Open science


From the mailbag, news of a new aging-related peer-reviewed journal, currently in its first issue: Pathobiology of Aging & Age-related Diseases. I haven’t had to check it out yet, but it looks like it will be of broad interest to biogerontologists from a variety of disciplines. The editorial board includes quite a few luminaries of the field, so it seems promising.

In their own words:

Aims: Pathobiology of Aging & Age-related Diseases (PBA) is a new peer reviewed journal serving as a forum for researchers to communicate pathology data as a primary scientific focus of aging; data that might be of less interest in other journals more focused on generic aging or specific scientific disciplines. We are especially interested in developing a focus for advancing the pathological basis of aging in mammalian systems, in particular the mouse and humans.

Scope: Pathobiology of Aging & Age-related Diseases is interdisciplinary in nature and covers all aspects of pathology of aging related to disease phenotypes including cancer, cardiovascular disease, neurological disorders, metabolic dysfunction, renal and gastrointestinal disorders, endocrine dysfunction, musculoskeletal conditions and skin disorders. The underlying theme is based on the sound scientific principles of the pathogenesis of aging and age-related diseases as well as intervention data with resolution of pathological endpoints. The emphasis will be on preclinical studies as well as clinical studies related to strategies developed in animal models and will be image intensive. Papers on the basic biology of aging in invertebrates will not be considered unless comparative mammalian data is also included.

We welcome Research papers, Review articles, Brief reports, Case reports, New animal models, Technical reports, Images, PhD thesis Summaries, and Commentaries.

Target groups: Anatomical and molecular pathologists, gerontologists, geriatricians, transgenic mouse geneticists, toxicologists, and scientists, veterinarians and physicians focused on basic and clinical research in cardiovascular disease, cancer, gastrointestinal disease, endocrine disorders, metabolic dysfunction, renal disease, neurological disorders including Alzheimer’s disease, skin disorders, and musculoskeletal disease.

PBA is open-access; the publisher, Co-Action Press, is a relatively new entity whose small but growing stable consists entirely of open-access journals spanning a wide range of fields.

My personal feeling is that there are probably already too many journals, mostly because I don’t think I or my colleagues actually interact with journals as entities. Mostly we just do literature searches, and choose papers to read based on titles and abstracts. The exception is when we’re submitting papers, but then the diversity of formats and author requirements creates obstacles to rapid submission (and re-submission, if necessary).

I wouldn’t mind seeing individual journals be replaced by a robust tagging system on a relatively laissez-faire neo-journal such as PLoS ONE (to allow scholars to create communities and filters on the firehose of new papers), and a little time spent teaching everyone how to set up PubMed RSS feeds. That said, if we’re going to start new enterprises, this is probably the right way to go, so good luck to PBA.

When it’s not gouging academic libraries with outlandish subscriptional fees, Elsevier finds other ways to boost its bottom line: Publishing bogus journals for pharmaceutical companies. From The Scientist:

Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles–most of which presented data favorable to Merck products–that appeared to act solely as marketing tools with no disclosure of company sponsorship.

“I’ve seen no shortage of creativity emanating from the marketing departments of drug companies,” Peter Lurie, deputy director of the public health research group at the consumer advocacy nonprofit Public Citizen, said, after reviewing two issues of the publication obtained by The Scientist. “But even for someone as jaded as me, this is a new wrinkle.”

The Australasian Journal of Bone and Joint Medicine, which was published by Exerpta Medica, a division of scientific publishing juggernaut Elsevier, is not indexed in the MEDLINE database, and has no website (not even a defunct one). The Scientist obtained two issues of the journal: Volume 2, Issues 1 and 2, both dated 2003. The issues contained little in the way of advertisements apart from ads for Fosamax, a Merck drug for osteoporosis, and Vioxx.

The article contains links to PDFs of the “journal,” which contains one very useful page: the list of members of the editorial board. You never know when you’ll need an Australian clinical researcher whose good name is for sale. (Update: For a more charitable interpretation of the editorial board’s role, see shwu’s comment below. Update #2: And this comment too. )

Elsevier’s defense, described later in the article, is pretty thin. They acknowledge that they failed to include full disclosure of the publications’ commercial mission, but claim that the error was inadvertent. (Given their usual fastidiousness about legal permissions, this can be dismissed as nonsense.) They also point out that the “journal” in question was published several years ago and that they don’t do things like this anymore — also utter crap, since if they were genuinely contrite about the error and had reformed their disclosure policies, they should have gotten in front of it and made an announcement of the fakery before they got caught.

Taking money to publish a fake journal to advance a corporate marketing agenda cheapens the process of peer-reviewed scientific publishing. I don’t imagine that Elsevier is engaging in pay-to-play in their flagship journals, but the fact that they were willing to cast aside their integrity in this once instance casts a shadow over their whole operation.

How many times will Elsevier have to disappoint the scientific community (you remember us, right? we’re the ones who produce their content, peer-review it for free, pay page charges to publish our own work and then pay again for the privilege of accessing those publications) before we get smart and move on? There are other models for scientific publication that are working just fine; we don’t need ethically challenged behemoths like Elsevier to disseminate scientific knowledge. At some point we just have to stop sending them papers.

P.S.: One wonders whether Merck suppressed unfavorable data about their products in their fake journal, as well.

Update: I wrote a follow-up here, and there’s a roundup of blogging about this issue at Tree of Life.

Just a reminder: Registration for SciBarCamp Palo Alto went live today. We’re limited to 75 people so if you’re in the Bay Area (or able to get here on your own dime), of a scientific inclination, and seriously committed to attending, move quickly — and then spread the word.

The registration site is here, and there’s more info at the main website.

Which journals are the most influential? The answer obviously depends on the individual who is answering, and is sensitive to variables like one’s field, subfield, position, and recent professional history — but that doesn’t stop people from compiling lists of the most important publications within broad disciplines like “biology”.

The methodology by which one makes the comparison is also important. If one proceeds by “impact factor” (a complex, proprietary, and increasingly challenged function of how frequently papers in a given journal are published), the answers tend to converge on a few very high-profile journals. If one takes a poll of librarians and experts chosen by librarians, the resulting list overlaps somewhat with the one derived from impact factor, but with far greater diversity (possibly as a result of honoring journals that were once great but whose readership has fallen off somewhat in the past few decades). Neither list mentions open-access journals at all.

But citation is just one means to measure the importance of a paper. Speaking personally: there are lots of papers that change the way I think, and contribute tremendously to the intellectual “backstory” of my projects, but never end up getting referenced in a primary paper. Beyond that, citations take a long time to accumulate; they generally don’t even start appearing until more than a year after a paper is published.

What if we were able to measure the actual use of a paper by scientists, irrespective of whether they eventually got cited? One could measure the rate at which papers were downloaded from journal websites, and indeed this is already being proposed as an alternative metric of journal impact.

There’s also a lot of free information floating around on social bookmarking sites like Connotea and Mendeley. One could ask which journals are publishing the articles most likely to be bookmarked and shared by users of those sites. Doing so reveals that open-access journals may be a good deal more influential — in the sense of actually being read by a large number of working scientists — than predicted by conventional metrics.

Of course, all of this discussion presupposes that there is some reason why we need to pick a “best” journal at all. Good search engines, in conjunction with rapid indexing of the primary literature, have greatly flattened out the landscape — however, at the same time, the proliferation of journals have caused that same landscape to greatly expand. We need some filter on the literature, but it’s increasingly unclear to me whether selecting papers to read based on the brand name on the journal’s cover (which I never see anyway) is a good solution to that problem.

UCSC, the institution that brought you the industry-standard genome browser, has now launched the UCSC Cancer Genomics Browser:

The browser is a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. This browser displays a whole-genome and pathway-oriented view of genome-wide experimental measurements for individual and sets of samples alongside their associated clinical information.

This site hosts the public UCSC Cancer Genomics Browser. The public site contains a rapidly growing body of publicly available cancer genomic data, including 12 published studies, datasets from the TCGA consortium, and others.

We encourage you to explore these data with our tools. The browser enables investigators to order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways, and user-edited collections of genes. Standard statistical tools are integrated to provide quantitative analysis of whole genomic data or any of its subsets.

I suspect that the Cancer Genomics Browser will provide an indispensable tool for biogerontologists who are seeking to explore the mechanistic connections between aging and cancer. I’m currently trying to think up an interesting way to use the service (and publicly available data) in my own work: e.g., tumors all have to undergo cellular senescence; would it be possible to find some fingerprint of senescence bypass mechanisms by looking at expression data from large numbers of tumors?

The new interactive Timeline of Discoveries in the Science of Aging (which I mentioned previously) is growing at a reasonable pace — it has roughly doubled in size since I first saw it, and now requires users to scroll down a bit.

I’ve added two articles and intend to do more:

Feel free to stop by and check those out.

If you feel that a major event in the history of biogerontology is missing from the timeline, I would encourage you to make an addition. Thanks to the site’s proprietor, Paul House, posting is relatively easy and entirely painless — though it’s not currently possible to go back and edit an entry yourself, so it probably makes sense to write and proofread your post before you start entering data into the form. If you know of a critical paper that’s not listed but don’t want to post yourself, you can still suggest it on the forum.

As I said before, I think this is a great idea and will be a fantastic educational and reference tool for the field, so I hope others will support the effort as well.

Last year I enjoyed attending two great “unconferences”, Scifoo andBioBarCamp. Although nominally similar in structure, the events had very distinct feels: Scifoo was a massive, invitation-only affair sponsored by Google, Nature and O’Reilly, whereas BioBarCamp (spearheaded by Attila Csordás of Partial Immortalization and organized by him and John Cumbers, now at NASA-Ames) was more freely accessible and intimate. I ended up getting a lot out of both events: I learned a lot, got inspired about open science, and met a lot of delightful people with whom I’m still in touch.

This year Attila is in Hungary and unable to plan a BioBarCamp in coordination with Scifoo, but will be putting one together for later in the year. The pre-foo unconference torch has been passed to Jamie McQuay of Scimatic Software, who has a slightly more expanded vision for a SciBarCamp that is inclusive of all fields. I’ve signed on to help organize, along with several others whom I met at BioBarCamp last year:

The conference will be free but space-limited to an as-yet-undetermined extent, so if you’re interested it behooves you to sign up early. As Jamie just announced on Scimatic’s blog, registration will open May 1. In the meantime, there’s a SciBarCamp website already up, and a FriendFeed room for discussion.

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