Of Polymers and Phages

After the my recent rantings about publishers and their antics, it is highest time for a polymer post. So here is a lovely piece of work: Graff et al., PNAS, 99(8), 5064 (2002) (doi: 10.1073/pnas.062654499, freely accessible via PubmedCentral).

There is a great deal of research interest in nanocontainers at the moment, specifically those produced via the self-assembly of block copolymers. In this particular example, a poly(2-methyl-2-oxazoline)-block-poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (PMOXA-PDMS-PMOXA) triblock copolymer (M_n(PMOXA) = 1800 gmol^-1, M_n(PDMS) = 5400 gmol^-1, PDI = 1.7) is used for the generation of micelles with a diameter of approximately 250 nm in an aqueous phase. Subsequently, the LamB receptor (a porin, which normally forms trimeric channels in the walls of gram-negative bacteria and is used for the transport of maltose and and maltodextrins) was incorporated into the walls of micelles through simple diffusion. Both this paper as well as others have shown that incorporation of proteins into synthetic polymer membranes leaves the proteins functionally intact, although synthetic membranes normally tend to be thicker and more densely packed than natural lipid bilayers.

As it happens, the porin not only acts as a channel, but is also a binding site for the lambda-phage. So when the latter is let loose on the micelles, the authors could observe binding of the phage tail to the protein receptor. Here’s a schematic:

(Reproduced with permission, Copyright PNAS 2002)

and here’s some micrographs:

(Reproduced with permission, Copyright PNAS 2002)

The top micrograph shows a phage bound to a single polymer vesicle, whereas the bottom one shows binding to a vesicle aggregate.

Using a fluorescent dye, the authors could show that, analogous to the process in natural, the phage injects its DNA into the polymer vesicle, where it is protected from the action of hydrolytic enzymes such as DNAse.

I don’t know about you, but I find this type of interface work beautiful and extremely elegant from a purely scientific point of view. The potential usefulness of DNA loaded vesicles in gene therapy applications is obvious and given the wide variety of co-polymer chemistry that we can choose from nowadays, it is even conceivable that one might find a system that has a specific target.

But even if we don’t – it is simply beautiful work.

P.S.: Thank you PNAS for making blogging about this so easy.

Running Joseki

In previous posts I have already alluded to the fact that we are interested in the use of OWL ontologies and RDF for our polymer informatics project. As part of this, we are investigating Joseki, which is a RDF publishing server, which provides a web interface for running SPARQL queries over RDF graphs.

The Joseki documentation is sparse and I always like a take-you-by-the-hand-and-walk-you-through-in-babysteps type of tutorial to getting things up and running. So I have attempted to supply one and the link is here. Seems to work on my fruit machine (MacBook Pro), so something must have gone right…….

Aesthetic Data

I have a confession to make: I am a sucker for bright ideas and bright people – particularly when those ideas resonate with my academic work, or when they strike a particular aesthetic cord with me. And there are a number of places on the web, where both can usually be found abundantly. One of these places is a podcast, “Entrepreneurial Thought Leaders” produced by the Stanford Department of Management Science and Engineering. Another one is the homepage of the TED (Technology, Entertainment, Design) conference and in particular their videocasts.

When browsing their website, I came across a short presentation by Jonathan Harris, who has done work, which not only resonated with our own, but is just simply beautiful. Jonathan is both a computer scientist and an artist, who is trying to understand the world and us human beings by analyzing the content and artefacts they are contributing on the web. He does this by collecting huge amounts of data, which he then visualizes in incredibly beautiful displays. One of his most impressive projects is the “We feel fine” project.

In “We feel fine” he scours the world’s blogs and extracts all those sentences from blog entries which contain the phrases “I feel” and “I am feeling”. If a sentence like this is found, it is scraped and transferred into a database. Using language processing it is then scanned to determine whether it contains a set of “pre-defined” feelings. If the blog post contains a picture, that is scraped too and associated with the sentence. Using statistics and a lot of visualization, Jonathan can draw an amazing amount of conclusions about “how the world feels” at the moment. I did a search just now, asking, how both men and women in the UK feel, when the weather is sunny between 2005 and 2007. The results speak volumes: the top 10 emotions in descending order are: ill, old, free, tired, weired, sorry, down, guilty, sad and happy.
Conceptually, there is so much in this that is analogous to the work some of my colleagues are doing here in the Centre (data gathering and analysis in Crystal Eye for example…..I am sure that if we were allowed to gather a bit more metadata than we are, we could tell so much about what’s occupying science at the moment, follow scientific progress etc…..just by looking at the molecules people are working on), and so much that we will have to learn about yet (e.g. analysis and visualization of large data sets, useful representations of data for chemistry).
But enough of me, best let Jonathan do the talking and the presentation. And I urge you to spend some time with the “We feel fine” website….it is fascinating.

Copyright Permissions – How they can also be done!

Having recovered from my hopping madness vented in my last post by taking a brisk walk round the chemistry department, I sat down to request more re-use permissions. One of the figures I wanted to use came from PNAS – the Proceedings of the National Academy of Sciences. Their current copyright policy was explained in a PNAS editorial in 2004 (I quote the entire thing):

Liberalization of PNAS copyright policy: Noncommercial use freely allowed

Nicholas R. Cozzarelli, Editor-in-Chief, Kenneth R. Fulton, Publisher, and Diane M. Sullenberger, Executive Editor

We have changed our copyright and permissions policies to make it easier for authors and readers to use material published in PNAS for research or teaching. Our guiding principle is that, while PNAS retains copyright, anyone can make noncommercial use of work in PNAS without asking our permission, provided that the original source is cited. For commercial use (e.g., in books for sale or in corporate marketing materials), we approve requests on an individual basis and may ask for compensation. We have revised our copyright assignment form to make the changes clear (www.pnas.org/misc/copyright.pdf) and added to our web site a “frequently asked questions” (FAQ) section on author and reader rights (www.pnas.org/misc/authorfaq.shtml).

As a PNAS author, you automatically have the right to do the following:

* Post a PDF of your article on your web site.
* Post a webcast containing material from your article.
* Make electronic or hard copies of articles for your personal use, including classroom use.
* Use, after publication, all or part of your article in a printed compilation of your work, such as collected writings or lecture notes.
* Include your article in your thesis or dissertation.
* Reuse your original figures or tables in your future works.
* Post a preprint of your article on a public electronic server, provided that you do not use the files created by PNAS.
* Present your paper at a meeting or conference, including those that are webcast, and give copies of your paper to meeting attendees before or after publication in PNAS. For interactions with the media prior to publication, see the PNAS policy on media coverage (www.pnas.org/misc/forms.shtml).
* Permit others to use your original figures or tables published in PNAS for noncommercial use (e.g., in a review article), provided that the source is cited. Third parties need not request permission to use figures and tables for such use.

Given that authors and readers can automatically use original material in PNAS for research or teaching, why do we request copyright transfer? We do so for three reasons: to allow us to publish, archive, and migrate articles to new media; to remove the administrative burden of rights and permissions management from authors; and to provide protection from copyright abuse.

We do not feel that this or any copyright policy is the only one possible. In fact, our policy has changed through our 90 years of publishing and surely will change again. We have requested that authors transfer copyright only since 1993. From the first issue of PNAS in 1915 through 1992, authors held copyright to their articles. From 1978 to 1992, we registered copyright for each journal issue as a collected work but did not request copyright for individual articles. In 1993, we began requiring that authors transfer copyright “in all forms, languages, and media now or hereafter known,” which granted us the rights to publish papers online in 1997 and to then digitize selected back issues and post them online.

We think that our current policy best meets the needs of readers, authors, and the journal, for the following reasons:

1. To store and migrate archival formats of the journal. We are committed to facilitating permanent, freely accessible archives of the scientific literature. PNAS is a charter member of PubMed Central, a digital archive of the life sciences journal literature (www.pubmedcentral.nih.gov), and is a participant in the National Library of Medicine’s effort to digitize and post back issues of journals. Not holding copyright to individual articles from 1915 to 1992 delayed our posting of this older material online because we do not have the legal rights to do so. In the end we proceeded without explicit permission from the original authors or their heirs. We accept the risk in doing so because we believe it is clearly in everyone’s best interest. If a copyright holder objects, however, we will immediately remove the article from our online collection. Full copyright transfer allows publishers explicit rights to invest in long-term archiving strategies.
2. To provide an administrative convenience for everyone. Despite our liberal rights and permissions policies, PNAS still receives more than 50 commercial and noncommercial permission requests per week. We routinely agree to noncommercial use, so such requests waste everyone’s time.
Unfortunately, PNAS cannot provide permission for others to use all or part of articles published from 1915 to 1992 because we do not hold copyright. Only the original authors or their designees can grant permission. Researchers are frustrated when they contact us for permission to use seminal works and we are unable to grant their requests.
3. To provide international protection regarding infringement or plagiarism. On the rare occasion that material is misused, authors appeal to PNAS to intervene on their behalf to enforce copyright protection. In such cases, a formal query from PNAS or the threat of a copyright infringement lawsuit has prompted expeditious action. In cases of redundant publication we sanction authors for violating journal and copyright policy. Because international standards and copyright law are complex, PNAS leaves interpretation of global copyright standards to our expert legal counsel.

We also support creative efforts such as charting, mining, analyzing, sorting, navigating, and displaying information contained in PNAS. The highly successful Sackler Colloquium “Mapping Knowledge Domains” (www.pnas.org/content/vol101/suppl_1) is a prime example (1). We encourage authors to use standard forms of data presentation to facilitate this process.

References

1. Shiffrin, R. M. & Börner, K., eds. (2004) Proc. Natl. Acad. Sci. USA 101, Suppl. 1, 5183–5310.[Free Full Text]

This is reaffirmed on the up-to-date 2007 PNAS copyright faq page:

Can others (nonauthor third parties) use my original figures or tables in their works without asking PNAS for permission?

Yes, PNAS automatically permits others to use your original figures or tables published in PNAS for noncommercial and educational use (i.e., in a review article, in a book that is not for sale), provided that the original source and copyright notice are cited. Commercial reuse of figures and tables (i.e., in promotional materials, in a textbook for sale) requires permission from PNAS.

Now this is an entirely sensible and science friendly policy. Now open access according to the BBB declaration, but a huge step in the right direction, certainly in comparison with the last example:

• automatic grant of re-use rights for non-commercial puposes (because asking for permission and credit card numbers is a WASTE OF TIME)

• re-distribution rights for authors

• self-archiving rights (of original manuscript etc.)

• free classroom use etc.

Thanks PNAS – you guys made everyone’s life a bit easier.

Requesting Permissions for Re-use of Copyrighted Material.

Now I am not normally one to rant, at least not on a blog, but today I encountered something that makes me just mad…..and I mean hopping mad.

I have just finished writing a review paper on poly(2-oxazolines)…a class of polymers close to my heart. As it is a review paper, I have included some figures, which were taken from the original research papers forming part of the review. Given that these were not my figures and that I respect and honour the copyright of other authors who have worked hard to produce high-quality and illustrative figures for their publications and the copyright of publishers who have been assigned those rights by an author, I went off to request permissions for re-use of copyrighted material from the relevant publishers. The review was based on about 150 papers, and I had taken figures from a few of them…ACS, RSC…no problem. Their procedures are all more or less automated and relatively pain free, although time consuming. And then, well then I came to Elsevier……

Elsevier has outsourced their copyright clearance procedure to a company called the Copyright Clearance Centre (I have included the link for your edification), which, on its website claims to “help to advance education, innovation and the free flow of information.” So far so good. Following Elsevier’s instruction, the first thing I have to do to obtain permission, is to go and find the resource I took the figure from on ScienceDirect. So off I go and locate the relevant journal (Talanta) and citation on Science Direct. Next, the website instructs me to find the abstract of the paper and to press the “Request Permissions” button.

Pressing this button launches a pop-up window which asks me what I want to do and I make my selections:

I am somewhat curious as to why it asks me which currency area I am currently in, but decide to ignore it for the moment. Having made my choices, I hit the “continue” button. I am then asked to set up an account as I have never used rights link before. Ok, getting tedious, but I hit the button to set up an account (note: none of this is necessary with the other publishers). I am now taken to a page where the anger really sets in: they are asking me how I want to pay.

How I want to pay?? All I want is to request permission for reuse of one small figure. I do not want to pay anything – my institution is subscribing to the journal for me. Why on earth would you want to lump requests for re-use of copyrighted material together with a business process that may be appropriate for the purchase of pay-per-view access? If I do not want to have pay-per-view access, why do I need to hand over payment details? However, the dropdown menu only gives me the opportunity to choose between a credit card payment and an invoice.

Hmmm…..on I go and fill in my details hoping that the “payment” thing is just going to go away down the line. But no such luck and sure enough, on the next screen I am being asked for my credit card details IN ORDER TO BE ABLE TO SET UP AN ACCOUNT to request re-use permissions.

At this stage, I broke off the procedure. I understand that it might be convenient for the “Copyright Clearance Centre” to set up an account for me in such a way, that if I ever wanted to purchase a journal article from one of their customers, they have all the necessary information. IT IS NOT CONVENIENT FOR ME. All I want is permission to re-use a figure in a paper. I do not think that I should have to hand over my credit card details for this and I refuse to do so.

So what is the consequence of this? I am not prepared to set up a Rightslink account with the Copyright Clearance Centre under these circumstances. Therefore I cannot obtain permission to reproduce the figure I wanted and therefore I cannot use the figure in my paper. Furthermore, there is the personal inconvenience: I now have to throw the figure out of the manuscript and to renumber all of my figures in the text. This will cost me at least half an hour.

More significantly though, this has a negative impact on scientific dissemination. On the grand scale of things, it is only a tiny thing, but in effect this has stopped me from re-using a figure created by other scientists, which, I am sure, have a vested interest in their research being talked about, evaluated and disseminated. That is part of a scientist’s core business. The Copyright Clearance Centre has neither helped to advance education and innovation, nor indeed the flow of information, but rather has impeded it. And Elsevier is indirectly guilty: they have not done their best for their authors by helping to disseminate their science, but are collaborating with an organisation which actually puts people off reusing science. They have allowed requests for re-use of material to be lumped into the same procedure used for the purchase of pay-per-view articles. At best that is thoughtless and very poor customer service.

Now as I say, I don’t like to rant, but this kind of thoughtlessness makes me mad.