Michael Eisen
I'm an evolutionary biologist at UC Berkeley and an Investigator of the Howard Hughes Medical Institute. My research focuses on the evolution and population genomics of gene regulation in flies, and on the ways that microbes control animal behavior. I am a strong proponent of open science, and a co-founder of the Public Library of Science. And most importantly, I am a Red Sox fan.

"The infinite bookshelf is already a problem for us. To add to the fun, once we enter the world of ebooks, nothing ever goes out of print. So works going back many years or decades are presented with equal priority to the latest new titles.

Upshot: we badly need better curation. Amazon and their competitors could present the results of author searches pre-sorted by time since publication and by language and by series. But that's barely a start.

Genre, in the ebook space, is a ball and chain. It stops you reaching new audiences who might like your work."

Some typologies on length and style of fictional series.

"After I recommended that the major publishers drop mandatory DRM from their ebook products, I realized that my essay had elided a bunch of steps in my thinking, and needed to reconsider some points. Then I realized that it's not a simple, straightforward argument to make. Consequently, I ended up writing another essay, although I've tried to summarize my conclusions below. "

As a way of fighting unauthorized sharing of digital files, DRM is particularly stupid. It not only doesn't work -- DRM is always broken, and DRM-less versions quickly produced -- it also makes the official versions less valuable than the pirated ones, since they are less convenient to use in multiple ways. As a result, DRM actually makes piracy more attractive, which is probably why most of the music industry eventually decided to drop it.
Sadly, the world of ebooks seems unable to learn from that experience, and insists on making the same mistakes by using DRM widely. But it turns out that there are even more problems in the publishing domain, as this fascinating tale of how DRM acts as a barrier to entry in the online bookstore market makes clear

"Making revisions in response to referees' comments can be challenging and sometimes discouraging. A pragmatic step-by-step approach can help overcome barriers."

"Since its inception in the early part of the 20th century, the theory of quantum mechanics has consistently baffled many of the great physicists of our time. But while the ideas of quantum physics are challenging and notoriously weird, they seem to capture the public imagination and hold an enduring appeal. Evidence of this comes in part from the numerous popular-science books that have been written on the topic over the years. This episode in the Physics World books podcast series looks at the popularity of quantum mechanics in science writing"

"TJM.org is the website of Tim McCormick. I work for HighWire Press, Stanford University, in Palo Alto, CA, as Sr. Product Manager for Emerging Content. Also reader, writer, library student."

Annotated link http://www.diigo.com/bookmark/http://www.techdirt.com/articles/20120330/12402418305/why-missing-20th-century-books-is-even-worse-than-it-seems.shtml

"To understand newspapers’ 15-year attachment to paywalls, you have to understand “Everyone must pay!” not just as an economic assertion, but as a cultural one. Though the journalists all knew readership would plummet if their paper dropped imported content like Dear Abby or the funny pages, they never really had to know just how few people were reading about the City Council or the water main break. Part of the appeal of paywalls, even in the face of their economic ineffectiveness, was preserving this sense that a coupon-clipper and a news junkie were both just customers, people whose motivations the paper could serve in general, without having to understand in particular."

Nature Education is delighted to announce the launch of a new series of affordable, high quality interactive textbooks in college-level science. The first textbook in the series, Principles of Biology, is intended for university-level biology courses. The first title in the series is Principles of Biology, intended for introductory biology classes.

A collaboration of scientists, artists, students, and anyone else interested in science, this project produces small zines and web comics on a variety of topics . Read online, download zines, and share your ideas here!

"Although the “mass media era now looks like a relatively brief and anomalous,” it is seen as normal by those who have spent their careers in those organisations. Those stuck in the “old paradigm” have great difficulty imagining and accepting the “new paradigm.”

Scientific journals are lagging behind newspapers, but they are surely on the same course. Many find unacceptable the domination of a few journals and the huge profits made by some publishers from the scientific value produced by others, and the open access has begun for these and other reasons. Open access articles are increasing rapidly, and just in the past few years we have seen the appearance of many “megajournals” like PLoS One and BMJ Open, which are aiming to publish rapidly after light peer review that does not attempt the largely impossible job of “spotting winners” but leaves readers to decide. "

"CKAN is the Comprehensive Knowledge Archive Network, a registry of open knowledge packages and projects (and a few closed ones).

CKAN makes it easy to find, share and reuse open content and data, especially in ways that are machine automatable."

"Scientific publishing as it stands is an inefficient way to do science on a global scale. A lot of time and money is being wasted by groups around the world duplicating research that has already been carried out. FigShare allows you to share all of your data, negative results and unpublished figures. In doing this, other researchers will not duplicate the work, but instead may publish with your previously wasted figures, or offer collaboration opportunities and feedback on preprint figures."

More concerns about publishing, e-books, licensing, ownership, etc.

Detailed discussion of the HarperCollins proposal to limit e-book library checkouts to 26.

"But in the end, most authors have themselves to blame. Having immersed themselves in a subject, almost all succumb to the hubristic idea that they can find new and unique ideas for solving intractable problems. They rarely do, and even works that do usher in specific reforms or broad social transformations — from “The Jungle” to “The Feminine Mystique” — do so by raising awareness about an issue, not by providing ready-to-go blueprints.

Yet solutions seem to be what our national temper demands. “It is one of the peculiar intellectual accompaniments of democracy that the concept of the insoluble becomes unfashionable — nay, almost infamous,” Mencken wrote in “Notes on Democracy” (1926).."

"The decision highlights a tension between the need for rigorous peer review of scientific research and the desire to provide as much data as possible to the scientific community.

"More data, in and of itself, is always a good thing -- if there aren't adverse effects," said Maunsell, who is also a neuroscientist at Harvard University. But peer review was becoming less effective because many reviewers failed to evaluate the supplemental materials, which the journal wasn't even required to provide, he explained. "We were taking a hit on peer review for something that wasn't formally our responsibility." "

"The tipping point for digital textbooks is defined as that point on the industry/product continuum at which current financial variables and market factors make the eventual dominance of digital over print an inevitable outcome within 5-7 years. It is our argument in this report that the Higher Education textbook industry in the U.S. is now at that tipping point. In support of this argument, we will discuss both the current status of the Higher Education textbook market as well as the primary market/financial factors influencing its evolution."

"The loss of ownership creates a downward spiral in value, and erodes the very notion of paying for books at all.

Defining ownership down. We used to own our books. With most ebooks we own them in name, but effectively we lease them. As Jane documents, the slide toward more and more attenuated concepts of ownership continues."

"champions books from around the world that are..underappreciated"

"This paper presents the first meta-analysis for the inter-rater reliability (IRR) of journal peer reviews. IRR is defined as the extent to which two or more independent reviews of the same scientific document agree."

"Which academic articles get published in the more prestigious journals is a pretty random process."

"Open Research Computation publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers in any field. Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries. Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software. "

Articles receiving the Open Access treatment received significantly more readership (as measured by article downloads) and reached a broader audience (as measured by unique visitors), yet were cited no more frequently, nor earlier, than subscription-access control articles. A pronounced increase in article downloads with no commensurate increase in citations to Open Access treatment articles may be explained through social stratification, a process which concentrates scientific authors at elite, resource-rich institutions with excellent access to the scientific literature. For this community, access is essentially a non-issue. The real beneficiaries of Open Access are the communities that consume, but do not contribute to, the scientific literature.

So let’s say for the sake of argument that you can narrow your choices to two journals, roughly equivalent in prestige. Here’s how you might choose between them...

OASIS aims to provide an authoritative ‘sourcebook’ on Open Access, covering the concept, principles, advantages, approaches and means to achieving it. The site highlights developments and initiatives from around the world, with links to diverse additional resources and case studies. As such, it is a community-building as much as a resource-building exercise. Users are encouraged to share and download the resources provided, and to modify and customize them for local use. Open Access is evolving, and we invite the growing world-wide community to take part in this exciting global movement.

Award winning SHERPA is investigating issues in the future of scholarly communication. It is developing open-access institutional repositories in universities to facilitate the rapid and efficient worldwide dissemination of research. SHERPA services and the SHERPA Partnership are both based at the Centre for Research Communications at the University of Nottingham.

By open data in science we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to software or use them for any other purpose without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. To this end data related to published science should be explicitly placed in the public domain.

Formally, we recommend adopting and acting on the following principles:

On August 11, the Journal of Neuroscience published an Announcement Regarding Supplemental Material by Editor-in-Chief John Maunsell. In it John Maunsell announces that the journal in November will stop accepting supplementary material in article submissions. The announcement has lead to an extensive discussion in the science blogosphere with a number of relevant posts listed below

he basic logic is that sharing work with the general public is a means of circumventing the "serious" peer review process, and as such is necessarily "unserious." The problem with that explanation is that the peer review process is itself a monument to unseriousness.

As originally identified, the Matthew effect was construed in terms of enhancement of the position of already eminent scientists who are given disproportionate credit in cases of collaboration or of independent multiple discoveries. Its significance was thus confined to its implications for the reward system of science. By shifting the angle of vision, we note other possible kinds of consequences, this time for the communication system of science. The Matthew effect may serve to heighten the visibility of contributions to science by scientists of acknowledged standing and to reduce the visibility of contributions by authors who are less well known. We examine the psychosocial conditions and mechanisms underlying this effect and find a correlation between the redundancy function of multiple discoveries and the focalizing function of eminent men of science—a function which is reinforced by the great value these men place upon finding basic problems and by their self-assurance.

Since the publication of Robert K. Merton's theory of cumulative advantage in science (Matthew Effect), several empirical studies have tried to measure its presence at the level of papers, individual researchers, institutions, or countries... Using an original method for controlling the intrinsic value of papers—identical duplicate papers published in different journals with different impact factors—this paper shows that the journal in which papers are published have a strong influence on their citation rates, as duplicate papers published in high-impact journals obtain, on average, twice as many citations as their identical counterparts published in journals with lower impact factors. The intrinsic value of a paper is thus not the only reason a given paper gets cited or not, there is a specific Matthew Effect attached to journals and this gives to papers published there an added value over and above their intrinsic quality.

Matthew Nisbet remarks to University Research Magazine Association. "The shift over the past decade has been away from a transmission and science literacy model to a view focused on public engagement, which means empowering, enabling, motivating, informing, and educating the public around not just the technical but also the political and social dimensions of science....but remembering what the public does with the acquired knowledge, motivation, skills, and resources and how they participate on the issue, is up to them."

The professoriate may be more liberal politically than the most latte-filled ZIP code in San Francisco, but we are an extraordinarily conservative bunch when it comes to scholarly communication.

We don’t need more filters or better filters in scholarly communications – we don’t need to block publication at all. Ever. What we need are tools for curation and annotation and re-integration of what is published. And a framework that enables discovery of the right thing at the right time. And the data that will help us to build these. The more data, the more reseach published, the better.

The guardians of learning can no longer allow the Library to be surrounded with barbed-wire fences. It is time for the academe to liberate scholarship

No, these ideas are worthy, but they don't get to the real problem. It's not like all the crappy papers are coming from younger faculty who are bucking for tenure, you know. Plenty more are emitted by well-entrenched groups who just generate things that no one ever really wants to read. I think we've made it too possible for people to have whole scientific careers of complete mediocrity.