I am discussing really amazing new techniques to see inside cells this month, and have already posted about the magic that is Array Tomography. Today we'll look at another amazing new technique that (like array tomography) combines nano-scale detail with a scale large enough to see many neurons at once. This technique is called Serial Block-face Electron Microscopy (SBEM), and was recently used to investigate how starburst amacrine cells control the direction-sensitivity of retinal ganglion cells.
SBEM images are acquired by embedding a piece of tissue (like a retina) in some firm substance and slicing it superthin (like 10s of nanometers thick) with a diamond blade. The whole slicing apparatus is set up directly under a scanning electron microscope, so as soon as the blade cuts, an image is taken of the surface remaining. Then another thin slice is shaved off and the next image is taken, and so on.
Using this technique, Briggman et al. (2011) are able to trace individual neurons and their connections for a (relatively) large section of retina. What is so great about this paper is that before they sliced up the retina, they moved bars around in front of it and measured the directional selectivity of a bunch of neurons. Then, using blood vessels and landmarks to orient themselves, they were able to find the exact same cells in the SBEM data and trace them.
The colored circles above represent the cell bodies and the black 'tree' shape are the blood vessel landmarks.
Once they found the cell bodies, the could trace the cells through the stacks of SBEM data. What is really neat is that you can try your hand at this yourself. This exact data set has been turned into a game called EYEWIRE by the Seung lab at MIT.
Reconstructing the cells, they could not only tell which cells connected to which other cells, but they could also see exactly where on the dendrites the cells connected. This is the really amazing part. They found that specific dendritic areas made synapses with specific cells.
Briggman et al. (2011) Fig4: dendrites as the computational unit
This starburst amacrine cell overlaps with many retinal ganglion cells (dotted lines represent the dendritic spread of individual RGCs)...BUT its specific dendrites (left, right, up down etc) synapse selectively onto RGCs sensitive to a particular direction. Each color represents synapses onto a specific direction-sensitivity. e.g. yellow dots are synapses from the amacrine cell onto RGCs which are sensitive to downward motion.
This suggests that each individual dendritic area of these starburst amacrine cells inhibits (probably) a specific type of RGC, and that these dendrites act relatively independently of one another.
"The specificity of each SAC dendritic branch for selecting a
postsynaptic target goes well beyond the notion that neuron A
selectively wires to neuron B, which is all that electrophysiological
measurements can test. Instead the dendrite angle has an additional,
perhaps dominant, role, which is consistent with SAC dendrites acting as independent computational units." -Briggman et al (2011)(discussion)
These cells are weird for so many reasons, but the ability of the dendrites to act so independently of one another is a new and exciting development that I hope to see more research on soon.
Briggman KL, Helmstaedter M, & Denk W (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471 (7337), 183-8 PMID: 21390125
I have just finished reading Jane McGonigal's book Reality is Broken: Why games make us better and how they can change the world. It is a fascinating book which presents a strong case for games (including video games) doing good in the world.
Reality is Broken by Jane McGonigal
I have to admit, part of me wanted to read this book to make me feel better about my own video game habit. It certainly helped solidify the vague ideas I had about what good they might be doing me.
Specifically, the book made me think that scientists of all people might benefit greatly from playing games. There is one major reason why:
Games make you more resistant to failure
If there is one thing that scientists need to persist in their research its resilience in the face of failure. If you didn't know this already, just start following some 'life in academia' bloggers on twitter. Failure is a staple of scientific life.
Just yesterday I awoke to a small grant rejection. I started thinking about just how many things I had applied for during my (still new) scientific career, and just what proportion of those applications had resulted in rejections. I tallied it up on a chart (similar to a failure C.V.), and discovered that for about every 3.5 things I have applied for, only one was successful. This includes grant applications, travel fellowships, paper submissions and re-submissions, and miscellaneous things like applying to be an SfN Neuroblogger. (I did not include abstract submissions or applications to graduate school.) I actually think this is a relatively good ratio, and I expect this ratio to get worse in the future, because the competition for the things I am applying for will be even tougher.
Part of the reason I wanted to calculate my success/attempt ratio was to see how many things I had actually applied for. I was glad that the list was long, and that I applied for lots of things, even if it means that my 'ratio' is the worse for it. I would posit that having a good success/attempt ratio is not really that great if you only ever apply for a few things that are easy to get.
In science, you will fail; there is absolutely no scientist EVER who hasn't been rejected from something.
So back to games. Reality is Broken explains that games teach you to persist in the face of failure, and that games increase your optimism.
"Learning to stay urgently optimistic in the face of failure is an important emotional strength that we can learn in games and apply to our real lives. When we're energized by failure, we develop emotional stamina. And emotional stamina makes it possible for us to hang on longer, to do much harder work, and to tackle more complex challenges. We need this kind of optimism in order to thrive as human beings." -Reality is Broken, chapter 4
When I think of my own resistance to failure (which is decent, but could be better), I think of my time spent learning from games that failure is not the end of the world. Ever since I repeatedly failed to jump Mario over the first Goomba, video games were teaching me to try again, and again, and again.
Jane McGonigal brings up Tetris, one of the most popular video games of all time. Tetris is a game with no possible outcome except failure. You keep playing until you lose, and yet the game is immensely fun and ultimately rewarding. Each time you fail you want to try again, and you feel that you will probably do better next time.
In summary, games reward persistence and desensitize you to failure. When you play video games you learn implicitly that trying again is worth it and that failing isn't the end of the world. These skills are great to have in life and are essential to have in an academic career.
Reality is Broken lists 13 other ways that games 'fix' reality. Some of these fixes are about personal betterment (like persistence in the face of failure), but some of these fixes are about how games can ultimately change the larger reality. Games that combat global warming, for example, or games like Fold-It that actually further scientific progress and human knowledge. Whether you already play games or not, you can get something out of this book.
A nice addition to this book is the appendix "Practical advice for gamers" in which Jane McGonigal lays out some guidelines for getting the most out of games. For example, one rule is to never play more that 21 hours in a week. While video games have benefits, there are problems that can result from compulsive video game play, and you shouldn't think think that you are doing something healthy if you play video games for 50 hours a week and completely ignore reality. The idea is that playing games can help you function in reality. If you never venture into reality, you won't make any use of the benefits that the game might have given you.
Ferguson, C. (2011). Reality is broken, and the video game research field along with it. PsycCRITIQUES, 56 (48) DOI: 10.1037/a0026131 Farhangi, S. (2012). Reality is broken to be rebuilt: how a gamer’s mindset can show science educators new ways of contribution to science and world? Cultural Studies of Science Education, 7 (4), 1037-1044 DOI: 10.1007/s11422-012-9426-y
Sure playing video games (and therefore shooting in video games) releases dopamine, and sure if you inject dopamine into people while they shoot real guns they will like shooting guns better. BUT the key implication here, that shooting guns in video games makes you like shooting real guns demands evidence.
As a female Halo player myself, I think these Lady Spartans are awesome! (source)
Personally, I like shooter video games. I'm playing Halo 4 like the rest of the world right now and I played the heck out of Mass Effect earlier in the year. I have also shot real guns.
And guess what? shooting real guns is just not really my thing. I find it a little bit scary and not that fun or exciting. The idea of going to a shooting range and shooting guns at paper targets for an hour sounds really boring to me. Shooting skeet or something moving, like an animal, also sounds pretty boring.
I am skeptical about the idea that the dopamine released during shooting video games transfers to more enjoyment while shooting real guns. I am willing to change my mind upon seeing some data, but having seen nothing to support this direct transfer, I don't think it exists.
This post is written in response to "Addicted to the Bang: The neuroscience of the gun." by Steve Kotler and Jim Olds. (They don't actually claim that dopamine release during video game shooting directly causes addiction to real shooting, but I think that someone might get that idea from the article.)
In non-cellular news, I just beat Mass Effect 3 and had some thoughts.
Femshep or noshep
First let me say that I loved this game and still stand by my statements that everyone should play it.
****Spoilers****
There has been a lot of hoo ha about the different (barely) endings available in Mass Effect 3. Having just finished it, I have to say I pretty much agree. There is a fantastic (and lengthy) post at Game Front by Ross Lincoln that explains exactly what is disappointing about these ending choices. At Kotaku you can watch a sample of the 16 available endings and see for yourself (how similar they are).
So yeah, I do agree that the ending is a little disappointing (for pretty much exactly the reasons Ross Lincoln points out in his article). It was a huge info-dump on themes and topics not essential to the main plot of the game, and that seriously just didn't make sense. Bioware should have hired Brandon Sanderson to write the ending of this game because that guy knows how to wrap sh*t up.
so yeah, disappointing, but the end of my world, no.
Would I buy a new downloadable ending from Bioware? no, probably not. Will I complain endlessly on twitter that Bioware 'owes us' a better ending? no, I think they delivered an amazing game and I had a great time playing it. Am I going to write my own endings on my blog? ...Yes...
Here are some endings divided up into categories to make everyone happy:
1. Sad, but worth it endings
a. Control the Reapers:
Shepard dies, and you see the reapers leave. Then you should see Shepard in that digital-shape that the kid is in at the end, implying that Shepard takes the place of that kid as the reaper-controller. She becomes god, basically. Also you should see Shepard looking down at some of her teammates (like Garrus, who she specifically tells she will 'watch over' if she dies and he doesn't)
b. Destroy the Reapers:
Shepard dies, along with all synthetics. So you see a scene on Rannoch where the Quarian and Geth are working together to rebuild a new world (if you saved the Geth), and all of a sudden all the Geth just fall over dead. Sad, but interesting. Also, you see EDI die because she is, of course, synthetic, and you see Joker freak out. Also very sad. Your love interest from the game should find out your are dead and be miserable. But then you see some great scenes of the new Krogan utopia (if you cured the genophage) with little krogan babies (awww), and Wrex being a dad with his kid Mordin, how cute right? This is the Galaxy that you sacrificed yourself and everyone else to save. Maybe a scene of Kolyat praying, Jacob and his new family, Jack and her students, Miranda laughing with her sister... you know nice stuff that lets you know It was worth it.
c. Synthesis:
To be honest, I liked this ending as it was. I like the Joker and EDI =Adam and Eve look of the whole thing. It's a good ending to support the idea that there is a completely new age starting, one where synthetics and organics are merged. However, the third person should NOT walk out of the normandy though, seriously why the 3rd wheel?
Joker and EDI = Adam and Eve (Eden Prime Prime?)
2. Happy, everything is perfect endings
I am glad that Mass Effect 3 didn't go the cheesy route of everything being perfect. A happily-ever-after just doesn't fit The Shepard. But it is fun to think about, so here are some scenes that would make delightful endings for the disney-lovers out there. In each ending, Shepard lives, her/his love interest lives, earth is saved, and the galaxy is back to 'normal.' The endings mostly involve babies:
a. Liara: Little babies in blue running around Thessia, messing with mommy's shadow broker VI. b. Thane: Yeah, he's dead, but a scene of shepard visiting his grave or seeing his son wouldn't be horrible. Also, everyone wants to go to the Hanar-Drell homeworld and cure Keprel syndrome. c. Garrus: ok no babies here, just some totally fun hanging out and being happy together scene of Shepard and Garrus on a newly rebuilt Palovan. d. Kaiden: Some super sweet scene where Kaiden and Shepard look out at the sunset from their porch-swing on Kaiden's land on the Sun Coast. Also...Shepard's pregnant. e. Jacob: Just like Kaiden's ending but with Jacob. f. Ashley: Just like Kaiden's ending but with male shepard and Ashley's pregnant. g. Tali: Retiring to a beautiful house on Rannoch, you get to see her face! and you have a geth nanny to help out with the kids. h. Miranda: no babies (if you are astute, you may have read the shadow broker's intel explaining that she can't have kids), but you see her and Shepard being happy together somewhere beautiful just like all the other endings. i. Jack: I can't really think of anything good here, but she'd be happy.
ha, ok my teeth are sore from all this sugar.
3. Really Sad Ending
Another possibility is that a huge portion of your team dies, but Shepard her/himself doesn't. It's pretty clear that Shepard is the only one to survive that ending blast, so the two people you bring with you to the last fight should both die. If one of those is your love interest for the game or if one is EDI, there should be a sad scene of you lonely and wondering if it was worth it, and/or of Joker freaking out. The main theme of the whole game is what is worth it? You tell the Illusive Man that he "Sacrificed too much" but maybe you did too.
4. Epilogue-style endings
Another idea entirely, that would not be too much work for Bioware in the animation department, would be to expand the epilogue scene with the grandfather and kid to actually 'show' the legend of The Shepard. As in have a story-book style book that you can flip through at the end detailing Shepard's major choices throughout all three games. Just some stylized drawings (I'm thinking Fable here) and text.
Everything could be taken into account here and basically every playthrough could have a slightly different story at the end. It would also be cool if some clever writer could put in little interesting twists that could represent the story being destorted as it is passed down through generations. For example, if you choose the Krogan over the Salarians on Tuchanka, the story might show the Salarians as bad guys with their 'antennae' turned into devil horns or something. Similarly if you support the Salarians, the Krogan would be depicted as dangerous and evil.
Anyway, I think this story book ending would be the best solution because it would be easy enough for bioware to put together, it would be different depending on the choices made, and it would be satisfying to see that your decisions made a difference in the future mythology of the galaxy.
UPDATE 7/2/12: Thank you Bioware for following my advice and adding the story-book style epilogue to each ending! I was really delighted that in the destroy ending there were no geth and no EDI and that the Quarians were still in their suits. The ending choice now has actual consequences, and is therefore much more satisfying.
Another adventure outside of the 'cellular neuroscience' walls for The Cellular Scale. Today we are traveling to the land of video games, video games and women.
Commander Shepard, the most badass woman in the galaxy
Mass Effect 3 is being released in a few days and I thought I would use this time (while my xbox is downloading the free demo) to write about why the world would be a better (or at least slightly more gender-neutral) place if all women played Mass Effect.
Update: Just beat Mass Effect 3, see my thoughts on the endings here.
There are four main reasons people (especially women) should play this video game.
4. it's fun.
This is reason enough to play the game. Mass Effect is a sci-fi video game with some of the best world-building in book, movie or game to date (I expect angry comments bringing up Star Wars, Star Trek or Dune below, but I'm standing by that statement). Mass Effect presents a rich world with a cohesive believable history. You can literally read volumes about each species, each planet, each mercenary group, and each weapon if you are so inclined. There are nuances and details hidden everywhere that subtlety but strongly enrich the game.
A quick summary **SPOILERS**
You play as Commander Shepard (you can choose to be male or female), who is a human in the Alliance military.
troubled, but handsome
In Mass Effect 1, you have to track down and defeat a rogue spectre, Saren. He is an obvious bad-guy (the first thing you see him do is shoot his 'friend' point blank), but he does the job. You have to deal with some anti-human speciesism from the alien council, but they are generally on your side. You recruit some companions: a badass soldier in pink, a troubled but handsome biotic, an engineer on her pilgrimage, an ex-cop, an archaeological scientist, and a merc-for-hire tough guy. Then you go save the galaxy. Upon saving the galaxy your realize that the threat was much bigger than just the one rogue spectre.... which brings us to Mass Effect 2 (in which the shooting-game play is much improved)
'being perfect is so difficult'
In Mass Effect 2, you have been dead for two years, but are being rebuilt by Cerberus, a company that you only heard about in passing in ME1, but what you heard was bad. Cerberus is a human-supremacist group and it rebuilt you to help humanity, not the galaxy. So under the Cerberus logo, you attempt to face the 'bigger threat' that you discovered at the end of ME1. Human colonies are being destroyed, but in a really weird way where everything is left perfectly intact but all the humans are gone. You investigate these colonies, discover the reason behind these weird disappearances. Of course, you recruit some companions: a woman who likes to complain about being genetically modified to be 'perfect', a troubled but handsome biotic (not the same one), the same engineer after her pilgrimage, the same ex-cop, a killing-addict tattooed biotic, a pod-grown tough-guy, a geneticist/doctor, a morally rigid monastic biotic (or her evil daughter), a negligent father/assassin, and a robot. In this game you spend most of your time recruiting these companions and doing 'loyalty' missions for them. Then you save the galaxy.... and in saving the galaxy, you realize the threat isn't over...which bring us to Mass Effect 3 (in which a cooperative multi-player aspect has been added)
So the game is fun. The graphics are good, the action play is fun, leveling up is fun, the characters are great, the story is entertaining, but what really brings this game up a notch from other is the:
3. Complex morality
Like a lot of modern video games, you can make decisions in Mass Effect that have short and long term consequences. In fact, the decisions you make in ME1 effects who you see in ME2 and how you interact with them. Like other games you can become 'good' or 'bad' (Fable and Knights of the Old Republic are some of the games which pioneered this morality system), but in Mass Effect it is called "Paragon" or "Renegade" and it is a little more complex than in the other games. Paragon isn't necessarily good and everyone likes you, and Renegade isn't necessarily evil and everyone dies.
Paragon/Renegade
source: 'facebook' if this is yours,
let me know and I will credit you
Some of the moral dilemmas you face in this game remind me of game theory and morality experiments. Do you follow the law in all situations or do you break it for the greater good? Do you kill one to save many, or do you protect your friends and let strangers die?
The biggest moral dilemma in Mass Effect 1 is when you have to decide between two of your teammates, you don't have time to save both of them. Who do you choose?
Interestingly, it's not all 'thanks for saving me' from the person you rescue either, they feel guilty and upset because you chose them instead of the other person. This choice carries over all the way to ME3, where whichever person you saved apparently plays an important part.
My favorite moral dilemma is in Mass Effect 2 though, because it is related to science! Your teammate, the geneticist, confesses to you that he took part in producing the genophage, a mutation that drastically reduces the fertility rate in a particularly aggressive alien species. These aliens previously lived on a very hostile world and the constant environmental threats kept their population low. However, when they came into contact with other aliens and moved off their hostile world, their population exploded under their new non-threatening conditions. The geneticist in your group had lead the initiative to infect this alien species with a mutation (yes the fake science gets iffy here) that would decrease the fertility rate in females to like 1%. In your discussion with him he makes a convincing argument for 'galaxy safety' and this not being 'sterilization' or 'genocide' but simply a check on the population. But the other side is easy to see too, deploying the genophage is playing god with this species, deciding for them what their population should be. Why does the geneticist on your ship get to decide that? and how can he possibly know what the right population should be for this species? But then again, do you really want the galaxy completely over-run with these aggressive aliens? Tough choices.
This game is good because aside from being entertaining, there are points in this game that actually make you think.
2. Seeing women in positions of power
As explained in an Io9 article, by Kyle Munkittrick, sci-fi is historically able to push boundaries further than other media. A quote from that article:
"Science fiction is one of the best forms of social satire and critique. Want to sneak in some absolutely scandalous social mores, like, say, oh, I don't know, a black woman into a position of power in the 1960s? Put her on a starship command deck."
And Mass Effect does that. The 'tough soldier with a lot of health' character (you know the one, it shows up in every video game ever) is the second character you meet in ME1 and she is named Ashley. The all-powerful ruler of Omega who no one in their right mind would mess with is named Aria (also is voiced by Carrie-Ann Moss, who you might recognize from The Matrix and Memento). The game is full of stereotype-destroying characters. It's not another sci-fi story where all the male characters have distinct personalities, but the one token woman character has the personality of 'woman'. The women in Mass Effect show the same range of morality, toughness, power, and emotion that the men do.
Omega only has one law: Don't fuck with Carrie-Ann Moss
However, Mass Effect is not a completely non-sexist game or anything. There are plenty of females with comic-book proportions and there are even strip clubs. The characters aren't all respectful of Commander Shepard when she is a woman (or man for that matter). In a particularly brutal corner of the galaxy (Miranda calls it a 'piss hole'), you go to sign up for a mercenary mission and the jackass at the counter says 'sweetie, you're in the wrong place, strippers sign up over there.' (You can put him in his place for that remark if you choose to though). It's not only sexism that runs rampant in the galaxy, people are speciesist to you too, one bar tender even tries to poison you because you are human. The thing that makes it a good game for women to play is because you see commander Shepard deal with people being rude to her, confront them, earn respect, do her job, and save the galaxy.
1. Being a woman in a position of power.
More important and more effective than just watching women in power, is actually 'being' a woman in power. Modern video games like Mass Effect are highly immersive. You move a character around, you see through her eyes, and you can even make her look like you.
In 2008, Galinsky et al. published a paper testing the effects of perspective taking. That is, they had people pretend to be someone else, either by writing about their day as that person or by pretending to be that person in an interview. They found that after pretending to be someone else, the participants of the study actually took on some of the stereotypes associated with the person they were imagining themselves to be. For example, when they pretended to be a university professor, they rated themselves as smarter and actually performed better on an analytical task. In contrast when they pretended to be a cheerleader, they rated themselves as more attractive but actually did worse on the analytical task. The most interesting thing here is that the effect was stronger when the participants were told to 'write about your day as if you were this cheerleader' than when they were told 'here is a cheerleader, write about her day.'
In short, pretending to be someone can influence how you feel about yourself and even how you act.
This is where Mass Effect can potentially have benefits even beyond watching a powerful woman role model on tv. You actually pretend to be this woman: the commander of the ship, the leader of the team, the hero of the galaxy. You answer as her during conversations. You make the tough decisions described above in Reason 3: Complex Morality. You stand up for yourself when you know you are right, but the alien council doesn't believe you. The fate of the galaxy rests on your shoulders.
If the perspective effect works in a video game setting, then pretending to be a strong woman for an hour a day, might actually make you a more confident person in real life.
I would love to see a study actually using this game to test the perspective taking effect in video games. Galinsky, are you listening? you should do this study:
Have women play Mass Effect (select some key conversations where respect is shown or tough decisions are made) and test whether it affects their self-reported confidence or intelligence. An interesting control might be to have these women play Mass Effect as the male character and run through the exact same conversations.
Does taking the perspective of Commander Shepard boost confidence or ability? And if so is the effect increased when a woman plays as female Shepard compared to male Shepard? What if a man plays as female or male Shepard? The Cellular Scale wants to know!
Galinsky AD, Wang CS, & Ku G (2008). Perspective-takers behave more stereotypically. Journal of personality and social psychology, 95 (2), 404-19 PMID: 18665710
