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Doushantuo is that the fossils recovered are microscopic and preserve fine structural detail, the original cells having been replaced by phosphate minerals.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

Fossil instrument plays "Flintstones" theme

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

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

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

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?

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

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

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.

Riding ants all the way

EO Wilson has had a storied career in evolutionary biology: the originator of island biogeography and sociobiology, one of the world's leading experts on ants, and two-time Pulitzer Prize winner. Recently, he plunged into scientific controversy again with the publication of a paper authored with two Harvard mathematician colleagues, Corina Tarnita and Martin Nowak, claiming that kin selection is unnecessary to explain the origin of eusociality (Nature paper, Biology Refugia blog post).

A new profile of Wilson in the Atlantic magazine tells us what he has been up to lately: participating in a conservation project at Gorongosa Park in Mozambique, traveling, and still reveling in collecting and identifying ants and other insects.

...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

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: