Category Archives: the act of doing science

Lab notebooks, lab websites, the future.

About a year ago I went through a phase of rabid excitement regarding my lab’s website. Then I had to do some experiments, write grants, move across the country. And then today I became rabidly excited again.
Things in the Snyder lab are at a critical moment. My first 2 undergrads have retired, and new undergrads, a grad student, and postdocs have arrived or are arriving soon. Fledgling projects that I initiated are being handed off and I can tell things are going to grow rapidly. Now is the time to institute strange lab protocols so they become the norm. Today’s question is how to keep abreast of it all that is going on. Typically, one uses hardcover lab notebooks and the only person that ever looks at them is the experimenter, and occasionally other lab members when that person has left and there’s work to tidy up. As long as there’s decent communication this model can work just fine. But sometimes communication is hard, sometimes lab notebooks are messy, but most of all, there’s so much more that a lab notebook could be.

My re-rabidness (re-raBIDniss) was spawned as I was passing on my experimental notes to a student. The notes were in a Google doc so I could either copy and paste them, or just invite them to share the document. And if everyone in the lab used it then we’d all be on the same page (whose rats for which expt, who has expertise in certain protocols, general curiosity about lab projects). And then I wondered, is it a concern for one lab member to see another’s experimental notes? It sounds crazy but given the amount of secrecy involved in producing scientific research and the fact that no ever reads another’s lab book I wondered if it might just “feel weird”. Since in my heart open notebook science is the way to go, and since some actually put this into practice, I figure there are no real issues with simply sharing notes thoughout the lab, and any weirdness will be temporary and far outweighed by the positives.

At the moment I envision something like: A WordPress blog as the lab home page, containing links to Google spreadsheets (colony, orders, etc), documents (individuals’ experimental notes), calendars, files etc. But if this is where we go every day to organize our science, why have a separate site to present ourselves to the world? Why not make our lab notebook and lab website the same thing? And that’s where the blog comes in, where we can share data, pretty pix, random lab occurrences, literature reviews, whatever. There would likely be different views depending on whether you’re logged in (a lab member) or viewing from the outside. So this wouldn’t be completely open notebook science or anything, but I think it would help unify many of our responsibilities as scientists, namely to effectively and intelligently plan experiments, record our findings, communicate and educate (of course, great venue for jokes too).

RSS is (not) dead (to me)

I’ve thought of writing about RSS feeds for scientists for a couple of years now so it’s kind of funny that I’ve only gotten around to it 3 days before Google shuts down Reader. And it must be important to me because this is my first post in 6 months (except for a post on new neuron connectivity over at In the last year or so I’ve heard a number of people say that RSS is dead and, frankly, I have no idea what they’re talking about. I suppose social media has grown enormously during this time and has become a valuable way to discover new information but I still find that many new papers go unnoticed if I don’t systematically scan that table of contents of all my favorite journals. And this is what RSS does best. The fact that many scientists don’t use RSS feeds, or have never heard of them, is the inspiration for this post. So I would argue that RSS may not be dead but, rather, has not fully come to life.

my google readerRSS is Really Simple Syndication. It’s a way to subscribe to your favorite websites so that their new content shows up in your RSS reader. Subscribing is usually as easy as clicking on one of these things: 29146 or copying and pasting a url. Email for the internet, some have said. Instead of having to revisit dozens of websites that update with varying regularity one can simply open their RSS reader, see the sites that have updated content, and read the new content directly in the RSS reader (or at least the title or abstract¹). If you don’t have time to read a full article you can flag items for later viewing². I subscribe to 25 journals and about 50 blogs. I also subscribe to Google Alerts and Pubmed searches, feeds that track citations to my articles, and feeds that tell me when someone comments on a Flickr photo or edits a Google spreadsheet. It’s the only way I know to stay on top of everything, be all knowing, etc³. And I’ve backed up my Google Reader data so that when it closes on July 1 I can spend Canada Day not with my family but instead testing out a bunch of alternative RSS readers. Or at least testing out a bunch of RSS readers on my phone, in close proximity to my family⁴.


¹some journals only allow you to see the title in the RSS reader, forcing you to click through to their website to see the abstract. Sometimes I refuse to click and say (in my head) “I hate you”.

²for example you can see in the image that I flagged an article on Lunar Mascon Basins, because I’m really into them.

³On the other hand, I simply cannot actually read everything I come across. So another approach is to use something like Google Scholar’s “My Updates” feature as it selectively notifies you of papers that are similar to your own. Given the number of grey haired academics with Google Scholar profiles, the effectiveness of Scholar’s citation data, and the fact that it’s Google I’ve often wondered why they don’t extend its functionality just a bit, so you can follow other scientists and their papers etc.

⁴So that when my son sees a float at the parade and says “Look daddy!” I can glance up and feign excitement for a moment and go back to my phone when he’s distracted again⁵.

⁵I’m so kidding⁶.

⁶Okay, 80% kidding.

New neurons mature slower in the temporal/ventral dentate gyrus

I’ve previously written about the functional differences between the septal (aka dorsal aka rostral¹ aka posterior²) and temporal (ventral/caudal/anterior) hippocampus and how studies are increasingly not treating the hippocampus as a single homogeneous structure. Myself and others have extended this perspective to studies of adult neurogenesis and now I’m happy to report that we had a new paper come out on the topic last week.

The study was a bit of a fun learning experience for me for several reasons. As many of you know I recently changed labs and will be starting my own lab soon. So things are on the go and I haven’t had the time to dive deep into a study that is going to take several years to complete. But some research projects can be done quickly and still are able to produce very useful results. As I prepare for my own lab I was probably thinking, “What kind of projects could a Master’s student accomplish??”. And indeed we had a strong postbaccalaureate fellow in the lab for about a year who fit this description pretty well (she’s the middle author). Also, we had lots of tissue remaining from a recent study where we compared neurogenesis in mice and rats that could be used to answer other questions, thereby saving time, money and importantly, animals. So we decided to ask whether the maturation and survival of adult-born neurons differ between the aforementioned functionally-distinct hippocampal subregions.

The basic idea of the study.

experimental designBrdU was injected to birthdate+label new neurons and at various intervals kainate was given to “activate” all the neurons that had integrated into the circuitry, and formed synapses. This integration (a major step in the new neuron maturation process) can then be measured by immunohistochemically staining for gene products such as Arc that are expressed after synaptic activity. Our tissue was cut in the coronal plane, however, which is not ideal for isolating the septal and temporal ends of the hippocampus (though others have found that there are meaningful differences along this rostrocaudal axis). Since the rostral sections are purely septal (see blue portions, above) this subregion was not a problem. We then decided to basically “cut” the caudal sections in half and by analyzing only the ventral portion we were able to specifically target neurons located in the far temporal dentate gyrus (shown in red). We were also able to investigate whether new neurons are more likely to survive in one subregion than another, by counting the number of cells present before (at 7d old) and after (at 28d old) the period of cell death.

Since this article is completely open access you can see the actual data for yourself here. The short story is that new neurons matured faster in the septal dentate gyrus (all cells could express Arc by 3w of age whereas in the temporal dentate gyrus this didn’t occur until somewhere between 4-10w of age). The other new finding was that there were many more new neurons initially added to the infrapyramidal blade of the dentate gyrus but these neurons were much less likely to survive than neurons born in the suprapyramidal blade.

What is the significance of these findings? To me, they provide a framework for future studies. If you want to investigate new neurons specifically during their immature stage (when they might have unique functions) you certainly have to consider the anatomical location. But what if the main function for new neurons is not realized until they are fully mature? Well, if you plan to ablate or silence new neurons and examine behavioural effects, then you might want to wait longer if you’re planning on investigating emotion/stress-related behaviours that might rely more heavily on the temporal hippocampus. They also suggest that new neurons in the temporal dentate gyrus might have an extended unique role since they remain immature for longer. The peculiar survival difference between the infrapyramidal and suprapyramidal blades doesn’t do much to clarify the functions of these two regions, but it adds to the ever-growing list of differences that suggests they are truly distinct.

Often findings across labs do not match up as well as one would like so I am rather happy that Piatti et al. have found similar maturation differences in another species (mice) and using different methods (electrophysiological recordings from virally-labelled new neurons). So this is probably for real!

Lastly, a reviewer pointed out something very helpful, which is that it can be very difficult to discern the two blades of the dentate gyrus in caudal coronal sections (like this or those slightly more caudal where the dentate gyrus is essentially a blob). I spent a fair bit of time looking perplexed as I played with 3D paper models of the dentate gyrus but felt pretty cool doing so because similar strategies have been used by some of the foremost neuroanatomists of our time – see here. A 3D computer model that incorporated the blades of the dentate gyrus would have been very convenient (talking to you, Allen). In any case, we decided to remove our caudal blade analyses from the paper and instead only focussed on the septal infrapyramidal vs. suprapyramidal differences.

Reference: Snyder JS, Ferrante SF, Cameron HA (2012) Late Maturation of Adult-Born Neurons in the Temporal Dentate Gyrus. PLoS ONE 7(11): e48757. PMID: 23144957

¹in rodents

²in humans

A formal invitation to join the Snyder lab

dentate gyrus neuronsMy UBC Psychology page and Neuroscience links are up. Grad school application deadlines are approaching. I think it’s time to formally advertise that…


The lab’s goal is to identify the role of adult neurogenesis in memory and stress-related behaviours. We inhibit neurogenesis with transgenic animals in order to understand how they contribute to these behaviours, viral tools for labelling and modifying neurons, immunohistochemistry to quantify and characterize the neurogenesis process, and in vitro electrophysiology to understand the circuit mechanisms by which these new neurons regulate behaviour. The neurobiology of behaviour extends far beyond adult neurogenesis, however, and so we are also generally interested in how neurons throughout the dentate gyrus, hippocampus, and related structures interact to guide behaviour.

I’m excited about the science but I’m also excited about doing it in the open. Discoveries exist well before they’re printed in a journal but in most cases people don’t appreciate this, since discoveries are rarely shared as they happen. I’d like to do things a little differently and get our science out in the open. Early. To assist others and stimulate discussion. I’d like to see undergrads in my lab have have their data available online in a citable format. You don’t need a peer-reviewed publication or a graduate degree to contribute something valuable to the scientific record (and perhaps your CV).

If this sounds like the bomb:

Potential postdocs can email me ( directly to inquire about joining the lab. External funding deadlines are approaching and would go a looong way at this point.

Potential graduate students can contact me and apply through the Psychology or Neuroscience programs. Deadlines for a September 2013 start date are December 15 and January 30, respectively. There is also a June/July deadline for starting Neuroscience graduate studies in January 2014.

Potential undergraduates that are interested can email me directly. Previous lab experience is not a prerequisite to join the lab!

The lab will officially open in January 2013 and, after setting up, will be ready for real business around summertime. Oh, and I will be at the Society for Neuroscience meeting if interested folks would like to chat in person.

Google Scholar vs. Scopus & Web of Science

citation-battleA couple of interesting correspondences (here and here) just appeared in Nature on the legitimacy of Google Scholar for tracking citations. Interesting because I’ve recently been pondering the same issue but came up with the opposite conclusion, namely that Google Scholar is actually a better tool for tracking citations than either Scopus or Web of Science (and not only because it’s a pain to access the latter two).

The main concern by the authors is that citations for a given article are higher in Google Scholar than Scopus or Web of Science (well, one mainly focusses on the fact that they’re different). Higher because they include theses, patents, websites etc. Maybe also false positives.

I started thinking about this issue when I began applying for jobs. I didn’t have any fancy papers and so, for people outside of my field, noting the number of citations in my CV seemed like a decent way to make the point that some of these articles have had an impact. As I sent my applications I’d go back to Web of Science and check for the latest numbers and, this past year, I noticed that citations of some of my articles suddenly increased by up to 20%. Yay! But then I’d check the next day and they were low again (perhaps relating to changes in how citations were detected). So there was some glitch and I certainly didn’t want to appear to be inflating the numbers so I turned to Google Scholar. The numbers were higher, but consistent. For the most part the citations seemed completely legitimate as well.

So why were Google Scholar’s citation counts higher? Looking at my most cited paper, which has been cited 367 times (Google Scholar) or 267 times (Web of Science) or 287 times (Scopus) I found that Google Scholar included 11 Chinese articles, 10 book chapters, 15 theses, 4 patents, 1 blog (yours truly), 1 grant application, and 6 mysteries. Eliminating these 48 still leaves 319. Quite a bit higher than Web of Science and Scopus, probably because Google counts citations from articles that are still in press (my Neurobiology of Aging paper was published online but “in press” for 23 months, during which citations could be tracked in Scholar but not Web of Science). This is probably also why Google Scholar counts 17 citations (16 “normal”) of my most recent paper whereas Web of Science only counts 9 – many of these citing articles were recently published.

So should Chinese articles be excluded? Are book chapters irrelevant? Theses, well, no one reads theses so maybe there’s a bit of inflation there. I do think it’s a sign of impact when a blog, grant, or patent refers to your paper and believe that these things should be included in the citation counts (Google still isn’t great in this regard – I know of several blog posts on my papers that haven’t been detected by Google).

These are the reasons I specifically decided to use Google Scholar when adding citation counts to my CV. And so it’s funny to read about the “limitations of Google Scholar’s personalized citation reports” and how “I would not recommend using the reports for decisions that could affect careers”.

(for what it’s worth I did get a job, though clearly it’s all downhill from here)

Can you enjoy a good cup of coffee in the thick of experimenting?

More specifically,

Can you enjoy a good cup of coffee when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a coffee and get back in time and you can’t make a coffee at home and bring it in a thermos or travel mug (which would be room temperature (the worst temperature for enjoying coffee) by the time you wanted it nay NEEDED it) because those items have already been moved to Canada where you’ll also soon be moving which explains why you couldn’t do these experiments according to a more relaxed schedule but instead have to get as much done as is humanly possible in the few weeks that remain?


Yes:ultrapure vacuum filtered coffee

*Stay tuned for “Can you enjoy a good meal when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a meal and get back in time and you can’t make a meal at home and bring it in a thermos or travel mug because it would lose its form upon being stuffed into a drinking vessel but then why are you so hung up on appearances stop being so superficial and just stuff it in a thermos.”