We the Kardashians are Democratizing Science

I had a good laugh this weekend at a paper published to Genome Biology. Neil Hall, the author of the paper and well-established Liverpool biologist, writes that in the brave new era of social media, there “is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices.” Wow, what a punchline! According to Neil, we’re in danger of forgetting that tweets and blogposts are, according to him, the worthless gossip of academia. After all, who reads Nature and Science these days?? I know so many colleagues getting big grants and tenure track jobs just over their tweets! Never mind that Neil himself has about 11 papers published in Nature journals – or perhaps we are left to sympathize with the poor, untweeted author? Outside of bitter sarcasm, the article is a fun bit of satire, and I’d like to think charitably that it was aimed not only at ‘altmetrics’, but at the metric enterprise in general. Still, I agree totally with Kathryn Clancy that the joke fails insofar as it seems to be ‘punching down’ at those of us with less established CVs than Neil, who take to social media in order to network and advance our own fledgling research profiles. I think it also belies a critical misapprehension of how social media fits into the research ecosystem common among established scholars. This sentiment is expressed rather precisely by Neil when discussing his Kardashian index:

The Kardashian Index
The Kardashian Index

“In an age dominated by the cult of celebrity we, as scientists, need to protect ourselves from mindlessly lauding shallow popularity and take an informed and critical view of the value we place on the opinion of our peers. Social media makes it very easy for people to build a seemingly impressive persona by essentially ‘shouting louder’ than others. Having an opinion on something does not make one an expert.”

So there you have it. Twitter equals shallow popularity. Never mind the endless possibilities of having seamless networked interactions with peers from around the world. Never mind sharing the latest results, discussing them, and branching these interactions into blog posts that themselves evolve into papers. Forget entirely that without this infosphere of interaction, we’d be left totally at the whims of Impact Factor to find interesting papers among the thousands published daily. What it’s really all about is building a “seemingly impressive persona” by “shouting louder than others”. What then does constitute effective scientific output, Neil? The answer it seems – more high impact papers:

“I propose that all scientists calculate their own K-index on an annual basis and include it in their Twitter profile. Not only does this help others decide how much weight they should give to someone’s 140 character wisdom, it can also be an incentive – if your K-index gets above 5, then it’s time to get off Twitter and write those papers.”

Well then, I’m glad we covered that. I’m sure there were many scientists or scholars out there who amid the endless cycle of insane job pressure, publish or perish horse-racing, and blood feuding for grants thought, ‘gee I’d better just stop this publishing thing entirely and tweet instead’. And likewise, I’m sure every young scientist looks at ‘Kardashians’ and thinks, ‘hey I’d better suspend all critical thinking, forget all my training, and believe everything this person says’. I hope you can feel me rolling my eyes.  Seriously though – this represents a fundamental and common misunderstanding of the point of all this faffing about on the internet. Followers, impact, and notoriety are all poorly understood side-effects of this process; they are neither the means nor goal. And never mind those less concrete (and misleading) contributions like freely shared code, data, or thoughts – the point here is to blather and gossip!

While a (sorta) funny joke, it is this point that is done the most disservice by Neil’s article. We (the Kardashians) are democratizing science. We are filtering the literally unending deluge of papers to try and find the most outrageous, the most interesting, and the most forgotten, so that they can see the light of day beyond wherever they were published and forgotten. We seek these papers to generate discussion and to garner attention where it is needed most. We are the academy’s newest, first line of defense, contextualizing results when the media runs wild with them. We tweet often because there is a lot to tweet, and we gain followers because the things we tweet are interesting. And we do all of this without the comfort of a lofty CV or high impact track record, with little concrete assurance that it will even benefit us, all while still trying to produce the standard signs of success. And it may not seem like it now – but in time it will be clear that what we do is just as much a part of the scientific process as those lofty Nature papers. Are we perfect? No. Do we sometimes fall victim to sensationalism or crowd mentality? Of course – we are only fallible human beings, trying to find and create utility within a new frontier. We may not be the filter science deserves – but we are the one it needs. Wear your Kardshian index with pride.

#MethodsWeDontReport – brief thought on Jason Mitchell versus the replicators

This morning Jason Mitchell self-published an interesting essay espousing his views on why replication attempts are essentially worthless. At first I was merely interested by the fact that what would obviously become a topic of heated debate was self-published, rather than going through the long slog of a traditional academic medium. Score one for self publication, I suppose. Jason’s argument is essentially that null results don’t yield anything of value and that we should be improving the way science is conducted and reported rather than publicising our nulls. I found particularly interesting his short example list of things that he sees as critical to experimental results which nevertheless go unreported:

These experimental events, and countless more like them, go unreported in our method section for the simple fact that they are part of the shared, tacit know-how of competent researchers in my field; we also fail to report that the experimenters wore clothes and refrained from smoking throughout the session.  Someone without full possession of such know-how—perhaps because he is globally incompetent, or new to science, or even just new to neuroimaging specifically—could well be expected to bungle one or more of these important, yet unstated, experimental details.

While I don’t agree with the overall logic or conclusion of Jason’s argument (I particularly like Chris Said’s Bayesian response), I do think it raises some important or at least interesting points for discussion. For example, I agree that there is loads of potentially important stuff that goes on in the lab, particularly with human subjects and large scanners, that isn’t reported. I’m not sure to what extent that stuff can or should be reported, and I think that’s one of the interesting and under-examined topics in the larger debate. I tend to lean towards the stance that we should report just about anything we can – but of course publication pressures and tacit norms means most of it won’t be published. And probably at least some of it doesn’t need to be? But which things exactly? And how do we go about reporting stuff like how we respond to random participant questions regarding our hypothesis?

To find out, I’d love to see a list of things you can’t or don’t regularly report using the #methodswedontreport hashtag. Quite a few are starting to show up- most are funny or outright snarky (as seems to be the general mood of the response to Jason’s post), but I think a few are pretty common lab occurrences and are even though provoking in terms of their potentially serious experimental side-effects. Surely we don’t want to report all of these ‘tacit’ skills in our burgeoning method sections; the question is which ones need to be reported, and why are they important in the first place?

Birth of a New School: How Self-Publication can Improve Research

Edit: click here for a PDF version and citable figshare link!

Preface: What follows is my attempt to imagine a radically different future for research publishing. Apologies for any overlooked references – the following is meant to be speculative and purposely walks the line between paper and blog post. Here is to a productive discussion regarding the future of research.

Our current systems of producing, disseminating, and evaluating research could be substantially improved. For-profit publishers enjoy extremely high taxpayer-funded profit margins. Traditional closed-door peer review is creaking under the weight of an exponentially growing knowledge base, delaying important communications and often resulting in seemingly arbitrary publication decisions1–4. Today’s young researchers are frequently dismayed to find their pain-staking work producing quality reviews overlooked or discouraged by journalistic editorial practices. In response, the research community has risen to the challenge of reform, giving birth to an ever expanding multitude of publishing tools: statistical methods to detect p-hacking5, numerous open-source publication models6–8, and innovative platforms for data and knowledge sharing9,10.

While I applaud the arrival and intent of these tools, I suspect that ultimately publication reform must begin with publication culture – with the very way we think of what a publication is and can be. After all, how can we effectively create infrastructure for practices that do not yet exist? Last summer, shortly after igniting #pdftribute, I began to think more and more about the problems confronting the publication of results. After months of conversations with colleagues I am now convinced that real reform will come not in the shape of new tools or infrastructures, but rather in the culture surrounding academic publishing itself. In many ways our current publishing infrastructure is the product of a paper-based society keen to produce lasting artifacts of scholarly research. In parallel, the exponential arrival of networked society has lead to an open-source software community in which knowledge is not a static artifact but rather an ever-expanding living document of intelligent productivity. We must move towards “research 2.0” and beyond11.

From Wikipedia to Github, open-source communities are changing the way knowledge is produced and disseminated. Already this movement has begun reach academia, with researchers across disciplines flocking to social media, blogs, and novel communication infrastructures to create a new movement of post-publication peer review4,12,13. In math and physics, researchers have already embraced self-publication, uploading preprints to the online repository arXiv, with more and more disciplines using the site to archive their research. I believe that the inevitable future of research communication is in this open-source metaphor, in the form of pervasive self-publication of scholarly knowledge. The question is thus not where are we going, but rather how do we prepare for this radical change in publication culture. In asking these questions I would like to imagine what research will look like 10, 15, or even 20 years from today. This post is intended as a first step towards bringing to light specific ideas for how this transition might be facilitated. Rather than this being a prescriptive essay, here I am merely attempting to imagine what that future may look like. I invite you to treat what follows as an ‘open beta’ for these ideas.

Part 1: Why self-publication?

I believe the essential metaphor is within the open-source software community. To this end over the past few months I have  feverishly discussed the merits and risks of self-publishing scholarly knowledge with my colleagues and peers. While at first I was worried many would find the notion of self-publication utterly absurd, I have been astonished at the responses – many have been excitedly optimistic! I was surprised to find that some of my most critical and stoic colleagues have lost so much faith in traditional publication and peer review that they are ready to consider more radical options.

The basic motivation for research self-publication is pretty simple: research papers cannot be properly evaluated without first being read. Now, by evaluation, I don’t mean for the purposes of hiring or grant giving committees. These are essentially financial decisions, e.g. “how do I effectively spend my money without reading the papers of the 200+ applicants for this position?” Such decisions will always rely on heuristics and metrics that must necessarily sacrifice accuracy for efficiency. However, I believe that self-publication culture will provide a finer grain of metrics than ever dreamed of under our current system. By documenting each step of the research process, self-publication and open science can yield rich information that can be mined for increasingly useful impact measures – but more on that later.

When it comes to evaluating research, many admit that there is no substitute for opening up an article and reading its content – regardless of journal. My prediction is, as post-publication peer review gains acceptance, some tenured researcher or brave young scholar will eventually decide to simply self-publish her research directly onto the internet, and when that research goes viral, the resulting deluge of self-publications will be overwhelming. Of course, busy lives require heuristic decisions and it’s arguable that publishers provide this editorial service. While I will address this issue specifically in Part 3, for now I want to point out that growing empirical evidence suggests that our current publisher/impact-based system provides an unreliable heuristic at best14–16. Thus, my essential reason for supporting self-publication is that in the worst-case scenario, self-publications must be accompanied by the disclaimer: “read the contents and decide for yourself.” As self-publishing practices are established, it is easy to imagine that these difficulties will be largely mitigated by self-published peer reviews and novel infrastructures supporting these interactions.

Indeed, with a little imagination we can picture plenty of potential benefits of self-publication to offset the risk that we might read poor papers. Researchers spend exorbitant amounts of their time reviewing, commenting on, and discussing articles – most of that rich content and meta-data is lost under the current system. In documenting the research practice more thoroughly, the ensuing flood of self-published data can support new quantitative metrics of reviewer trust, and be further utlized in the development of rich information about new ideas and data in near real-time. To give just one example, we might calculate how many subsequent citations or retractions a particular reviewer generates, generating a reviewer impact factor and reliability index. The more aspects of research we publish, the greater the data-mining potential. Incentivizing in-depth reviews that add clarity and conceptual content to research, rather than merely knocking down or propping up equally imperfect artifacts, will ultimately improve research quality. By self-publishing well-documented, open-sourced pilot data and accompanying digital reagents (e.g. scripts, stimulus materials, protocols, etc), researchers can get instant feedback from peers, preventing uncounted research dollars from being wasted. Previously closed-door conferences can become live records of new ideas and conceptual developments as they unfold. The metaphor here is research as open-source – an ever evolving, living record of knowledge as it is created.

Now, let’s contrast this model to the current publishing system. Every publisher (including open-access) obliges researchers to adhere to randomly varied formatting constraints, presentation rules, submission and acceptance fees, and review cultures. Researchers perform reviews for free for often publically subsidized work, so that publishers can then turn around and sell the finished product back to those same researchers (and the public) at an exorbitant mark-up. These constraints introduce lengthy delays – ranging from 6+ months in the sciences all the way up to two years in some humanities disciplines. By contrast, how you self-publish your research is entirely up to you – where, when, how, the formatting, and the openness. Put simply, if you could publish your research how and when you wanted, and have it generate the same “impact” as traditional venues, why would you use a publisher at all?

One obvious reason to use publishers is copy-editing, i.e. the creation of pretty manuscripts. Another is the guarantee of high-profile distribution. Indeed, under the current system these are legitimate worries. While it is possible to produce reasonably formatted papers, ideally the creation of an open-source, easy to use copy-editing software is needed to facilitate mainstream self-publication. Innovators like figshare are already leading the way in this area. In the next section, I will try to theorize some different ways in which self-publication can overcome these and other potential limitations, in terms of specific applications and guidelines for maximizing the utility of self-published research. To do so, I will outline a few specific cases with the most potential for self-publication to make a positive impact on research right away, and hopefully illuminate the ‘why’ question a bit further with some concrete examples.

 Part 2: Where to begin self-publishing

What follows is the “how-to” part of this document. I must preface by saying that although I have written so far with researchers across the sciences and humanities in mind, I will now focus primarily on the scientific examples with which I am more experienced.  The transition to self-publication is already happening in the forms of academic tweets, self-archives, and blogs, at a seemingly exponential growth rate. To be clear, I do not believe that the new publication culture will be utopian. As in many human endeavors the usual brandism3, politics, and corruption can be expected to appear in this new culture. Accordingly, the transition is likely to be a bit wild and woolly around the edges. Like any generational culture shift, new practices must first emerge before infrastructures can be put in place to support them. My hope is to contribute to that cultural shift from artifact to process-based research, outlining particularly promising early venues for self-publication. Once these practices become more common, there will be huge opportunities for those ready and willing to step in and provide rich informational architectures to support and enhance self-publication – but for now we can only step into that wild frontier.

In my discussions with others I have identified three particularly promising areas where self-publication is either already contributing or can begin contributing to research. These are: the publication of exploratory pilot-data, post-publication peer reviews, and trial pre-registration. I will cover each in turn, attempting to provide examples and templates where possible. Finally, Part 3 will examine some common concerns with self-publication. In general, I think that successful reforms should resemble existing research practices as much as possible: publication solutions are most effective when they resemble daily practices that are already in place, rather than forcing individuals into novel practices or infrastructures with an unclear time-commitment. A frequent criticism of current solutions such as the comments section on Frontiers, PLOS One, or the newly developed PubPeer, is that they are rarely used by the general academic population. It is reasonable to conclude that this is because already over-worked academics currently see little plausible benefit from contributing to these discussions given the current publishing culture (worse still, they may fear other negative repercussions, discussed in Part 3). Thus a central theme of the following examples is that they attempt to mirror practices in which many academics are already engaged, with complementary incentive structures (e.g. citations).

Example 1: Exploratory Pilot Data 

This previous summer witnessed a fascinating clash of research cultures, with the eruption of intense debate between pre-registration advocates and pre-registration skeptics. I derived some useful insights from both sides of that discussion. Many were concerned about what would happen to exploratory data under these new publication regimes. Indeed, a general worry with existing reform movements is that they appear to emphasize a highly conservative and somewhat cynical “perfect papers” culture. I do not believe in perfect papers – the scientific model is driven by replication and discovery. No paper can ever be 100% flawless – otherwise there would be no reason for further research! Inevitably, some will find ways to cheat the system. Accordingly, reform must incentivize better reporting practices over stricter control, or at least balance between the two extremes.

Exploratory pilot data is an excellent avenue for this. By their very nature such data are not confirmatory – they are exciting in that they do not conform well to prior predictions. Such data benefit from rapid communication and feedback. Imagine an intuition-based project – a side or pet project conducted on the fly for example. The researcher might feel that the project has potential, but also knows that there could be serious flaws. Most journals won’t publish these kinds of data. Under the current system these data are lost, hidden, obscured, or otherwise forgotten.

Compare to a self-publication world: the researcher can upload the data, document all the protocols, make the presentation and analysis scripts open-source, and provide some well-written documentation explaining why she thinks the data are of interest. Some intrepid graduate student might find it, and follow up with a valuable control analysis, pointing out an excellent feature or fatal flaw, which he can then upload as a direct citation to the original data. Both publications are citable, giving credit to originator and reviewer alike. Armed with this new knowledge, the original researcher could now pre-register an altered protocol and conduct a full study on the subject (or alternatively, abandon the project entirely). In this exchange, it is likely that hundreds of hours and research dollars will have been saved. Additionally, the entire process will have been documented, making it both citable and minable for impact metrics. Tools already exist for each of these steps – but largely cultural fears prevent it from happening. How would it be perceived? Would anyone read it? Will someone steal my idea? To better frame these issues, I will now examine a self-publication practice that has already emerged in force.

 Example 2: Post-publication peer review

This is a particularly easy case, precisely because high-profile scholars are already regularly engaged in the practice. As I’ve frequently joked on twitter, we’re rapidly entering an era where publishing in a glam-mag has no impact guarantee if the paper itself isn’t worthwhile – you may as well hang a target on your head for post-publication peer reviewers. However, I want to emphasize the positive benefits and not just the conservative controls. Post-publication peer review (PPPR) has already begun to change the way we view research, with reviewers adding lasting content to papers, enriching the conclusions one can draw, and pointing out novel connections that were not extrapolated upon by the authors themselves. Here I like to draw an analogy to the open source movement, where code (and its documentation) is forkable, versioned, and open to constant revision – never static but always evolving.

Indeed, just last week PubMed launched their new “PubMed Commons” system, an innovative PPPR comment system, whereby any registered person (with at least one paper on PubMed) can leave scientific comments on articles.  Inevitably, the reception on twitter and Facebook mirrored previous attempts to introduce infrastructure-based solutions – mixed excitement followed by a lot of bemused cynicism – bring out the trolls many joked. To wit, a brief scan of the average comment on another platform, PubPeer, revealed a generally (but not entirely) poor level of comment quality. While many comments seem to be on topic, most had little to no formatting and were given with little context. At times comments can seem trollish, pointing out minor flaws as if they render the paper worthless. In many disciplines like my own, few comments could be found at all. This compounds the central problem with PPPR; why would anyone acknowledge such a system if the primary result is poorly formed nitpicking of your research? The essential problem here is again incentive – for reviews to be quality there needs to be incentive. We need a culture of PPPR that values positive and negative comments equally. This is common to both traditional and self-publication practices.

To facilitate easy, incentivized self-publication of comments and PPPRs, my colleague Hauke Hillebrandt and I have attempted to create a simple template that researchers can use to quickly and easily publish these materials. The idea is that by using these templates and uploading them to figshare or similar services, Google Scholar will automatically index them as citations, provide citation alerts to the original authors, and even include the comments in its h-index calculation. This way researchers can begin to get credit for what they are already doing, in an easy to use and familiar format. While the template isn’t quite working yet (oddly enough, Scholar is counting citations from my blog, but not the template), you can take a look at it here and maybe help us figure out why it isn’t working! In the near future we plan to get this working, and will follow-up this post with the full template, ready for you to use.

Example 3: Pre-registration of experimental trials

As my final example, I suggest that for many researchers, self-publication of trial pre-registrations (PR) may be an excellent way to test the waters of PR in a format with a low barrier to entry. Replication attempts are a particularly promising venue for PR, and self-publication of such registrations is a way to quickly move from idea to registration to collection (as in the above pilot data example), while ensuring that credit for the original idea is embedded in the infamously hard to erase memory of the internet.

A few benefits of PR self-publication, rather than relying on for-profit publishers, is that PR templates can be easily open-sourced themselves, allowing various research fields to generate community-based specialized templates adhering to the needs of that field. Self-published PRs, as well as high quality templates, can be cited – incentivizing the creation and dissemination of both. I imagine the rapid emergence of specialized templates within each community, tailored to the needs of that research discipline.

Part 3: Criticism and limitations

Here I will close by considering some common concerns with self-publication:

Quality of data

A natural worry at this point is quality control. How can we be sure that what is published without the seal of peer review isn’t complete hooey? The primary response is that we cannot, just like we cannot be sure that peer reviewed materials are quality without first reading them ourselves. Still, it is for this reason that I tried to suggest a few particularly ripe venues for self-publication of research. The cultural zeitgeist supporting full-blown scholarly self-publication has not yet arrived, but we can already begin to prepare for it. With regards to filtering noise, I argue that by coupling post-publication peer review and social media, quality self-publications will rise to the top. Importantly, this issue points towards flaws in our current publication culture. In many research areas there are effects that are repeatedly published but that few believe, largely due to the presence of biases against null-findings. Self-publication aims to make as much of the research process publicly available as possible, preventing this kind of knowledge from slipping through the editorial cracks and improving our ability to evaluate the veracity of published effects. If such data are reported cleanly and completely, existing quantitative tools can further incorporate them to better estimate the likelihood of p-hacking within a literature. That leads to the next concern – quality of presentation.

Hemingway's thoughts on data.

Quality of presentation

Many ask: how in this brave new world will we separate signal from noise? I am sure that every published researcher already receives at least a few garbage citations a year from obscure places in obscure journals with little relevance to actual article contents. But, so the worry goes, what if we are deluged with a vast array of poorly written, poorly documented, self-published crud. How would we separate the signal from the noise?

 The answer is Content, Presentation, and Clarity. These must be treated as central guidelines for self-publication to be worth anyone’s time. The Internet memesphere has already generated one rule for ranking interest: content rules. Content floats and is upvoted, blogspam sinks and is downvoted. This is already true for published articles – twitter, reddit, facebook, and email circles help us separate the wheat from the chaff at least as much as impact factor if not more. But presentation and clarity are equally important. Poorly conducted research is not shared, or at least is shared with vehemence. Similarly, poorly written self-publications, or poorly documented data/reagents are unlikely to generate positive feedback, much less impact-generating eyeballs. I like to imagine a distant future in which self-publication has given rise to a new generation of well-regarded specialists: reviewers who are prized for their content, presentation, and clarity; coders who produce cleanly documented pipelines; behaviorists producing powerful and easily customized paradigm scripts; and data collection experts who produce the smoothest, cleanest data around. All of these future specialists will be able to garner impact for the things they already do, incentivizing each step of the research processes rather than only the end product.

Being scooped, intellectual credit

Another common concern is “what if my idea/data/pilot is scooped?” I acknowledge that particularly in these early days, the decision to self-publish must be weighted against this possibility. However, I must also point out that in the current system authors must also weight the decision to develop an idea in isolation against the benefits of communicating with peers and colleagues. Both have risks and benefits – an idea or project in isolation can easily over-estimate its own quality or impact. The decision to self-publish must similarly be weighted against the need for feedback. Furthermore, a self-publication culture would allow researchers to move more quickly from project to publication, ensuring that they are readily credited for their work. And again, as research culture continues to evolve, I believe this concern will increasingly fade. It is notoriously difficult to erase information from The Internet (see the “Streisand effect”) – there is no reason why self-published ideas and data cannot generate direct credit for the authors. Indeed, I envision a world in which these contributions can themselves be independently weighted and credited.

 Prevention of cheating, corruption, self-citations

To some, this will be an inevitable point of departure. Without our time-tested guardian of peer review, what is to prevent a flood of outright fabricated data? My response is: what prevents outright fabrication under the current system? To misquote Jeff Goldblum in Jurassic Park, cheaters will always find a way. No matter how much we tighten our grip, there will be those who respond to the pressures of publication by deliberate misconduct. I believe that the current publication system directly incentivizes such behavior by valuing end product over process. By creating incentives for low-barrier post-publication peer review, pre-registration, and rich pilot data publication, researchers are given the opportunity to generate impact for each step of the research process. When faced with the vast penalties of cheating due to a null finding, versus doing one’s best to turn those data into something useful for someone, I suspect most people will choose the honest and less risky option.

 Corruption and self-citations are perhaps a subtler, more sinister factor. In my discussions with colleagues, a frequent concern is that there is nothing to prevent high-impact “rich club” institutions from banding together to provide glossy post-publication reviews, citation farming, or promoting one another’s research to the top of the pile regardless of content. I again answer: how is this any different from our current system? Papers are submitted to an editor who makes a subjective evaluation of the paper’s quality and impact, before sending it to four out of a thousand possible reviewers who will make an obscure  decision about the content of the paper. Sometimes this system works well, but increasingly it does not2. Many have witnessed great papers rejected for political reasons, or poor ones accepted for the same. Lowering the barrier to post-publication peer review means that even when these factors drive a paper to the top, it will be far easier to contextualize that research with a heavy dose of reality. Over time, I believe self-publication will incentivize good research. Cheating will always be a factor – and this new frontier is unlikely to be a utopia. Rather, I hope to contribute to the development of a bridge between our traditional publishing models and a radically advanced not-too-distant future.

Conclusion

Our current systems of producing, disseminating, and evaluating research increasingly seem to be out of step with cultural and technological realities. To take back the research process and bolster the ailing standard of peer-review I believe research will ultimately adopt an open and largely publisher-free model. In my view, these new practices will be entirely complementary to existing solutions including such as the p-curve5, open-source publication models6–8, and innovative platforms for data and knowledge sharing such as PubPeer, PubMed Commons, and figshare9,10. The next step from here will be to produce useable templates for self-publication. You can expect to see a PDF version of this post in the coming weeks as a further example of self-publishing practices. In attempting to build a bridge to the coming technological and social revolution, I hope to inspire others to join in the conversation so that we can improve all aspects of research.

 Acknowledgments

Thanks to Hauke Hillebrandt, Kate Mills, and Francesca Fardo for invaluable discussion, comments, and edits of this work. Many of the ideas developed here were originally inspired by this post envisioning a self-publication future. Thanks also to PubPeer, PeerJ,  figshare, and others in this area for their pioneering work in providing some valuable tools and spaces to begin engaging with self-publication practices.

Addendum

Excellent resources already exist for the many of the ideas presented here. I want to give special notice to researchers who have already begun self-publishing their work either as preprints, archives, or as direct blog posts. Parallel publishing is an attractive transitional option where researchers can prepublish their work for immediate feedback before submitting it to a traditional publisher. Special notice should be given to Zen Faulkes whose excellent pioneering blog posts demonstrated that it is reasonably easy to self-produce well formatted publications. Here are a few pioneering self-published papers you can use as examples – feel free to add your own in the comments:

The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae), Zen Faulkes

http://neurodojo.blogspot.dk/2012/09/Ibacus.html

Eklund, Anders (2013): Multivariate fMRI Analysis using Canonical Correlation Analysis instead of Classifiers, Comment on Todd et al. figshare.

http://dx.doi.org/10.6084/m9.figshare.787696

Automated removal of independent components to reduce trial-by-trial variation in event-related potentials, Dorothy Bishop

http://bishoptechbits.blogspot.dk/2011_05_01_archive.html

Deep Impact: Unintended consequences of journal rank

Björn Brembs, Marcus Munafò

http://arxiv.org/abs/1301.3748

A novel platform for open peer to peer review and publication:

http://thewinnower.com/

A platform for open PPPRs:

https://pubpeer.com/

Another PPPR platform:

http://f1000.com/

References

1. Henderson, M. Problems with peer review. BMJ 340, c1409 (2010).

2. Ioannidis, J. P. A. Why Most Published Research Findings Are False. PLoS Med 2, e124 (2005).

3. Peters, D. P. & Ceci, S. J. Peer-review practices of psychological journals: The fate of published articles, submitted again. Behav. Brain Sci. 5, 187 (2010).

4. Hunter, J. Post-publication peer review: opening up scientific conversation. Front. Comput. Neurosci. 6, 63 (2012).

5. Simonsohn, U., Nelson, L. D. & Simmons, J. P. P-Curve: A Key to the File Drawer. (2013). at <http://papers.ssrn.com/abstract=2256237>

6.  MacCallum, C. J. ONE for All: The Next Step for PLoS. PLoS Biol. 4, e401 (2006).

7. Smith, K. A. The frontiers publishing paradigm. Front. Immunol. 3, 1 (2012).

8. Wets, K., Weedon, D. & Velterop, J. Post-publication filtering and evaluation: Faculty of 1000. Learn. Publ. 16, 249–258 (2003).

9. Allen, M. PubPeer – A universal comment and review layer for scholarly papers? | Neuroconscience on WordPress.com. Website/Blog (2013). at <http://neuroconscience.com/2013/01/25/pubpeer-a-universal-comment-and-review-layer-for-scholarly-papers/>

10. Hahnel, M. Exclusive: figshare a new open data project that wants to change the future of scholarly publishing. Impact Soc. Sci. blog (2012). at <http://eprints.lse.ac.uk/51893/1/blogs.lse.ac.uk-Exclusive_figshare_a_new_open_data_project_that_wants_to_change_the_future_of_scholarly_publishing.pdf>

11. Yarkoni, T., Poldrack, R. A., Van Essen, D. C. & Wager, T. D. Cognitive neuroscience 2.0: building a cumulative science of human brain function. Trends Cogn. Sci. 14, 489–496 (2010).

12. Bishop, D. BishopBlog: A gentle introduction to Twitter for the apprehensive academic. Blog/website (2013). at <http://deevybee.blogspot.dk/2011/06/gentle-introduction-to-twitter-for.html>

13. Hadibeenareviewer. Had I Been A Reviewer on WordPress.com. Blog/website (2013). at <http://hadibeenareviewer.wordpress.com/>

14. Tressoldi, P. E., Giofré, D., Sella, F. & Cumming, G. High Impact = High Statistical Standards? Not Necessarily So. PLoS One 8, e56180 (2013).

15.  Brembs, B. & Munafò, M. Deep Impact: Unintended consequences of journal rank. (2013). at <http://arxiv.org/abs/1301.3748>

16.  Eisen, J. A., Maccallum, C. J. & Neylon, C. Expert Failure: Re-evaluating Research Assessment. PLoS Biol. 11, e1001677 (2013).

http://wl.figshare.com/articles/875339/embed?show_title=1

Short post: why I share (and share often)

If you follow my social media activities I am sure by now that you know me as a compulsive share-addict. Over the past four years I have gradually increased both the amount of incoming and outgoing information I attempt to integrate on a daily basis. I start every day with a now routine ritual of scanning new publications from 60+ journals and blogs using my firehose RSS feed, as well as integrating new links from various Science sub-reddits, my curated twitter cogneuro list, my friends and colleagues on Facebook, and email lists. I then in turn curate the best, most relevant to my interests, or in some cases the most outrageous of these links and share them back to twitter, facebook, reddit, and colleagues.

Of course in doing so, a frequent response from (particularly more senior) colleagues is: why?! Why do I choose to spend the time to both take in all that information and to share it back to the world? The answer is quite simple- in sharing this stuff I get critical feedback from an ever-growing network of peers and collaborators. I can’t even count the number of times someone has pointed out something (for better or worse) that I would have otherwise missed in an article or idea. That’s right, I share it so I can see what you think of it!  In this way I have been able to not only stay up to date with the latest research and concepts, but to receive constant invaluable feedback from all of you lovely brains :). In some sense I literally distribute my cognition throughout my network – thanks for the extra neurons!

From the beginning, I have been able not only to assess the impact of this stuff, but also gain deeper and more varied insights into its meaning. When I began my PhD I had the moderate statistical training of a BSc in psychology with little direct knowledge of neuroimaging methods or theory. Frankly it was bewildering. Just figuring out which methods to pay attention to, or what problems to look out for, was a headache-inducing nightmare. But I had to start somewhere and so I started by sharing, and sharing often. As a result almost every day I get amazing feedback pointing out critical insights or flaws in the things I share that I would have otherwise missed. In this way the entire world has become my interactive classroom! It is difficult to overstate the degree to which this interaction has enriched my abilities as a scientists and thinker.

It is only natural however for more senior investigators to worry about how much time one might spend on all this. I admit in the early days of my PhD I may have spent a bit too long lingering amongst the RSS trees and twitter swarms. But then again, it is difficult to place a price on the knowledge and know-how I garnered in this process (not to mention the invaluable social capital generated in building such a network!). I am a firm believer in “power procrastination”, which is just the process of regularly switching from more difficult but higher priority to more interesting but lower priority tasks. I believe that by spending my downtime taking in and sharing information, I’m letting my ‘default mode’ take a much needed rest, while still feeding it with inputs that will actually make the hard tasks easier.

In all, on a good day I’d say I spend about 20 minutes each morning taking in inputs and another 20 minutes throughout the day sharing them. Of course some days (looking at you Fridays) I don’t always adhere to that and there are those times when I have to ‘just say no’ and wait until the evening to get into that workflow. Productivity apps like Pomodoro have helped make sure I respect the balance when particularly difficult tasks arise. All in all however, the time I spend sharing is paid back tenfold in new knowledge and deeper understanding.

Really I should be thanking all of you, the invaluable peers, friends, colleagues, followers, and readers who give me the feedback that is so totally essential to my cognitive evolution. So long as you keep reading- I’ll keep sharing! Thanks!!

Notes: I haven’t even touched on the value of blogging and post-publication peer review, which of course sums with the benefits mentioned here, but also has vastly improved my writing and comprehension skills! But that’s a topic for another post!

( don’t worry, the skim-share cycle is no replacement for deep individual learning, which I also spend plenty of time doing!)

“you are a von economo neuron!” – Francesca 🙂

Fun fact – I read the excellent scifi novel Accelerando just prior to beginning my PhD. In the novel the main character is an info-addict who integrates so much information he gains a “5 second” prescience on events as they unfold. He then shares these insights for free with anyone who wants them, generating billion dollar companies (of which he owns no part in) and gradually manipulating global events to bring about a technological singularity. I guess you could say I found this to be a pretty neat character 🙂 In a serious vein though, I am a firm believer in free and open science, self-publication, and sharing-based economies. Information deserves to be free!

Twitter Follow-up: Can MVPA Invalidate Simulation Theory?

Thanks to the wonders of social media, while I was out grocery shopping I received several interesting and useful responses to my previous post on the relationship between multivariate pattern analysis and simulation theory. Rather than try and fit my responses into 140 characters, I figured i’d take a bit more space here to hash them out. I think the idea is really enhanced by these responses, which point to several findings and features of which I was not aware. The short answer seems to be, no MVPA does not invalidate simulation theory (ST) and may even provide evidence for it in the realm of motor intentions, but that we might be able to point towards a better standard of evidence for more exploratory applications of ST (e.g. empathy-for-pain). An important point to come out of these responses as one might expect, is that the interpretation of these methodologies is not always straightforward.

I’ll start with Antonia Hamilton’s question, as it points to a bit of literature that speaks directly to the issue:

antonio_reply

Antonia is referring to this paper by Oosterhof and colleagues, where they directly compare passive viewing and active performance of the same paradigm using decoding techniques. I don’t read nearly as much social cognition literature as I used to, and wasn’t previously aware of this paper. It’s really a fascinating project and I suggest anyone interested in this issue read it at once (it’s open access, yay!). In the introduction the authors point out that spatial overlap alone cannot demonstrate equivalent mechanisms for viewing and performing the same action:

Numerous functional neuroimaging studies have identified brain regions that are active during both the observation and the execution of actions (e.g., Etzel et al. 2008; Iacoboni et al. 1999). Although these studies show spatial overlap of frontal and parietal activations elicited by action observation and execution, they do not demonstrate representational overlap between visual and motor action representations. That is, spatially overlapping activations could reflect different neural populations in the same broad brain regions (Gazzola and Keysers 2009; Morrison and Downing 2007; Peelen and Downing 2007b). Spatial overlap of activations per se cannot establish whether the patterns of neural response are similar for a given action (whether it is seen or performed) but different for different actions, an essential property of the “mirror system” hypothesis.”

They then go on to explain that while MVPA could conceivably demonstrate a simulation-like mechanism (i.e. a common neural representation for viewing/doing), several previous papers attempting to show just that failed to do so. The authors suggest that this may be due to a variety of methodological limitations, which they set out to correct for in their JNPhys publication. Oosterhof et al show that clusters of voxels located primarily in the intraparietal and superior temporal sulci encode cross-modal information, that is code similar information both when viewing and doing:

Click to go to PDF.
From Oosterhof et al, showing combined classification accuray for (train see, test do; train do, test see).

Essentially Oosterhof et al trained their classifier on one modality (see or do) , tested the classifier on the opposite modality in another session, and then repeated this procedure for all possible combinations of session and modality (while appropriately correcting for multiple comparisons). The map above represents the combined classification accuracy from both train-test combinations; interestingly in the supplementary info they show that the maps do slightly differ depend on what was trained:

Click to go to SI.
From supplementary info, A shows classifier trained on see, tested on do, B shows the opposite.

Oosterhof and colleagues also investigate the specificity of information for particular gestures in a second experiment, but for our purposes lets focus on just the first. My first thought is that this does actually provide some evidence for a simulation theory of understanding motor intentions. Clearly there is enough information in each modality to accurately decode the opposite modality: there are populations of neurons encoding similar information both for action execution and perception. Realistically I think this has to be the minimal burden of proof needed to consider an imaging finding to be evidence for simulation theory. So the results of Oosterhof et al do provide supporting evidence for simulation theory in the domain of motor intentions.

Nonetheless, the results also strengthen the argument that more exploratory extentions of ST (like empathy-for-pain) must be held to a similar burden of proof before generalization in these domains is supported. Simply showing spatial overlap is not evidence of simulation, as Oosterhof themselves argue. I think it is interesting to note the slight spatial divergence between the two train-test maps (see on do, do on see). While we can obviously identify voxels encoding cross-modality information, it is interesting that those voxels do not subsume the entirety of whatever neural computation relates these two modalities; each has something unique to predict in the other. I don’t think that observation invalidates simulation theory, but it might suggest an interesting mechanism not specified in the ‘vanilla’ flavor of ST. To be extra boring, it would be really nice to see an independent replication of this finding, since as Oosterhof themselves point out, the evidence for cross-modal information is inconsistent across studies. Even though the classifier performs well above chance in this study,  it is also worth noting that the majority of surviving voxels in their study show somewhere around 40-50% classification accuracy, not exactly gangbusters. It would be interesting to see if they could identify voxels within these regions that selectively encode only viewing or performing; this might be evidence for a hybrid-theory account of motor intentions.

leoreply

Leonhard’s question is an interesting one that I don’t have a ready response for. As I understand it, the idea is that demonstrating no difference of patterns between a self and other-related condition (e.g. performing an action vs watching someone else do it) might actually be an argument for simulation, since this could be caused by that region using isomorphic computations for both conditions. This an interesting point – i’m not sure what the status of null findings is in the decoding literature, but this merits further thought.

The next two came from James Kilner and Tal Yarkoni. I’ve put them together as I think they fall under a more methodological class of questions/comments and I don’t feel quite experienced enough to answer them- but i’d love to hear from someone with more experience in multivariate/multivoxel techniques:

kilner_reply

talreply

James Kilner asks about the performance of MVPA in the case that the pattern might be spatially overlapping but not identical for two conditions. This is an interesting question and i’m not sure I know the correct answer; my intuition is that you could accurately discriminate both conditions using the same voxels and that this would be strong evidence against a simple simulation theory account (spatial overlap but representational heterogeneity).

Here is more precise answer to James’ question from Sam Schwarzkopf, posted in the comments of the original post:

2. The multivariate aspect obviously adds sensitivity by looking at pattern information, or generally any information of more than one variable (e.g. voxels in a region). As such it is more sensitive to the information content in a region than just looking at the average response from that region. Such an approach can reveal that region A contains some diagnostic information about an experimental variable while region B does not, even though they both show the same mean activation. This is certainly useful knowledge that can help us advance our understanding of the brain – but in the end it is still only one small piece in the puzzle. And as both Tal and James pointed out (in their own ways) and as you discussed as well, you can’t really tell what the diagnostic information actually represents.
Conversely, you can’t be sure that just because MVPA does not pick up diagnostic information from a region that it therefore doesn’t contain any information about the variable of interest. MVPA can only work as long as there is a pattern of information within the features you used.

This last point is most relevant to James’ comment. Say you are using voxels as features to decode some experimental variable. If all the neurons with different tuning characteristics in an area are completely intermingled (like orientation-preference in mouse visual cortex for instance) you should not really see any decoding – even if the neurons in that area are demonstrably selective to the experimental variable.

In general it is clear that the interpretation of decoded patterns is not straightforward- it isn’t clear precisely what information they reflect, and it seems like if a region contained a totally heterogeneous population of neurons you wouldn’t pick up any decoding at all. With respect to ST,  I don’t know if this completely invalidates our ability to test predictions- I don’t think one would expect such radical heterogeneity in a region like STS, but rather a few sub-populations responding selectively to self and other, which MVPA might be able to reveal. It’s an important point to consider though.

Tal’s point is an important one regarding the different sources of information that GLM and MVPA techniques pick up. The paper he refers to by Jimura and Poldrack set out to investigate exactly this by comparing the spatial conjunction and divergent sensitivity of each method. Importantly they subtracted the mean of each beta-coefficient from the multivariate analysis to insure that the analysis contained only information not in the GLM:

pold_mvpa

As you can see in the above, Jimura and Poldrack show that MVPA picks up a large number of voxels not found in the GLM analysis. Their interpretation is that the GLM is designed to pick up regions responding globally or in most cases to stimulation, whereas MVPA likely picks up globally distributed responses that show variance in their response. This is a bit like the difference between functional integration and localization; both are complementary to the understanding of some cognitive function. I take Tal’s point to be that the MVPA and GLM are sensitive to different sources of information and that this blurs the ability of the technique to evaluate simulation theory- you might observe differences between the two that would resemble evidence against ST (different information in different areas) when in reality you would be modelling altogether different aspects of the cognition. edit: after more discussion with Tal on Twitter, it’s clear that he meant to point out the ambiguity inherent in interpreting the predictive power of MVPA; by nature these analyses will pick up a lot of confounding a causal noise- arousal, reaction time, respiration, etc, which would be excluded in a GLM analysis. So these are not necessarily or even likely to be “direct read-outs” of representations, particularly to the extent that such confounds correlate with the task. See this helpful post by neuroskeptic for an overview of one recent paper examining this issue. See here for a study investigating the complex neurovascular origins of MVPA for fMRI. 

Thanks sincerely for these responses, as it’s been really interesting and instructive for me to go through these papers and think about their implications. I’m still new to these techniques and it is exciting to gain a deeper appreciation of the subtleties involved in their interpretation. On that note, I must direct you to check out Sam Schwarzkopf’s excellent reply to my original post. Sam points out some common misunderstandings (of which I am perhaps guilty of several) regarding the interpretation of MVPA/decoding versus GLM techniques, arguing essentially that they pick up much of the same information and can both be considered ‘decoding’ in some sense, further muddying their ability to resolves debates like that surrounding simulation theory.