It has been a long time

It has been so long. I am so behind…



I have so many papers to post that it is overwhelming. Plus I know everyone is hanging on the edge of their collective seats begging for me to post my list of the top papers from 2014! ūüėõ

However, in the mean time I cannot possibly resist directing everyone towards a great blog post from DrugMonkey.

You absolutely must read this wonderful, provocative blog post!


I just love so much about this post. I loved being scandalized when I realized I had completely forgotten about the subfornical control of drinking lessons from biology classes in the past.

But please don’t stop with the post itself. The continued¬†discussion in the comments is even better!! So good!!!!

I love the comments about optogenetics.

Let me be clear – I have mentioned before I am a huge Optogenetics Fan – I constantly strive to make everything I do in science linked with optogenetics. If I could, I would have my entire lifestyle saturated with the glorious method. I would ride from place to place on a sled pulled by thousands of cre-rats with ChR2 in their motor cortex… but I wont get carried away.

The point is as much as I love optogenetics, I also really enjoy when people question the use of the method. I like when people point out the limitations; how important certain controls are; or when optogenetics is used wrong.

But even better than the optogenetics discussion is the underlying point about science publishing and the glorified status of Nature and Science. I know I have said that I am passionate about the flaws in our science publishing system before, but I like the points that are brought up in the commentary especially from rxnm.

One of the things that makes me so frustrated about science publishing is not just the often talked about money madness, but how the ridiculous weight we give to these journals allows them to essentially dictate the direction of science itself. I hate the fact that getting a¬†Nature or¬†Science paper can make or break an entire career in science – jobs, funding, etc.. When this ultimately manifests into a situation where¬†an editor for a magazine is given the power to determine what is and isn’t valuable science. Of course… this discussion is very nuanced and I could go on, but I’ll stop while I can.

Anyway I have to at least repost the one comment from rxnm ,

“Nature is a private company, they can publish whatever the fuck they want and sell the ad space next to it. The chumps are the people who admire a paper because it’s published there. Believing that NPG’s primary goal is rigorous scientific standards instead of whatever is splashy and marketable is like believing Facebook is here to try to bring people closer together and make the world a better place.”

So great! I just love it!


Anyway if you still haven’t, please do check out the blog post and the comments here. I hope you enjoy it as much as I do.

I have no idea when.. but hopefully I’ll post some papers sometime in the next ten years ūüôā





CLARITY finally published!

If you were at SFN last year, you might have managed to catch a glimpse of this¬†poster buried inside a large crowd of neuroscientists. I didn’t even attempt to see the poster up close; instead I gathered what I could from those who escaped to the fringe of the mob after seeing the poster and video demonstration playing on an ipad. Those who I spoke to where wide-eyed and giddy. They told me tales of a magical method that could turn brains invisible..

Of course making tissue transparent for subsequent optical investigation is nothing new, but then that wasn’t the whole story! Supposedly with this magical technique you could subsequently perform whole brain immuno-staining.. and not just that.. you could do it multiple times!!

Ok, so on the surface this sounds pretty cool… but then you see the videos like the one from Nature’s video channel here¬†and you start to realize this is pretty amazing…

…then you read more about the method itself (from a commentary here¬†and the actual publication here)¬†and you start to really comprehend how useful this technique could be for understanding projections in the whole brain…

…and then you read that this can be applied to not just a mouse brain, but ANY brain… so you can do this to a brain from a rat, zebrafish, non-human primate … really any model organisms being used for¬†neuroscience¬†research! Of course you can forget using a model system and¬†just use actual¬†human tissue…the paper even shows an interesting finding using some human cortex from an autistic patient that had been stored in formalin for over 6 years!! …

… and then finally it makes sense why most of the neuroanatomists at SFN where walking away from the CLARITY poster looking like this…

I should add, this exciting new technique was developed in the lab of Karl Deisseroth, who you might recognize as one of the developers of optogenetics. I think it’s safe to say that he is feeling pretty good right about now.

Dr. Deisseroth this morning when the CLARITY paper was officially published.

I’ll end this overload of animated GIFs with a link to just one of several articles that are popping up all over the internet. This one had a link to a video of Dr. Deisseroth himself describing the process in an interview. You can check that out here as well.


Highlights of 2012

Everyone and their mom makes one of these Best of The Year lists or something related, so here is my version. Join me in looking back at what I consider some of the highlights from 2012 in neuroscience. As always I will present a numbered list. This is not supposed to be a ranking; I just like lists.

1. The Great Debate

The Great Brain Mapping Debate (Brain Brawl): Tony Movshon versus Sebastian Seung (link)

This was just fantastic. I highly recommend watching the video of this great debate. I had a wonderful time watching this live from my hotel room when I was in Chicago for grad school interviews. You can read some of the articles about this here, here, and here.

2.  Optogenetic activation of an engram!?

Optogenetic stimulation of a hippocampal engram activates fear memory recall Xu Liu, Steve Ramirez, Petti T. Pang, Corey B. Puryear, Arvind Govindarajan, Karl Deisseroth & Susumu Tonegawa ; Nature 2012 (link)


Generation of a Synthetic Memory Trace Aleena R. Garner, David C. Rowland, Sang Youl Hwang, Karsten Baumgaertel, Bryan L. Roth, Cliff Kentros, Mark Mayford ; Science 2012 (link)

 Ok that is certainly a bold description, but I think it is fairly appropriate for both. When these two papers came out I was extremely excited. I think what these papers accomplish represents a pretty big milestone for neuroscience. Of course I favor the Tonegawa manuscript because I have a known weakness for a certain scientific method. You can read about the two papers and how a similar accomplishment was shown in a previous SFN poster in 2009 here (I recommend reading the comments as well).

3. ¬†Zebrafish in the matrix (sort of.. ok not really.. but it’s so cool)

Brain-wide neuronal dynamics during motor adaptation in zebrafish Misha B. Ahrens, Jennifer M. Li, Michael B. Orger, Drew N. Robson, Alexander F. Schier, Florian Engert & Ruben Portugues ; Nature 2012 (link)

My list is dangerously close to becoming a highlight reel from the Nature Action Potential blog and you can certainly read an interesting commentary about this paper from them here. But let me just say I think this might be my favorite paper of the year. What really made this paper special for me was watching the first supplementary movie showing real time motor adaptation as they switch the gain for neural activity controlling the perceived motion. Seeing and hearing the neurons fire while the fish tries to “swim against the current” in order to stay still is really awesome.

4. PV+ neurons and their effect on visual cortex

Activation of specific interneurons improves V1 feature selectivity and visual perception Seung-Hee Lee, Alex C. Kwan, Siyu Zhang, Victoria Phoumthipphavong, John G. Flannery, Sotiris C. Masmanidis, Hiroki Taniguchi, Z. Josh Huang, Feng Zhang, Edward S. Boyden, Karl Deisseroth & Yang Dan ; Nature 2012 (link)


Division and subtraction by distinct cortical inhibitory networks in vivo Nathan R. Wilson, Caroline A. Runyan, Forea L. Wang & Mriganka Sur ; Nature 2012 (link)

even though it didn’t make the 2012 cut these should¬†be considered along with..

Parvalbumin-Expressing Interneurons Linearly Transform Cortical Responses to Visual Stimuli Bassam V. Atallah, William Bruns, Matteo Carandini, and Massimo Scanziani ; Neuron 2011 (link)

How specific subtypes of interneurons are involved in neural function is a question that is going to be asked for a long time. The battle to classify neurons into subtypes is itself an ongoing process (popular 2004 Markram review here). I constantly wonder if the subtypes we can target in optogenetics right now are even all that relevant or specific enough. It seems to be a case of the tail wagging the dog with so many papers looking at specific roles of what has become the holy trinity of genetically targetable subsets: PV+, SOM, and VIP interneurons. But I should save a discussion on neural subtypes for another time. Let me tell you what I liked about these papers. I enjoyed them because they are a perfect example of multiple papers asking almost the exact same questions, using almost the exact same methods getting published at almost the exact same time (sometimes this happens in different journals as you can see above for the engram papers or sometimes in the same journal with a nice little editorial to compare the two). When this happens it creates a wonderful opportunity for comparison. It is especially great when the papers come up with drastically different conclusions! I find it to be a sobering reminder that we are all doing science and sometimes just because results are published in¬†Nature or Science¬†it doesn’t mean the findings are ready to be engraved in stone. Of course there are interesting methodological differences between these three papers – awake verses anesthetized for example; however they still come up with fundamentally different results that anesthesia alone might not explain. ¬†So I think it is fun to question whether the differences are due to preparations and methods or our lack of understanding on another level. Only time will tell.

And again I can’t shake the pesky problem of questioning how specific our subgroups are to begin with. Sorry to beat the dead horse but just keep in mind this question, what does it mean to target PV+ neurons in the first place? How arbitrary are our classifications? Papers such as this one certainly have to be considered when reading these papers.

Ok I tried my best to avoid the subtype classification conundrum… oh well. I promise I’ll try and touch on it again in more detail another time.

5. Primate Optogenetics continues to mature

Saccadic eye movements evoked by optogenetic activation of primate V1 Mehrdad Jazayeri, Zachary Lindbloom-Brown & Gregory D Horwitz ; Nature Neuroscience 2012 (link)

This paper was¬†particularly¬†important to me this year because it was very relevant to some of my own work (shameless plug here). I have several thoughts on this paper as well as the recent influx of primate optogenetic publications that came out this year. I’m going to save that rant for a later post. Below are the other papers that came out involving primate optogenetics. Again, I will write a whole post about these later because I have a pretty long winded rant about the Jazayeri et al. and Cavenaugh et al. papers in particular.

Optogenetically Induced Behavioral and Functional Network Changes in Primates Annelies Gerits, Reza Farivar, Bruce R. Rosen, Lawrence L. Wald, Edward S. Boyden, Wim Vanduffel ; Current Biology 2012 (link)

Optogenetic Inactivation Modifies Monkey Visuomotor Behavior James Cavanaugh, Ilya E. Monosov, Kerry McAlonan, Rebecca Berman, Mitchell K. Smith, Vania Cao, Kuan H. Wang, Edward S. Boyden and Robert H. Wurtz ; Neuron 2012 (link)

In Vivo Optogenetic Control of Striatal and Thalamic Neurons in Non-Human Primates Adriana Galvan, Xing Hu, Yoland Smith,Thomas Wichmann ; PLoS One 2012 (link)

6. Wait.. what makes a Place Cell?

Hippocampal Place Fields Emerge upon Single-Cell Manipulation of Excitability During Behavior Doyun Lee, Bei-Jung Lin, Albert K. Lee ; Science 2012 (link)

So this year also marked the beginning of my diving into the world of hippocampus literature.. just picture that scene where¬†Alice falls down the rabbit hole. The world of place cells, grid cells, head direction cells, episode cells, and phase precession continues to blow my mind with every new paper I read.¬†One of the small joys of playing catch-up in a new field of research literature is starting with the early stuff and moving in chronological order. It’s always great when you read an old paper and think, “Woah that’s amazing! ….but I wonder what would happen if they looked at _______” and then finding a paper a couple years later that asks and answers your exact question!

But back to this paper. Place cells and place fields are a staple of hippocampal literature and I think their discovery is one of the more amazing phenomena in neuroscience research. This paper from the Lee lab¬†(had to have a shameless plug for my friends at the farm) is great because it takes the standard model of what makes a place cell a place cell and completely flips it upside down! In fact the implications and questions this paper raises kind of scares me! I mean.. I can barely wrap my head around what the paper might mean. If all it takes to make a pyramidal cell a “place cell” is to depolarize it a little… then what does that mean about the wiring of the neurons themselves? Do the anatomical connections not matter? Of course they matter, but I just love the questions this paper raises. Definitely an exciting step forward in our attempt to understand the brain.

So this post turned out much longer than I anticipated. I can promise if you think they will all be this long then you should definitely lower your expectations

but hopefully as (and if) I continue to do this blog, posts will improve and become more concise; because the last thing anyone needs is to waste all of their time reading my rants when there are so many papers to catch up on!


What papers did you enjoy this year? What were some of the neuroscience reports that you thought where most interesting? Please please please share at least one of them in the comments!

Testing 1…2…3…

So I already don’t like the format of this theme.. I need links and menus on the side or something.. plus the font is huge..¬† Switched to a different one… maybe better..

Anyway the gist of a typical post would be kind of like the following (for this I will use papers that were referenced at a recent dinner conversation)

1. Layer-Specific Entrainment of Gamma-Band Neural Activity by the Alpha Rhythm in Monkey Visual Cortex Eelke Spaak, Mathilde Bonnefond, Alexander Maier, David A. Leopold, and Ole Jensen ; Current Biology 2012 (link)

2. Quantitative inference of population response properties across eccentricity from motion induced maps in macaque V1 Malte J Rasch1, Ming Chen, Si Wu, Haidong D Lu, and Anna W Roe ; Journal of Neurophysiology 2012 (link)

3. The smallest stroke: occlusion of one penetrating vessel leads to infarction and a cognitive deficit Andy Y Shih, Pablo Blinder, Philbert S Tsai, Beth Friedman, Geoffrey Stanley, Patrick D Lyden & David Kleinfeld ; Nature Neuroscience 2012 (link)

4.¬†Hippocampal‚Äďcortical interaction during periods of subcortical silence ¬† ¬†¬†N. K. Logothetis, O. Eschenko, Y. Murayama, M. Augath, T. Steudel, H. C. Evrard, M. Besserve & A. Oeltermann ;¬†Nature 2012¬†(link)

5. Decorrelated Neuronal Firing in Cortical Microcircuits Alexander S. Ecker, Philipp Berens, Georgios A. Keliris, Matthias Bethge, Nikos K. Logothetis, Andreas S. Tolias ; Science 2010 (link)

I guess if I want to be really nice and really snazzy I should include some sort of link for each one.. or is it not too much to ask someone to just copy and paste the title into google scholar? But then sometimes it might not show up? Then with links I have to worry about them being broken or linking something that requires institutional access? Personally I like to download the papers and supplementary material and then combine them into one single PDF. I guess the ultimate service would be if I made those and linked/posted them but I am pretty sure that is illegal.

Oh to test out a poll?

Alright, see how this works.

UPDATE: I started including links – figured it can’t hurt- but of course you need permissions to get the papers from them.

Starting from scratch

So this isn’t the first time I have attempted to start a blog of some sort, but perhaps this time something will stick. The idea behind this blog is to provide a way for me to share the lists of papers that I find interesting after my weekly sifting through the newly published neuroscience literature.

Anyway as you can see this is very much a work in progress. If I do make this happen getting feedback / comments from people who check/ read the blog would be extremely useful. Hopefully the wordpress platform fosters an easy way for commenting.

remember when websites used to have tons of funny animated GIFs showing construction tape and stuff? Those were the days :)

remember when websites used to have tons of funny animated GIFs showing construction tape and stuff? Those were the days ūüôā