New Species Discovered Near Antarctic Seafloor

A plethora of new species have been discovered around hydrothermal vents near Antarctica. As always, the ocean has many surprises for us.

From ScienceDaily:

‘Hydrothermal vents are home to animals found nowhere else on the planet that get their energy not from the Sun but from breaking down chemicals, such as hydrogen sulphide,’ said Professor Alex Rogers of Oxford University’s Department of Zoology, who led the research. ‘The first survey of these particular vents, in the Southern Ocean near Antarctica, has revealed a hot, dark, ‘lost world’ in which whole communities of previously unknown marine organisms thrive.’

Highlights from the ROV [Remotely Operated Vehicle] dives include images showing huge colonies of the new species of yeti crab, thought to dominate the Antarctic vent ecosystem, clustered around vent chimneys.

We heard about yeti crabs earlier, when we learned that one species of them off the coast off Costa Rica may farm bacteria on its claws by waving them over methane-seeping fissures to feed them, then chowing down. Obviously cold fissures by Costa Rica are very different from hydrothermal vents by Antarctica, but it would be awesome if we found that a species had the same strategy there.

Elsewhere the ROV spotted numbers of an undescribed predatory seastar with seven arms crawling across fields of stalked barnacles and found an unidentified pale octopus nearly 2,400 metres down on the seafloor.

A seastar is a starfish, something I did not know. A predatory seven-armed starfish sounds like a thing of nightmares – if you’re a tiny sea animal anyway.

‘What we didn’t find is almost as surprising as what we did,’ said Professor Rogers. ‘Many animals such as tubeworms, vent mussels, vent crabs, and vent shrimps, found in hydrothermal vents in the Pacific, Atlantic, and Indian Oceans, simply weren’t there.’

The team believe that the differences between the groups of animals found around the Antarctic vents and those found around vents elsewhere suggest that the Southern Ocean may act as a barrier to some vent animals. The unique species of the East Scotia Ridge also suggest that, globally, vent ecosystems may be much more diverse, and their interactions more complex, than previously thought…

‘These findings are yet more evidence of the precious diversity to be found throughout the world’s oceans,’ said Professor Rogers. ‘Everywhere we look, whether it is in the sunlit coral reefs of tropical waters or these Antarctic vents shrouded in eternal darkness, we find unique ecosystems that we need to understand and protect.’

Very cool, as always. Scientists who look for new ocean species must laugh at their terrestrial counterparts; it’s like exploring space versus exploring your backyard. But now the real question: how do these new species taste?

Blinking Bacteria As Biological Sensors

You’re probably aware that making lab organisms – or at least parts of them – glow a certain colour is relatively commonplace. Biologists frequently attach the gene for green fluorescent protein (GFP) or its differently coloured family members to a gene that they’re interested in, so whenever the gene of interest is activated GFP is produced and the relevant target fluoresces, a nice visible marker. 

In the last few years a group of researchers found a way of tying fluorescence to the cycle of bacteria’s biological clocks, producing rhythmic blinking. Last year they managed to coordinate this blinking in large groups of bacteria, which they compare to living neon signs. Now, they’ve shown that this system can be used as a living sensor for environmental pollutants.

From ScienceDaily:

Using the same method to create the flashing signs, the researchers engineered a simple bacterial sensor capable of detecting low levels of arsenic. In this biological sensor, decreases in the frequency of the oscillations of the cells’ blinking pattern indicate the presence and amount of the arsenic poison.

Because bacteria are sensitive to many kinds of environmental pollutants and organisms, the scientists believe this approach could also be used to design low cost bacterial biosensors capable of detecting an array of heavy metal pollutants and disease-causing organisms. And because the sensor is composed of living organisms, it can respond to changes in the presence or amount of the toxins over time unlike many chemical sensors.

“These kinds of living sensors are intriguing as they can serve to continuously monitor a given sample over long periods of time, whereas most detection kits are used for a one-time measurement,” said Jeff Hasty, a professor of biology and bioengineering at UC San Diego who headed the research team in the university’s Division of Biological Sciences and BioCircuits Institute. “Because the bacteria respond in different ways to different concentrations by varying the frequency of their blinking pattern, they can provide a continual update on how dangerous a toxin or pathogen is at any one time.”

They go on to explain that there are too many bacteria on their “microfluidic chips” (up to 60 million cells) for the bacteria to all coordinate in their usual way, which is called quorum sensing (roughly, relaying signaling molecules between them). They found, though, that colonies released gases that could be used to coordinate between them, while cells within colonies still coordinated by quorum sensing.

This is a pretty interesting idea. I trust biologists to be able to make bacteria sensitive to various molecules and react in various ways; I see no reason why bacteria wouldn’t be able to glow different colours based on the environment, for example. There may be more possibilities with living versus non-living sensors simply because of the incredible complexity of living things, which we can take advantage of without reconstructing from the ground up.

A New Dinosaur Related to the Triceratops

A new dinosaur species has been announced, a whopping 95 years after the discovery of its fossil. It’s called Spinops sternbergorum (“Sternberg’s spine-face”, after the Sternberg father and son team who discovered the fossil).

A recreation of Spinops via ScienceDaily, copyright Dmitry Bogdanov.

From ScienceDaily:

Spinops was a plant-eater that weighed around two tons when alive, a smaller cousin of Triceratops. A single large horn projected from the top of the nose, and a bony neck frill sported at least two long, backward-projecting spikes as well as two forward-curving hooks. These unique structures distinguish Spinops from related horned dinosaurs…

Parts of the skulls of at least two Spinops were discovered in 1916 by Charles H. and Levi Sternberg, a father-and-son fossil collecting team. The Sternbergs recognized that their find represented a new species and sent the fossils to The Natural History Museum (London). However, the fossils were deemed too scrappy for exhibit, and consequently were shelved for decades. It wasn’t until Farke and colleagues recognized the importance of the fossil that the bones were finally cleaned for study.

I don’t really understand how that happens. How do you discover a new species and then just… let it lie? This field of science definitely seems different than what I’m used to. In any case, I’m glad the discoverers eventually got the credit they deserved.

Creating Light From a Vacuum

Quantum theory predicts that in a vacuum, virtual particles are constantly being created in pairs and then quickly destroying each other. Up until now, outside of theory there hasn’t been any proof that they actually exist. Now, researchers have managed to make some of these particles materialize: by giving energy to virtual photons, they created “real”, measurable photons. Did they say “Let there be light!” as they did it? Let’s just pretend so. 

From ScienceDaily:

Chalmers scientist, Christopher Wilson and his co-workers have succeeded in getting photons to leave their virtual state and become real photons, i.e. measurable light. The physicist Moore predicted way back in 1970 that this should happen if the virtual photons are allowed to bounce off a mirror that is moving at a speed that is almost as high as the speed of light. The phenomenon, known as the dynamical Casimir effect, has now been observed for the first time in a brilliant experiment conducted by the Chalmers scientists.

“Since it’s not possible to get a mirror to move fast enough, we’ve developed another method for achieving the same effect,” explains Per Delsing, Professor of Experimental Physics at Chalmers…

The “mirror” consists of a quantum electronic component referred to as a SQUID (Superconducting quantum interference device), which is extremely sensitive to magnetic fields. By changing the direction of the magnetic field several billions of times a second the scientists were able to make the “mirror” vibrate at a speed of up to 25 percent of the speed of light.

“The result was that photons appeared in pairs from the vacuum, which we were able to measure in the form of microwave radiation,” says Per Delsing. “We were also able to establish that the radiation had precisely the same properties that quantum theory says it should have when photons appear in pairs in this way.”

What happens during the experiment is that the “mirror” transfers some of its kinetic energy to virtual photons, which helps them to materialise. According to quantum mechanics, there are many different types of virtual particles in vacuum, as mentioned earlier. Göran Johansson, Associate Professor of Theoretical Physics, explains that the reason why photons appear in the experiment is that they lack mass.

“Relatively little energy is therefore required in order to excite them out of their virtual state. In principle, one could also create other particles from vacuum, such as electrons or protons, but that would require a lot more energy.”

That’s crazy. What’s the wear and tear like on something vibrating at 25% the speed of light? It’s unimaginable. Whoever engineered that must’ve had an incredibly difficult time.

I was torn about posting this article since on the one hand it sounds awesome, but on the other hand it’s definitely over my head, so I can’t exactly help break it down for you any more than they already did. Anyway, it’s clear at least that this is a very cool experiment and very big news for physics, so let’s bask in this moment of awesome. Are you basking? Bask!

The Possible Birthplace of Life on Earth

I wanted my 100th post on this blog to be about something suitably epic; this article should do. It’s about the identification of a group of volcanoes in Greenland that may have had the right conditions for creating life 3.8 billion years ago, something that hasn’t been found anywhere else. 

From Science Daily:

The mud volcanoes at Isua, in south-west Greenland, have been identified as a possible birthplace for life on Earth by an international team headed by researchers from the Laboratoire de Géologie de Lyon: Terre, Planètes et Environnement (CNRS/Université Claude Bernard Lyon 1/ENS de Lyon). Almost four billion years ago, these volcanoes released chemical elements indispensable to the formation of the first biomolecules, under conditions favorable to life. It is the first time that such an environment, meeting all the requirements for the emergence of life, has been identified by scientists in 3.8 billion year-old formations…

Mud volcanoes are cooler than igneous volcanoes, and don’t eject lava. According to Wikipedia, “Ejected materials are often a slurry of fine solids suspended in liquids which may include water, which is frequently acidic or salty, and hydrocarbon fluids.” Sounds nasty. 

Serpentinite is a dark green mineral used in decoration and jewelry. In nature, it is formed when sea water infiltrates into Earth’s upper mantle, at depths that can reach 200 km in subduction zones. According to the scientists, this mineral, often found in the walls of hydrothermal sources, could play a major role in the appearance of the first biomolecules…

The team of scientists publishing this article focused their studies on serpentinites from Isua, in south-west Greenland, which date from the start of the Archean [4 to 2.5 billion years ago]. Dating back some 3.8 billion years, the rocks of Isua are some of the oldest in the world. Using isotopes of zinc as indicators of the basic or acid nature of an environment, the researchers highlighted the basic character of the thermal fluids that permeated the Isua serpentinites, thus demonstrating that these minerals formed a favorable environment for amino-acid stabilization…

Nearly four billion years ago, at a time when the continents only occupied a very small part of the surface area of the globe, the oceanic crust of Isua was permeated by basic hydrothermal fluids, rich in carbonates, and at temperatures ranging from 100 to 300°C. Phosphorus, another indispensable element to life, is abundant in environments where serpentinization takes place. As this process generates mud volcanoes, all the necessary conditions were gathered at Isua for organic molecules to form and be stable. The mud volcanoes at Isua thus represent a particularly favorable setting for the emergence of primitive terrestrial life.

So that’s pretty cool. However, as fun as it may be to point at a specific place as the origin of life, we have to of course keep in mind that this is just one possibility. Life is generally thought to have originated near hydrothermal vents, so those are still a possibility. It’s also hard or impossible to say that this location at Isua is more likely than others, since, as they say, those are some of the oldest rocks in the world; there’s no way to compare them to equally old rocks everywhere else.

Could still make for a good tourist attraction though…

Nanoparticle Exposure May Not Be An Issue After All

The study of nanoparticles is a growing field relevant to nanotechnology. Nanoparticles – tiny particles of a material, anywhere between 1 and 2500 nanometres in diameter – are particularly interesting because they can have different properties than the same material in larger quantities. They have size-dependent properties, because the proportion of atoms on a particle’s surface is non-negligible compared to the atoms inside the particle, unlike with larger objects. 

For example, from Wikipedia

Nanoparticles often possess unexpected optical properties as they are small enough to confine their electrons and produce quantum effects. For example gold nanoparticles appear deep red to black in solution. Nanoparticles of usually yellow gold and gray silicon are red in color. Gold nanoparticles melt at much lower temperatures (~300 °C for 2.5 nm size) than the gold slabs (1064 °C). And absorption of solar radiation in photovoltaic cells is much higher in materials composed of nanoparticles than it is in thin films of continuous sheets of material.

However, the unusual properties of nanoparticles means, naturally, that they could be harmful to human health in some way. This has been a worry for some time now as nanotechnology has risen to prominence. In what seems like a big relief, a new study shows that we may actually be exposed to nanoparticles all the time, so if they have any dangerous effects, we should already know about them.

From ScienceDaily:

Since the emergence of nanotechnology, researchers, regulators and the public have been concerned that the potential toxicity of nano-sized products might threaten human health by way of environmental exposure.

Now, with the help of high-powered transmission electron microscopes, chemists captured never-before-seen views of miniscule metal nanoparticles naturally being created by silver articles such as wire, jewelry and eating utensils in contact with other surfaces. It turns out, researchers say, nanoparticles have been in contact with humans for a long, long time…

Using a new approach developed at [the University of Oregon] that allows for the direct observation of microscopic changes in nanoparticles over time, researchers found that silver nanoparticles deposited on the surface of their SMART Grids electron microscope slides began to transform in size, shape and particle populations within a few hours, especially when exposed to humid air, water and light. Similar dynamic behavior and new nanoparticle formation was observed when the study was extended to look at macro-sized silver objects such as wire or jewelry.

“Our findings show that nanoparticle ‘size’ may not be static, especially when particles are on surfaces. For this reason, we believe that environmental health and safety concerns should not be defined — or regulated — based upon size,” said James E. Hutchison, who holds the Lokey-Harrington Chair in Chemistry. “In addition, the generation of nanoparticles from objects that humans have contacted for millennia suggests that humans have been exposed to these nanoparticles throughout time. Rather than raise concern, I think this suggests that we would have already linked exposure to these materials to health hazards if there were any.”

Any potential federal regulatory policies, the research team concluded, should allow for the presence of background levels of nanoparticles and their dynamic behavior in the environment.

So that’s good news. Nanotechnologists, nanotechnology away!

A Mechanical DNA Clock Determines Embryos’ Segmentation

Researchers have discovered a mechanism for how animal embryos segment themselves (roughly from head to tail) with extreme precision and consistent timing: the DNA responsible for determining the fate of different segments unravels in the same order and with the same timing as the segmentation itself. Remember that DNA is generally twisted and looped up as tightly as possible, so that molecules that could span 6 feet end-to-end are crammed up into a few nanometres; specific DNA sequences get unwound when they’re needed so that they can be read and transcribed by proteins, and then have an effect on the cell. 

From Science Daily:

During the development of an embryo, everything happens at a specific moment. In about 48 hours, it will grow from the top to the bottom, one slice at a time — scientists call this the embryo’s segmentation. “We’re made up of thirty-odd horizontal slices,” explains Denis Duboule, a professor at EPFL and Unige. “These slices correspond more or less to the number of vertebrae we have.”

Every hour and a half, a new segment is built. The genes corresponding to the cervical vertebrae, the thoracic vertebrae, the lumbar vertebrae and the tailbone become activated at exactly the right moment one after another… How do the genes know how to launch themselves into action in such a perfectly synchronized manner? “We assumed that the DNA played the role of a kind of clock. But we didn’t understand how.”

Very specific genes, known as “Hox,” are involved in this process. Responsible for the formation of limbs and the spinal column, they have a remarkable characteristic. “Hox genes are situated one exactly after the other on the DNA strand, in four groups. First the neck, then the thorax, then the lumbar, and so on,” explains Duboule. “This unique arrangement inevitably had to play a role.”

The process is astonishingly simple. In the embryo’s first moments, the Hox genes are dormant, packaged like a spool of wound yarn on the DNA. When the time is right, the strand begins to unwind. When the embryo begins to form the upper levels, the genes encoding the formation of cervical vertebrae come off the spool and become activated. Then it is the thoracic vertebrae’s turn, and so on down to the tailbone. The DNA strand acts a bit like an old-fashioned computer punchcard, delivering specific instructions as it progressively goes through the machine.

“A new gene comes out of the spool every ninety minutes, which corresponds to the time needed for a new layer of the embryo to be built,” explains Duboule. “It takes two days for the strand to completely unwind; this is the same time that’s needed for all the layers of the embryo to be completed.”

This system is the first “mechanical” clock ever discovered in genetics. And it explains why the system is so remarkably precise.

I wanted to share this article both because it seems like a very novel discovery and because it touches on some DNA and development fundamentals, but to be honest it’s a bit confusing to me, and I wish I could read the actual article in Science for an explanation. This article basically reads like the embryo is one cell with one set of DNA, which, unless I’m thoroughly off the mark, is not the case during segmentation, by which I’m assuming they mean somitogenesis. This begs the question: in which cells are they noticing this Hox activity? How is this pattern being communicated between cells? 

I may be missing something obvious, but I wish this Science Daily article were clearer. Anyway, in conclusion, here’s an interesting time-keeping mechanism during embryogenesis 🙂

Side note: Apologies for the gap in posts since Thursday; like I said in the previous post, I was marathon cramming for my GRE biochemistry test on Saturday, and my brain has been hibernating since then. It’s slowly recovering from the trauma. Fear not, though, we won’t miss a thing: I’ll be going through every article in my RSS feed since Thursday, all 1000+. No science will escape us!

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