Don't let the nutrients fly away!

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

Nepenthes bicalcarata (by David Sucianto, via Wikimedia Commons)

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

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

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

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

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

Cockroach vs. human arms race

German cockroach (via Wikimedia Commons)

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

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

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

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

Hey there sailor...

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

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

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

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

How periodic cicadas evolved their timing

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

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

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

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

Contrary to expectations, the old species, defined by morphology and period, do not correspond to the evolutionary history as uncovered by molecular phylogeny and haplotyping. The three big species groups are still supported, representing two evolutionary splits at about 3.9 and 2.5 million years ago (Mya). The splits within the species groups, however, are relatively recent, mostly less than 0.5 Mya. Furthermore, the splits correspond more to geographical regions than to life cycle period. The split between 13- and 17-year periods have also evolved multiple times. To quote from the paper:

Our results are broadly consistent with the previous idea that an ancestor of all Magicicada diverged into three species allopatrically, and later, the three became sympatric and each species independently diverged into 13- and 17-y cicadas. Surprisingly, however, the divergence of 13- and 17-y cicadas was asynchronous among the species groups and occurred repeatedly even within a species group. This finding is all of the more interesting given that each species group shows similar eastern, middle, and western phylogeographic divisions similar to post-Pleistocene patterns observed in other North American taxa, suggesting that the three Magicicacda groups shared multiple refugia during the last glacial maximum.

This is a nice surprise, and as the authors point out, the repeated switching between 13- and 17-year forms suggests that there is a single genetic "switch" involved, because it is unlikely that a complex mechanism could be repeatedly gained and lost in such a manner.

Taxonomists are not going extinct

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

---

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

How to foster good science in Singapore?

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

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

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

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

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

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

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

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

---

Some other comments:

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

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

Light and deep-sea organisms

Did you know that...

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

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

Battle of the species hunters

Scientists are not the only ones who are hunting for new species. Animal and plant collectors too, searching for new exotic species to add to their collections, pose a threat to the survival of newly-described species. They monitor the scientific literature for new species descriptions, which essentially tell them exactly where to pick up the loot and what it looks like!

That at least is the message of a new podcast from the BBC documentary series One Planet, titled "The New Species Dilemma" (mp3 download). New podcasts are available for 30 days after broadcast.

In some cases, though, scientists are aware of this problem. When the famous Wollemi Pine (which even has its own official website) was discovered in Australia, its location was not made publicly known, and I think that still is the case to this day.

At the same time, proper scientific description requires full documentation, and that includes geographical data. It's an unexpected problem, and I don't think something that most taxonomists have to think about. But if you're working on a particularly "charismatic" group of organisms (and standards for "charisma" vary; some people collect exotic frogs, for instance) it might be something worth giving some thought to!

Are they embryos or not?

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

The world's largest virus

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.

Afterword on "arsenic-life" affair

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.

Frogs can "drink" water from air

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.

How the bean got its twist

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.

Plant gives birds a place to stand

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.

How many species - why do we care?

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 mole's new thumb

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

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

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:

• S Wada, K Kawakami, S Chiba. 2011. Snails can survive passage through a bird's digestive system. Journal of Biogeography published online 21 June 2011, doi: 10.1111/j.1365-2699.2011.02559.x
• BBC News article

"Mismeasure of Man" Revisited

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