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).

Impaired adult neurogenesis leads to depression – is it realistic?

depressionAbout a year ago we published a paper linking adult neurogenesis to depression. A causal sort of ‘linking’, right? I mean, we found that, when adult neurogenesis was eliminated, mice had elevated glucocorticoids in response to stress and showed depressive-like behaviours1. So doesn’t this mean that impaired adult neurogenesis could lead to depression in humans, in the real world?

Well, it could…and we did end our paper with the following:

Because the production of new granule neurons is itself strongly regulated by stress and glucocorticoids, this system forms a loop through which stress, by inhibiting adult neurogenesis, could lead to enhanced responsiveness to future stress. This type of programming could be adaptive, predisposing animals to behave in ways best suited to the severity of their particular environments. However, maladaptive progression of such a feed-forward loop could potentially lead to increased stress responsiveness and depressive behaviours that persist even in the absence of stressful events.

We had to end it somehow – I was just happy that after 3 years of work we were DONE2! But our final speculation makes it clear that, while this chapter may be done, the story is not. And this fact was rightly pointed out in a recent commentary by Lucassen et al. in Molecular Psychiatry3, where they continue the discussion and bring up some good points. Here is a loose elaboration on some of the outstanding issues they bring up. Continue reading

The White House wants your thoughts on open access to scientific publications! Deadline January 12!

Do you live on planet earth? Then you probably pay taxes. And if you pay taxes then you’re supporting scientific research. Thanks a lot – that’s really great. Thanks to you scientists can make discoveries that lead to cures for diseases. And we’d really love to share these discoveries with you…but you can’t afford them.

There are lots of problems with the way scientific findings are communicated but this is perhaps the saddest one. The public pays for scientific research and then is charged again to read the results. People who do not have access to massive library holdings simply cannot access scholarly publications. Many scientists themselves cannot even access the papers they need because their institution cannot afford the subscriptions.

Fortunately, things are changing. For example, the National Institutes of Health requires that all federally-funded research be deposited into Pubmed Central where it is freely available to the public within 12 months of publication (this allows publishers to still make money off the article for a while, which is very kind of the US government). Another example is the new publishing model put forth by PLoS One and other journals, where the authors pay a fee that covers the costs of publication, archiving etc. Then the articles are made freely available to all because subscriptions are not needed to cover costs.

The way things are going, it is only a matter of time before scholarly publications and scientific information becomes freely communicated to those that paid for it. How long this transformation will take is the big question and there are two big movements in the US government that will play a big role. Two big movements that need your input. Continue reading

How to share all of your data

Figshare is one of the greatest new tools for scientists. It allows you to publish any piece of data, no matter how small or insignificant, in a citable fashion. This is a big deal because ALL scientists have (tons of) data of this sort. Pilot experiments are performed to get the conditions right for the real experiments. And they never get published. The manuscript is written up or the paper is reviewed and some data is judged irrelevant or incomplete and is excluded. And never gets published. An experiment is performed and there is a null result, or the data are hard to interpret without further experiments, or the project doesn’t get funded, and so the project is dropped. And the experiment becomes nonexistent outside of the lab that performed it. There are many reasons why this should not be the case: 1) effort was spent on the experiment and so publishing it gives the scientist credit, 2) taxpayer money was spent on the experiment and so publishing these data gives back to the system that enables us to do this work in the first place, 3) data that are not useful or exciting to the scientist that acquired them can be incredibly useful and time-saving to other scientists that are working on related problems. The list could go on.


Figshare may not be the only option, and others will likely crop up in the near future, but it is a good example of a solution. We all know about the internet, right? A medium for immediately publishing anything you want? I’m a little baffled that this has taken so long.

For my part, in my spare time, I will be scouring my hard drive for findings that have been forgotten. The beauty of publishing in a place like Figshare is that it is easy. Most of these experiments have already been analyzed (I mean, they were graphed so that we could discuss what to do/not do with them, now it’s just a matter of uploading the already-presentable data). Also, there’s no obligation to discuss the data ad nauseum (you’ll see some data descriptions are pretty short) though some degree of explanation is required to make the data useful. Furthermore, should the story evolve, there’s no reason why it can’t be also published in a traditional journal format. Check out Nature Publishing Group’s policy – they’re ok with publishing data (even full manuscripts) on preprint servers prior to submitting to their journals.

Of course, some data may still not be “shareable” such as patient data or data that is closely related to an ongoing project. But interestingness should never be a factor in my mind, because you never know what will be valuable to others.

So, if you’re “just” a summer student who thinks your 2 months of work can’t possibly amount to hard, citable evidence, think again. Ask your boss first, but think again.