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.

Animal Research Makes Me Feel Bad

This week Imperial College London came under heat for inadequate treatment of research animals. Facilities were understaffed and poorly supervised, while caretakers received “patchy training.” The university has held a press conference and promised to correct the wrongs.

While I know animal research provides a massive amount of scientific insight that can be gained no other way (that we know of), I’m still uncomfortable with the idea of subjecting animals to research: growing tumors on their backs, injecting them with diseases, keeping them isolated in a sterilized cage for their entire life.

The topic fits well with another piece of recent news: the Nonhuman Rights Project has filed a lawsuit claiming chimpanzees should have the same basic rights as humans. They’re focusing specifically on a chimp in New York named Tommy who “is being held captive in a cage in a shed at a used-trailer lot.” Right now chimps are classified as property and the owners have a right to keep him confined in a cage. They’re asking the court to assign personhood to Tommy so that he can be removed from that environment and placed in a sanctuary.

This court case is not so cut and dry (the owners claim they rescued Tommy from even worse conditions and have been trying to place him, without luck, in a sanctuary), but that’s not what I want to focus on. I’ve been reading books on animal cognizance and thinking a lot about the topic lately and it’s my opinion (though it’s shared by many others) that animals have emotional lives. Elephants mourn their dead, dogs get anxious when their masters leave, and I once had a cat that was perpetually pissed until it found a best friend.

Now, I’m not saying their emotions mimic human emotion, or that they’re as strong (but I’m not saying they’re aren’t as strong either), or that they have a way to classify those emotions and rationally act on them (I don’t believe that at all). I’m saying animals can feel sad and worried and scared.

I feel animal research can bring negative emotions to the test animals and that makes me uncomfortable. Even in laboratories where the animals are well cared for, they still undergo human handling, confinement in an unnatural habitat, and testing (sometimes not-so-nice testing). But as I said before, I’m conflicted because I know the human benefits of animal testing. Maybe better computer models would take some of the burden off live animals. Hopefully, all those biologists quitting wet labs for so called “dry labs” (i.e. computers) will fix this problem and animal testing will phase out. Until then, I’ll feel bad about it.

Give Those Women Some Space

When I grew up I wanted to be an astronaut. I loved outer space (specifically that of the Star Trek variety) and I thought it would be fun to float around in space and fiddle with the scientific instruments, maybe take a stroll on the moon.

Then I learned (slightly erroneously) that most astronauts are in the military. (A person can gain flying experience in the military, which is handy, but civilian astronauts are common, too.) I didn’t want to join the military. Even though I was a kid not too long ago (in the 90’s) the military wasn’t really a place for women, or at least wimpy petite women like me. I mainly gained life experience through movies/TV and there just weren’t women soldiers… or if they were they were buff and bald and manly (I’m looking at you Demi Moore).

So I gave up my dream of being an astronaut. And maybe that was better. The Guardian just reported that the number of women in space and just surpassed the number of dogs in space. But times are changing. Many women are looking into careers in space. Astronaut Cady Coleman noted that some people have the misconception that women don’t belong in space, they can’t do the jobs or won’t be as good as men. (Of course, since “normal people don’t care about science” they had to equate women in space to a popular movie. So skip to the end if you want to hear her quote.) But she’s been working hard to show people that women are just as capable. Mae Jemison, the first African American woman in space, also offers hope to young women wanting to go into space: “Never let yourself be limited by other people’s limited imagination.”

The End [of the big research group] Is Nigh

Nobel laureate Robert Grubbs, of the Grubbs’ catalyst fame, answered some interesting questions in an interview recently in Nature. He was asked “Is academic science research becoming dependent on industry funding?” A question I’ve been interested in since I started graduate school. From reading through the literature and talking to people about their work, the obvious trend of application-based research leaps out. Being in academia and studying ‘basic science,’ I understand how hard it is to get funding (in four years, I’ve only been on RA a single summer). Grubbs says that,

industry is having similar financial problems to academia and has also cut back on its funding of basic research… Now, most of the commercialization is done by small companies who are bridging the gap between the laboratory and industry.

For someone interested in how things work and not necessarily their utility, this is sad to hear. At the same time, it is understandable. I attended a talk by the famous chemist George M. Whitesides this weekend at the NASW conference and he supported the trend of application-based research. But he took a slightly different aspect. Instead of finding a problem and applying known chemistry (or physics or biology), researchers should find a problem that can’t be solved with what we know. Then, after much hard work and new discoveries, we’ll have both a solution to the problem and a deeper understanding of the universe. That is an opinion both the pure and applied researchers can get behind.

In the interview, Grubbs goes on to talk about how funding is increasingly difficult to find, saying it’s hard to even get into a career in the sciences. “We will probably have to reduce some of that [graduate] support and make tenure decisions earlier. The day of the really big research group is over.” In a not-so-promising ending to the (published) interview he says, “I must admit that I am sort of glad I’m old!”

Just something I want to point out

I don’t know why people think animals are generally stupid. Maybe because they don’t have language (although sperm whales have regional accents, so that must say something) and haven’t taken over the world (opposable thumbs really helped us with that one). Maybe it’s from the religious notion that animals don’t have souls. Either way, it’s left us with an undue pride of being the only truly cognizant species on the planet.

Recent years have shown that animals do think and reason—some researchers even go as far to say animals have rudimentary feelings, though in the scientific literature they are careful in their phrasing. Now, we’ve learned that elephants can understand what a human means when they point. The researchers pointed and the elephants found food. Apparently, they’re the first wild animal to do this. (Wolves are known to follow a human’s gaze,  but don’t understand pointing.) Elephants already use their trunks to point so it makes sense that they understand what a little creature is doing when they wave their two tiny side trunks.

I’m reading Animal Wise by Virginia Morell and she really highlights the ability for animals, even insects, to think and learn. I think (I hope) that in the next few decades we’ll come to realize that how we see the world isn’t so different from how animals see the world. Rather than categorizing their actions under the broad topic of “animal instinct” we’ll realize that these creatures think and learn just like us. Sure, humans have the benefit of being able to mold the world around them, but maybe, just maybe, we’ll realize that we’re not so much better.

Age of Anthropocene: Let the Sunshine In

I learned today that there’s a chronological term (like Jurassic and Cretaceous) to mark when human activities negatively impacted (I’m a little hasty with the past tense here) the Earth’s ecosystems. The Anthropocene, to my surprise, started 8,000 years ago when humans first started clearing forests and fields to cultivate crops. Our effects were pretty stagnant until about 2,000 years ago when Romans and Chinese were running around building their empires and dynasties. But our destruction really gained speed during the Industrial Revolution when we started spitting plumes greenhouse gases, soot, and metals into the air.

We’ve messed up a lot of things. We know that. Or, at least, most of us know that.

To further prove that our actions really do have consequences, a recent publication in Nature Communications studied the effect of human influence on global tree cover. I had hoped they used Google Earth to map the tree cover, but they were more advanced than my armchair science. To get topography information they used data from Shuttle Radar Topography Mission and something called MODIS, which makes me think of TARDIS but is actually nothing like that (I’ve been watching a little too much Doctor Who lately). Both are NASA projects using satellites to map various aspects of Earth.

They found slopes “act as a refugee for trees.” The more humans came the more trees fled to the slopes, like frightened cats running up the stairs every time the front door opens and someone new struts in. With enough people around, our activities start to dictate where the trees go. Areas with low fertility rates and low projected population growth (they mentioned Switzerland by name) managed to increase tree density on slopes. Which is nice, we’re learning to cohabitate with plants… as long as they stay on the bumpy parts.

Taken from Figure 3.

Relationship between slope and tree cover, which is “strongly skewed” towards positive values.

Another interesting aspect is that they found political and economic models could predict changes in tree coverage. And they made a decent model of just how much our (not so) little human dealings affect the environment. Surprisingly they found tree coverage actually increased between 2000 and 2005 (why they studied tree coverage almost a decade ago is beyond me).

Hopeful researchers predict a transition into the Sustainoscene through renewable energy (the paper I linked was very excited about solar cells) and more environmentally friendly industrial practices. Maybe one day we’ll learn to live on this world without ripping it up. That or discover FTL space travel and a suitable world so we can keep ripping shit up.

Simplify the Universe

Particle interactions calculated with a single term all done by hand?! That’s crazy. In case you have nothing to base calculating particle interactions in quantum field theory on, just imagine having thousands of puzzle pieces scattered everywhere to suddenly, without all the pesky pieces, having a single, unified picture. All it takes is some new thinking and a little geometry.

In this new model, physicists describe the universe by an amplituhedron, an infinite-dimensional geometric object. The volume of this object is equal to the scattering amplitude—the holy grail of particle physics—which physicists at the Large Hadron Collider use to describe particle interactions. In some amplituhedrons the amplitudes can be calculated directly. In others diagrams called “twistors” are needed.

What’s more, they’ve found the solution to everything. The volume of an infinite-sided “master amplituhedron” represents the amplitudes of all physical processes. The italics are supposed to impress you. Interactions between a finite number of processes, what us humans normally consider, are contained on various faces. Interesting to me, but probably not to anyone else, is that the master amplituhedron simplifies to a circle in 2D.


Amplituhedron representing an 8-gluon particle interaction, which normally needs ~500 pages of algebra.

The amplituhedron removes locality and unitarity. Particles that aren’t near either other in space or time can interact (what?) and the sum of the probabilities for all possible particle positions doesn’t have to be 1 (what?!). That works out for gravity though, which explodes—yes, explodes—in equations with locality and unitarity. Connecting gravity to particle physics is a big deal—no one’s been able to do it yet. Jacob Bourjaily, one of the researchers, described this method as “a starting point to ultimately describing a quantum theory of gravity.”

Nima Arkani-Hamed, the lead author (the main man, the head honcho), gave a talk about amplituhedrons at the SUSY 2013 conference, which is posted online. Warning: the talk is very technical, but interesting nonetheless (if only to watch a man in shorts and a shirt two sizes too large give a spitfire professional talk). Although, in the talk he says amplituhedrons can be “explained to a smart junior high school student,” which left me feeling like a stupid graduate student.