I’m like a rat. I only fly away.

A decade ago, scientists at the University of Florida taught a Petri dish rat brain to fly a flight simulator. They grew a culture of 25,000 rat neurons and, using 60 electrodes, hooked it up to a common desktop computer. At first, the neurons were simply scattered in the dish, but they quickly started to form connections. “You see one extend a process, pull it back, extend it out – and it may do that a couple of times, just sampling who’s next to it, until over time the connectivity starts to establish itself,” Thomas DeMarse, the lead biomedical engineer of the work, described in a ScienceDaily release. When the neural network was joined to the computer, more connections formed as the “brain” learned to control the simulated F-22. Eventually, the “brain” could control the pitch and roll of the aircraft in a variety of conditions, including hurricane-force winds.

flightsim

Would a Petri dish brain get motion sickness?

According to the release, “As living computers, they may someday be used to fly small unmanned airplanes or handle tasks that are dangerous for humans, such as search-and-rescue missions or bomb damage assessments.” A prescient statement for a time before drones (or at least before the public knew). Who knows, maybe the next generation of war will be fought by rat brains.

(For anyone who doesn’t understand the title of this post, I thought I’d bring back some early 2000s references. Remember this?)

Hemp: Not Just for Rope and Granola

Hemp is back, man, and more energizing than ever. David Mitlin, then at the University of Alberta and now at Clarkson University, has developed a method for making supercapacitors out of hemp that is not only much cheaper than graphene (the cream of the crop as far as organic conductors go), but also outperformed standard devices by nearly 200%.

In a press release from the American Chemical Society, Mitlin gives the best quote possible on his research: “We’ve pretty much figured out the secret sauce of it. The trick is to really understand the structure of a starter material and to tune how it’s processed to give you what would rightfully be called amazing properties.” Right on.

hemp

The American Society of Mechanical Engineers is down with hemp.

To make the supercapacitors, his group heated hemp waste at 180 °C (~350 °F) for a day to get a nice char going, then blasted it at 800 °C (~1470 °F) with a little potassium hydroxide. That final burn turned the char into carbon nanosheets (as so nicely depicted in the above picture from the American Society of Mechanical Engineers). The hemp precursor left a lasting impression on the nanosheets, giving them the unique molecular structure that Mitlin claims is key to his device performance. The sheets were riddled with holes 2–5 nanometers in diameter, making nice paths for charges to move in and out.

Yury Gogotsi, materials scientist at Drexel University, in a comment to Chemical & Engineering News, says that scaling up the process may be difficult (read: costly), what with the high temperatures and day-long heating process.

But that’s just, like, his opinion, man.

City frogs like to look for mates in the gutter, according to a report in the Journal of Zoology. Researchers in Taipei found that male tree frogs were congregating in storm drains. It turns out that the structures amplify their mating calls by about 4 decibels, which could help to attract the ladies. The verdict is still out on whether this technique works, but I suspect frogs aren’t too picky about the setting of their romantic trysts.

treefrog

Our little buddy desperately calls for a mate.

Read a bunch of articles on the paper here: Nature News, Live Science (which got picked up by Mother Nature Network and for some reason The Christian Science Monitor), CityLab (complete with “Sexy Sewer Mix” recording) and News Tonight Africa.

That Spider Looks Like Shit

Bird shit, to be specific. In a sad-for-you but funny-for-me play by evolution, the Cyclosa ginnaga orb-web spider has somehow learned to fashion its nest so, when sitting in it, the spider looks like bird poop. This is, like most evolutionary advances, done in an effort to avoid predators (thankfully, these spiders don’t dress up like poop to find a mate). To predators such as ants and wasps, the color of the spider’s body and its web decorations are indistinguishable from each other and from bird dukes. A group in Taiwan published these findings in a recent issue of Scientific Reports (which is open-source, hooray).

(a) Our spider friend pretending to be poop and (b) a reference in case you don't know what bird poop looks like.

(a) Our spider friend pretending to be poop and (b) a reference in case you don’t know what bird poop looks like.

 

In the paper, the authors noted  that many have pointed out that the spider looks like shit, but no one has ever done a scientific experiment to confirm this “hypothesis”.  So they gathered up 10 spiders and waited for them to spin their webs. Then they measured the specific wavelengths of light emitted by the spider’s bodies, their webs, and, of course, bird turd for comparison. Using a computer program to analyze the emitted patterns, they found that bees and wasps couldn’t distinguish between the spider and its web—it all looked like one big blob to them. What’s more, they couldn’t distinguish the spider-web blob from a pile of bird dinks either.

Then, they went out in the wild and decided to color some of the webs black so that the spiders could no longer hide. In short: “When the color signal of decoration silk is altered the predator attack rate increased significantly,” I-Min Tso, an ecologist at Tunghai University and co-author of the paper, told Smithsonian Magazine. The spiders not only needed to blend in with their web, but the entire setup had to blend in with the background, the forest. Black was just too obvious of a disguise.

Oddly enough, “it’s really not all that uncommon. Several other spiders, like Bolas spiders, also use this disguise,” Cornell University arachnologist Linda Rayor, who was not involved in this study, told National Geographic.

So the next time you think you look like shit, remember our little friend C. ginnaga and realize you don’t look so bad after all.

Journal of Proteomics Gets Weird

Harry Belafonte and the secret proteome of coconut milk sounds like a bad detective novel from the 50s (maybe even a radio show). Really, it’s the title of a January 2012 paper in the Journal of Proteomics. After the title, the abstract calms down a bit. They talk about mapping the proteome (proteins expressed by a genome) of coconut milk. Their reason for doing this pain staking work is to create a starting point to discover the proteins responsible for the beneficial health effects often attributed to coconut milk.

And then there’s the graphical abstract:

Image

And their wonderful caption: “Here is your coconut woman, as perhaps envisioned by Harry Belafonte. For its proteome, though, have a look at the report inside!”

They also have a list of highlights about coconut milk.

  • The beverage promoted by Harry Belafonte since at least 1957!
  • A most nutritious beverage in vogue in the Caribbean and all over the world.
  • A grand total of 307 unique gene products detected.
  • Now you know what is the proteome in your Mocha Coconut or Coconut Crème Cappuccino or even in your Piña colada.

In the introduction they even have a recipe for a Batida de Côco coctail (“coconut milk is mixed with sugar and cachaça”). The paper then goes on to talk about proteomics and gel electrophoresis and mass spectrometry, but, man, did they really put some effort into making their work “interesting.”

The Day The Anaerobes Died

A little over 2 million years ago the atmosphere filled with oxygen, and quite rapidly by geological times. The world went through the Great Oxygenation Event (GOE), or if you’re feeling saucy the Oxygen Catastrophe. Cyanobacteria had been chugging away 200 million years prior, going through photosynthesis and releasing oxygen. Before the GOE their released oxygen was trapped by organic matter or dissolved iron (FeS2 and other easily oxygenated molecules). The majority of life, living around these few cyanobacteria, were anaerobic—they didn’t need oxygen. In fact, oxygen was poison to them. The anaerobic lifeforms depended on these oxygen traps, so I’m sure they weren’t pleased to find out that the cyanobacteria had filled up the traps. The cyanobacteria kept producing oxygen and it went straight into the atmosphere. Anaerobic life died. It was one of the biggest extinctions our planet has known. A catastrophe. A second oxygen jump, up to the levels we know today, happened a couple million years later when the deep ocean was oxygenated. This seems completely reasonable, so much so that it’s accepted almost universally as a scientific truth.

oxy1

Oxygen in the atmosphere increases over time. The red line show the traditional two-step oxygenation event, where everything happened in big jumps. The blue line shows the new proposed model, where things are a little more gradual. Arrows are poorly understood “whiffs” of oxygen arising from anomalous metal enrichments in Australian shale.

But a new model, published in Nature Reviews, suggests the GOE isn’t as step-wise as previously thought. Proponents of the model say that the oxygen level spiked, then decreased. That the one billion or so years of atmospheric consistency had relatively low levels of oxygen. Large pockets of hydrogen sulfide in the oceans harbored life during this time, and it wasn’t until the final oxygen jump that most of life on Earth died. To them, the GOE is less of an event and more of a process.

The only way to test these kinds of theories is to look at rocks. For example, by looking at the sulfur isotope fractions, which are greatly affected by the amount of oxygen present. But this, they claim, may be tainted by rivers flushing their sulfur to the ocean, creating a sort of false positive. If this did, in fact, occur then oxygen levels may have risen more gradually than previously assumed—tens of millions of years more gradually. To support the challenge to current theory, they tied in the Archaean-Proterozoic boundary (defined in time and geology), where tectonic plates reorganized into the first volcanoes, and the “Snowball Earth,” the first of the global cooling cycles (or glaciations), saying these events contributed to both the sulfur isotope fractions (further obscuring the data) and accumulation of atmospheric oxygen.

But even before the GOE (or, as they suggest, the GOT for transition) animal life was rare—estimated at less than 1% of today’s diversity. Some research suggests that, instead of the rise in animal life being a coincidence, it was the emergence of animals that triggered the GOE. Others suggest that without the GOE life as we know it would not have abounded. Either way, this is one catastrophe we should feel good about.

Big Ball Scars

Buckyballs are weird. They’re little soccer balls that collect electrons—one of the few materials used as electron acceptors in solar cells. They’re the largest object to show particle–wave duality, and that’s quite a feat for sixty carbon atoms. If an alkali-metal is shoved in the center, the whole thing acts metallic and, in some cases, superconducting. They even have a toy named after them. And we can’t forget that the 1996 Nobel Prize in Chemistry went to the discoverers of fullerene. Needless to say (of course, I’m about to say it anyways), these large spherical molecules are a hot topic.

Some researchers are moving away from the “small” fullerenes, C60 and C70, to larger versions. But as the size grows so do the problems. A recent report in ACS Nano by David Wales of the University of Cambridge details the defects that arise in larger configurations (sorry for the paywall link). This work is entirely theoretical, as causing defects in a specific arrangement is as difficult (or maybe more so) than forming defect-free molecules. The molecule can get a “scar” when the pentagon–hexagon–pentagon structure is dislocated to a pentagon–heptagon–pentagon structure.

bucky3

C860 and C1160 fullerenes with red scars.

Defects are unavoidable in large spheres and the configuration of them constitutes a Thomson problem, the location of repulsive points on a sphere, which is one of eighteen unsolved mathematical problems on the list of Smale’s problems for the 21st century. While the Thomson model was previously used to describe the configuration of electrons in an electron shell (and has since been abandoned since it’s failure to do so), the problem is now being applied to fullerenes.

bucky1

Defects in different sized fullerenes.

 

The paper also looked at funnels, or outward curving structures, and showed that defects can occur there, too. Interestingly, the fourth to last structure below (which is akin to a carbon nanotube) shows no defects (at least in their picture, they didn’t discuss the lack of defects in the text).

bucky2

Defects in curved surfaces.

So what does this mean? What can defects do? Well, they can disrupt aromaticity and conjugation which would change the electronic structure of the molecule, diminishing conductivity and widening the band gap so that they’d be unsuitable for solar cells or other electronic applications. (That was a mouthful… fingerful?) But it’s not all bad. A paper from last year in the Journal of Physical Chemistry C (paywall again) states that defects in a graphene surface can lead to reactive sites. In other words, chemistry can happen. I don’t think it’s too far fetched to say there would be a similar situation with fullerenes. After all, they’re just balled-up graphene.