Monday, May 27, 2013

What is an Experiment?

What is an experiment?
Experimenting with color (source)

People use the term 'experiment' to meant a lot of things. One may say "she experimented with drugs" or "she performs experimental music". Someone might 'experiment with ones hair' or 'perform a thought experiment'.

All of these uses of the word experiment have distinct connotations, but most of them essentially mean 'to try something and see what happens'. In the examples above, most of the phrases also imply that the experiment is something new. If she experiments with her hair, she's probably trying some new style and seeing if she likes it. If she performs experimental music, she's probably not following the conventional rules for the music she is playing.

Are these kinds of 'experiments' different from the experiments that scientists do? Well yes and no.  The basic definition of an experiment as 'trying something [often new] and seeing what happens' is pretty much what scientists do. So what's different? Why isn't someones 'hair experiment' publishable in a scientific journal?

Mythbusters would have you believe that the only difference between science and screwing around is writing it down:

And that is sort of true.

But what really makes a scientific experiment scientific is controls. In our hair example, you can experiment with your hair by dying it black, and seeing if you like it. But that's not the scientific experiment. To be scientific you would have to decide how to measure how much you like your new hair color. You could do this by filling out a survey each day asking you how many times you thought you were pretty or rating your confidence on a scale of 1-10. You could fill this survey out for a week and then dye your hair and fill the survey out for another week. You could then compare the scores and decide if the new black hair had a 'significant' impact on your self-image. 

Lets say it does impact your self image and you report higher self-confidence that second week. But what if you feel different just because you have a new hair color, not because you have black hair?

Well, you would want to do a control experiment, which controls for the newness of the hair color. You could control for novelty by dying your hair yet a different color, and taking the survey for another week. Or you could take the survey two months after you dyed your hair black to see if you still report higher confidence or if your confidence has dropped back down to normal.

This is not a perfect experiment by any means, it's not even a clever or well-designed one, but it is somewhat scientific. And illustrates what I think is the most important difference between experimenting as in trying something new, and experimenting as in trying to find something out:

The control group

In addition, here is a great example of how important the control group is in science. (See the epilogue)

© TheCellularScale

Saturday, May 18, 2013

Homeostatic platsicity in a thorny situation

Synapses, the connections between neurons can strengthen and weaken depending on the specific activity at that synapse. This is called synaptic plasticity, and we've talked about it a lot on this blog (here, here, here and here).

the strengthening and weakening of synaptic connections corresponds to the spine growing or shrinking (Matsuzaki 2007)

However, there is another kind of plasticity that can occur at synapses. This is called homeostatic plasticity. And instead of the synapse strengthening or weakening depending on the specific activity at that synapse, the synapses strengthen and weaken in homeostatic plasticity depending on the activity of the whole cell.

To drastically simplify, each cell 'wants' to fire about a certain amount, if it suddenly starts to fire a lot less, it will take steps to strengthen its connections or make itself more 'excitable' so it can get back to its preferred amount of firing. Similarly if the cell starts to fire a lot more than normal, it will take steps to make itself less excitable and to weaken its connections until it reaches the right amount of firing. 
Thorny Excrescences from Lee et al., (2013)
A recent paper from the Pak lab explains how in some specific neurons in the hippocampus (CA3 pyramidal cells), the activity of the whole cell is strongly controlled by a some very peculiar synapses. These synapses are close to the cell body, and are on these HUGE weirdly shaped spines (see above) called "Thorny Excrescences". For comparison 'normal' spines look more like this:
Spines from Lee et al. (2013)
The Thorny Excrescences (TEs) are massive spines that contain many separate synapses on them, but connect to the dendrite through 1 neck. 'Normal' spines, on the other hand, usually have 1 synapse at the spine head, and connect to the dendrite through 1 neck.

The size of the TEs, and their proximity to the soma makes them an extremely powerful way to control the signals that the soma receives. Lee et al (2013) shows that when you drastically reduce activity by blocking action potentials (using TTX), you get massive growth of these TEs, but the normal spines further away from the soma stay the same.

They test 3 things to determine whether the TEs have undergone homeostatic plasticity. They look at the morphology (they are bigger), the activity (the electrical signals from them are bigger) and the molecular signatures (the molecules indicative of new synapses are more plentiful). The paper is a really nice complete story showing that these TEs have a lot of control over the general activity of the cell.

It also solves an important problem with homeostatic plasticity. That is, how can the general activity of the cell be modulated without the specific differences between synapses being erased, and consequently the memories or pieces of information they encode? If homeostatic plasticity occurs at spines dedicated to it, then the other spines can still encode specific signals while the activity of the cell as a whole changes.

© TheCellularScale

Lee KJ, Queenan BN, Rozeboom AM, Bellmore R, Lim ST, Vicini S, & Pak DT (2013). Mossy fiber-CA3 synapses mediate homeostatic plasticity in mature hippocampal neurons. Neuron, 77 (1), 99-114 PMID: 23312519

Sunday, May 12, 2013

The Inadvertent Psychological Experiment

Escape from Camp 14 is deeply disturbing, and I highly recommend it.

Escape from Camp 14 by Blaine Harden
Escape from Camp 14 is a chilling tale of Shin Dong-hyuk's escape from a North Korean prison camp. What is so interesting about Shin Dong-hyuk's story as written by Blaine Harden is that he was born inside this North Korean prison camp. Apparently they allow breeding between prisoners as a reward for 'good behavior.'

Escape from Camp 14 reveals the obscene violations of human rights that occur in North Korean prison camps, and was especially poignant because I am a similar age to Shin Dong-hyuk and could directly compare my memories during the specified years to his. For example he escapes on January 2nd, 2005 and I couldn't help but think of the New Years party I was at that year and how absurdly different my life has been from his.

This book struck me in a way that reading about the horrors of the Holocaust never could. Those atrocities happened long before I was born. But the atrocities in North Korea are happening right now. I mean right this minute in a prison camp, a child is likely being beaten, a woman is likely being raped by a guard (later to be killed if she happens to become pregnant), someone may be picking undigested corn kernels from cow dung to ease hir starving belly, and maybe two lucky prisoners are getting to have 'reward breeding' time. Right now. This minute. That is just nuts.

The other thing that struck me about this whole situation is that having children born into a hostile prison environment is an inadvertent psychological experiment. These children are raised without love and without trust. One of the sharpest points in the book is the reveal that Shin Dong-hyuk turned his own mother and brother in to the guards for planning an escape. He watched his mother's execution shortly thereafter and felt nothing but anger at her for planning an escape.

When he finally escaped, it was shocking to him to see people talking and laughing together without guards coming over to (violently) stop it. In Camp 14, gathering of more than 2 people was forbidden. These prison children are being raised on fear of the guards and suspicion of each other. One of the easiest ways to be rewarded is to tattle on another prisoner for something (stealing food, for example), and the children learn this quickly.

If something drastic happens and North Korea dissolves, these children raised in prison camps will have a near impossible time trying to adjust to a life of freedom and will have a difficult time forming attachments and trusting others (as seen in Shin Dong-hyuk and other refugees from North Korea). Their personalities and psychological profiles could be fundamentally different from any other group on earth. These atrocities should be stopped and these people should be studied and rehabilitated.

© TheCellularScale
Lee YM, Shin OJ, & Lim MH (2012). The psychological problems of north korean adolescent refugees living in South Korea. Psychiatry investigation, 9 (3), 217-22 PMID: 22993519

Monday, May 6, 2013

Everyone should learn everything.

Today I am getting on a bit of a soapbox about things.  Specifically about things scientists should learn.
Scientists should learn everything (source)
In an ideal world everyone would be good at everything, but as you have probably noticed this is NOT the case. Some people are good at lots of things and some people are really good at specific things, but terrible at others, and some unfortunate people are generally bad at a lot of things and mediocre at a few.

Recently, I've been hearing increasing noise for scientists (or scientists-in-training) to learn X, Whatever X is. 'Scientists should learn art"; "Scientists should learn creative writing"; "Scientists should learn how to communicate to the public more clearly" ; "Scientists should learn managerial skills" and so forth.

This bothers me for a couple of reasons.

1. Why should the scientists learn all this stuff? Why aren't people clamoring for artists to learn microbiology, or for novelists to brush up on their molecular genetics?


2. What is wrong with some people being good at science and NOT being good at much else?

Yes, if waving a magic wand could suddenly make scientists good communicators, artists, and managers, I wouldn't object. But these things (like science itself) take training. And god knows, graduate students already get a lot of training.

And yes, running a lab takes managerial skills and grant writing requires clear communication and story-telling skills. But instead of requiring one person to be good at all these things, why not divide up the labor a little and have a 'lab manager' help run the lab, and a 'departmental grants guru' to help polish the grants.

It is really easy to say 'scientists should learn X' because...

1. there is a perception that scientists are smart and can learn things easily


2. it is always impossible to argue that things wouldn't be better if scientists were good at X. (Wouldn't it be great if all scientists were excellent public speakers? yes of course.)

The problem is implementing the extensive training in X that a scientist should have, and what current training to replace. Therefore I propose that the 'scientists should learn X' statements should all be adjusted to say 'scientists should get extensive training in X rather than Y'.

© TheCellularScale

Thursday, May 2, 2013

a STORM inside a cell

We've been talking about some of the most cutting edge intracellular visualization techniques lately. Array tomography and Serial block-face electron microscopy have been featured. Today we'll talk about STORM imaging.

STORM imaging (Xu et al., 2013)

STORM stands for Stochastic Optical Reconstruction Microscopy. While Array tomography and Serial block-face EM are both revolutionary in that they can combine very high resolution imaging with relatively large volumes of tissue, STORM is an advancement that lets you see tiny tiny little molecules within the cell.

The problem with 'normal' imaging is that molecules are smaller than the diffraction of light.
Example of the STORM resolution (from Zhuang lab's webpage)
In the figure above, imaging some tiny molecules next to each other is impossible with traditional fluorescence microscopy, but with STORM, you can resolve 10s of nanometers (nm).

To do this, STORM uses photoswitchable dyes, which means that the dye can be turned on or off. This allows researchers to turn on tiny little areas and then turn them off. If all the dye is turned on all at once, the image will look like a big mess because the signals will all overlap each other. But turning on only a few at a time allows you to estimate where the actual protein or molecule is.
"The imaging process consists of many cycles during which fluorophores are activated, imaged, and deactivated. In each cycle only a subset of the fluorescent labels are switched on, such that each of the active fluorophores is optically resolvable from the rest. This allows the position of these fluorophores to be determined with nanometer precision." -Zhuang lab webpage
So what amazing things can they do with this STORM?
A recent paper by Xu et al. (2013) found that the actin which plays a huge role in the intracellular structure of a neuron, has a specific ring-like structure along the axons.

Xu et al., 2013 Figure 4F

This is the kind of research that will immediately go into neuroscience and cell biology textbooks. Xu et al. discovered how actin was structured along the axon simply by being able to 'see it'.

Not only did they discover the structure of actin and spectrin (magenta above) in the axon, but they also found some other interesting molecular patterns that appear to relate to the actin ring structure. The sodium channels, which control action potential propagation down the axon, are concentrated about half way between the ends of the spectrin tetramers. The potential for super-resolution microscopy like STORM is huge. The location of molecules with relation to one another probably plays a huge role in the function of cells and now we have the tools to map them.

© TheCellularScale
Xu K, Zhong G, & Zhuang X (2013). Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science (New York, N.Y.), 339 (6118), 452-6 PMID: 23239625