Pathobiology of Aging & Age-related Diseases: a new open-access journal

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.

 

AGING indexed by PubMed

I follow the aging literature using (among other tools) a set of RSS feeds that monitors recent journal articles in PubMed.

Today, my feeds were all overflowing, and with great titles, way more than usual…and then I noticed that all of the papers seemed to be from the same journal.

What’s going on? PubMed has started indexing AGING, the open-access biogerontology journal that launched a little less than a year ago, and several issues at once were added to the database (and, therefore, to my feeds). This was announced last year but it’s taken a while for the full catalog of articles to make it into the database.

Getting indexed is an important step for a new publishing effort, since if an article isn’t in PubMed it’s basically invisible to scholars around the world. So, congratulations are in order.

Looking over the last year of AGING, I’m reasonably impressed. For such a new journal, they’re getting lots of papers from major labs, and publishing quite a few nice studies. This bodes well for measures of importance such as impact factor and article-level metrics (though neither is yet available for AGING).

The great thing about open-access journals is that content is free to everyone — so if the lack of journal subscriptions has been holding you back, now is a great time to jump into the aging literature. AGING is highly technical, but it represents a rare confluence of universal accessibility and a high concentration of aging-related articles, so it’s a good place to start exploring.

 

“What if you could think a thought at the world and have the world think back?”

In collaboration with the estimable Vivan Siegel, I’m writing a series of op/ed articles on the future of scientific publishing. The first of these was about the challenges of filtering the scientific literature. The second piece, explores the prospect of using “Web 2.0″ approaches to accelerate scientific progress. The article starts from the assumption that sharing is a good thing, and considers the ways in which social networking and other types of internet-powered tools might help scientists share more efficiently. We begin with a description of a long-term, somewhat pie-in-the-sky goal before returning to earth to evaluate the current state of the art (link):

This revolution will be digitized:
online tools for radical collaboration

But let us entertain the thought that the ideal size of the collaborative unit might be much larger than the average research group of today, and that we lived in a world in which scientific efforts were organized around this principle. How might evolving information technologies allow science to progress more rapidly? In such a world, we might choose to organize scientific efforts differently: not according to physical proximity in labs or departments, but rather by aptitude, expertise and availability. Rather than thinking of projects as the virtual property of small groups, we would simply broadcast ideas (or data) until they reached the right person(s) to take the next step. …

In other words, what if you could think a thought at the world and have the world think back? What if everyone in the world were in your lab – a ‘hive mind’ of sorts, but composed of countless creative intellects rather than mindless worker ants, and one in which resources, reagents and effort could be shared, along with ideas, in a manner not dictated by institutional and geographical constraints?

There’s another piece in the works, probably about the publication of results that fall below the threshold of a “publishable unit”. Others have written extensively on this subject, and there are a number of solutions to this problem out in the wild, so I’m currently absorbing all of that information and determining whether I have original thoughts on the subject.

Patil, C., & Siegel, V. (2009). This revolution will be digitized: online tools for radical collaboration Disease Models and Mechanisms, 2 (5-6), 201-205 DOI: 10.1242/dmm.003285

 

Why We Blog

A couple of months ago I lamented that scientific blogging would probably be unable to serve as an effective “filter” for the scientific literature. Scientists struggle to keep up with the literature in their own field (let alone related fields), and it would be nice if someone could pre-screen emerging papers in a way that would decrease the time and effort involved in keeping current. For a variety of reasons, I think it’s unlikely that science blogs will be able to serve this function.

But filtering isn’t the only justification for the existence of science blogs, as is made clear by a recent bumper crop of blog posts and articles about science blogging. Blogging can help an individual scientist share ideas with colleagues and spread the word about one’s own work. Some see blogs as increasingly essential to the process of self-promotion, whereas others see an opportunity to fill growing holes in the fabric of conventional science journalism. There is a consensus that blogging is less prestigious than other kinds of scientific publishing, but as participation grows, this may change.

In rough order of the ideas presented in the previous paragraph, I present these pieces here for your delectation:

• It’s good to blog (Nature editorial)
• Is it becoming dangerous to not blog? (Useful Chemistry)
• Scientific blogging: Ignore it and be ignored? (Depth-First)
• Filling the void (Nature editorial)
• Science journalism: Supplanting the old media? (Nature news feature)
• Science Blogging plus/vs Science Journalism (A Blog Around The Clock)
• How to broaden the reach and legitimacy of blogging to practicing scientists (Terra Sigillata)

 

Reflect: Linking protein names to rich content, as you read

Continuing with my current fascination with cool ways to enhance the experience of searching and engaging the literature online…

Deepak Singh at business|bytes|genes|molecules tells us about Reflect, a new tool for adding value to online articles:

Essentially, Reflect is an entity extraction engine with a specific purpose, recognizing molecular entities, both compounds and proteins. I have spoken at length about the value of entity extraction, and the availability of a service like Reflect just shows you how useful something like this can be. Using either the Reflect website where you can enter a URL, or the Firefox plugin, you can use extract molecular entities on a webpage quite easily. The service highlights recognized entities, and using your mouse you can get additional details as shown in the screenshot below.

Reflect identifies the names of proteins/genes or small molecules that appear in a body of text and generates a live link to a floating window containing informations (and further linkage) about that entity.

You can check it out at the Reflect website.

I had a lot of fun plugging in blog posts from Ouroboros and seeing what Reflect thought of them. It did a great job with genes and a fairly good job with small molecules, though the higher false positive rate in the latter case was a little disappointing (identifying words as small molecules that weren’t, and linking to things that aren’t small molecules at all, like the word “reset” that appears in a graph about something else).

(P.S.: By the way, Reflect was the winner of the Elsevier Grand Challenge, and its development may have been motivated by the incentive of the prize. In light of that, I just want to clarify that I still think Elsevier is the devil.)

Update: The developers of Reflect have a preprint up at Nature Precedings. Thanks to Hilary Spencer for the heads-up.

 

The plot thickens: More fake journals in the Elsevier/Merck story

Earlier in the week we learned about Elsevier publishing a fake “journal” for the pharmaceutical giant Merck. The Australasian Journal of Bone and Joint Medicine presented itself as a peer-reviewed publication with a prestigious editorial board, but in reality consisted entirely of reprinted articles and material favorable to Merck products like Fosamax. I assume that copies of the journal were used as marketing material, stuffed into conference schwag bags and clinicians’ hospital mailboxes — one step down from those ads that look like single-column articles in the newspaper, since neither Elsevier nor Merck took the trouble to write “ADVERTISEMENT” in little block letters at the top of AJBJM.

Now, a cunning bit of “forensic librarianship” has revealed that this may have been merely the tip of the iceberg, and that AJBJM may have been one of a large stable of fake journals (“Excerpta Medica”), all devoted to accomplishing similar goals in different fields. In other words, Elsevier didn’t run a few copies of a bogus journal — it ran a whole bogus label. The original analysis can be found at Bibliographic Wilderness, with commentary at Caveat Lector and Open Reading Frame.

(Hat tip to @kaythaney of Science Commons, whose tweet this morning pointed me in the direction of this news.)

 

Elsevier publishes fake journal for Merck

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.

 

Science radio for scientists

There are a number of good science-related shows on Public Radio: Science Friday, Radiolab, and Tech Nation top my personal list, and there are many others. This type of programming is an important means of disseminating scientific ideas to a general audience, and as I scientist I think I enjoy the shows more than the average listener. Still, I often find myself wanting more: more detail, more description of methods and controls used to obtain results, more erudite discussion about the context of a given finding within the larger edifice of scientific inquiry. More.

So it’s been with great satisfaction that I’ve discovered several podcasts administered by scholarly journals:

• Nature Podcast
• Science Magazine Podcast
• Science Signaling Podcast (registration required)

This is “science radio” but with a twist: the intended audience is us. The producers aren’t targeting a general audience, and as a result they’re free to include highly technical content. Especially with the Science Signaling podcast, which often involves an interview with the author of a recent paper featured in STKE, the stories sound more like a lab group meeting than a radio show.

Granted, this comes at a cost: the journal podcasts have high production values but not quite as high as on general-audience NPR shows, and sometimes the phone interviews sound like they were conducted underwater, making it harder to listen in noisy environments like a car moving at 70 MPH down a California freeway.

But that’s a small price to pay. This is exciting! Podcasting is democratizing broadcasting to the extent that people are creating high-quality professional programming for a small minority of people diffusely scattered all over the world.

What are you waiting for? Check it out. All three of the podcasts I’ve mentioned are available (for free) via iTunes and the websites linked above

Two questions:

1. Does anyone else have a science-for-scientists podcasts they’d like to share?
2. When will an open-access journal step up to the mike?

 

Best journal? Depends on whom you ask

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.

 

Cognition: Using natural language to query Medline semantically

You know by now that I love literature search tools (check out the small but growing “Links: Search” category in the right-hand column on the main page). I am strongly motivated by a desire to filter the huge and growing biological literature so that I can find the most relevant papers with the least amount of effort. Therefore, I’m always curious when I hear of a tool that purports to do an old task (searching Medline) in a new and unusual way.

A company called Cognition (“Giving technologies new meaning”) claims to enable the user to use semantic natural language processing to search the literature. Here’s their elevator pitch:

Cognition’s Semantic Natural Language Processing (NLP) technologies add word and phrase meaning and understanding to computer applications, providing a technology and/or end-user with actionable content based upon semantic knowledge. This understanding results in simultaneously much higher precision and recall of salient data within the universe of possible results. Cognition’s Semantic NLPTM makes technologies and applications more human-like in their understanding of language, thereby resulting in more robust applications, greater user satisfaction and new capabilities available for exploitation. On the Web in particular, powering applications with Cognition’s semantic understanding technology drives these applications ever closer to Web 3.0 (the semantic Web).

They have various commercial applications for sale but their semantic MEDLINE product is freely available on the web.

I’m not going to lie to you — it’s pretty great. You can ask the interface a real English question, like “Which genes are expressed in senescent fibroblasts?” and get real answers. (OK, to be fair, it’s fine with just “genes expressed senescent fibroblasts”, but I enjoy being able to use my native language when I talk to a computer.) I encourage you to play around with it; it’s fun.

One feature that seemed promising at first didn’t seem to work well at all. On the right-hand side of the search results screen are a series of dropdown menus; each menu contains several different meanings for keywords within the query. The idea is that one could refine a search by choosing the specific meaning of an ambiguous term, rather than having to slog through a search result that allows all meanings of the term in question. Unfortunately, this feature doesn’t deliver. Allow me to illustrate.

In the query example mentioned above, the dropdowns allowed for six meanings for the word “express”. The results had initially come back with one of these meanings (“6. to make a protein in bacteria or cells in culture”) already selected (I assume because this meaning gave the largest number of hits: ~12 papers, a totally manageable number, all of which were good answers to the question).

That definition is OK but I felt like another meaning (“5. to make a protein from a gene”) was slightly closer to the original intent, so I chose that definition and resubmitted. This culled the list down to only 1 paper, which wasn’t a very good match, and eliminated all the excellent answers from the earlier version of the search.

I can’t even begin to guess how the “sense” of a word is determined algorithmically by the Cognition software, but I do know that the outcome of my twiddling didn’t conform to my intuitive understanding of the words involved — which, after all, is the whole point of natural language processing. So I have to list this under “room for improvement”.

Which is all just to say that this search engine isn’t perfect yet — but please don’t let that stop you from checking it out. I like a lot of things about Cognition semantic Medline, and I’m going to be using it a lot.

What do you think? I’d love to hear about other people’s experience with the software.

(Hat tip to Code-Itch. Yes, I’ve had that post bookmarked since September.)