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.

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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.

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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.

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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).

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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.

John Rogers In The 24th and a Half Century

In the lab of University of Illinois Urbana-Champaign Professor John Rogers, electronics fall apart or, more accurately, dissolve in water. Transient electronics, as they’re called, are designed to be temporary. They have the potential to be implanted in the body, monitor vital signs or fight infection, and slowly dissolve into harmless components. If scaled up to manufacturing levels, these devices have the potential to revolutionize electronics. And his group has been working hard by publishing a lot of papers on the subject.

So I was surprised when I saw a recent report by the Rogers group in Nature Communications on a wholly different class of electronics. (Though maybe I shouldn’t be surprised since Rogers got his Ph.D. under none other than George Whitesides who may be the most diverse chemist of today.) In this new report, he’s using fractal patterns to integrate metal wires into a stretchable substrate. At first I thought, “How the hell is he going to make an infinite recursion wire.” Then I found out that space-filling curves are fractals (thanks Wikipedia). You can think of the patterns like a winning game of Snake, lines packed as close as possible without overlapping. An excited group of mathematicians figured out mathematical functions for different varieties of packing and left us with the below patterns. (Traditionally, the mathematical functions have hard edges, but Rogers has replaced the edges with arcs to improve the mechanics—hard turns create stress points which break easily.)

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Different fractal patterns used in the devices.

So wires of different patterns are embedded in a polymer substrate. So what? Well, it turns out interesting mechanical properties arise with the different patterns. These things can stretch. The “stretchability” is well above the 20% necessary to mimic skin. So that’s what they did. Using the Peano layout, they spelled out the word ILLINOIS and mounted it on someone’s actual skin. Then, using a “skin-replica” they took optical and scanning electron microscopy images to prove that the wires conform to the valleys and hills of normal human skin.

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The word ILLINOIS was embedded on actual, living skin. Boxes e and f are optical and scanning electron microscopy images on a skin-replica.

“Amazing,” I thought. Wearable electronics may soon be reality. And if this was my work, I would probably stop there, too excited not to publish. But it’s not and a good thing, too. They went on to make actual functioning devices able to heat, sense temperature, and take electrocardiograms (ECGs). They made tiny heart monitors.

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And not only that. The devices are compatible with MRIs. Because there are no closed loops in these devices, there aren’t any circulating magnetic currents that may cause signal loss. They’re completely invisible in an MRI scan.

It’s not often that math-inspired work crops up in chemistry (for a hard science, chemists are surprisingly squeamish about math), but when it does it’s always beautiful. It seems that John Rogers has made it his personal mission to advance us to the next level of technology… and into the twenty-fourth and a half century!

“Never give up. Never surrender.”

One of my favorite research projects to follow is Whitesides’ soft robot. Part of his platoon (since he has enough graduate students to call it such) has been developing a mobile robot made purely of polymers. No metal necessary. The body of the robot is divided into air sacs that are pumped full or evacuated to create movement. They’re supposed to resemble starfish, but they look more like army commandos crawling under enemy gates.

By filling the sacs in the right order, the soft robot can slip under a raised barrier.

By filling the sacs in the right order, the soft robot can slip under a barrier, such as your bedroom door at night.

Soft robots are cheap, easy to fabricate, lightweight, and have the advantage of picking up delicate objects, like an egg, without crushing it.

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In a new paper in Advanced Functional Materials, the group shows that the robots can resist blunt impacts “better than hard robotic structures (and also most animals of comparable weight and size).” Though I hope they didn’t have a control for that parenthetical joke. The group wanted to quantify exactly how much damage these robots can take. So, in a comically sad fashion they hit their robot with a hammer. If you have access to the paper, check out the Supporting Information for some videos that will make you feel a little bit bad for laughing. Of course, the “hammer test” was in addition to more traditional scientific methods for measuring stress and strain.

You can knock him down, but he'll get right back up.

You can knock him down, but he’ll get right back up.

Since whacking the poor guy with a hammer wasn’t enough, they ran him over with a car. And when that wouldn’t stop him, they ran him over again but this time with a pile glass underneath. Yet, he continued to grip. They proved that these little guys are highly resistant to mechanical stress. Of course, if the glass had managed to poke a hole in one of the sacs the robot would cease to inflate, in effect maiming it, but the polymer they use, an Ecoflex silicone, is fairly puncture resistant.

He's a survivor.

He’s a survivor.

These flexible robots really delight me. They’re not creepy enough to give me chills (Boston Dynamics, I’m looking at you)  and they’re not human enough to make me think of bad sci-fi movies. Well, maybe my science fiction thoughts aren’t totally gone, because, after reading the paper and opening this text editor, I started to type:  I’m glad these guys aren’t sentient… yet.

New Skool

I’ve been talking to a few professors lately who are doing really exciting stuff in the classroom. Instead of the normal lecture then homework format, they’re having students do in depth research projects during class hours. After half a semester of lecturing, the students break up into small groups, decide on a topic, and then develop a project. The professor is in the room while the students are working out the details so that the students are guided in the right path, rather than presenting a project in the end and getting half of it wrong. And they’re not choosing simple topics. The two specific professors (I won’t name them, but it probably wouldn’t be hard to Google-guess them) are focusing on conjugated polymers and paper electronics. New cutting edge stuff where there’s not a lot of information out there (that’s not written at the graduate/professional level). One of the groups in the polymer class continued their project after the semester ended and got a publication out of it! So not only are students learning about the cutting edge of science, but they’re actually contributing. (And they published open-source, which I think is also great.)

I really hope this kind of classroom setting catches on. Of course, this takes a lot of effort and time for both the students and the teachers and if the project turns into a full-fledged research project it could get expensive, but I think for students who are working toward graduate school that a undergraduate course like this would be invaluable. The first year for any graduate student is diving into the literature and learning advanced techniques, not really discovering anything new yet. This helps students develop their chemical intuition which imparts creativity and a quick understanding without having to search through the literature every time a problem comes up. After an in depth class that focuses on new topics and has the students doing actual research, the students will have already started to develop that chemical intuition.

Some people think that we’re producing too many science PhDs (see this post in Scientific American for a nice summary and debate in the comments). Maybe a way to counteract that would to be to produce better BSs, and going away from the typical lecture-based format will definitely help. Plus, it’d be way more interesting than listening to someone drone on for an hour then doing homework problems that can be googled.

Future Made of Virtual Insanity

A team from Utrecht University and University of British Columbia have developed an amazing algorithm for “flexible muscle-based locomotion for bipedal creatures.” Their paper is available online (open-access) and they have a great video on Vimeo demonstrating their algorithm.

The “creatures” determine their own walking gait based on repeated cycles. There’s even a part in the video where they show walking at various cycles in the experiment. The first cycle creature falls down almost immediately. As the cycles progress, the creatures walk a little longer and a little straighter before falling over seemingly at random. Around cycle 1000 (or a few before) the creature finally gets the hang of walking and can move around without falling over.

The creatures (either humanoid or dinosaur-looking) aren’t given initial input on how to walk, but are “driven entirely by simulated muscle-based actuation.” The simulated muscles aren’t even put in a specific location. They start with an approximate structure and let the machine determine the best structure for walking. Essentially, the computer is evolving this creature, it’s muscles and it’s mechanism of walking, to make it stable.

Not only can these creatures walk, they can run (or hop in some cases), change directions, walk up and down small inclines, and, as for this unfortunate fellow, keep plodding along as boxes fly at him from all different directions.

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An apt metaphor for the human condition.

There are great possibilities for the future of this research: understanding how creatures evolved for bipedal locomotion on Earth, simulating how creatures would evolve on another planet (maybe if we find water on a planet in a Goldilocks Zone, we could simulate what creatures living there would look like), animations could be more realistic without the need for input from an actor, or if we get really advanced we could simulate an entire universe, creating simulated life that evolves and grows, maybe even watch as they develop a philosophy saying that they’re just a simulation. It’s this kind of work that really makes you question our universe, but then makes you laugh when you see the guy above get pummeled by a giant box.

An Out of This World Collaboration

This is a work of historical fiction. Liberties have been taken with events and timeline.

Harold Kroto and Robert Curl gazed into the Sussex night sky, imagining molecules floating in the space dust.

“If only we could make some of what’s out there down here,” Kroto sighed.

“I may know someone who can help,” Curl said.

The next day, Curl called his friend Richard Smalley, an expert in experimental physical chemistry. If there was anyone who could make the unsaturated carbon chains Kroto and Curl so desperately desired, it was Smalley.

“Smalley, my old friend. Harold and I have come upon an interesting topic and would like you involved. We’d like to synthesize some of the more unstable spacely carbons for direct characterization here on Earth.”

“You want me to create outer space,” Smalley said, “in my lab.”

“Precisely,” said Curl. “I’ll be back in the US soon. I’d like it if we could sit down and chat.”

“Absolutely,” said Smalley as he hung up the phone.

Weeks went by before Curl returned to his academic home, Rice University, but time had not eroded his interest. Directly after landing, eyes heavy with jet lag, Curl drove to the university.

He arrived in the chemistry building to find Smalley’s door open, lights on, but Smalley nowhere in sight. He waited for half an hour without the return of his friend before he gave up. His head hurt. His back hurt. He was tired. Maybe it would be best to return home. He could try again tomorrow.

I’ll just take a quick look in the lab, Curl told himself.

The whirring of pumps grew louder as Curl approached Smalley’s lab. A red light blinked over the door, warning unsuspecting visitors to dawn a pair of yellow-tinted glasses, lest they be blinded from a beam gone awry. Taking a pair of glasses from the bin at the door, Curl entered the lab.

Thick metal tubes connecting thick metal boxes took up the majority of the room. Lenses, bolts, and wires littered what little counter space was left. Three people in lab coats dotted with curious brown rimmed holes were gathered around one of the boxes.

“Try the 1064. That should arouse some excitement.” Smalley said. He turned from the group and saw Curl waiting in the door.

“Robert,” he said. “Good news and bad.” He slung his arm around Curl and led him out, away from the flashing lights and whirring pumps. “We’ve got the setup working nicely. The results though…”

“You’ve already started?” Curl asked, surprised. “We haven’t had time to talk.”

“I did some research of my own. My setup will make your outer space, of that I have no doubt, but we may find space to be more perplexing than we thought.”

“What makes you say that?”

“We’re getting…,” Smalley paused as his eyes drifted upwards, “clusters.”

“Clusters?”

“Clusters. Sixty connected carbons.”

“In chains?”

“Not chains. Spheres.”

“Spheres?”

“Or as close to a sphere as a molecule can get.”

“Let’s get Harold on the phone,” Curl said.

Minutes later Kroto was fumbling with the phone in his office, trying to accept the collect call Curl and Smalley had placed.

As soon as the call clicked through Kroto exclaimed, “This will cost a fortune.”

“Sorry about that,” Curl said. “We didn’t have time to request international minutes. You know how tight the administration is with money…”

“Yes, well, get on with it,” Kroto said.

“We’ve found spheres,” Smalley said.

“Spheres?” Kroto asked.

“Spheres,” Smalley and Curl said together.

“I better get out there.”

Three days later Smalley, Curl, and Kroto were gathered in Smalley’s cramped lab. Smalley pushed aside a pile of bolts and, as they clinked against the linoleum floor, pulled a ream of paper from the printer. The three, each holding a different colored pen, scribbled furiously.

“I’ve got it!” Kroto shouted. He had drawn a football with dots, representing carbons, at seemingly random points.

Smalley and Curl examined the drawing closely.

“You drew sixty-one,” Curl said and they all went back to scribbling.

A pair of graduate students walked in the lab and froze at the sight of three professors huddled close. They crept across the lab, trying not to gather attention. As they shuffled their feet, they came upon the abandoned bolts Smalley had flung and stepped down hard.

“OUCH!” one yelled. The other punched him in the arm.

The professors turned their heads in unison to look at the intruders. As the unfortunate student jumped in place holding his foot, the other grabbed a soccer ball from his desk.

“We came to get our ball,” he said.

The professors turned to each other, eyes wide.

“That’s it!” they shouted.

And so fullerene was born.

This Year In Space

There’s a lot to be excited about this year, especially if the study of outerspace is your thing.

New Year’s Day ushered in the Curiosity rover’s 500th sol (or Martian day) and her mission isn’t over. Curiosity’s ready for the coming year, showing us her excitement by tweeting: “Goals for 2014: Finish driving to Mars’ Mount Sharp & do all the science I can.” Once at Mount Sharp (officially called Aeolis Mons), Curiosity will test for water and organic molecules in sedimentary rock layers, as her search for life continues.

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Panoramic of Mount Sharp taken by NASA’s Curiosity rover.

With Curiosity considered a success, NASA has moved on to their next Mars project. The mission, called Mars Atmosphere and Volatile EvolutioN, MAVEN for short, will explore the thin atmosphere hovering above the red planet. Data from the probe, which launched this past November, should tell us about the planet’s history in terms of atmosphere, climate, and liquid water. We won’t see results until mid-to-late 2014, as the journey to Mars takes a long 10 months.

India is also hosting their own Mars Orbiter Mission, but the mission’s goals aren’t solely about Mars. Three of the four listed goals were about developing the technology to achieve deep space exploration, including design and realization of a Mars orbiter, long-range communication, and the creation and addition of autonomous features in the spacecraft. The probe was launched in early December and is expected to travel 300 days before reaching Mars. Once there, the probe will remain in orbit to study surface features such as morphology, mineralogy, and atmosphere composition.

In a final exciting mission, the European Space Agency’s Rosetta spacecraft will finally reach its target. The European Space Agency has been playing the long game, as one must do when playing in outerspace. The probe first launched in 2004 and only now (and by now I mean in almost a year) is it coming in contact with its target. The plan is to both orbit and land on the comet Churyumov–Gerasimenko. If successful, Rosetta will be the first probe to land on a comet and give us the first images of what the surface actually looks like. Part of the probe will stay in orbit to collect gas and dust samples from the coma (the head of the comet) and the tail.

I expect there will be a lot of news coming from these projects in 2014 and 2015. I’m most excited about the photos the probes will send back, especially from the Rosetta spacecraft. Everything we know about the surface of comets is a well-educated guess. Now we’ll finally confirm or, even more exciting, disprove that guess. We’re exploring new frontiers and proving that that exploration isn’t dead. It’s a good time to be alive.

Grad School Needs Its Own Change.gov

Nathan L. Vanderford wrote a bold article in Nature Biotechnology last month. In it, he called out graduate education, saying that the system was broken but fixable. He made some statements that I think most graduate students, especially those from the sciences, can relate to. I know I sure can.

What I found was that graduate school was not impossibly difficult from an intellectual standpoint, but it was painfully hard from an emotional and physical standpoint. I felt as though faculty had the mentality of putting students (and postdocs) though, well, torture—because that’s how they went through graduate school and their postdoctoral fellowship.

And the quote that really spoke to me:

I also found it mentally frustrating that graduate education is narrowly focused on preparing students to eventually become faculty in major universities in which they would be running their own research programs.

There just isn’t enough room for every Ph.D. student to gain a faculty position. What’s more is that a lot of students don’t want faculty positions. I know I don’t.

Vanderford’s main areas of change focused on faculty supporting of alternative career paths, multidisciplinary course work, and active work experience (job work, not lab work).

As some of you (hi, mom) may know, I’m working toward a career in science communication. Although I’ve had to seek out opportunities and resources on my own (including finding a way to fund a trip to the National Association of Science Writers conference last November), my PI has been extremely supportive. When I first told him I wanted to go into science writing, he tried to convince me that academia would provide a better job. And, yes, I’d make more money in academia, but if I was in it for the money I’d have gone to business school. After he realized that my mind wouldn’t be swayed, he gave me a contact at the Materials Research Society (where I sometimes write articles for their website, shameless plug) and he lets me spend time working on my writing goals (as long as I have research results).

I love science. But I don’t love the culture in academia. I don’t love the isolation and the tedium and the ridiculously narrow focus. I want to know everything about science and I want to share that knowledge with others, so I’ve chosen an alternative career path that will let me do just that.

Judging from a poll on Benchfly.com, where the article originally appeared, a whopping 77% of people think graduate education “needs a complete overhaul.” Only 4% say it should stay the same. (The remaining 19% are wishy-washy about it.) I don’t think making the changes that Vanderford proposed would be too hard to implement. Many schools are already focusing on multidisciplinary research and coursework (I took a graduate level engineering course and it counted towards my requirements). I’ve also been told that taking an internship during my education is fully possible—structures are in place to handle a temporary leave—but I was offered no help in obtaining one (and ultimately didn’t). The most difficult change will be removing the mindset that academia is the be-all-end-all of doctoral education. A Ph.D. is no less of a Ph.D. if they choose to go into industry or work for a non-profit or go into science communication or do something else entirely. These academic biases may not so easily be removed, but if they are then graduate education would be infinitely more helpful to achieve what most of us are here for: to get a job.