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:

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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.

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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.

Preceptor? Like in Harry Potter?

The University of Delaware is taking a hint from medical fields like nursing and pharmacy to join together two difficult topics: chemistry and biology. The goal is to help students learn complicated chemistry in relation to basic biology ideas, which C&EN reported in this week’s issue.

Basically, the program is taking graduate level scientists who have their Ph.D. or masters and having them act as a learning guide. These preceptors play a role between TA and professor. They’re in the labs and classes getting their hands dirty, but aren’t involved in grading or assessment. They’re mentors which give no judgement. Michael Weir, one of the preceptors, equates his role to that of a “friendly uncle” who will answer questions and solve problems without students being afraid of punishment. Students are divided into smaller groups (though still 48 large) and assigned to a specific preceptor. The students have more access to the preceptor as opposed to a professor overseeing a class of 200.

I really hope the idea catches on. Not only will the undergraduates have access to more personalized help (which I think is absolutely important for first and second year undergraduates) but the preceptors will have experience teaching at the university level. One thing I think larger schools suffer from is the larger class sizes, which is absolutely necessary unless you want a huge staff of professors whose priority is to teach rather than do research (which would cost more money and drive up tuition prices even more). Though I’m not sure that the preceptors need to be staff members as they are at University of Delaware. I think upper level graduate students who want to go into academia could nicely fill this role. It would give them a one-up on their resume, too.