the names suggest showed up in the Caribbean. A new strain of this fungal pathogen has emerged in recent decades to attack the Cavendish variety, which is now under threat. The new strain, called Tropical Race 4, has spread through the Asia-Pacific region, and has yet to hit Latin America, that other bastion of banana agriculture, but it's only a matter of time.

Possible solutions include genetically-modified strains of the Cavendish banana plant, or increasing the genetic variety of bananas in cultivation. Preserving genetic variation in crop foods is now an important concern, given the susceptibility of Green Revolution-style monoculture projects to pathogens. Seed banks around the world store varieties of important crops like the potato and rice as an insurance policy, as traditional cultivars are being abandoned for 'modern' high-yield plants. There is also a thriving trade in so-called 'heirloom seeds' among gardening enthusiasts and smaller-scale farms.

Will such measures be enough to save the banana? Time will tell, but the days of the big, starchy, and seedless Cavendish may be numbered. (Another fun new fact: India "grows and consumes more bananas than any other country in the world." Who knew?)

(via Gawker)

The mole's new thumb

2011-07-19T12:05:00.000+08:00

Two instances of making do with what you have at hand.

With their huge hands, pointy snouts, and apparent lack of eyes, moles certainly appear to us as very peculiar creatures. These traits, however, are adaptations to a subterranean lifestyle. Those big front paws, in particular, are used for digging tunnels into the soil. Aside from being large relative to the rest of its body, the paws also have an elongated and enlarged radial sesamoid bone just beside the thumb. In some species of mole, this false 'thumb' (although it doesn't actually protrude as a distinct digit) is actually capable of some independent movement, spreading outwards to widen the hand.

This same wrist bone is also modified in giant pandas to form their peculiar 'thumb'. The panda uses its false thumb in feeding, to strip down the bamboo shoots that comprise its diet. (A photo of this in action can be found here.) This was the subject of a well-known essay by Stephen Jay Gould that later titled one of his published collections. As an example of what he called 'Tinkertoy evolution', it illustrates how evolution often makes do with existing structures to fulfill new functions. It is examples like these, which are less than perfect and highly contingent functional solutions, that break the illusion of a perfect world as posited by natural theology, and demonstrate evolution in action, he argued. (It's also the name of a popular evolution blog.)

The case of the mole's 'thumb' also bears out this theme. Developmental biologists have recently found that Sox9, a gene involved in limb chondrification (the formation of cartilage tissue), is expressed in the region of the enlarged radial sesamoid during the development of the front paws of a mole embryo. This gene is also expressed in the 'normal' developing digits. However, the timing is different: it is expressed in that region of the wrist after Sox9 expressed has faded away in the normal digits. They compared this pattern of gene expression in embryos of the shrew, which are the closest relatives to moles, and did not find any Sox9 expression in the wrist at the same developmental stages.

Therefore, similar developmental mechanisms (the 'toolbox') have been co-opted to form the mole's false thumb, but their timing has been changed. That seems an easier option than to invent an entirely new set of tools.

Instances of obvious 'tinkering' such as this one make the messiness of evolution more apparent to us. Even structures of of evident perfection such as the eye (or eyes, since image-forming eyes have evolved multiple times) evolved by a long process of making do with existing structures to form new ones (clip from the BBC science show 'Bang Goes the Theory'). After all, isn't this just descent with modification, the very concept of biological evolution itself? Even at the level of genes and genomes, new genes often originate by duplication of existing genes (or even entire genomes, in the phenomenon of polyploidy) followed by divergence in function of these new copies from their originals. A whole book has recently been published on this subject.

What intrigues me is that the evolution of language also seems to have a similar pattern, and not just in terms of coining new words or borrowing vocabulary from other languages, but in the very grammatical structure of a language. Apparently 'perfect' systems like the Latin noun cases are actually the intermediate products of an ancient and on-going process of decay, accretion, and modification. A readable account is found in a popular-linguistics book I recently read, The Unfolding of Language.

Perhaps I'm straying too far from the original point of this post, and making a mountain out of a molehill, but the parallels to be found throughout the natural world and between the different sorts of evolution, biological and cultural, continue to fascinate me. Nature has immense and dizzying diversity, but that doesn't mean it has to be opaque to our understanding.

Sources:

BBC News story by Jennifer Carpenter
C Mitgutsch et al. (2011) Circumventing the polydactyly 'constraint' - the mole's thumb. Biology Letters published online 13 July 2011. doi: 10.1098/rsbl.2011.0494

MacClade at 25, now available free

2011-07-14T13:59:00.000+08:00

MacClade is one of the most popular computer tools for phylogenetics today. It's commonly used for editing data sets and analyzing phylogenetic trees, though it can't be used itself for inferring trees. It recently celebrated its 25th birthday, and has been available for free online since 1 May. It will no longer be supported on the upcoming version of MacOS ("Lion") so the Maddison brothers, who authored the program, suggest using Mesquite instead, which is also developed by them.

Snails surviving being eaten by birds

2011-07-12T22:30:00.000+08:00

Japanese scientists have found that small land snails of the species Tomatellides boeningi can survive being eaten by birds. They fed live snails to Japanese white-eyes and a brown-eared bulbul, and found that about 15% of the snails remained alive after passing through the birds' guts.

Just as birds are important dispersers of plant seeds, it appears that they can contribute to the dispersal of small animals too.

Wild populations of T. boeningi on Hahajima Island in the W Pacific show genetic heterogeneity within populations and no evidence of isolation, and there is a statistically-significant positive correlation between genetic variation and the density of Japanese white-eyes, lending support to the idea of bird-borne dispersal.

Sources:

Who's a climate scientist?

2011-07-06T12:49:00.000+08:00

Climate science researchers appear in a video produced and aired by the Australian satirical TV show Hungry Beast, titled "I'm a Climate Scientist." Among their reasons for doing so was to "[highlight] the issue of unqualified opinions on climate science by politicians, economists etc. in the media." (Source)

A sample of the lyrics:

Who's a climate scientist?
I'm a climate scientist!
A penny-farthing cyclist?
Not a climate scientist!
A Fox News journalist? -- No!
A paleontologist? -- No!
A clean coal lobbyist? -- No!
A cashed-up alarmist? -- No!

The video is embedded below, but warning: loud music and strong language. Via an article on scientist-turned-activist James Hansen in the Guardian.

Islamic creationism in Malaysia

2011-06-28T15:56:00.000+08:00

Salman Hameed is an astronomer and sociologist of science at Hampshire College in the US. He has been conducting an extensive survey on Muslim attitudes to science and religion in several Muslim-majority countries around the world.

"[Hameed] has found that attitudes about evolution vary greatly from country to country. For instance, most Pakistani doctors accepted evolution, even human evolution. "But in Malaysia, we were really surprised to find a major rejection of not only human evolution but evolution in general," he says.

"Hameed expected to find more acceptance of modern science because Malaysia has a sophisticated high-tech industry. He and his colleagues now speculate that Muslims are trying to carve out a cultural niche that's distinct from the more educated Indians and Chinese in Malaysia. "We think the rejection of evolution has become part of their Muslim identity," he says."

(Source: Chronicle of Higher Education)

The article goes on to discuss other findings that were presented at a symposium on Islam and science held at Cambridge University this past May. One of the major figures in the world of Islamic creationism is Harun Yahya from Turkey, the pen name of Adnan Oktar. A previous blog post here on creationism in Hong Kong schools mentioned him in passing. He was responsible for sending a hefty, full-color tome titled the Atlas of Creation to major universities and research institutions world-wide, to the amusement and befuddlement of academics and scientists who received them. He has an extensive media empire publishing creationist titles, but a profile in the New Scientist magazine suggests that politics are also at play.

The apparent growth of creationism in Malaysia is as much a sociopolitical issue (of "identity politics") as it is a scientific one. Therefore the standard solution of "more education" on its own may be insufficient to overcome this obstacle to promoting scientific and technical literacy in the country.

Indigenous peoples opposed to Indonesian carbon swap

2011-06-24T16:01:00.000+08:00

Forest-dwelling communities in the Indonesian state of Kalimantan, on the island of Borneo, have expressed their objection to the REDD (Reducing Emissions from Deforestation and Degradation) agreements signed by Indonesia with other countries and non-governmental groups.

REDD schemes are designed to put an economic value on forested lands for biodiversity and ecosystems services, where previously the only ways to extract monetary value from them were logging and clearing land for agriculture. Under such schemes, many of which are bilateral, governments are paid money in exchange for preserving tracts of forest. (Example: UN-REDD programme in Indonesia)

To quote a forest reserve executive in Guyana: "We have a resource we would like to get money for. Either you pay us for biodiversity services or we will sell the forest to Malaysian logging companies." (source)

Indigenous peoples who claim customary use of forests have objected to them because they feel that their rights to the land have been overlooked in the process, displacing them from their livelihood and dwellings. It seems like there may be more than one indigenous organization making public statements against REDD programmes.

I've previously blogged about how deforested land is being 'swept under the carpet' due to poor oversight. Related concerns have been expressed about the tremendous potential for corruption that they bring. It seems obvious to state that corruption is possible when large sums of money are being given to a central government to pay for a rural commodity (ecosystem services) which is hard to define and which you can't take conventional delivery of.

Transparent animals as art

2011-06-19T21:42:00.001+08:00

The technique of 'clearing and staining' is used to prepare anatomical specimens of small animals to show their bones and cartilage in situ. It involves digesting away the protein in a preserved animal body with enzymes, and rendering them transparent with other chemicals. The skeleton is then colored with brightly colored stains, creating specimens that look almost like stained glass and definitely as beautiful (if somewhat macabre).

Japanese artist Iori Tomita has been making cleared and stained specimens since 2007. His project, called New World Transparent Specimen, is his effort to "help people feel closer to the wonders of life." Much of the appeal of his works, he points out, is because "they appear as if they were beautifully sculpted from minerals."

(Source: New World Transparent Specimen website.)

The website is definitely worth a look. I've always found anatomy to be oddly compelling. Quite a few of them are invertebrates (like the shrimp in the picture above), which I've not seen before as cleared specimens. The technique is typically used to prepare fish, amphibians, and other small vertebrates.

(via sarzha)

Spellchecker to Weed Out Botanical Typos [Updated]

2011-06-16T10:33:00.002+08:00

[Update 17/6/11]
Following the comments by araygoza to this article (see below), I ran my list of misspelled plant names through the TNRS spellchecker and voila! it works!

That's really cool! The new URL is here.

****
Scientific nomenclature - the business of giving names to organisms - is a huge book-keeping exercise that is notoriously error-prone. Not only may one species be given multiple binomials, as scientists argue whether it should be classified one way or another, but misspellings and typos are easy to make.

Typos directly affect scientific research, which often relies on analyzing data from species databases. For example, a simple count of how many species are present in a certain place may be inflated because some name records have been misspelled. For botanists, there is now a possible solution available online. A team from several institutions has launched the Taxonomic Name Resolution Service, which uses technology similar to spell-checking software to detect erroneous names and suggest corrections.

I decided to give the system a try (click on "Try it now!" on the main page), using the names of four common plants with single-letter misspellings, listed below:

Cocos nuciferra
Samana saman
Pterocarpus indicum
Ficus grossulariodes

The results showed that these names were not found in the database, but it couldn't suggest any possible matches, which was a disappointment. Just in case they weren't actually in the database (it's based on TROPICOS, which focuses on plants from the Americas), I ran the correctly-spelled names through the checker and got a 100% match on each one.

From this small trial, which admittedly is not very thorough, I would say that the fuzzy-logic system for suggesting correct names is not really effective right now. However, the batch-check function is useful if one has a large database of records to sort through for validity. They have posted their source code and also are developing an API (application programming interface) for the service, so developers (or botanists with some computing savvy) can readily plug in their own systems.

(Via Nature News.)

"Mismeasure of Man" Revisited

2011-06-15T21:21:00.000+08:00

Stephen Jay Gould's 1981 book, The Mismeasure of Man, made the case against 'scientific racism'. He opened the book with an attack on the 19th-century physical anthropologists, the craniologists, who measured skulls as a way to classify different races as superior or inferior. Later on, he examined the origins of the IQ test and argued against its validity and statistical basis. In 1996, the book was reissued with a set of new essays, in response to the controversial 1994 book The Bell Curve. This was welcomed by those who opposed the Bell Curve's revival of biological determinism in intelligence.

Fifteen years on, Gould's book is back in the news but to criticism, rather than acclaim. One of the bodies of work that he analyzed and apparently refuted was that of Samuel George Morton, an American craniologist who amassed a large collection of skulls from around the world. Gould claimed that Morton's measurements exhibited bias, unconscious or not, that bolstered the preconceived notion that Europeans should have larger brain volumes than other, 'inferior' races. Morton supposedly fudged his analysis by selective reporting (see my previous blog post on other ways to fudge your science) and improper measurement. However, Gould did not remeasure the skulls himself, basing his criticism only upon his re-analysis of the published data. Now, a study by anthropologists who painstakingly remeasured Morton's skull collection has absolved Morton of misconduct. There was no mismeasurement, contradicting Gould's thesis that unconscious bias had influenced Morton's scientific methodology. The research team says: "Ironically, Gould's own analysis of Morton is likely the stronger example of a bias influencing results."

Read more at the New York Times, and the original article in PLoS Biology.

Reference:
Jason E Lewis et al. 2011. "The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias." PLoS Biology 9(6): e1001071. doi:10.1371/journal.pbio.1001071

Tongues without cheek

2011-06-08T10:25:00.000+08:00

It helps to have cheeks. We humans drink by forming a seal around the liquid (and often also the edge of a cup or bottle) with our lips, and then sucking inwards (with the help of our cheeks) to draw it into our mouths. This simple process is not available to other animals, such as dogs and cats, which don't really have cheeks to speak of.

I blogged some months ago about how cats lap up liquids. They don't use suction like we do, but as anyone who's watched a thirsty cat knows, it's all in the tongue. They touch their tongues to the surface of the water, and the liquid naturally adheres to the underside of the tongue. By pulling the tongue back quickly, the adhesion of tongue to water and cohesion between water molecules draws up a thin column of liquid into the mouth of the cat. This happens so quickly that it seems like they are 'flicking' water into their mouths - but no spooning or scooping is involved at all.

They're neat and classy, unlike dogs, right? Dogs seem to make a mess whenever they drink, and in the Times article that I linked to in my previous post, the scientists are quoted as saying that dogs scoop water up with the backs of their tongues, instead of elegantly lapping with the tips of their tongues. But this isn't really the case.

New research by a retired zoologist Alfred Crompton who used his 8-year-old dog Matilda shows that dogs do the same thing as cats do: adhesion followed by quick retraction of the tongue, except that where cats use the underside, dogs use mostly the dorsal surface. In neither case is any scooping of water involved. (via sarplus)

X-ray video of lapping in a dog from AW Crompton on Vimeo. (via Nature News blog)

So it's not true that dogs are dumb 'scoopers' while cats are sophisticated 'lappers'. As Crompton said, "Let's hear it for the dogs." But why are they still so messy? Probably because "the dog's tongue tip penetrates more deeply into the liquid than in cats, and consequently sprays more liquid around as the tongue rapidly withdraws".

Hummingbirds use a completely different mechanism to drink nectar from flowers. Because of their small size they are able to use a different realm of physical phenomena to aid in the drinking process: surface tension, instead of adhesion and bulk inertia. In this case, scientists were also debunking another long-held notion, that they drink nectar by capillary action up a tubular tongue (Steven Vogel's commentary is, as always, an informative read).

The hummingbird tongue is thin and forked at the ends. Two stiffening rods run down the length of the tongue, and each half is curled up like a straw that has been slit down lengthwise. So far so good. But what happens when the tongue is immersed in nectar is surprising: the 'lamellae' of the tongue unfurl themselves, and become flatter, no longer tube-like. The nectar sticks to the hydrophilic inner surface of the tongue.

As the tongue is withdrawn, the liquid surface of the nectar is now exposed to air; because of the surface tension of the air-nectar interface, the edges of the tongue are drawn inwards, causing it to re-furl passively. This limits the loss of nectar from the tongue. The bird brings the tongue back into its mouth, and then closes its bill leaving only a small gap. It squeezes its tongue through this narrowed opening, to wring the nectar off the tongue, starting a new cycle. This whole process is really quick, occurring over as little as 50 milliseconds, and is repeated over and over again.

Sources:

Big Bad Science

2011-06-06T18:36:00.000+08:00

If you talk to some people, you might walk away thinking that science is medicine's poor cousin. "Oh you study biology! That means you'll be working in the pharmaceutical industry, right?"

No, but you just can't convince some people.

Not being able to make money might be a good thing, in so far as science is concerned, though. A damning article by Harriet Washington (probably to promote her forthcoming book) recently published in The American Scholar has a familiar moral to its story: commercial concerns can get in the way of doing good science. But boy is it one heck of a story. (A similar sad tale is told in the context of psychiatric drugs in a recent book review by Marcia Angell.)

Medical research suffers from severe conflict-of-interest issues,

"Today, medical-journal editors estimate that 95 percent of the academic-medicine specialists who assess patented treatments have financial relationships with pharmaceutical companies, and even the prestigious NEJM gave up its search for objective reviewers in June 1992, announcing that it could find no reviewers that did not accept industry funds."

... from the seedy plague of ghostwriting,

"Many biased medical-journal articles are the work not of physicians or scientists, but of ghostwriters who script them in accordance with the drugmakers’ marketing messages. A medical expert is found who, for a few thousand dollars, is willing to append his or her signature, and then the piece is published without any disclosure of the ghostwriter’s role."

... advertisements passed off as genuine research journals,

"Elsevier, the Dutch publisher of both The Lancet and Gray’s Anatomy, sullied its pristine reputation by publishing an entire sham medical journal devoted solely to promoting Merck products. ... its Australasian Journal of Bone and Joint Medicine, which looks just like a medical journal, and was described as such, was not a peer-reviewed medical journal but rather a collection of reprinted articles that Merck paid Elsevier to publish. At least some of the articles were ghostwritten, and all lavished unalloyed praise on Merck drugs, such as its troubled painkiller Vioxx. There was no disclosure of Merck’s sponsorship."

... and much, much more.

Washington cites a satirical 2003 article published in the British Medical Journal, titled "HARLOT plc: an amalgamation of the world’s two oldest professions" (free registration required to see the full article). HARLOT stands for "How to Achieve positive Results without actually Lying to Overcome the Truth", and was the brainchild of two doctors who effectively catalogued the various ways that one might distort the truth to present a favorable outcome in clinical trials.

Here's where I think the relevance is, for us regular basic science people. It's also a quick tutorial in bad science - what we know we should not do (by commonsense or otherwise) but may be tempted to do, in the interest of making our results look nicer or getting a paper published faster. Some tips from HARLOT, if you want to go down that path:

Cherry-pick your data - Selectively ignore negative results.
Shifting the goalposts - Use one set of standards for your experiments and another for your controls or comparisons.
"Munchausen's statistical grid" - Slice your data in as many ways as you can until you find a statistically significant result.
Overinterpreting positive results

And that's just what you can do with your data and experimental design. The human element is important too: hiring 'experts' to sell your snake oil, celebrity endorsements, and behind-the-scenes moves like lobbying government agencies, using litigation as a tactical weapon....

Ultimately the lesson we should take from all this is the one lesson that formal education cannot really teach: critical thinking and appraisal. Should I trust a certain research finding, even if it's been published in a big-name journal?

This affirms my thinking on how one should read a scientific paper. One of my tutors told me something offhandedly that has stuck with me since freshman year of college: the materials and methods are the most interesting part of a paper. Get to know how an experiment was really done, and look at the actual data as much as possible, instead of just buying the conclusions and interpretations that the authors try to feed you. Many students make the mistake of jumping straight from the Introduction to the Results and Discussion, but these are precisely the parts where the authors are trying to spin their research as being 'relevant' and 'important'. Also: discussion is cheap. It is the data which are the hardest-won; perhaps our attention should be proportional to the effort put into producing it.

Otherwise we might eventually end up buying that snake oil.

German nuclear shut-down - what next?

2011-06-03T11:17:00.000+08:00

Germany has recently announced that it will shut down all its nuclear power plants by 2022. This comes in the wake of the disaster at Japan's Fukushima nuclear power plant, and election gains by the German Green Party in the key state of Baden-Württemburg. The Green Party is a major player in German politics, and supports the cause of denuclearization.

What does this mean for the politics of energy production in Europe and beyond? On the one hand, we want to reduce our dependence on fossil fuels. Existing sources will eventually run out, and the carbon dioxide released by burning them is believed to be the key factor driving climate change. On the other, are nuclear power and renewable energy may be inadequate to meet the shortfall. Nuclear power, in particular, is fraught with difficulties. Not only are people fearful of potential disastrous accidents ('Fukushima' may eventually become a cultural keyword in the same way that 'Chernobyl' is now), but there are practical concerns regarding the disposal of nuclear waste. If we forgo the nuclear option, will wind, solar, wave, and other so-called 'renewables' be enough?

This seems like a good time to introduce an important book on the issue, Sustainable Energy - Without the Hot Air, written by David McKay, a physicist at Cambridge University. The whole book is available for free online, in addition to a 10-page synopsis for those who want to get the gist of it quickly. An even shorter summary has been written by him for the BBC website.

McKay's analysis, which is essentially a straightforward, but necessary, accounting of the relevant figures and facts, shows that relying exclusively or heavily on renewable energy sources would be hugely disruptive and intrusive to both our existing way of life and, ironically, to the environment. The main fact is that wind farms, solar farms, and the like are not energy 'dense' - they require large tracts of land to produce the same amount of power as a conventional or nuclear power plant. Given existing levels of energy consumption (the book focuses on the UK but other industrialized nations are comparable), there would be hardly any land left for other purposes!

Wind farming projects around the world, for example, are already running into opposition from local citizens who find the windmills, and the electrical pylons required to connect them to the grid, hugely unsightly. Their constant whir is also a form of noise pollution. Biofuels and solar energy harvesting, two commonly-proposed alternatives, would possibly squeeze out farming and natural woodland. Even so, they would not yield very much. The figure below, from Without the Hot Air, shows to scale the quantity of land required for biofuels, wood harvesting, and other forms of renewable energy, required to meet the UK's current demand (the last five symbols in the legend are not to scale, but the rest are).

Therefore, if nuclear were out of the question entirely, it seems unlikely that renewable energy, in the state of technology that is available now, would be able to carry the day. Realistically speaking, it is likely that the Germans will find that after the closure of their nuclear plants, the supply of energy from renewables will not be able to keep up and they will be forced to revert in some degree to fossil fuel, or to importing energy from neighboring countries.

Nuclear energy is something even Singapore has to take into account. Even if our country decides that the risks are simply too high for our island-state, we still have to consider the possibility that neighboring countries will adopt nuclear power. It is important to have a frank discussion of the risks and realities now, than to be enveloped in doubt and fear later.

Imitation, flattery, and body-plans

2011-05-20T02:01:00.000+08:00

If imitation is the highest form of flattery, then ants might be among the most celebrated creatures of the insect world. A delightful essay in Current Biology describes some of the more uncanny cases of ant-mimicry among arthropods, among them the treehopper Cyphonia clavata.

Ant-mimicking treehopper Cyphonia clavata. Via Flickr.

The 'ant' that's apparently riding on the back of the treehopper is actually an extension of its headshield. The green coloration of the rest of its body blends in with its leafy background, so on first glance you only see the black 'ant'. The mimic is seated in reverse: if you look carefully at the 'abdomen' of the 'ant', you'll see the green eye of the treehopper staring right back at you. This makes sense because in their defensive posture, ants move backwards.

Creatures that mimic ants are called myrmecomorphs ('ant-shaped', from Greek). There are certainly a lot of ants out there to be imitated (Antweb has high-resolution scans of ant specimens from around the world). One statement in this essay got me thinking:

"... there are about 2,000 species that mimic ants. Not surprisingly, these are nearly all insects or spiders, as a certain degree of body plan resemblance to ants is probably a prerequisite to becoming a myrmecomorph. ... ant mimicry must have evolved many times independently."

Treehoppers are true bugs (Hemiptera) in the family Membracidae. They are known for their headshields, also called helmets, which are responsible for the great diversity of form in this family. Some of them look like they may have inspired the fascinators worn by some of the women at the recent Royal wedding.

Diversity of treehopper headshield forms - Cyphonia clavata is at bottom right. Via Nature

Developmental biologists have now found that the helmet is actually a body plan innovation (original paper abstract), something that's incredibly rare in evolution. New structures are typically formed by modifying or reducing existing parts of anatomy, but innovations such as new appendages or new body segments are much rarer.

Insects typically have a pair of legs on each of the three thoracic segments (T1 to T3), and wings on the 2nd and 3rd (T2 and T3). The helmet arises from the 1st thoracic segment (T1), and anatomical observations have suggested in the past that they might be homologues of wings. By looking at gene expression in a developing treehopper, biologists found that wing-specific transcription factors (which control the expression of other genes), especially Nubbin, are expressed in the developing helmet, which indicates that it's developmentally homologous to wing appendages. They suggest that the Hox genes responsible for suppressing wing formation in T1 have been suppressed in treehoppers, allowing the evolution of the helmet. Because they aren't needed for flight, they aren't faced with the same physical constraints and so have been able to develop into a wild variety of shapes and sizes.

So coming back to the statement about body plan resemblances quoted above, perhaps the idea is more beguiling than it actually should be. An ant mimic for sure will have to be bilaterally symmetrical, of the right ant size, but beyond that I don't think the prerequisites for mimicry can be quantified. For conceptual proof of this, watch this famous octopus species mimic in turn a brittlestar, lionfish, and sea snake.

"Primitive" fungi discovered... in a pond!

2011-05-14T05:12:00.000+08:00

The microbial world is ubiquitous (there are microbes everywhere!) and vast (there remains so much to be discovered). Basic discoveries are made on a fairly regular basis, and new taxonomic groups of microorganisms are routinely identified when people sequence DNA from the environment.

We don't necessarily have to go to exotic locations like hot springs or the deep sea to discover something new. A new group of "primitive" fungi has recently been described from samples taken from a variety of locations around the world, including a pond in Devon near Exeter University in the UK, where the scientists worked.

This group, called the cryptomycota (not capitalized, because it's not yet officially described according to the rules of taxonomy), has characteristics which make it apparently a 'missing link' between the fungi and other eukaryotic microbes. Sequences of a number of genes place it as a sister group to the rest of the fungi; that is to say, on the family tree of the fungi, it branches off at the very base of the tree.

Although the term "primitive" is often used for groups that fall out at the base of phylogenetic trees, like the cryptomycota, it's important to note that they don't necessarily resemble the ancestors of these groups in every respect. That is to say, just because one branch of your family split off many generations ago from your own lineage, it's not true that this branch more closely resembles your great-great-grandparents. Likewise with other living organisms.

However, in this case, the cryptomycota are called a 'missing link' precisely because they have some characters which were presumed to be present in the ancestors to fungi. They have flagella, which are absent in all 'true' fungi except the chytrids. In fact, chytrid fungi were originally not considered to be true fungi, because they had a flagellated stage in their life cycle. Aside from the cryptomycota, the chytrids are the next-most-basal group of fungi. Furthermore, in every intro biology class we learn that fungi have a chitinous cell wall. These are lacking in the cryptomycota, and presumably also lacking in the precursor to fungi, because it's a feature that's unique to the 'true fungi'.

Fluorescence microscopy image of cryptomycota. Flagella are labeled with an antibody (red), the nuclei with a fluorescent stain (blue), and the ribosomal RNA labeled with an in-situ hybridization probe (green). Via BBC News.

As before, it's important to point out that the term 'missing link' is often misinterpreted. Just as the word 'primitive' has commonsense connotations of being somehow worse off than the 'advanced' species, the same goes for 'missing links'. In the context of systematics, what it refers to is the fact that some species retain traits that are present in ancestral species (either known from fossil evidence or inferred by reconstruction), and their having a mixture of 'derived' and 'primitive' characters provides additional confirmation for how we reconstruct the phylogenetic relationships of these related species.

Also notable is how these fungi were identified. It's fairly routine now to study microbes from the environment without needing to culture them in the lab. Sequences of a well-known gene, such as the ribosomal RNA genes, can be produced from DNA extracted from the environment, and then compared with known sequences in databases, to see 'what's out there'. Novel sequences identified in this way can be related to actual cells under a microscope, by labeling them with probes that specifically target these unique parts of their ribosomal RNA, a method called in-situ hybridization. That's what's shown above in the micrograph, where the probe labeled with a green fluorescent molecule demonstrates that these peculiar flagellated cells were the mysterious fungus-like sequences that the scientists kept finding in environmental samples.

So the lesson here is: There's plenty out there waiting to be found, even in stagnant nondescript ponds! As DNA sequencing gets cheaper and labeling techniques become more convenient, I'm sure that we'll be hearing much more news like this, about cool new microbes that many years ago would have been impossible to identify or classify.

Sources:

Jones et al. "Discovery of novel intermediate forms redefines the fungal tree of life." Nature (published online: 11 May 2011) doi:10.1038/nature09984

BBC News

Highlights of the Week

2011-05-14T04:07:00.000+08:00

Some interesting news and articles from around the web for this week:

Cicadas are emerging en masse in the Midwestern United States after yet another 13-year cycle.
Cicadas are insects which are known for their loud and distinctive sounds produced by a mechanism called 'tymbalization' in their abdomens. Several species in the genus Magicicada in the US are called 'periodical cicadas' because they transition into the adult phase of their life cycle in a synchronized manner in cycles of 13 or 17 years. This summer the time has come for the emergence for the so-called brood XIX. These emergences happen in such numbers that early European settlers thought that the cicadas were the pestilential "locusts" of the Bible, and their carcasses litter forests in a deep crunchy layer. Find out more about cicadas at this website from the University of Michigan.

Mathematics and biology have a deep and subtle relationship.
Viruses, for example, have self-assembling coats made up of protein subunits, which tile together in specific geometric forms. Disrupt these geometries, and one might be able to render a virus harmless.... Other fields of mathematics, such as chaos theory, can help in modeling natural phenomena such as plankton dynamics in the ocean. (I wish this essay was illustrated, though.)

How do flatworms regenerate their missing body parts?
The planarians (flatworms) are favorite classroom examples for regeneration because of their freakish ability to regenerate a complete worm when cut into multiple pieces. New research shows that cells in the worms called neoblasts, which can be thought of as analogous to stem cells in other animals, are pluripotent, meaning that they can develop into any cell type in the body. Researchers have also found some of the factors that determine whether a newly divided cell in a regenerating animal will develop into part of the head or the tail.

Fire ants link up into waterproof rafts

2011-05-11T03:09:00.000+08:00

Many insects, such as the aptly-named water-striders, are able to exploit surface tension and literally walk on water. However, the majority are only moderately hydrophobic, and because they are denser than water, have to struggle all the harder to remain afloat the larger they are.

Fire ants live in places which are frequently inundated by water. Individual ants placed in water can float, but not very well. How then do they cope with flooding? It turns out that they assemble themselves into ant 'rafts', cooperating to improve their buoyancy and waterproofing.

Insect cuticle itself is already water-repellent to some extent, but alone it is not enough to explain how a clump of ants, gripping onto each other mandible-to-leg, is more buoyant per unit mass than an individual ant. The answer lies in their ability to trap a layer of air (called a 'plastron') around their bodies. By clumping together, they increase the size of these plastrons, and can entrap larger air bubbles within the clump. These lower the effective density of the ant mass, and also allow them to breathe (insects breathe through pores in their cuticle) even when submerged.

Quotable quotes from the paper:

"Ants were scooped with spoons into 100-mL beakers rimmed with talc powder and weighed to count their numbers. Using the natural adhesion of the ants, a few swirls of the beaker was sufficient to roll the ants into balls."
"Not surprisingly, ant spheres that are placed on solid surfaces quickly disintegrate as the ants flee in all directions."
"By harnessing two live ants with an elastic band, we found that the maximum tensile force between them is F = 620 ± 100 dyn (N = 11), or more than 400 times body weight."

Reference:
Mlot, Tovey, & Hu. "Fire ants self-assemble into waterproof rafts to survive floods." Proceedings of the National Academy of Sciences, USA (10 May 2011) vol. 108 no. 19 pp. 7669-7673.

Cuckoos mimic hawks to scare hosts

2011-04-18T06:14:00.000+08:00

Cuckoos have a bad reputation, and it's probably going to get worse. They're known for being brood parasites, depositing their eggs in the nests of other bird species. When these hatch, the cuckoo chicks aggressively demand food from the host parents and also eject their unfortunate step-siblings from the nest. As a result, the cuckoo gets a free pass on child-raising.

It is little surprise that cuckoos coming in to lay their parasitic eggs are often 'mobbed' by the birds that they target, in order to drive them away. However, a recent study has found that 'naive' birds are reluctant to approach cuckoos that have a barred (striped) pattern on their undersides, compared to cuckoos that lack such a pattern. This is interpreted as a form of Batesian mimicry by the cuckoos, taking on the stripes of sparrowhawks, which are birds of prey.

Cuckoos therefore may use two different kinds of mimicry in their lives: as adults mimicking birds of prey to prevent host birds from attacking them, and in the nest mimicking host chicks to convince the host parents to feed them.

Sources:

"Cuckoos mimic hawks to scare their hosts, says research," by Victoria Gill. BBC Earth News, 17 April 2011
Welbergen, J. A. & N. B. Davies, 2011. A parasite in wolf's clothing: hawk mimicry reduces mobbing of cuckoos by hosts. Behavioral Ecology. First published online 21 Mar 2011, doi: 10.1093/beheco/arr008 [abstract].

Organic material preserved in fossilized reptile skin

2011-03-27T23:56:00.000+08:00

Fossilized organisms shared the same fate as the poor folk who dared to look at the mythical beast Medusa with their bare eyes: they were turned into stone. Most fossils that show evidence of soft body parts (i.e. not bones, shells, teeth and the like) are impressions, like natural plaster casts. The original material has either decayed away, or remains as an amorphous carbon film on the specimen.

Occasionally, well-preserved fossils show up which apparently preserve some trace of organic material. A specimen of reptile skin from the 50 million year old Green River Formation in Utah, USA, is one such candidate. Scientists using a sensitive, non-destructive method called Fourier transform infrared spectroscopy (FTIR) have showed that organic substances, which can be related to the original beta-keratin of the reptile skin, are present in the fossil.

The method is common in organic chemistry and the study of materials. Different chemical functional groups absorb a different characteristic set of wavelengths when exposed to infrared light. These patterns of absorption can be used to identify the groups. They showed that the fossilized skin had amide, thiol, and hydrocarbon groups which can be related to the products of beta-keratin (the thiol would come from cysteine bridges) and lipid breakdown. This was comparable to the results obtained from modern gecko skin. What's even more exciting is that when the detected levels of these chemical groups were mapped across a portion of the specimen, they revealed a pattern that corresponded to the visible scaly skin pattern of the fossil (below).

The authors of this study were careful in how they worded their statement. They said that "biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved," and not that "proteins are preserved in the fossilized skin." This is because the original proteins are no longer detectable (they tried to see if any protein could be isolated for sequencing), and the FTIR method only detects functional groups, not entire molecules.

What's particularly exciting about this, aside from the fact that we can still "see" the traces of ancient organic matter after 50 million years, is that this is a non-destructive method. The sensitivity also allows the mapping of information across the specimen, providing spatial information too. As one of the researchers told the BBC: "We have learned that some of these compounds, if the chemistry is just right, can give us a bit of a whiff of the chemistry of these ancient organisms." A very tantalizing whiff indeed!

Human DNA contaminates genome databases

2011-02-18T03:55:00.000+08:00

Scientists rely extensively on public databases of genomic sequences, such as GenBank, based in the USA, and the European EMBL. They might use this for detailed and exacting statistical studies of molecular evolution, or for doing a quick search to check whether a sequence they've just amplified is indeed what it is. Most biology students today have done a BLAST search at some point, underscoring the ubiquity and usefulness of these bioinformatics tools.

One big problem that haunts these sequence databases, however, is contamination and mis-annotation. Sequences are not always what they say they are, and scientists who don't carefully check the provenance of their data, or who trust that "because it's in GenBank it should be ok" may find their painstaking analysis to be in vain if they had used the wrong data to start with. While this problem is widely acknowledged, it comes as a surprise, perhaps to hear that nearly 20% of non-primate genomes in public databases have some degree of contamination from human sequences, probably DNA shed from the skin of the very scientists and technicians who prepared the material for sequencing.

Why non-primate genomes in particular? The research team from the University of Connecticut decided to use a particular short (less than 300 bases) sequence in the human genome, called AluY, which is repeated in great numbers and is highly conserved among humans and other primates. Alu elements are retrotransposons and an example of SINEs (short interspersed elements) that make up much of the genome. The AluY subfamily is derived from an insertion event that happened in the common ancestor of primates, and its specificity to primates is a marker of our common ancestry.

This is a creative use of past evolutionary events for tackling what is effectively an applied, technical question. It really helps to know some history!

Highlights of the Week: Catching up on Blogging

2011-02-10T07:18:00.000+08:00

It's been a while since I've written anything new, and the explanation is straightforward: classes just started up again and have hit me like a freight train. Two weeks in, I've just had a chance to catch my breath.

But I've still been keeping an eye out for interesting articles and news on the Web, and here's my selection of cool stuff from the past week (okay, two weeks...):

Green Porno film star and director talks about her work. Isabella Rossellini's short film series, Green Porno and its follow-up Seduce Me ("A potential sponsor called to say they liked the films but that they couldn't support anything that had the word "porno" in it") are short (1-2 mins), award-winning gems about the peculiar sex lives of different animals. She stars in all of them as the animals, dressing up in fantastic paper costumes (see above).

Vladimir Nabokov's biogeographic theory on the origin of the Polyommatus blues butterflies has been confirmed by lepidopterists using molecular techniques. Aside from being a successful author in both his native Russian and his adopted English (in which he wrote his most famous book, Lolita), he was a great butterfly enthusiast and was for a time curator of Lepidoptera in Harvard's Museum of Comparative Zoology.

Woodpecker skulls inspire the design of more effective shock absorbers. Fun fact: woodpecker skulls decelerate by up to 1200 g each time it hammers (more than 20 times a second!), whereas humans would be concussed by an acceleration/deceleration between 80-100 g.

World Wildlife Foundation launches a new document format, similar to Adobe's PDF format, but which doesn't allow the document to be printed, to raise awareness about excessive paper use. As expected, the file extension is .wwf. Good idea, or gimmick?

The Galapagos Islands, biodiversity hotspot and inspiration for Darwin's theory of evolution, have been taken off UNESCO's list of endangered World Heritage Sites. Doesn't mean that they're out of danger, though. Ironically, the effects of tourism are the greatest threats to the islands today, as the booming tourist industry encourages development and immigration to the archipelago.

Photo gallery of the world's 10 most threatened rainforests, including Sundaland, the Philippines, and India-Burma.

Hidden costs of bioethanol

2011-01-27T10:49:00.000+08:00

Are biofuels really 'green' as they claim to be? This subject has come up before on this blog, usually on the side of 'no'.

A recent piece of correspondence to Nature (caution: paywall) from two scholars at the Federal University of Alagoas in Brazil points out the real costs associated with Brazil's experiment in sugarcane farming for bioethanol. Brazil was a pioneer in using sugar for vehicular fuel, decades before biofuels became fashionable in the rest of the world. They say that over 85% of the rainforest cover in the state of Alagoas in Brazil has been destroyed over the period of 35 years, since the beginning of the sugarcane to biofuel program. The loss of rainforest cover is thought to be responsible for landslides and flooding associated with heavy rains.

They call it "a dirty footprint in one of Brazil's poorest states." Biofuels gained popularity because they are supposedly 'renewable', as opposed to finite fossil fuels. Nothing comes for free, however, and this small planet we live on has only limited land available. For fuel crops to be grown, additional forested land has to be cleared, or land that would otherwise have grown food crops have to be converted. The former causes a net carbon gain to the atmosphere as well as a loss of biodiversity. The latter straitens the food supply, risking higher prices and endangering vulnerable populations.

There's no way to win!

Were 19th century naturalists also imperialists?

2011-01-26T04:35:00.002+08:00

The 19th century was a fertile time for Western natural history, in large part because of the curiosity that attended their newly acquired colonial dominions around the world, especially in the tropics. Naturalists and adventurers followed closely behind the footsteps of conquering soldiers and colonists, while officials and other colonial expatriates also sent specimens back home to the museums of London, Paris, and other European capitals. In many cases, colonial administrators and intrepid naturalists were one and the same person, as the examples of Rumphius and Stamford Raffles show.

Post-colonial sentiment, however, leads many people to question the Western narrative of the “heroic naturalist” opening up new vistas of knowledge, as the writer Richard Conniff comments upon in this blog post. Were they really discovering new species, or simply claiming credit for knowledge that locals long knew. After all, many European naturalists relied heavily upon local guides and informants, without giving them due credit (a practice that has changed considerably with modern co-authorship and local collaboration courtesies).

In particular he discusses Pére Armand David, a French missionary and naturalist who traveled in Qing dynasty China and discovered (for the West) many species such as Pére David's deer, which were already known to Chinese. Is it fair, then, to call him its discoverer? Some would say to do so would be cultural hubris and insensitivity.

Part of this is to do with how we are limited by past history. Western science was born of the response of European cultures to the newfound knowledge of the world beyond its borders. Its conceit of being universal is partly a historical accident, of being at the right place at the right time, so to speak. The fact that most of the modern world puts Western science in a privileged position as an explanatory framework through which to view the world is part of that historical accident (though see this article for a rejoinder). Now that it has been so widely adopted, to call it “Western” science might no longer be accurate or honest. Calling the European naturalists of old “imperialists” might be true in individual cases (many of them were certainly serving imperial projects or believed in the imperial cause), but to reject their science on these political grounds is a non sequitur.

In some cases, their work helped to preserve local knowledge that might have been lost otherwise (ironically through the socioeconomic change wrought by colonialism). I'm reminded, for example, of I.H. Burkill's monumental compendium, Dictionary of Economic Products of the Malay Peninsula, wherein he recorded many traditional uses of the seemingly innumerable plants, animals, and natural products of Malaya. With development, the traditional strand of transmission for this knowledge between generations has been broken, leaving those of us who are interested to have to acquire it from the written record. Hence the standard Malay dictionary in Malaysia, the Kamus Dewan, frequently refers the reader to Burkill's work and those of other colonial-era writers in the definitions associated with plant names, simply because that is the textual record that we have.

So yes, I would say that many naturalists were imperialists, but we should disentangle their imperial legacy from their scientific one. We can't correct the political injustices of the past, but their documentary record of the lost, rich world which we have lost continuity with can help us recover that heritage and begin to appreciate it again.

Latest named cat species actually two subspecies

2011-01-24T21:35:00.000+08:00

The Sunda clouded leopard (Neofelis diardi) was recognized as a distinct species, separate from the mainland Southeast Asian clouded leopard N. nebulosa, in 2008. Both are Vulnerable species, according to the IUCN.

Based on molecular genetic data, researchers suspected that the Sunda clouded leopard might actually represent two different subspecies, and this has been confirmed by a combination of molecular genetics and skull/dental features. There may be additional differences in coat patterning, but the number of specimens available for inspection is not enough to make a definitive statement.

The two subspecies are geographically separated: the Sumatran subspecies (N. diardi diardi) and the Borneo subspecies (N. diardi borneensis). They were probably isolated from each other after Sundaland land bridges were cut off when sea levels rose after the last ice age.

The BBC has a good summary article including a rare video of the animal from Dermakot National Park in Sabah, Borneo.

Rebirth of Bird Watching

2011-01-23T04:07:00.000+08:00

"Bird watching" sounds like such a back-to-nature pursuit: just me and my binoculars, hiding behind a bush and waiting for the birds to come out. But with digital cameras making high-quality photography cheap and accessible, and the Internet making sharing those pictures and swapping tips so much easier, birding has become a hobby for the technologically savvy too.

Today, there are crowd-sourced bird-mapping tools, birding packages that double as vacation getaways, birding blogs, birding iPhone apps, and remote-birding Web sites that don't require watchers to be present in the landscape at all. A few old-fashioned birders may still practice their hobby in isolation with binoculars and field guides, but the birding community, these days, has moved on to gather, check, and share sightings across great distances using the fruits of technological industry and the jumbo jet.

This is from an amusing article about the different kinds of birders and the kinds of communities that they form. What the writer calls "privileged aloneness"–getting up to go birding before other people are even awake–seems like a good way to describe the attitude that many birders have.

The way I see it, it's as much about the birds as it is about immersing yourself in the community and its special culture. Just like hardcore runners (or cyclists, or computer geeks) have their own magazines, fashions, gear fads, the same with birders.

Those birds don't stand a chance.

Thailand Closes 18 Coral Reef Diving Sites

2011-01-22T05:16:00.000+08:00

Dive sites in 7 national parks across Thailand have been closed in response to coral bleaching that has affected up to 80% of corals surveyed.

According to the Bangkok Post, the sites affected are:

Hat Chao Mai National Park in Trang, Mu Koh Petra and Tarutao national parks in Satun, Mu Koh Chumphon National Park in Chumphon, Hat Nopparat Thara-Mu Koh Phi Phi National Park in Krabi, and Mu Koh Surin and Mu Koh Similan national parks in Phangnga.

The bleaching is attributed to elevated sea temperatures in past years. Closing the sites off to tourists will certainly reduce damage from irresponsible divers and waders (see this photo (via NYT) for something horrifying), but it will not do anything about the coral bleaching itself.

'Avatar' Director Plans Deep Ocean Dive for Next Movie

2011-01-19T02:34:00.000+08:00

Director James Cameron has commissioned a deep-diving submersible, being built in Australia, to dive to the deepest point in the world's oceans, the Mariana Trench of the Pacific, in order to film undersea footage for his upcoming sequel to 2009's blockbuster movie Avatar.

The article linked to above has a great summary of the last (and only) successful dive into Challenger Deep, the deepest part of the Trench, which was the Trieste dive of 1960. The Trieste was a custom-built submersible, comprising a spherical capsule in which the two crew sat with their instruments, suspended underneath a giant container of gasoline. It functioned like an underwater blimp: the gasoline acted as the buoyant balloon, and they carried ballast to bring them down, which was jettisoned for the ascent. It's a great story of engineering and derring-do, unfortunately not much was learned about the biology of the deep sea from that expedition.

I particularly liked the writer's description of how life can survive at such high pressures in the deep:

One oceanographer described how as follows: a human is like a party balloon – taken down to great depths it will be crushed to nothing; but a deep-sea fish is like an untied balloon – take that down to the bottom of the ocean and the pressure has little effect. Perhaps the greatest difficulty is that intense pressure causes nerves to stop working, a problem that deep-sea life has side-stepped by evolving a more robust physiology at molecular level.

Cameron's quest is not really a scientific expedition, but is still an exciting opportunity for observation of life in the deep sea. The director is also known for his underwater documentary film-making, such as Volcanoes of the Deep Sea featuring the submersible Alvin). Given that the marine realm has inspired many of Cameron's cinematic works (Aliens, The Abyss, Avatar, and of course Titanic) it's only natural that he returns to it for inspiration, like marine enthusiasts all over the world, except with deeper pockets!

Melting Glaciers Reveal Plane Wrecks in Andes

2011-01-17T11:14:00.000+08:00

A bizarre and somber side-effect of retreating glaciers in the Andes mountains: decades-old aircraft wrecks and dead climbers, as well as older Inca mummies and 'icemen', are being revealed by the thaw:

"Some discoveries are personal, allowing families closure after years of mourning loved ones who appeared to have vanished. Others have added alluring clues into the history of human migration, diet, health and ethnic origins..."

Interspecies Monkey Play

2011-01-16T11:25:00.000+08:00

From the NY Times's "Scientist at Work" blog: primatologist Anthony Di Fiore from NYU writes about watching a juvenile spider monkey play with juvenile woolly monkeys in Ecuador, a "a rare, long bout of interspecies play". Sadly the video associated with the article doesn't seem to show the playing monkeys....

How to be a Famous Scientist

2011-01-14T08:17:00.000+08:00

Can you aspire to be as famous a scientist as Charles Darwin?

"Darwin's full name is invoked at least once in more than 2% of books published in the English language. (I know that is hard to believe, but we have carefully verified it. And it is on the rise. "Charles Darwin" appears in about 4% of English books published in the year 2000.)"

Science magazine feature The Gonzo Scientist teamed up with one of the team that gave us the recent culturomics study (pdf) and Google Ngrams, to assess the nature of scientific fame. Among the advice for making a name for yourself? Don't be a mathematician, and consider blogging....

John Hunter and the Giants

2011-01-14T00:20:00.001+08:00

This isn't the name of a band. John Hunter, the great 18th century surgeon whose anatomical collection now forms the Hunterian Museum of the Royal College of Surgeons, was fascinated by 'freaks' of nature. Among them, the Irish giant Charles Byrne, who measured 2.34 meters in height and became a celebrity when he showed up in London.

Hunter met Byrne in life, and had designs to acquire the giant's skeleton after his death, for his museum. However, Byrne tried to thwart Hunter's plans, and after he died at the age of 22, he had made his friends promise to bury him at sea. Hunter's hired hands, unfortunately for Byrne, managed to bribe or intoxicate the funeral party, or so the story goes, and stole the body away to Hunter's back door in the upmarket Leicester Square neighborhood, where in his basement the body was boiled down to a skeleton.

According to the Guardian, an endocrinologist named Márta Korbonits at London's Barts hospital has found a possible genetic cause for Byrne's gigantism. His growth spurt (and subsequent early death) was due to an excess of growth hormone produced by the pituitary gland. Pituitary tumors are the most common cause of gigantism, and today is treated by surgical removal of the tumor.

She studies a genetic condition called familial isolated pituitary adenoma, which is caused by a mutation in a gene called AIP (Aryl Hydrocarbon Receptor Interacting Protein). According to her work, Byrne's mutation (discovered by sequencing DNA from his teeth) came from a common ancestor as a population of people bearing the AIP mutation in Ireland today. As the article says:

Both Holland and McCloskey [a FIPA survivor and film-maker] came from Tyrone and were fascinated by the number of actual giants in the area, and by the way they figured in Irish folklore not as freaks, but as kings, seers and poets.

John Hunter himself was also a colorful character, living in a colorful age. He might be called the prototype of the 'brash surgeon', more interested in showing off their surgical chops (and in Hunter's case - acquiring specimens for his collection) than the comfort of their terrified patients.

A good recent biography of him is Wendy Moore's The Knife Man. In his time (and indeed until the modern age), there was no clear line between medicine and natural history, and many of his famous experiments and observation concern the latter subject.

He was one of the first to experiment with surgical grafting. Among the grafts he performed was that of a freshly-pulled human incisor onto the comb of a rooster. We are told that this required repeated trials–I wonder who donated all those teeth! Eventually, the graft did 'take', and he sacrificed the animal, in order to bisect its comb to see how it connected to the tooth. He found that blood vessels from the rooster had indeed penetrated the tooth pulp: "The uniting of parts of different animals when brought into contact he attributed to the production of adhesive instead of suppurative inflammation, owing to their possession of 'the simple living principle.' " (Encyclopedia Britannica).

After his death, his anatomical collection found its way to the Company of Surgeons. It suffered damage during World War II, but is still on display today in London.

Wilderness Parks May Change Beyond Recognition

2011-01-13T03:35:00.001+08:00

Climate change may cause changes to national parks in the US that will alter their very identity, according to scientists and conservationists interviewed by Nature magazine. It's not all about glaciers melting, either. Warm winters in the past few years have allowed populations of the mountain pine beetle to boom in Yellowstone National Park, where they previously were kept in check by winter cold. As a result, stands of dead trees killed by the beetle, which bores into the wood of living trees, are now a common sight. Park managers and conservationists

"... are coming to terms with the idea that the historical remit of most parks systems — to preserve a piece of land in its 'natural' state — is untenable. 'You can't fight the climate,' says Ken Aho, an ecologist at Idaho State University in Pocatello, who studies non-native species at Yellowstone National Park in Wyoming. 'Eventually you have to throw up your hands,' he says."

Aldo Leopold, author of A Sand County Almanac, and an influential pioneer of wildlife management in America, opined that "a national park should represent a vignette of primitive America." On the other hand, the very idea of an "untouched wilderness", as something apart from human civilization, and to which we should have recourse when we wish to seek Nature (with a capital N), is a recent invention.

It's an unrealistic idealization because there's really nothing that has escaped the human hand, being only a matter of degrees. Environmental historian William Cronon reflects on this in a thought-provoking 1995 essay entitled "The Trouble with Wilderness; or Getting Back to the Wrong Nature" (reprinted 2005 in Guernica magazine).

The concern about the fate of Yellowstone and other iconic American parks reminds me of a research talk I attended a long time ago; unfortunately I can't remember who gave it and when. It was about the gazetting of marine reserves, and the speaker pointed out that the fact of accelerated climate change meant that our intuitions about what to preserve are often wrong. Instead of drawing park boundaries only around the prominent patch of pristine reefs, which with rising temperatures and bleaching will eventually become an ugly dead zone, we should include in large part those areas which are less picture-perfect, but which contain communities which are more robust to change and which the future ecosystem will still rely upon.

The overall message is that we can no longer afford to think of nature as 'timeless', especially with the prospect of further anthropogenic change.

Glimpse of the Past - 'The Borneo Story' Online

2011-01-12T05:24:00.003+08:00

The Borneo Story: 'Birds Nest Soup' from The Doozer on Vimeo.

Catching up on leisure reading over New Year, I re-encountered the name of Tom Harrisson, who has been described as a "polymath" - pioneering British anthropologist, WWII hero, long-time director of the Sarawak Museum, conservationist, but also a prickly personality whose character invited controversy and divided opinions.

I was pleased to find that a series of documentaries that he co-produced in the 1950s, titled 'The Borneo Story', is available online. One of them, "Birds Nest Soup", which won a prize at the Cannes Film Festival, is embedded above.

These documentaries are a valuable glimpse into the state of Borneo in the postwar period, when it was still a tropical idyll, relatively untouched by large-scale plantation agriculture. Now, of course, birds nest soup is often commercially produced by inducing swifts to nest in abandoned buildings or purpose-built 'hangars', instead of being collected from the wild.

A 2006 BBC documentary, "The Barefoot Anthropologist" (YouTube), hosted by David Attenborough, gives a sense of the man and his exploits, including how he "restarted headhunting in Borneo". It's not all happy memories, though: one of the Australian soldiers under his command during the war describes how he wanted to shoot Harrisson, and is visibly agitated talking about him, half a century on!

More about his life can be read in the biography by Judith Heimann, The Most Offending Soul Alive.

Dolphins for Sentosa Resort Moved to Philippines?

2011-01-10T02:56:00.000+08:00

The proposed Marine Life Park run by Resorts World Sentosa (RWS) has come under fire for its planned dolphin show ever since word about it got out to the public. The dolphins were captured from the wild in the Solomon Islands and shipped first to the Philippines then to Langkawi, where they have been held for training.

Last October, two (out of seven) were reported to have died from a bacterial infection. In the last month, they have been moved again. According to Today Online:

An employee who wanted to be known as Ahmed, told MediaCorp that the dolphins were put into a container last month and sent to Langkawi's international airport, from where they shipped to the Philippines.

RWS has defended its decision to have a dolphin display by saying that it complied with CITES regulations on the trafficking of endangered species, and that the display would be "educating the public on marine life and environmental issues."

In reply, a member of the public claims that having "dolphins and whales in captivity is not about education or conservation, it is about one thing - profit,"and that the best place to learn from them is in their natural habitat.

Now that nature documentaries have become so advanced both in technical terms and in narrative sophistication, I think that one would learn more from watching a good film about the life and behavior of dolphins, filmed in the wild with wild animals, than from paying to see a handful of caged animals performing tricks. I'm not saying that zoos don't have value; what I have in mind are rare animals whose beauty and fascination lie as much in their behavior and interactions with their natural environment as with their physical appearance. Dolphins certainly fall in this category.

House Too Small? – Overlapping Genes in Viruses

2011-01-09T08:17:00.006+08:00

Protein coding genes are complicated things: the four bases of DNA are arranged into triplet codons, each of which codes for one of 21 (more or less) amino acids, which are strung up in a polypeptide chain, folded into a complex 3-dimensional structure where precise shape and chemistry determines function... It would seem that any perturbation would throw this finely-tuned system off-kilter.

Even more outrageous is the notion that genes can overlap and still code for perfectly functional proteins, because this implies that, for part of the gene at least, a different reading frame still has functional meaning. This flies against our intuition that frame-shift mutations are the deadliest of all, and has been likened to taking a paragraph of text, moving all the spaces between words down by a character, and still being able to read it, but this time with a completely different meaning!

Viruses, though, are capable of this sort of contortion, and a number of hypotheses have been proposed to explain why they find it necessary to do so. Is it a way to reduce the overall genome length in the face of a high mutation rate? Or is it a means to couple together the expression of more than one gene? Looking at a number of viral genomes, a team from Italy and the UK claim to have found the reason: overlapping genes are a response to the constraints placed by viral capsid size.

For viruses that use RNA for their genetic material, there is a known inverse relationship between genome size and gene overlap: the longer the genome, the less gene overlap is present. They confirmed that this also held for DNA viruses. But when they grouped viruses by the kind of capsids they have–icosahedral vs. flexible–they found that this relationship is strong in the icosahedral capsid viruses, but weak in those with flexible capsids. Capsids are protein 'coats' that encase the viral genome; icosahedral capsids are particularly rigid and constrained in size, because their geometric configuration (icosahedra are one of the five Platonic solids of classical geometry) is the result of the interlocking of the protein units that make up the coat. There are precise mathematical rules that govern the assembly of these units.

Icosahedral adenoviruses (electron micrographs) with cartoon of icosahedron. (Wikimedia Commons)

On the surface, it seems like an extreme solution, even reminiscent of the infamous Bed of Procrustes. These viruses appear to have found a way of surviving the ordeal. It's so striking because we wouldn't expect to see what is patently a physical constraint leaving such a distinctive genomic signature, the latter being strictly informational. At the molecular level, though, there may be a fuzzier line between the two.

This is one of those things which writers used to attribute to the 'ingenuity of Nature', but speaking in materialist terms:

"In effect, the capsid poses an engineering problem for the creation of genomic novelty, and gene overlap is the way around it."

History of Amazon Basin Shaped by Andes

2011-01-09T04:36:00.000+08:00

Here's something that has relevance to the name of this blog. The traditional model for the history of Amazonian biodiversity held that much of it weathered the Pleistocene period in forest fragments, or refugia, and from there spread out again to repopulate the basin when the climate again became amenable. These so-called diversity centers, however, have been shown to be artifacts of sampling, rather than a real biotic phenomenon, pushing back the origins of diversity in the Amazon to earlier periods of geological history.

Amazonia today. From Hoorn et al. 2010 (Link)

A recent review in Science magazine synthesizes what is known about the geological and biological past of the Amazon, to reconstruct a scenario where the uplift of the Andes mountains, which are relatively young, is responsible in part for the present-day patterns of diversity in the basin. Prior to the Andes uplift (which began in the Paleogene after the end-Cretaceous 65 Mya, and continues to the present day), the geology of Amazonia was 'cratonic', i.e. it was dominated by the rocks of the continental center. The rising mountain range changed both the climate, e.g. by intensifying rainfall to the East of the range, and also the landscape, as sediment eroded off the mountain faces and came to be deposited in the basin below. Extensive, inland wetlands (the Pebas system) first appeared in correlation with intensified uplift and then disappeared, replaced by a riverine, fluvial landscape.

The present-day biota of the Amazon is very much terrestrial. Therefore, the disappearance of the extensive wetlands, which formerly fragmented the terrestrial forests, was a prerequisite for the appearance of modern Amazonian fauna and flora. Furthermore, diversity as measured today for both mammals and tree species is highest where the soils are of Andean origin (swept down by erosion and deposited by the rivers), as opposed to where the original cratonic soils remain at the surface. Perhaps the nutrient levels are linked to both forest productivity and resultant diversity, but the climate engendered by the topographic relief may also have a role in patterns of diversity.

This is very much a 'big picture' review, and is worth reading to think about how the literal shape of the Earth has a role in defining the life that dwells as a thin film on its surface.

Prehistoric Human Remains found in Java

2011-01-08T10:27:00.001+08:00

Via our fellow SE Asian science blog SEAArch, the Southeast Asian archaeology newsblog, comes a report from Indonesian newspaper Tempo Interaktif on remains of prehistoric humans found in the Tata and Bonjong caves in Java.

Unfortunately, there is no further information in the article, nor has the research (apparently) been published yet, so there's not much more to say. Java, though, is where the celebrated skullcap of 'Java Man', a specimen of Homo erectus erectus, was found in 1891 by Eugene Dubois on the banks of the Solo River. Also in Java, close to the Java Man site, is the Sangiran Early Man site, which has been declared a UNESCO World Heritage Site, and has yielded many more hominid fossils and ancient tools.

Ammonite Jaws Reconstructed in 3D with X-rays

2011-01-08T06:20:00.000+08:00

Ammonites are common fossils with distinctive chambered spiral shells – so common that they're probably some of the first fossils most of us encounter, as decorative objects sitting prettily in someone's home or workplace. They're cephalopods, extinct relatives of the octopus, squid, and cuttlefish, but unlike these, have an external shell. The still-extant Nautilus is a cephalopod with an external shell, and is often confused with the ammonites, but these two actually represent two different lineages within the cephalopods.

Like most molluscs, ammonites had a (presumably) chitinous feeding apparatus comprising jaws and a radula–a rasping row of teeth-like structures unique to molluscs. These have been recovered occasionally in the past, but using X-rays, these have been studied in-situ in the ammonite Baculites from the Upper Cretaceous of South Dakota, allowing them to be reconstructed in breathtaking, 3-dimensional detail (paper in Science).

What's more, the food of these creatures can also be detected and identified. Within the buccal mass of these ammonites were fragments of small isopods, also called pill-bugs, which are crustaceans that, as their name suggests, look like rounded pills.

Unlike Nautilus and other nautiloids, the jaw structure and the kind of food they ate suggest that Baculites fed on small prey in the water column (i.e. zooplankton), instead of larger prey on the sea floor (benthic). They hypothesize that this preference for planktonic food may be responsible for the extinction of ammonites at the end of the Cretaceous, when the composition of planktonic communities changed considerably, but this theory will certainly have to be tested with more fossil data, as the commentary article points out.

Formosan Black Bears

2011-01-01T08:43:00.002+08:00

Hwang Mei-hsiu (黃美秀), assistant professor at National Pingtung University of Science and Technology, Taiwan relates the challenges to study the ecology of Formosan Black Bears in a dialogue with President Ma Ying-jeou.

Prof Hwang describes the difficulties of studying the black bears in the remote mountains of Taiwan and rarities of sighting the illusive animals. She responded regretfully that she has no exact population figure despite 15 years of research. With initial estimates of about several hundred for the island, she added that the viable population figure should be 2,000. This reflects the endangered status of the bear in Taiwan

Watch the enchanting "making of" clip with Willy the Bear-tracking Dog. This canine is trained to search for bear droppings!

Note: clips in Chinese.

Where Do Petals Come From?

2010-12-31T02:18:00.000+08:00

"From leaves, of course!" - would have been the answer given by Goethe, the German national poet and occasional scientist. He was one of the early proponents of the idea of homology, where two traits (which may be organs, limbs, tissues...) in two different species are said to be homologous if they are derived from the same organ in their common ancestor. Hence Goethe believed that "all plant is leaf", and that every part of the plant can be homologized with the leaves of the original, primeval Ur-plant.

We've come a long way since then. Floral development in particular has fascinated generations of botanists. Flowers comprise four parts, or 'whorls'–the sepals, petals, stamens, and carpel–listed from the outermost inwards. The sepals and petals, collectively called the perianth, are not always differentiated, and when they cannot they are called tepals. Non-flowering seed plants, or gymnosperms, such as pines, Ginkgo, and cycads, however, lack homologues to the perianth. Stamens and carpels, on the other hand, can be homologized to the male and female sexual organs of the gymnosperm cones (strobili). So where does the perianth come from?

One way to answer this question is to look at the genes involved in the development of the flower. We would expect that different genes are expressed in different whorls during development. The prevailing model used to explain this is the ABC (later the ABCE) model (Wikipedia): genes involved in floral development are expressed in a concentric, overlapping pattern, and the particular combination of gene expression in a tissue determines which whorl it becomes. For example, expression of class A genes alone produces sepals, class A+B produces petals, B+C give stamens, and C+E give the carpel. This model is based on work done on a handful of well-studied model plant species, especially Arabidopsis.

Diagram illustrating ABC model of floral development. Source: Wikimedia Commons.

A research team led by Pamela and Douglas Soltis (husband and wife) has used a comparative approach to try and answer some of these questions. Instead of just focusing on the gene expression pattern (transcriptome) of only one model species, they looked at the floral transcriptome of four different angiosperms, representing different 'grades' of plant evolution, from the relatively basal water lily and a magnoliid (the avocado), to relatively advanced California poppy and Arabidopsis. They also compared this to cone development in a gymnosperm, the cycad Zamia.

L to R: Flowers of avocado (a magnoliid, representing basal angiosperms), Arabidopsis, and female cone of Zamia (different species from that used in the featured study).

What they found was that the more basal angiosperms have a 'fuzzier' pattern of gene expression. Where the poppy and Arabidopsis have fairly sharp boundaries of gene expression between the different whorls, the basal species (water lily and avocado) have more genes that are expressed in two or more adjacent whorls. They interpret this to mean that the genetic programs for floral organ development have become more 'canalized' during angiosperm evolution.

What about the perianth? Water lily and avocado do not have clearly differentiated petals and sepals (and so have 'tepals'). When compared with the cycad Zamia, the genes expressed in the perianth of angiosperms have more in common with genes expressed in the in male cones of Zamia, than those expressed in the female cones. This supports earlier hypotheses that perianths (tepals, sepals, and petals) are evolutionarily derived from male parts of gymnosperm cones, at least as far as their developmental programs are concerned.

There are some caveats, of course. Having only four angiosperm species and one gymnosperm, it's always a bit of a stretch to say that they are truly representative of 'basal' and 'advanced' angiosperms. Furthermore, some systematists might object to the idea of thinking in evolutionary 'grades' to begin with. That is to say, just because a certain species is basal–i.e. it diverged early in angiosperm evolution–doesn't mean it represents an ancestral, primitive state; after all, it's experienced millions of years of subsequent independent evolution, too. We should at least be cautious not to equate the basal condition with the ancestral condition. This is best understood by analogy to a family genealogy. If you meet distant cousins who are descended from a branch of the family that split off three generations ago, you would not assume that they resemble your great-grandparents in every detail. Sure, they would give you some information about what your great-grandparents were like, but you shouldn't assume straight away that they are identical.

Despite all that, it's still good to see comparative studies being done on plant development. Framing developmental questions in an evolutionary context, or Evo-Devo, is a big field now and is so appealing as a research theme, I think, because it puts the science in a narrative context, and telling stories is what we humans intuitively are drawn to, right?

Singapore Mangroves "Smelly, Dirty"?

2010-12-30T11:59:00.000+08:00

Ron Yeo, who writes the nature blog The Tide Chaser, has written a paean to Singapore's under-appreciated mangrove swamps for The Online Citizen.

The mangrove habitat is a staple for school field trips and biodiversity classes, but being 'in the choir' (the one that is being preached to, in the idiom), I and maybe many of this blog's readers tend to forget that:

Dark, smelly, dirty, muddy, scary, mosquito infested, illegal immigrant infested… Ask the usual Singaporeans what they think of our mangroves, and these are some of the common responses. In fact, I even had a friend telling me that he did not like going to mangroves because he was afraid of snakes dropping down from the trees.

Yeo suggests that we should get people to break from these preconceived notions and actually go to see it for themselves. But let's be honest, mangroves do smell funky, and even if you do manage to get your city slicker friends or family to take a trip down to see what all the fuss is about, they might still complain about the heat and remember mostly the mosquitoes, especially if your stories aren't captivating enough or the otters are a no-show. Singaporeans can be a hard lot to please, right?

So I might add to what Yeo's suggests: if you care about nature in Singapore and spend time in our parks and forests, bring a camera and with just a little bit of luck you'll have some pretty pictures of flowers or animals to share online. Then you can answer the question "Singapore forests got anything to see, meh?", and show that appreciating nature is as much about how closely you look, as where you go. In this digitally-driven age, seeing it first on the computer screen might just be the 'hook' to bring people outdoors to see with their own eyes.

Bizzare/Funny Science Blog

2010-12-30T06:46:00.001+08:00

A friend told me about this, and it's too good not to share.

Two graduate students at UC Berkeley have a blog called NCBI ROFL where they post weird or humorous papers dredged up from the PubMed database.

Some recent gems include:
Unsuccessful treatment of writer's block
Doctor reinvents the calculus, names it after herself

They also have a Twitter feed.

Happy New Year!

The Elephants' New Tree

2010-12-22T12:19:00.000+08:00

Top (L to R): African Savannah Elephant, African Forest Elephant, Asian Elephant

Bottom (L to R): Woolly Mammoth, Mastodon

Source: Wikimedia Commons (click through for source pages)

African Elephants have big ears, Asian Elephants have small ears - that's how we usually learn to tell these two apart. The "African Elephant", though, actually comprises two species in the genus Loxodonta, the Savannah elephant (L. africana) and the Forest elephant (L. cyclotis). The Asian elephants are not as closely related as these two, and are in the genus Elephas. Whether the two species of African elephants are really distinct species, however, has been a subject of debate ever since they were first described by zoologists. New research, however, shows that they are indeed different species, and that this divergence is an ancient one. What's more, the Asian elephant is a closer relative to the woolly mammoth than it is to the extant African elephants!

A scientific team led by researchers from the Broad Institute at Cambridge, Massachusetts and the Max Planck Institute for Evolutionary Anthropology in Leipzig have used DNA from the three extant elephant species as well as ancient DNA from the Woolly Mammoth (Mammuthus) and the Mastodon (confusingly called Mammut) to reconstruct the Proboscoidean family tree. What's really novel about their methodology is that they have used tens of thousands of nucleotides of DNA sequence data, spanning several hundred loci (genes) on the nuclear genome of these elephants. Most phylogenetic studies (i.e. research that aims at reconstructing the genealogy of organisms) generally looks at only a handful of genes because large quantities of data are expensive (money-wise) to produce and computationally expensive to crunch through. They took advantage of the Broad Institute's expertise in next-generation pyrosequencing, where DNA is "sequenced by synthesis", based on technology that is fundamentally different from the decades-old Sanger sequencing technology that we learn about in school.

Their results are based on nuclear genes, but show a conflict with previous results obtained by analyzing the mitochondrial genome (mtDNA) of these elephants. mtDNA suggests instead that the African elephants share a relatively recent common ancestry, within the past half-million years or so. What could be happening is that mitochondrial and nuclear genomes are evolving under different circumstances, because the mitochondria are inherited only through the maternal line. The authors hypothesize that this difference is caused in part by the matriolcal behavior of elephants - matriarchal herds stay more or less in the same place, while waves of male migration spread out and fertilize herds elsewhere, displacing nuclear genes but not mitochondrial ones.

The value of ancient DNA is now well-recognized, and has entered the mainstream in science, where previously it tended to be viewed askance as a fringe endeavor more associated with science fiction than real science (think Jurassic Park). What I'd like to see this research group do in the future is to obtain sequences from a larger pool of animals. At present they have DNA sequences from only one or two individuals of each species. A larger data set would allow us to see how well-supported the nuclear-mtDNA divergence really is, and what degree of variation is present at the populational level for this species. As sequencing costs and computational costs go down, it will certainly be cheap enough, one day, to do large-scale population genetics at hundreds of loci. Also, it would have been valuable to see what tree topologies they would obtain using other tree-building methods, because neighbor-joining is known to produce branch lengths that are difficult to interpret, and information is lost when compressing data into distance metrics.

Is Nature 'Good'?

2010-12-21T23:32:00.002+08:00

What is 'natural' and 'organic' may not necessarily be good for you:

"Nonetheless, in resisting many things that I view as "unnatural"—nuclear weapons, global warming, chemical pollution, habitat destruction—while also honoring, respecting, defending, admiring, and nearly worshiping many things that are natural (sometimes just because they are natural), it is all too easy to get carried away, to forget that much in the world of nature is unpleasant, indeed odious. Consider typhoid, cholera, polio, plague, and HIV: What can be more natural than viruses or bacteria, composed as they are of proteins, nucleic acids, carbohydrates, and the like? Do you object to vaccination? You'd probably object even more to smallpox."

Read more

Singapore research changing gears

2010-12-20T07:55:00.000+08:00

Singapore is aiming high, and backing this up with serious cash, if the preponderance of ads from A-Star, Singapore's main science research agency, in top science journals like Nature and Science are anything to go by. Going by various metrics, Singapore is rapidly becoming one of the best cities in the world for science. What it has been particularly good at is picking up high-profile researchers to set up labs and to head local institutes, among them the Nobel laureate Sydney Brenner, who was also made an Honorary Citizen in 2003.

According to a recent editorial in Nature, however, the unusually generous terms on which science has been funded here may soon change:

"Rumours of purse-tightening measures have grown over the past year, but researchers in the city-state were still stunned by the news in September that almost one-third of the total research budget will be abruptly shifted to competitive 'industrial alignment funds'. Access to that funding will now depend on researchers' abilities to show that their work has industrial applications. The policy will affect all research but is aimed particularly at the biomedical sciences, which are senior figures feel are not pulling their weight."

It's clearly not the case that the money is drying up; in fact, A-Star claims to be planning to spend more on R&D. Instead, the new structure is intended to stimulate competition and, understandably for the pragmatist, economy-driven policy worldview that Singapore's government favors, show that the investment is bringing in results.

What's interesting to read are the comments to that editorial. Criticisms and general grievances include: policy changes implemented without warning, bureaucracy that is difficult to navigate, only a few big projects being funded at the expense of early-career researchers or small-scale projects, and review process that is opaque. On the other hand, other commentators point out that: basic research funding is actually being increased, what's being changed are the rules for translational research, which has always been about the bottom line, and also that the situation for researchers in Singapore is still very good compared to most developed countries, e.g. with the upcoming funding cuts to universities in the UK and elsewhere in Europe.

Arsenic claim petering out

2010-12-19T01:27:00.000+08:00

So it seems like the claim for bacteria using arsenic in their biomolecules was never strong to begin with. During the original press conference, the token skeptic was a chemist, and most of the criticism comes from those who are convinced that the chemistry of the matter is quite unlikely. The bacteria are not 'thriving' on arsenic, by any means, but merely tolerating it.

The original paper claimed that only a fraction of the phosphorus was being replaced by arsenic, but it seems likely that as other labs try to replicate their results, this value will be revised downwards.

Red faces all around - including this one! - for feeding the hype, and many people are pointing to NASA's infamous 'life on Mars' claim as prior precedent for the dangers of mixing science and the media.

Read more:
The authors released a technical statement responding to criticism on methods (pdf original, html version on USA Today)
A good newsy summary from the Philadelphia Inquirer.
Ed Yong at Discover Magazine summarizes the timeline and reflects on the practice of science journalism.

Highlights from BBC's Decade of Discovery

2010-12-18T02:10:00.001+08:00

A new program, "Decade of Discovery", by the BBC showcases the 'greatest hits' from the past 10 years of natural history exploration, including the first live images of the barreleye fish (which can only look up and has a transparent dome over its head), the world's longest stick-insect, and more. Some video clips are available on the BBC's YouTube channel or from the TV program's webpage linked above, and the Guardian newspaper has a picture gallery of highlights if you're in a hurry.

Can you fool a baby panda?

2010-12-13T15:38:00.000+08:00

Source: Reuters, via The Guardian

Workers at the panda conservation center in China's Wolong nature reserve dress up in panda suits when they have to handle panda cubs in their care. They claim that this is to minimize the human influences on the pandas, so that they won't be acclimatized to human presence before they are released to the wild.

How effective is this? Only time will tell. In the meanwhile, enjoy the bizarre photographs....

"Natural Security" in a world of scarcity

2010-12-13T14:51:00.000+08:00

The US military is starting to plan for potential future conflicts based on scarcity of natural resources such as water, arable land, mineral resources, and environmental degradation due to climate change. Policy makers have coined the term "natural security", and warn that these future scarcities can represent "triggers for conflict".

One would assume that the military would not have an ideological stance for or against acknowledging climate change, because there's no inherent reason to do so, if their mission is simply to protect their country's security interests. So it's interesting to watch the military essentially taking climate change into account in their plans, while some civilian politicians can still win votes by refusing to even consider the possibility that human activity can have global impact on the physical world that we live in.

"Green Energy" sometimes a different kind of green

2010-12-10T11:22:00.000+08:00

"Green Energy" is a buzzword in policy circles because what is "green" must be good for the environment, right? Unfortunately, the truth is that what sounds like a good idea on paper (or increasingly, online) can actually do more harm than good.

The advocacy group Survival International, which claims to represent the interests of "tribal peoples" around the world, has criticized the Malaysian Bakun dam project in Borneo, which not only has flooded large tracts of rainforest and disrupted river flow, but also has displaced members of the Penan tribe. They also have sharp words for the palm oil plantations which are razing forest in the name of biofuel, a subject which this blog has covered many times before. As one commentator on the Malaysia Today website (where the SI article is reposted) remarks, the only thing "green" about these projects is the money changing hands!

"Arsenic-life" under fire?

2010-12-09T09:31:00.000+08:00

Slate magazine reports on criticism of the recently-released report on bacteria that use arsenic in place of phosphorus. Much of the concern arises from the possibility that the arsenic detected in these biomolecules were not endogenous but instead contaminants. Some scientists are also dissatisfied with how NASA was performing "science by press release", pumping up the publicity machine ahead of the paper's publication.

It remains to be seen how the team that produced this paper will respond; they are willing to give cultures of the strain to any researcher who wants to investigate their claims, and detailed criticisms are presently being prepared for publication.

In all likelihood, though, the mass media will not be as interested in probably prolonged back-and-forth that will ensue, the news cycle isn't quite patient enough for such sustained coverage. This of course is a pity because it biases how the public views science: as a string of spectacular discoveries, but without any of the routine counter-checking that goes on afterward.

Egyptian crypt aids search for origin of dogs

2010-12-08T03:44:00.000+08:00

One of the most charming and enjoyable books about dogs is Man Meets Dog by Konrad Lorenz, who was one of the founders of the field of ethology, or the scientific study of animal behavior. This book popularized ethology but unfortunately one of Lorenz's other theories, that dogs were descended from jackals, has been found by more recent scientific work to be wrong. Dogs are most probably descended from wolves, which seems mind-boggling if we look at the tremendous variety of dog breeds. How did they all come about?

It is in this context that the rediscovery of a crypt for dog bones in Saqqara, Egypt is significant. These animals were sacrificed upon the death of their owners, and were entombed underground, sometimes mummified. Although ancient Egyptians were known for their love of cats, there was a significant interest in dogs and dog-breeding among them too. This crypt therefore preserves for us, like a snapshot in time several millennia ago, a cross-section of dog variation in the course of their domestication that may give some insight into the evolution of modern breeds, and their origin from wolves.

Bacterium using Arsenic instead of Phosphorus discovered

2010-12-03T12:05:00.001+08:00

Mono Lake in California is one of the so-called 'soda lakes', not filled with fizzy pop but with caustic alkali and high salt concentrations. What could possibly live in these harsh conditions? Well, microbes, of course. What's more, arsenic concentrations in this like are at levels which would be toxic to most organisms. If we're going to look for weird life forms, Mono Lake would be the place to go!

Mono Lake in California (Google Maps). View Larger Map

One such weird life form has just been discovered. It's a bacterium that uses arsenic in place of phosphorus in its biomolecules, including DNA. In intro biology we learn that all living things have DNA, and that DNA has a sugar-phosphate backbone along which the four bases (A, T, C, and G) are arranged. The phosphate groups in the backbone of DNA are supposedly universal, and it's hard to imagine how any organism could have a different chemistry for something so fundamental, but apparently such a creature does exist. In place of the phosphorus atoms in the phosphate groups, it has instead arsenic. Arsenic is an element that is in the same group as phosphorus, and so has the same chemical valence, and in theory can substitute for phosphorus because it can form similar chemical bonds. Until now such a scenario has seemed to be entirely in the realm of science fiction, but that appears now to be reality.

Using a combination of radioisotope labeling and spectroscopy, a team from NASA's Astrobiology Institute led by Felisa Wolfe-Simon (disclaimer: she was the TF for a class that I took two years ago) has shown that a strain of bacteria isolated from Mono Lake is capable of taking up arsenic, and further that the arsenic is localized in the biomolecules of the organism. This is an exciting discovery because it suggests that alternative chemistries of life are possible, and that organisms need not be limited to the canonical 'six fundamental elements of life': carbon, nitrogen, oxygen, phosphorus, sulfur, and hydrogen.

While this is a very important discovery, it is also crucial to emphasize what it is not, especially given the hype and publicity that this new piece of research has received. The fact that the work was done through the NASA Astrobiology Institute has led some to think that perhaps it has something to do with extraterrestrial life or new life forms. It is emphatically not the case: The bacterium is a member of the Halomonadaceae, a known family of the gamma-Proteobacteria. It is not part of the so-called 'shadow biosphere' (Wikipedia), which is the idea that alongside the canonical DNA/RNA/protein based life that we know of, there are 'organisms' based on fundamentally different chemistry (e.g. with some other form of information-coding molecules instead of DNA, or some other means of catalyzing biochemical reactions...). This discovery 'only' shows that one particular component of the highly-conserved basic biochemistry, namely the use of phosphorus in biomolecules like the nucleic acids, can be swapped out for an element with similar chemical properties. This is not a form of primitive life; if anything it represents an extreme form of specialization to an extreme habitat. Phosphorus is typically a highly limiting nutrient for life - this is why algae tend to form 'blooms' when phosphorus-containing fertilizers or detergents seep into water bodies - because the sudden influx of phosphorus allows a great burst of growth. In the case of this bacterium, called strain GFAJ-1, it is able to capitalize on the high arsenic concentration to replace some of its need for phosphorus.

Hence, not to detract from the excitement about this really cool piece of natural history, but these clarifications really needed to be made in the face of what was inevitably a lot of misunderstanding and misrepresentation in the popular press (with sensational headlines like "Alien life forms discovered?" and so on). What is exciting is certainly the fact that life like this has been discussed as a theoretical possibility for a long time, and is now finally known to be real.

Sources:

Update (3 Dec 2010, 0043 EST):
Even the geek-cool comic strip xkcd has gotten into the act:

Source: xkcd by Randall Munroe

Indonesian forest plan under threat?

2010-11-29T11:42:00.000+08:00

Indonesia is a testbed for so-called 'cash for carbon' plans (Reduced Emissions from Deforestation and Forest Degradation, or REDD), where developing countries are given credits for reducing deforestation; this not only preserves valuable forest habitat for wildlife, but curbs carbon emissions from deforestation itself.

Greenpeace, however, has released a report that says Indonesia is planning to go ahead with massive forest clearance despite signing a new REDD agreement with Norway. According to the New York Times's coverage:

Greenpeace said that government documents show plans to bring 63 million hectares, or nearly 156 million acres, of land into production by 2030, including 80 percent of its peatland and half its forested orangutan habitat, to support expansion of industries including pulp, paper and palm oil.

At the same time, the group said, a push is on to rebrand the clearing of forests for plantations (which results in a net release of carbon into the atmosphere) as the replacement of degraded land with new trees (which takes carbon out of the atmosphere). This, they say, could effectively mean international funds would be subsidizing forest destruction.

Tremendous disappointment, or 'more of the same'? How Indonesia handles this will certainly be watched closely. As with any current event it runs the risk of being swept under the carpet, or just sat upon until the media attention inevitably dissipates.

More coverage:

Greenpeace's original report, titled 'Protection Money'.
Blogger Chris Lang in REDD-Monitor gives a brief account of recent REDD-related developments in Indonesia.
The REDD-ALERT website describing various REDD initiatives around the world.

Book Review: The Art Instinct

2010-11-29T03:05:00.002+08:00

Book reviewed -- Denis Dutton. The Art Instinct. New York: Bloomsbury Press. 2009.

Modern humans have a profound fascination with our Pleistocene past, in part because many of us, disillusioned by technology and modernity, find something more authentic and natural in the ways of hunter-gatherers. A recent post by fellow Refugee, Alvin, highlights research suggesting that barefoot running may be better for our bodies. For some people, the 'Paleolithic Diet' is becoming fashionable, while even literary theorists are looking to Darwin and the hunter-gatherer psyche to explain the ins and outs of literature. Can other human endeavors, like art and music, be explained by our evolutionary past in the same way?

Those who would dismiss the field of evolutionary psychology (EP), which applies ideas from evolutionary biology (in particular sociobiology) to explain human behavior and mind, would consider all this to be various manifestations of what Marlene Zuk terms 'paleofantasy'. Practitioners of this field, it is claimed, make up 'just-so stories' and mine subjects like literature and art, previously the province of the humanities, to support conclusions about our purported hunter-gatherer past that have already been decided upon. In its crudest pop-sci form, EP is cited to support statements like 'art is merely a means to advertise for mates, just as the male bower-bird decorates its bower to attract females'.

Denis Dutton, a New Zealand philosopher, does indeed mention bowerbirds in his latest book, The Art Instinct, but his arguments are more nuanced and level-headed than the pop-sci version of EP. He argues that we humans have an instinct for liking art, and that what art is (a perennial debate among artists and critics) should be understood on the basis on that instinct. Dutton also runs the well known weblog Arts and Letters Daily, which posts daily links to thought-provoking articles in the arts and humanities. The book, in many ways, shows the same tendencies as his curation of the website - some of the hot topics he followed on the blog (such as the plagiarizing pianist Joyce Hatto) show up in the book, and both have a level-headed skepticism of fashionable ideas or trendiness.

Thus far there have been two broad classes of explanation for why humans like art. One is due to Stephen Jay Gould, and basically states that art is a kind of spandrel - it's a by-product of other true evolutionary adaptations in the mind, but has no functions of its own. The other holds that art itself is somehow adaptive, and points out for example how people like landscapes with lakes and hills, and that these are probably good places to forage and hunt. Dutton, as I understand him, proposes a third way. He acknowledges the role of instinctual preferences shaped by natural selection, but is not content to dismiss art as a spandrel (a concept which has always been contentious). He explains how sexual selection has shaped our minds and behavior, and ties all these disparate threads - sexual selection, natural selection, non-adaptive roles - together compellingly. Art, as it is seen today, is not easily explained as being adaptive for this or that purpose, but is a complex product of various kinds of innate instincts or even hypertrophied preferences.

Along the way (but admirably concisely), Dutton sorts out the issue of what art actually is. Are art-forms like Marcel Duchamp's Fountain (a urinal that the artist bought and signed) and other 'readymades' really art? Are Schoenberg's unlistenable atonal works really music? He acknowledges the difficulty that these cases present to definitions of art, and he proposes that art is a 'cluster concept' with these as fringe cases, hence to understand what art is we should not look to the fringe, but instead begin with the center, with things which are universally acknowledged to be art. With that understanding in place, we can then understand why our innate 'art instinct' makes it so difficult for us to accept those outliers, because they were designed to challenge our notion of art in the first place. But it is precisely because of that challenge that they have value as art, but only within the context of the point they were trying to make. Because of their status as experiments and singular statements, however, they are not really repeatable, and subsequent readymade art, for example, receive little sympathy from the viewing public.

This is an ambitious book, and covers a lot of ground, but although it is readable it does not sacrifice much rigor or clear-mindedness. To an evolutionary biologist, this is clearly not a scientific work, but it is of a much higher quality than much pop sci writing in the press and online. It is easy to dismiss humanists trying to grapple with the consequences of Darwinism for their own disciplines, but here Dutton shows the value that can be derived from a qualitative, conceptual analysis for a better understanding of our human condition.

Tuataras!

2010-11-26T03:00:00.002+08:00

Natalie Angier, a science writer at the New York Times, has written a great feature article on the tuatara, a 'living fossil' that is the only remaining representative of its group, the sphenodontids. All other lizards and snakes are members of a group called the Squamata, which is distinct from the Sphenodontidae (see a reptile phylogeny at Tree of Life).

Some fun facts include their 'third eye' (the pineal eye), a primitive light-sensing organ in the center of their head which has been lost in most living reptiles, and their longevity - individuals in the wild may routinely reach 100 years or more, and continue to reproduce despite their advanced age.

Her article highlights research that shows how certain parts of the tuatara genome are evolving at a rapid rate, despite their apparent morphological 'stasis'. This questions our popular notion of what a 'living fossil' is - although they may appear to be quite similar to fossilized relatives from millions of years ago, we shouldn't forget that these organisms have had corresponding millions of years of evolution since that time, and so morphological stability may conceal other advanced specializations. It would be a mistake to think of these organisms as 'primitive' in the common sense of backward and inadequate.

Panthers and Leopards in the Malay Peninsula

2010-11-26T00:56:00.000+08:00

The term 'panther' has a confusing history - it's been used to refer to any big, black (i.e. 'melanic') cat, usually the leopard in particular. Leopards and panthers used to be thought of as different species, but they are in fact merely different color variants, and this so-called melanic coat coloration is a recessive Mendelian trait. To complicate matters, the four big cats - leopards, tigers, lions, jaguars - have been grouped in the genus Panthera, based on the same etymological root.

In Southeast Asia, the leopard Panthera pardus exists in two color morphs: the usual spotted variety, and the melanic 'panthers'. However, a recent evaluation of camera-trap data could not find any spotted leopards South of the Isthmus of Kra; all the animals that were photographed by these traps were black leopards. Anecdotal evidence from interviews with aboriginal peoples living in national parks also found that they were unfamiliar with the spotted leopards but could recognize the black ones. Although 'absence of evidence is not evidence of absence', it does show that spotted leopards are at the very least rare in Malaysia. The authors of this study suggest that this trait has become genetically fixed because of a bottleneck event sometime in the history of this population. This is a neat intersection between basic natural history and genetics, having implications for the genetic variability of the Malayan leopards, and hence their conservation viability.

Stowaway Viruses

2010-11-19T11:04:00.001+08:00

Most of us tend not to think too much about viruses until we (or our computers...) get one, and then we start to wonder what medical science is up to if after all this time we still don't have a cure for viral disease.

What we don't realize is that lurking in our genomes, and indeed the genomes of most animals, are viral stowaways. Biologists are no strangers to stowaways - the mitochondrion is one of the best examples, once a free-living bacterium now captured to be the energy generators of the eukaryotic cell. But at least one can see a mitochondrion. Stowaway viruses, more properly called endogenous viral elements (EVEs), have worked their way right into the stuff of life itself, inserting the instructions for making more of themselves into our DNA.

For one group of viruses, the retroviruses, this does not come as a surprise. Retroviruses invade the cell carrying their genomes on RNA, and then use the enzyme reverse transcriptase (hence their name) to write their genome into DNA which is then inserted into the host genome. From this seat in the host genome, their genes are activated and set in motion the machinery for producing and assembling new virus particles. They can also lie quiescent for generations, piggybacking along the divisions of their (increasingly numerous) hosts. It's been known for a long time that much of the human genome is made up of former EVEs that have mutated and are no longer functional, becoming part of the 'junk DNA' that litters our genomes.

A recent intensive search of animal genome sequences, however, has found that non-retroviruses can form EVEs too. This is part of a clutch of recent studies on the diversity and evolution of EVEs, that seems to also pose a philosophical question - what does it really mean to be human? The human cells in our bodies are already outnumbered by the bacteria that live in our gut, on our skin, under our nails, and virtually every other surface on us. And now we find that our genomes don't really belong to us either?

EVEs in the genome sequence are being used as a 'fossil record' of viral infection events in our human past, being of value in reconstructing the history of virus and human evolution. Yet these ancient events still have very immediate consequences for us today. Schizophrenia is a widespread and serious mental disorder that is extremely debilitating to its sufferers. It has long been treated as a purely psychiatric disorder, with the exact physiological basis remaining obscure. Yet some puzzling observations about the disease remained:

Schizophrenia is usually diagnosed between the ages of 15 and 25, but the person who becomes schizophrenic is sometimes recalled to have been different as a child or a toddler—more forgetful or shy or clumsy. Studies of family videos confirm this. Even more puzzling is the so-called birth-month effect: People born in winter or early spring are more likely than others to become schizophrenic later in life. It is a small increase, just 5 to 8 percent, but it is remarkably consistent, showing up in 250 studies. That same pattern is seen in people with bipolar disorder or multiple sclerosis.

This observation has been used to support the hypothesis that schizophrenia is caused by an EVE called HERV-W, which has also been implicated in the onset of multiple sclerosis. Although the endovirus theory of schizophrenia is still far from being textbook truth (the theory's main supporter, Fuller Torrey, has weathered considerable controversy), it is certainly thought-provoking, and will certainly draw more attention to the burgeoning field of animal endoviruses.

Cats are classy drinkers

2010-11-16T14:03:00.000+08:00

Or lappers, to be precise. Unable to sip by suction like we humans do, cats and dogs lap up water with their tongues. However, dogs are much messier than cats, who elegantly flick water into their mouths without splashing it everywhere (what some cats do with their paws later is a separate matter.)

A team of engineers has recently analyzed high-speed photographs of cat lapping to find that they succeed by using only the tips of their tongues to draw up a thin stream of water and then closing their mouths just as the stream begins to break and fall back down again. Scaling up to big cats, they found that their model predicts the speeds that cats of different sizes should lap with (bigger cats lap more slowly).

Just how fast do house cats lap? Here's some trivia for cat lovers: cats lap four times a second, and their tongue moves at the speed of one meter per second, a really rapid, darting movement.

(Via NY Times)

Singapore Index on Cities' Biodiversity endorsed in Nagoya

2010-11-01T06:53:00.000+08:00

The Straits Times reports that the Singapore Index on Cities' Biodiversity (CBI) has been endorsed at a meeting of the Convention on Biological Diversity (CBD) in Nagoya. This index is a 'scorecard' for cities, rating them on the basis of several criteria which account for the extent of their remaining native biodiversity, ecosystem services, education and recreational value, and governance/management of biodiversity. Singapore's National Parks Board (NParks) played a key role in formulating this index for the CBD.

Further information: Singapore Index webpage at CBD, NParks website

Lost in the Clouds - Blog Action Day 2010 "Water"

2010-10-15T12:28:00.000+08:00

Blog Action Day is an annual event on 15 Oct (since 2007) that brings together bloggers around the world to write on a certain topic of pressing importance. This year's theme is "Water", and it ties in well with something that I've been meaning to write about for some time.

A week ago, I was fortunate to hear Dan Janzen, the ecologist and conservationist known for his work in setting up the Guanacaste National Park in Costa Rica, speak in person. His talk was great - you could tell that he's a no-nonsense personality who speaks his mind and is frank about his opinions on conservation. One very small part of his talk was a series of three photographs that he showed, of one of the cloud-forest mountain peaks in that park. In the first picture, taken in the 1970s (if I remember right), it's shrouded in a permanent fog. The next picture, taken a few years later, shows much sparser wisps, and the most recent one is completely bone-dry. The sky is blue and totally clear. Rising temperatures have lowered humidity and lifted cloud cover above the level of the mountains. The cloud forest has lost its cloud.

When we think of water issues and the environment, we tend to think about pollution in rivers, about salinization of groundwater, or eutrophication in lakes. This is water that we can see flowing or pooled up, that people can drink from, swim in, and fight over. But that's just one part of the water cycle we all learn about as children, when we drew arrows in our textbooks going from the ocean to the fluffy white clouds and back down as rain to the green fields below. In cloud forests, declining humidity has a strong biotic impact. They have been implicated in population crashes of frogs and other animals. As the fog rolls across these peaks, though, they also drip into streams and rivulets that feed waterways down below: a direct impact of climate change on water availability for both nature and people.

It's not just something that only affects picturesque spots far away in the exotic tropics, either. A major part of the water supply to the state of California comes from the spring thaw of the snowpack on the mountains of the Sierra Nevada range, which form part of the mountainous backbone that runs up the Western half of North America. Winds blowing in humidity-laden air from the Pacific is forced up the slopes of the Sierra Nevada, where it condenses in the cold upper reaches of the mountains and falls as precipitation; in the wintertime this is in the form of snow that accumulates until the thaw. This is also why Nevada is such a dry place - it sits in the 'rain shadow' of the range. As temperatures rise, however, the quantity of condensation and precipitation will decline and likewise the water that can be supplied to the inhabitants of California, both human and non-human. This water stress will force choices to be made between serving people and preserving the environment, as described in my previous post.

In the grand scheme of things, though, the environment will bounce back in some form. The Sierra Nevada is a relatively young mountain range, formed by uplift less than 10 million years ago. As they rose up, they cut off the formerly extensive lakes inland in the Great Basin behind them from the rivers that had led from them to the coast. The lakes eventually dried up and disappeared, causing the extinction of their fauna, as did the freshwater fishes in the former rivers. As the mountains grew further, however, rivers once again flowed, fed by the precipitation intercepted by the range. The fishes that now populated them were instead secondary re-invasions of freshwater habitats by marine fishes. (Oversimplified version of a much more intricate and fascinating story.) Life went on even in the face of drastic change. What's different about this time, though, is the time scale. The environment is now changing in tens and hundreds of years instead of thousands and millions. It's a sobering thought to think that long after we humans disappear, some alien paleontologist looking through the fossil record of the former Earth would find our age to be one of the great Mass Extinctions in the history of life. We manage to slake our thirst, but at the same time have poisoned the well for everyone.

(Stay tuned for Blog Action Day updates at our partner blogs: Coastal Cleanup Singapore, Otterman Speaks, Wild Shores Singapore.)