On Sci-Hub

Many readers will have heard of Sci-Hub which makes almost 50 million copyrighted journal articles freely available. Derek has blogged about Sci-Hub and has also suggested that it might not matter as much as some think that it does. Readers might also want to take a look at some other posts ( 1 | 2 | 3 ) on the topic. I'll focus more on some of the fallout that might result from Sci-Hub's activities but won't be expressing an opinion as to who is right and who is wrong. Briefly, one side says that knowledge should be free, the other side says that laws have been broken. I'll leave it to readers to decide for themselves which side they wish to take because nothing I write is likely to change people's views on this subject. 

Sci-Hub and its creatrix are based in Russia and, given the current frosty relations between Russia and the countries which host the aggrieved journal publishers, it is safe to assume that Sci-Hub will be able to thumb its nose at the those publishers for the foreseeable future.  Sci-Hub relies relies on helpers to provide it with access to to the copyrighted material and these helpers presumably do this by making their institutional subscription credentials available to Sci-Hub. It's worth noting that one usually accesses copyrighted material through a connection that is recognized by the publisher and only a very small number of people at an institution actually know the access keys/passwords. One important question is whether or not publishers can trace the PDFs supplied by Sci-Hub. I certainly recall seeing PDFs from certain sources being marked with the name of the institution and date of download so I don't think that one can safely assume that no PDF is traceable. If a publisher can link a PDF supplied by Sci-Hub to a particular institution then presumably the publisher could sue the institution because providing third parties with access is specifically verboten by most (all?) subscription contracts. An institution facing a legal challenge from a publisher would be under some pressure to identify the leaks and publishers would be keen for some scalps pour encourager les autres.

While it would be understatement to say that the publishers are pissed off that Sci-Hub has managed to 'liberate' almost 50 million copyrighted journal articles, it is not clear how much lasting damage has been done.  The fee for downloading an article to which one does not have subscription access is typically in the range $20 to $50 but my guess is that only a tiny proportion of publishers' revenues comes from these downloads. I actually think the publishers set the download fees to provide institutions with the incentive to purchase subscriptions rather than to generate revenue from pay-per-view. If this is the case, Sci-Hub will only do real damage to the publishers if, by continuing to operate, it causes institutions to stop subscribing or helps them to negotiate cheaper subscriptions.

There is not a lot that the publishers can do about the material that Sci-Hub already has in its possession but there are a number of tactics that they might employ in order to prevent further 'liberation' of copyrighted material. I don't know if it is possible to engineer a finite lifetime into PDF files but they can be protected with passwords and publishers may try to only allow a small number of individuals at each institution to direct access the copyrighted material as PDF files. Alternatively the publishers might require that individual users create accounts and change passwords regularly in order to make it more difficult (and dangerous) for Sci-Hub's helpers to share their access. Countermeasures put in place by publishers to protect content are likely to add complexity to the process of accessing that content. This in turn would make it more difficult to mine content and the existence (and scale) of Sci-Hub could even be invoked as a counter to arguments that the right to read is the right to mine.

Given that almost 50 million articles are freely available on Sci-Hub, one might consider potential implications for Open Access (OA). There is a lot of heated debate about OA although the issues are perhaps not as clear cut as OA advocates would have you believe and this theme was explored in a post from this blog last year.  Although there is currently a lot of pressure to reduce the costs of subscriptions, it is difficult to predict how far Sci-Hub will push subscription-based journal publishers towards a purely OA business model. For example, we may see scientific publication moving towards a 'third way' in the form of pre-publication servers with post-publication peer review. I wouldn't be surprised to learn that 'direct to internet' has usurped both subscription-based and OA scholarly publishing models twenty years from now. That, however, is going off on a tangent and, to get things back on track, I'd like you to think of Sci-Hub from the perspective of an author who has paid a subscription-based journal $2000 to make an article OA. Would it be reasonable for this author to ask for a refund?       

   

Looking back at 2015

I'll start the year by taking a look back at some of the 2015 blog posts. The dynamic range of the bullshitometer was severely tested last year and there was an element of 'pour encourager les autres' to more than one of the posts. I thought that it'd be fun to share some travel pics and the first is of the Danube in Belgrade (I'd dropped by to catch up with friends and deliver a harangue at the university).  The early evening light was quite perfect although I hope that I won't spoil your experience of the photo by telling you that there was a pig carcass floating about 100 m from it was taken.

 

I changed the title of the blog this year. I've not been involved with FBDD for some years now and molecular design was always my main interest. One of the ideas that I try to communicate is that there's more to design than just making predictions. After Belgrade, I dropped in at Fidelta in Zagreb where I delivered another harangue before heading south to Sarajevo.  I'm a keen student of history so it was inevitable that this would be the first photo I'd take in Sarajevo.

It seems so bizarre today. There had already been one assassination attempt for the day when the driver of the car took the fateful wrong turn that gave Gavrilo Princip the opportunity to fire two shots at the royal couple. Back in Vienna, Sophie was not always allowed out in public with Franz Ferdinand so the trip to Sarajevo may have been a special treat for her. What if SatNav had already been invented but, then again, what if Queen Victoria's eldest child had succeeded her to the throne?

Part of the problem was that, as a lowly Czech countess, Sophie was not considered an appropriate match for the Habsburg heir by Franz Josef (the reigning emperor and a puritanical old killjoy) and there were rules (although metrics and Lean Six Sigma 'belts' had, thankfully, not yet been invented). One of the rules was that the children of Sophie and Franz Ferdinand were barred from succession. It is somewhat ironic that poor Franz Ferdinand was never even supposed to be crown prince in the first place and only got the job because his cousin Rudolf had abruptly removed himself from the Habsburg line of succession a quarter of a century previously. 

All this talk of puritanical rules serves as a reminder that, before moving on, I need to point you towards a friend's blog post on roundheads (who were bigger killjoys than Franz Josef or even Lean Six Sigma 'belts') and cavaliers in drug discovery.  I really like the term 'roundhead' and I think you do have to agree that it's a lot politer than 'compound quality jackboot'. Terms like 'roundhead' and 'jackboot' are invariably associated with pain and that brings me to the next topic which is PAINS. My interest in this topic was piqued by a PAINS-shaming post at Practical Fragments and I have to thank my friends there for launching me on what has proven to be a most stimulating, although at times disturbing, line of inquiry.

My first post on PAINS examined some of the basic science and cheminformatics behind the substructural filters used. One observation that I'll make is that cheminformaticians would have done themselves rather more credit if, instead of implementing PAINS filters quite so enthusiastically, they'd first taken a more forensic look at how the filters had been derived. Singlet oxygen is an integral component of the AlphaScreen technology used in all six assays that formed the basis of the original PAINS study and the second post explored some of the consequences of this reliance on singlet oxygen. The third post was written as a 'get out of jail' card for those who need to get their use of PAINS past manuscript reviewers but, on a more serious note, it does pose some questions about how much we actually know about the behavior of PAINS compounds. The final PAINS post emphasized the need to make a clear distinction in science between what we know and what we believe. If we are unable (or unwilling) to demonstrate that we can do this in drug discovery then those who fund our work may conclude that the difficulties we face are of our own making.

There's actually a lot more to Sarajevo than dead Habsburgs and the city hosted the  1984 Winter Olympics. I took a taxi to the top of the bobsled run and walked back down to the city. Here are some photos. 

  

  

  

So I guess you're wondering where the 1984 bobsled run fits into drug discovery.  Ligand efficiency is, in essence, about slopes and intercepts and, like bobsledders, ligand efficiency advocates prefer not to think about intercepts.  I did two posts on ligand efficiency in 2015. The first post was a response to an article in which our criticism of ligand efficiency metrics was denounced as noise although, in the manner of Pravda, the article didn't actually say what the criticism was and I was left with the impression of a panicky batsman desperately trying to fend off a throat ball that had lifted sharply off just short of a length. The second post explored the link between ligand efficiency and homeopathy. 

I have described ligand efficiency as not even wrong and it also fits snugly into the voodoo thermodynamics category. Sometimes I think that if a coiled dog turd could be converted to molar energy units and scaled by coil radius then it would get adopted as a metric (which we might call 'scatological efficiency'). Voodoo thermodynamics is likely to feature more frequently in 2016 although I did manage one post on this topic in 2015. 

I took the train from Sarajevo to Mostar and the next four photos show a guy jumping, as is the local custom, off the reconstructed Stari Most into the Neretva River.

 

Now I guess you're wondering what a guy jumping off a bridge in Herzegovina has to do with molecular design and the quick answer is nothing at all. During the course of the year I jumped off a bridge of sorts (more accurately out of my applicability domain) with a post on Open Access and there'll hopefully be more of this sort of thing this year. This is probably a good point to wrap up the review of 2015 and I look forward to seeing you towards the end of the month when you'll meet the boys who cried wolf.

On open access

I’ve been meaning to write something about open access (OA) for some time and I do genuinely believe that true OA is a worthwhile (and achievable) ideal. This blog post is not intended as a critique of OA although I will suggest that its advocates do need to think a bit more carefully about how they present the benefits. I'll be writing from the perspective of authors of scientific journal articles and disclose, in the interests of openness, that all but one of my publications have been in paywall journals. One general observation that I will make is that the sanctimonious, holier-than-thou attitude of some OA advocates (who may occasionally avail themselves of the advantages of publishing in paywall journals) does tend to grate at times.  Although there is actually a lot more to OA than who pays for journal articles to be published, I'll not be discussing those issues in this post. The principal theme of this post is that it may be helpful for those who opine loudly on the benefits of OA to take a more author-centric look at the relevant issues and this is especially important for those advocates whose contributions to the scientific literature have been modest.  

One of my gripes is that OA is sometimes equated with open science and I believe that the openness of science is actually a much bigger issue than who pays for scientific articles to be published in journals. Drug discovery research is my primary focus and a certain amount of what (we think that) we know in this field comes from analysis of proprietary databases.  Some of this analysis falls short of what one might feel entitled to expect from journals that would describe themselves as premier journals and you’ll find some examples in this presentation.  I have argued here and here that studies of this genre would actually pack a much heavier punch if the data was made publicly available. However, it is not only datasets that are undisclosed in drug discovery papers.  In some cases, models built from the data are not disclosed either (this does not inhibit authors from comparing their models favorably with previously published models). If the science in a data modelling study is to be accurately described as open then the data and models associated with the study have to be disclosed. This is not just an issue for paywall journals and the models described in the following OA articles do not appear to be fully disclosed:

JCheminform2010:2:11 | JCheminform2012:4:29 | JCIM2014:54:944 
 JCIM2015:58:4066 | PLoSNTD2015:9:e0003878

The point that I'm making here is that a the science in a paywall journal is not necessarily less open than that in an OA journal. In my view, the openness of the science presented in a journal article is determined by how much its authors disclose rather than whether or not one needs to pay to read the article. It's also worth remembering that internet access is not free.

This is a good point to say say something about the economics of publishing articles in scientific journals. In economic terms, a journal article represents a service that the journal has provided for the author rather than the other way round (which many would regard as more sensible).  The author typically pays for the service by either signing over rights to paywall journal or by paying an article processing charge (APC) to a journal (OA or paywall) which means that the article can be freely viewed online and rights are (hopefully) retained by the author.  I need to note that not all OA journals levy APCs and, in these cases, it's a good idea to check how the journal is funded and whether or not articles are peer-reviewed. Payment of an APC implies that the journal article is technically an advertisement and this has interesting (and potentially even troubling) implications if the journal also publishes conventional advertisements. All articles in a paywall journal are usually considered (e.g. by download cost) to be of equal value and this is one of the bigger fictions in the scholarly publishing business.  The situation becomes more complicated with OA journals because the APC may vary with geographical region or be waived completely for some individuals. In the interest of openness and accountability, shouldn't open access journals disclose the actual APC paid for each article published?

There are compelling arguments that can be made in support of OA and, like many, I believe that the results of publicly-funded research should be fully visible to the public. This is probably a good point at which to raise the question of who should own intellectual property generated by publicly-funded research. OA broadens participation (by citizen scientists and emerging scientific communities in developing countries) and increases the likelihood of a study being read (and used) by the people with the most interest in it. OA greatly facilitates mining of the ever-expanding body of published literature which adds to its value and, unsurprisingly, some of the loudest voices calling for scientific literature to be made public property are those of informaticians and data scientists.  One question that OA advocates need to address is whether the results of mining and analysis of freely available literature should also be considered to be public property. While a strong and coherent case can be made for OA, it might not be such a great idea to invoke morality (can get a bit subjective) or fundamental human rights (people under siege in Syria might consider it less than tasteful that their suffering is being equated with their inability to access the latest articles in Nature).

There are a few hurdles that will need to be overcome if OA vision is to translate to OA reality. Advocates for OA typically demonize the paywall journals although the cynic might note that easily-recognized enemies are needed by the leaders of mass movements in order to galvanize the proletariat. Some declare that they will only review manuscripts for open access journals while others assert that they are boycotting Nature and Science (I scarcely dare to think of the mirth of that would result from me announcing to colleagues that I will no longer be submitting manuscripts to Nature). While demonizing paywall journals may make people feel good (and righteous), it misses the essential point that the OA movement needs to win hearts and minds so that authors (the creators of content) come to see OA journals as the most attractive option for publishing their studies. Put more bluntly, authors are as at least as much to 'blame' as the journals for their articles 'disappearing' behind paywalls. It's also worth remembering that journal editors are also usually authors as are the people on academic hiring committees who might use journal impact factor to to decide that one research output of one applicant is worth more than that of another applicant.

One nettle that the OA movement does need to grasp is that journal publishing is frequently a business and, from the perspective of the 'customer', the terms 'paywall' and 'open access' simply describe alternative business models.  I'm certainly not saying that it has to be that way and there are other areas, such as the provision of health care, education and religion, where a case can be made for the exclusion of commercial activity.  However, the issue remains and, like or not, the OA movement is effectively lobbying in favor of one set of commercial interests over another set of commercial interests. This means that OA advocates need to be clear (and open) about the sources of any funding that should come their way.  The other nettle that the OA movement needs to grasp is that it should be very careful about whom it allows to speak on its behalf.  OA propaganda sometimes takes the form 'open access good, paywall bad' and the message loses some of its bite if it turns out that Napoleon has been publishing in Nature while denouncing Beall's List as reactionary and counter-revolutionary.

So let's take a look at OA from the perspective of a scientist who is trying to decide where to send a manuscript.  Typically the decision will be made by the principal investigator (PI) who will be well aware that funding and, if relevant, tenure decisions will be influenced by which journals in which the PI's articles have been published.  In some areas (e.g. biomedical), academic research is particularly competitive and PIs are well aware that an article published in an elite journal is visible to the PI's peers and all those who will be making decisions about the PI's future.  As such, publishing in an OA journal can represent a risk without compensating benefits (in competitive academic science, knowing that everybody on the planet can see your article fits into the 'nice to have' category). Another factor that inhibits authors from publishing in OA journals is the paucity of options in some disciplines (e.g. chemistry). I don't believe that there is currently a credible OA equivalent to Journal of Medicinal Chemistry and would be concerned about the ability of a general purpose OA journal to identify and recruit specialist reviewers. I'm not a computational biologist but, if I were, I'd definitlely be thinking twice about submitting an article to a computational biology journal that published Ten Simple Rules of Live Tweeting at Scientific Conferences. Finally there is the issue of cost because publishing in OA journals (or paying for OA in a paywall journal) does not usually come cheap and, in some cases, funding needs to be specifically sourced (as opposed to simply paying out of one's grant). Those scientists for whom the APC represents a significant expense will also be aware that they are effectively subsidizing other scientists for whom the APC has been waived. Something that may be going through the mind of more than one scientist is the direction in which APCs might head should all scientific publishing be forced to adopt an OA business model.

I think this is a good point at which to wrap things up and I should thank you for staying with me.  If you're an OA opponent and had been hoping to see OA skewered then please accept my apologies for having disappointed you. If you're an OA supporter, you may well disagree with many (or all) of the points that I've raised. If, however, something in this post has prompted you to think about things from a different angle then it will have achieved its purpose.