Enjoy the Disruption

My thoughts on Mendeley/Elsevier & why I left to start PeerJ

I joined Mendeley as head of R&D at the start in early 2009 and left end of 2011. Here are my thoughts about my time there and why I eventually left to start PeerJ. 

First, in terms of business success, regardless of your stance on Elsevier acquiring Mendeley, this was a win for the Mendeley team, so congratulations. I hear many saying that Elsevier overpaid (FT states £45M), but Elsevier is smart and they are getting a huge team in Mendeley that knows how to operate like a startup. That’s very near to impossible to grow organically with an established organization the size of Elsevier. This also gives Elsevier a major operational unit in London, which they did not have before.  That and other factors say to me that the amount paid is about right give or take a few percentage points. 

In terms of mission success, however, I am uncertain if this was a win. Mendeley had become known as the darling of openness, which in my view was already closing off when I left. Selling to Elsevier sets up a new challenge to maintain that open ethos, and unfortunately we can’t immediately gauge what the outcome will look like. 

I joined Mendeley after abandoning my own fledgling online article manager and recommendation tool that I had started while still finishing up my doctorate. I started talking with the Mendeley founders in the Summer of 2008 just before they opened for a beta program. I was really impressed with their plans to “disrupt” the academic market then held by EndNote and also to allow wider discovery of the literature. At Mendeley I was responsible for building out new discovery tools with the data that we were collecting. 

The R&D group did a lot in a few years (deduplicating 200M documents, real-time stats, search, Mendeley Suggest, etc), so I’ll mention just three of my projects below and what type of indication it creates about how Elsevier approaches things that are open.

One of my early projects was the “Open API.” It took some convincing at first to the founders that by releasing the extracted article data we would actually grow, but to their credit it didn’t take long for them to agree. I wrote the spec in late 2009 and worked with Ben Dowling (now an engineer at Facebook) to develop the first beta version of the API that was released in April 2010. After Ben left, Rosario jumped in to improve and expand the API and still heads it up in engineering. The API is now used internally at Mendeley for its own tools. From the start, the API was very controversial as we were now giving away metadata for free (titles, abstracts, etc) that publishers had always held onto tightly unless you were willing to pay for it. 

Next up were “PDF previews” that display anywhere from 1-3 pages of a PDF on each of the article landing pages on Mendeley web. The inspiration here was the 30 second previews that iTunes gives (and now every other digital music provider). The thinking was that this would benefit publishers by sending them traffic that was ready to engage with their articles, something that only seeing the abstract can limit. And we were right, the data we saw showed that articles with previews sent more traffic to publishers than without previews. To many publishers however, this was even more controversial than the Open API, as we were now showing even more content, although you couldn’t get access to it via the API. 

The third project was a JISC funded grant, DURA, that we co-wrote with Symplectic (now owned by Digital Science) and the University of Cambridge. The idea was to utilize the Mendeley Desktop client to connect to institutional repositories to allow drag & drop depositing. Put your authored papers into Mendeley and they are automatically deposited with your institution’s Green Open Access archive. 

All three of these projects were impacted by Elsevier. With the PDF Previews out, Elsevier came out hard to limit what we could do. The Mendeley founders, citing little choice, cave to removing Elsevier abstracts from the API and taking down PDF previews of Elsevier articles. Meanwhile, another publisher, Springer, surprisingly took the opposite approach and wanted us to do more with the PDF previews.

With the JISC funded DURA project, I got word that behind closed doors Elsevier was allegedly trying to stop the project altogether at JISC. That project has since stalled since I left Mendeley. 

These events were entirely against my personal open ethos and why I had originally agreed to join Mendeley. It was clear that the founders and I no longer agreed on the future (a blog post I had written calling out Elsevier’s actions was censored during the intense Elsevier talks) and tensions led me to reconsider my time there. It eventually came to a head and we agreed to part amicably. 

If one is honest, from a business perspective the Mendeley founders did the right thing to comply with Elsevier’s demands. My personal passions about Open Access hindered that, so no surprise it didn’t work out for more than a few years. What I learned was that my next project had to have open at its core, rather than just tacked onto the side. For that reason then I co-founded PeerJ, an Open Access journal, with one aim of never being in the position to take shit ever again from a closed publisher. 

I think that Mendeley as it stands today will continue to be useful even at Elsevier. That said, I think it will be challenging for Mendeley to become a truly transformative tool in science, which is what had originally convinced me to move from San Francisco to London four years ago. I cannot take all of the credit for the “open street-cred” Mendeley has gained over the years, but the projects I worked on had a big contribution to that and I can’t help to think that the day I left was the last day of further open innovation. It will be interesting to see what happens. I sincerely wish Jan, Paul, Victor and the team at Mendeley well.

Updated (10 April 2013): Let’s keep it classy Internet. Since I’ve witnessed some personal attacks against a few current Mendeley staff I thought I’d step in and state that there are still voices for change at Mendeley. I don’t want to leave anyone out, but since I saw attacks against them; three such people are William Gunn, Steve Dennis, and Ricardo Vidal. I know their character having worked together for years and know that they will do their best to make changes from within and wish them the best.

Another example of research hidden for months due to academic publishing norms

This is the latest paper, published in PLOS Genetics, from one of my former PhD advisors in graduate school.

Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

This one isn’t even all that bad, from submission to publication took seven months. However, I didn’t have the heart to ask him if it had been submitted elsewhere and been rejected. I didn’t want to shit all over what is a great feeling to have another publication out the door.

Sadly, most papers do go through multiple rejections from other journals before finding a home. And that’s if they are not “scooped” while doing the long journal dance. This means that advances in research are tied up for 1-2 years in many cases. 

Why I am upset and concerned

Delaying research helps no one. The paper above is an important one, that doesn’t immediately translate to saving lives, but is core basic research that one day could be applied as such. And this happens every day.

I cannot wait for PeerJ PrePrints to come out this Spring, which will put a stop to this nonsense.

Biology is in a slump - we need error logs to get out of it

It isn’t lost on me that what I am about to say is rather cliche and pronounced at least twice a month somewhere in the world. I feel that biological research isn’t progressing like it should be. First some background.

The two paragraph background

In circa 2000, about the time I was looking at grad schools, I read the book “Gene Dreams.” The book rehashes the biotech scene of the 1980’s and 90’s, along with all of the promises that biotech + gene therapy would bring to the world. It notes that all of those ‘dreams’ failed, but that the 2000’s would make it right. I was a believer! I entered graduate school determined to use gene and stem cell therapy to cure the entire F'ing planet. Spoiler alert, I failed.

I wasn’t alone though. Many others have failed in that pursuit as well. Gene and stem cell therapy is largely an 'applied science’ versus being a 'basic science’ (aka learning about the building blocks of what makes things tick). So, for a long time I felt that it was just applied science that had issues. The “issues” being that no solid or common frameworks to make discoveries or breakthroughs exist. And that it was better to do basic science if you wanted to succeed more easily. Years after completing grad school though, I think my bitterness was too narrow. I’m an equal opportunist, and would therefore like to bash basic science as well for lacking a modern toolset to take “it” (whatever “it” is) to the next level.

That’s the quick, slightly incoherent two paragraph background, now on to the (somewhat) present thinking.

I was at FooCamp last June 2012 and wound up in a session about biology (don’t remember the title). I think a discussion was brought up originally over the question of how programmers could get more involved with science in a DIY approach by Jesse Robbins. By this time, I had been several years removed from doing actual science on an actual bench with an actual pipette. Instead, I had taken up what I originally started out doing (at age 5) by programming shit; albeit shit related to science now.

Something that was said during that discussion brought me back to my graduate school days of failed experiment after failed experiment. Jesse asked, “Jason, how can I get more involved in science?”

My first reaction was, “Don’t! You’ll end up depressed.” All of those failed experiments, and all of the failed work by others in gene therapy, and most of the time we had no-f-ing-clue-why-they-were-failing. That was the biggest drain on me in grad school, not knowing why. Equally, if I did some kind of PCR directed-evolution experiment and found ONE good result amongst a thousand failed wells in a plate, my next step would be to toss those 999 failed wells and evolve the good well in another PCR round. How, stupid, was, I.

Having gotten back into programming after grad school, I immediately realized my error. Instead of concentrating on the one good well in a thousand, I should have taken the 999 bad wells to see why they went wrong. In programming, this is debugging by looking at your error logs, or similarly, test-driven development.

Moreover, what was missing was some sort of stack trace that would tell me exactly at which point the antibiotic I was testing started to kill the cell all the way up to the point of death (antibiotics were often used to test PCR evolved enzymes used in gene/cell therapy). It was then that I realized that not just applied science, but basic science was missing these “error logging” tools as well. We usually don’t know why experiments fail because 1) we hardly care about failures in science and 2) no one, AFAIK, has built the tools to examine the “why” stuff fails. Such an approach would be laughed at in programming.

Instead, in programming you check your error logs to figure out how to make things work as expected. And the reason we can do that is because someone in the past spent the time building error reporting tools. What is missing in biology (again, AFAIK) is a comprehensive set of error logging within cells.

This is why we’re in a progression slump; we can’t make the huge mental leaps in science because we’re now at the point where better tools are needed. This happens once a generation or so, where we’ve surpassed the infrastructure that was built by the previous generation. A more methodical approach within a framework is needed. A new respect for failed experiments is needed.

And I wouldn’t be surprised if building such error reporting within cells was more universal than we might expect at first, no matter what the cell type or species whence it came. Error reporting I suspect, much like DNA itself across species, could be generalized enough to require little modification per cell, protein interaction, or whatever. A common set of error messages could bubble up to a logging system to be investigated post-experiment. Even the act of building such error reporting would result in a giant number of new discoveries.

Of course, like any idea, good or bad, this has probably been “thunk” before, possibly at the same time. The thing is, I’ve yet to see anyone do it. Perhaps because they did and it failed, and so the research was tossed per usual.

Meg Hillier, my local MP, actually did something about my UK Visa

Running a startup is difficult enough. Being a foreigner doing a startup is about 100x as difficult. The last thing you want to be worrying about is your Visa and not having a passport to do business.

I’ve lived in the UK for nearly four years now on a Tier 1 Visa. I moved here from San Francisco to join Mendeley as Head of R&D [note: left to found PeerJ before Elsevier moved in to buy them :)].  

Last August I needed to send my Visa in for a two year extension. It has now been five months, and I still have not received my passport and new Visa. This is not an uncommon thing these days (read any Visa forum) for the UK Border Agency, the agency in charge of immigration decisions.

Obviously being without your passport is rather hampering as a co-founder of an Open Access tech/publishing startup with locations in both London and San Francisco. It’s outrageous actually, and the UKBA knows exactly what my business is. 

I know for certain that I am not the only entrepreneur going through this. A shame, as startup companies are the ones bringing new investment to the UK economy and creating new jobs. And with the RCUK pushing for Open Access, you’d think there would be added incentive in this case. David Cameron is full of a lot of hot air, professing to be on the side of foreign entrepreneurs. From where I sit, we’ve received no help.

Finally, this week I decided to do something besides futile attempts at contacting the UKBA for information on the delay. I wrote to my local MP, labour party member Meg Hillier. And behold, a written reply within two days of my emailing.

“… I have immediately written to the Home Office’s UK Border Agency (UKBA) on your behalf and have asked for a cause for the delay as well as an assurance that a decision will be made on your case as soon as possible. I regret that the UKBA is a very far from satisfactory organisation and that the service it provides to my constituents is deteriorating at present. …”

- Meg Hillier MP - 17 January 2013, private correspondance (see image in this post)

Thank you Ms. Hillier.

When stealing isn’t stealing - The most disturbing part of the Aaron Swartz story

Probably the most disturbing thing to me about the Aaron Swartz tragedy is this statement in 2011 from US Attorney Carmen Ortiz:

“Stealing is stealing whether you use a computer command or a crowbar, and whether you take documents, data or dollars.”

That is teaching our children that the law is always correct and that discretion should not be used when enforcing the law. It’s teaching our children not to question what they are being told by those in power. Had the American fore-fathers believed that “treason is treason” then the United States would have never had its Revolution and founding.

There is no physical law that governs the Universe that outlines stealing, killing, lying, etc. These are human fabrications to govern us as a society, tribe, and culture. We equally have the capacity to dictate when stealing isn’t stealing, or when an act of treason is the right thing to do as the American fore-founders discovered. That is how we advance as a  civilization.

There is a tremendous difference between stealing for personal gain, and “stealing” [1] to release academic papers paid for with tax-payer money. A true leader would recognize that. It’s been reported that Carmen Ortiz had political ambitions to one day run as Governor of Massachusetts. Is that the kind of leader a state would want? A false leader who doesn’t recognize when an act has morally justified grounds? A real leader would act to make changes, not throw the book at someone.

MIT should be ashamed as well, whether they were actively pressing charges or passively standing by [reports are conflicted over this]. MIT as well is supposed to be leading us. In the past they were one of the first universities to offer free and open classroom lessons online. Here, they failed miserably to lead by example that academic research should be made open.

The Aaron Swartz story is bigger than just a 26 year-old doing some computer hijinks and getting bent-over by those in a position of power. It’s even bigger than the importance of Open Access to academic research. It’s surfacing some major issues that we have in society in both the U.S. and beyond about true leadership [note: I am a US citizen currently residing in London, UK]. Ortiz was put into a position to use her discretion. Instead, she let her ambitions dictate Aaron’s fate.

At the end of the day, if it is against the law to steal whether morally motivated or not, then you’ve broken the law. Laws can be changed though. New countries can be formed. And leaders in power can use their discretion to apply fair judgment, not to further their own ambitions. Where have all the true leaders gone?

footnote

1. Note that Aaron wasn’t even technically stealing in terms of the law, at most it was breach of contract [according to several reports].

Are academic publishers creating or extracting value from scientists?

This morning, by way of @SimonBayly, I came across the article “Towards fairer capitalism: let’s burst the 1% bubble” in yesterday’s Guardian.

There’s a nice late 1800s/early 1900s quote that I can’t help but correlate with today’s academic publishers:

“The barbarous gold barons do not find the gold, they do not mine the gold, they do not mill the gold, but by some weird alchemy all the gold belongs to them.”  

- Haywood, William D. The Autobiography of Big Bill Haywood. New York: International Publishers, 1929, p. 171

What this is saying, and the thesis of the Guardian article, is that the gold barons of the 19th Century and the financial bankers of the 21st century are wealth extractors, rather than wealth creators.

The Guardian thesis goes on:

Value creation is about reinvesting profits into areas that create new goods and services, and allow existing goods to be produced with higher quality and lower cost.

Think about that. When was the last time we saw academic journals lower their prices? Subscription-based (and in cases even Open Access based) academic publishing is the opposite of value creation, it is value extraction.

The byproduct of innovation of the Internet has turned a wealth creating industry of academic publishing into a wealth extracting one. Make no mistake, today’s publishing executives are equal to yesterday’s gold barons and hedge fund managers. The Internet has given publishers the opportunity to lower prices, but they’ve chosen to do the opposite. That’s value extracted from scientists.

An important aspect of the Guardian thesis on economics isn’t that profits are inherently bad, but that they need to be reinvested to create more value.

I’d like to think this is what we are trying to do at PeerJ by creating value for the community. We made the price ridiculous at $99 for lifetime publishing. You’re forced to innovate with a price tag like $99. What’s more, we’re experimenting with free publishing as well with PrePrints (non peer-reviewed and non-typeset academic articles).

The thing is, we don’t know what the right price is for academic publishing today [1]. I don’t think it is what subscription journals have been charging, or most Open Access journals have been charging for that matter either. I suppose the thesis, of hedge fund managers and academic publishers robbing value, shall be proven if PeerJ continues to survive. 

If you’re not lowering your prices then you’re not innovating. And if you’re not innovating, then you’re not creating value.

Footnotes:

1. It’s definitely not free, as it costs money to run servers and pay staff who maintain those servers, etc. ArXiv (non peer-reviewed) is a good example of what the right price might be, though even they have substantial costs that need support.

Aaron Swartz found dead, but lives on with Open Access

If it weren’t for Aaron’s heroic actions to release academic research articles in 2011, I am unsure if PeerJ would have ever been born. 

Today’s news was shocking. Aaron Swartz was found dead from apparent suicide on the 11th of January, 2013 at the age of just 26. For the science community and Open Access advocates, Aaron was the man responsible for the (near) liberation of all pay-walled JSTOR content in mid 2011. He also co-wrote the first RSS 1.0 specification at the age of 14 and led the early development of Reddit. 

JSTOR and MIT eventually dropped the civil case against him (publicly anyway), but the U.S. government continued criminal proceedings against him. JSTOR, it should be noted, was not his first attempt at freeing information. Aaron was facing up to 35 years in prison for the act of setting academic research free. It’s unknown if this was the reason for his suicide, but that’s not why I am writing. 

The events around JSTOR and Aaron’s prosecution were probably the final straw for me. What kind of world do we live in, where such harsh punishment is sought for liberators of publicly funded information? The indictment of Aaron and the severity of the probable punishment angered me.

I wrote the following in July 2011 after learning about Aaron’s fate:

Will the JSTOR/PirateBay news be Academic Publishing’s Napster moment? i.e. end of the paywall era in favor of new biz models?

(Twitter reference)

Something had to be done. I wanted to turn Aaron’s technically illegal, but moral, act into something that could not be so easily thwarted by incumbent publishers, agendas or governments. Over the next few months I let that desire build up inside, until one day the answer came in the Fall of 2011.

It was then that the groundwork for PeerJ was first laid; a new way to cheaply publish primary academic research and let others read it for free. Aaron was significantly responsible for inspiring the birth of PeerJ and what I do now trying to make research freely available to anyone who wants it. 

I hope that when the history books are written in decades time, that Open Access crusaders like Aaron will still be remembered. My thoughts go out to Aaron’s friends and family. Know that Aaron’s light and efforts will live on. Thank you, Aaron, for inspiring us.

A bone to pick: not enough product-market fit

How often do we hear this, “We’ve just raised a small seed round and are using it see if we can gain product-market fit.”? In other words, they’re spending time and money without any inclination that there is a market available. I’ve not done the research, but at what point in history did this become a good strategy for the founders involved? The odds of success are tiny.

Building a startup with a huge market available to it is hard enough. Building a startup and trying to create its own market is a disaster waiting to happen. Far too often, I see startups trying to do the latter. You are wasting your time if you don’t start with an idea that has product-market fit from day one.

I’ve often heard people say that Apple created an entirely new market when it introduced the iPad. Same with the iPhone when the app store was launched. This isn’t true though. The ‘market’ already existed, it was the media/entertainment market. The iPad was just another device to leverage that market. Apple knew what it was doing.

I mention Apple, because they are a good example, for this specific case, in knowing your product-market fit before you even begin. For startup companies that manage to raise a small seed round (<$500K) it means you’ve been given a chance to demonstrate that product-market fit. For the Angel(s) involved, that’s great if you go on to prove that, and if not, well, they’ve invested in enough startups to hedge their losses. For >95% of startups though, you will never achieve that product-market fit if you don’t already have it from the start.

The best way to tell if your idea/startup has product-market fit is to ask yourself what other companies are successful and doing what you are thinking of doing. By success, I don’t mean raised a round (or even multiple rounds), I mean profitable and a staple in a large portion of people’s lives. If you can’t name several companies in your area, then 1) you don’t have enough knowledge of your area or 2) your idea doesn’t have an audience.

Startup pitch contests. Worst idea, perhaps ever.

Unless you are trying to find out who the best actor might be that is. It’s like saying, “they just won the ‘Presidential debate,’ therefore they must be an awesome President.”

There is absolutely no correlation between the ability to deliver a pitch and the ability to successfully run a business.  

What has spurred this bit of a rant is a blog post I woke up to this morning about the Founder’s Institute training their “student entrepreneur’s” on the fine art of pitching. Basically every incubator does this, so FI isn’t alone. And they do it for a reason, because this is what investors expect when you sit down with them, a well-polished pitch. And to be fair, investors usually don’t throw down money just because of a pitch, there is a lot more due diligence, usually.

I think that last point though, further due diligence, further backs up my claim that startup pitch contests do not actually determine the best business opportunity. They determine the best pitch, and that is all. In fact, winning a pitch contest might actually be harmful to your company, because it can bring a false sense of success; that you’ve achieved 'product-to-market fit.’ It will certainly raise the level of your profile for a short-while, but I don’t believe there are any self-fulfilling prophecies when it comes to becoming a successful business.