This evening just after sunset, the crescent Moon was positioned in a beautiful triangular alignment with Venus and Jupiter. (view the skymap) I took the kids out to try using the binoculars to see the Moon — which they certainly also just used to walk around the yard finding one another! — and to talk a little about the two planets and how cool it is that we can see them with our own eyes.
These slightly in-focus images were taken with a very simple Nikon CoolPix S8100 auto focus in night landscape mode on a tripod.
We have just begun reading the recently released review book, “Connectome,” from Sebastian Seung of MIT. The basic notion of the book is that you are the emergent result from the interconnections of some 100 billion neurons in your brain. “You are your connectome.”
This is not a novel idea at its most basic level, however, Dr. Seung is bringing this exciting hypothesis to a broader popular understanding, which will help guide future generations of appreciation for the utterly incredible mass of flesh lodged in our skulls.
Mapping the complete interconnections of neurons remains to this day a daunting task for neuroscientists, but a task in which Dynamic Patterns Research is particularly interested. It took decades of manual labor by White, et al. to map the mere 302 neurons in the wee little worm C. elegans. The complete structural architecture of its neuronal connections–it’s connectome–is now readily available for research and exploration. Now, imagine extending this task to the human brain, but plan on taking a 300+ million-fold leap that would necessarily require technological advances not yet fully realized.
Despite this apparent impossibility, there is just something awesome about the human brain that makes us who we are, and we just have to plow forward and try to discover more. There’s something “in there,” or, something that emerges from what’s inside that especially sets us apart from all other known life on this planet. If we could tap into that “something,” then we might just have a better understanding of who we are as an organism. Tapping into the structure of our brains–our connectome–is the best place to start.
Watch Sebastian Seung’s TED Talk, “I am my connectome.” :: July 2010
It seems that we will have to patiently wait for technological advances–although they are increasing at accelerating rates–to get us to the ability to efficiently map our personal connectomes. In the mean time, we do have an extraordinarily powerful tool that is ready today to help with developing procedures for mapping neuronal connections in living brains: this tool is the brains of citizen scientists.
It is from the laboratory of Sebastian Seung and enthusiastic collaborating scientists who bring to the citizen science community the exciting opportunity to directly map interconnections in neural tissue. The online system is called eyewire, and provides images from 3-D stacks of neuronal tissue from the retina and guides citizen scientists through a process of identifying connecting features. By visually evaluating two-dimensional cross-sections of tissue images created with electron microscopy, users work through the layers by recognizing connecting features between each image. The identified cross-layer features from the efforts of citizen scientists can then be reconstructed into a three-dimensional structural map of the neurons–and their connections–throughout the tissue.
A waiting list is currently in place to control the influx of interested citizen scientists, so Dynamic Patterns Research has not yet had the opportunity to test out the system (but, we are on “the list”!). We hope to be in soon so that we can participate in this great project that is at one of the core interests of Dynamic Patterns Research. If you are already participating now, please let us know what you think of the system.
Your brain is the most awesome thing in the Universe. We know so little about it, but we are on the cusp of a revolution in a new understanding of what it is and how it works. Now, citizen scientists can be an integral part in this revolution so that anyone can scientifically better know their inner self.
Accessing the absolute latest in scientific communications directly by the independent amateur or citizen scientist has been a financially daunting prospect for decades; practically impossible. The top research journals carry high subscription rates (price out for yourself one of the best), and the science professional relies on their employing institution to cover the costs of access through the resident library budget, save for a personal subscription to their most treasured journal.
Of course, a great deal of front-line scientific research is funded by governmental agencies, which translates into taxpayer dollars. So, shouldn’t the taxpayer be able to access the fruits of their financial investments? Or, should the taxpayer just expect to later benefit from the results of research after implementation by companies and institutions? To avoiding opening a messy can of political warfare here, we will instead focus on the fact that there has been a rapidly growing trend from part of the scientific publishing industry itself to provide open access (“OA”) to the most recent articles from scientific research. This trend has been influenced from both the scientific authors and their funding agencies.
A traditional culture about to change
The traditional business model for scientific journal publications is for professional scientists to submit their draft papers to a group of peers — typically in related fields of expertise — who brutally review, critique, and feedback on the work. Revisions are made until acceptance of the peers is reached and the paper is published in a future volume of the journal. Individuals or, most typically, institutions then pay for access to obtain printed and digital versions of the published papers. Prices for access are high. It’s expensive to pay for the printing, editing, and the peer review process for such technically challenging and critical information and a bit of profit has to fit in there as well.
To change this culture and allow for the free dissemination of scientific advances, new models are being developed and tested. Money still has to be made, of course: the expenses are still present, even if the published materials are openly available to the readers, and even if they are solely digital presentations. One such model requires the author to pay a significant fee to be published (assuming they passed muster with the peer review), or if the author can’t bite the financial bullet, then their funding grant money or institution can help out with the bill. This approach is referred to as “Gold OA.”
An alternate version, which fits into the traditional subscription publishing model, is self-archiving of published work by the individual author. If the journal offers this permission, which is more often now required by funding agencies, the author maintains a digital copy of the work on a personal or institutional resource separate from the publisher. This “Green OA” approach is dependent on the individual author’s follow-through on archiving and requires a separate cataloging service to provide any sense of organization.
The OA Explosion
The Open Access movement significantly expanded during the first decade of the 21st Century. A detailed study of this growth of open access by Laakso, et al.  published in 2011 (available as open access, of course) found that about 19,500 open access articles in 740 journals were available in 2000, and by 2009, nearly 192,000 articles could be accessed for free in 4,769 journals.
The Public Library of Science (PLoS), starting simply as an advocacy group in 2000 and then expanding to an OA publisher in 2003, has been arguably the most successful innovator and proponent of the open access movement in scientific communications. PLoS currently follows the model of author-pays-to-publish-post-peer-review and has been publishing cutting edge scientific research featuring seven journals with tens of thousands of peer reviewed articles.
Quite recently announced (January 30, 2012), an even more extreme model of open access will begin later in 2012 that utilizes post-publishing open peer review with the ability to revise published work after releasing it to the public. This new approach being launched by the “Faculty of 1000” (F1000) group will require a similar pay-to-submit model. Called F1000 Research, this system will also allow for an “open” format for how information is presented, which may include poster presentations, traditional written articles, graphs and charts, and even raw data. The published information will be immediately available after a simple formal check from F1000 advisers that the submission is scientifically relevant, and registered readers will have the opportunity to provide comments and ratings.
The other side of OA
On the other hand of this seemingly exciting new trend for the seeker of open knowledge, the author-pay-to-publish model can potentially be a major hurdle for independent amateurs wanting to publish their work in peer-reviewed journals. The fees certainly are steep and it might be assumed that the majority of amateurs do not have the personal funds to move their work through the publishing system. Just as major funding agencies, like the National Science Foundation, require and provide assistance with publication fees for open access availability for scientific professionals, the independent researcher will need to search for outside financing to support the work if it is to intermingle with the professionals.
Although it certainly isn’t required that an independent publish their work through a traditional or open access route, it is the peer-review process that really is required to vet the work and help develop it into a final form that provides accurate and valuable information to the rest of the world. The principal of the peer-review process is a critical resource for the scientific community to ensure that rigorous information is disseminated, and the independent should not be outside of this, or at least some form of, quality control. If the independent wants to be taken seriously, they should try to play with the majors, and deal with the financial burdens in innovative ways.
So, it seems that the long-term success of Open Access is rather exciting for the amateur and citizen scientist. It is certainly exciting for Dynamic Patterns Research, which is not a large academic or commercial organization with massive budgets to cover massive journal subscriptions. However, the OA development is not a straightforward path for the future of the business of scientific publishing. Quality is never really free, and for organizations to provide this important peer review and publication services that we need and desire, expecting it to be free might mean significant sacrifices somewhere else.
The debate between the traditional and OA models has been brewing for years, and although growth in OA resources has been substantial in recent years, there is still a long way to go to discover that secret formula for a sustainable business model for Open Access publishers. The premier publishing group, Nature, (and rather expensive journal publisher) hosted a web debate forum  in 2004 on the issue of access to scientific literature. In particular, Kate Worlock wrote a “pros and cons” review describing many important concerns that OA would bring to publishers, all of which would directly impact the end-user.
Most notable, in the digital age publishing is heavily dependent on new technologies, and advances and innovations require great investments to develop and implement. With the popular pay-per-article model at current typical rates ($500 to $2,500), publishers will expect a great deal less revenue to meet operational expenses, invest in the future, and make a profit. And, making a profit is not an evil activity: it is from this profit that future growth and beneficial investments can be made possible. With reduced profits, the potential lack of investment ability could bring scientific publishing to stagnation and irrelevancy in the marketplace, obviously resulting in a direct negative impact on the scientific community.
As suggested above, although author fees could be covered by funding sources, host institution libraries might also be on the hook to support their resident research. The open access payment model only shifts the costs from one line item category to the next, and as fees grow higher in the future, budgets may continue to be equally stressed. In addition, larger research-focused academic institutions with significant output might end up subsidizing the pay-per fees from smaller teaching-centric colleges or commercial organizations with fewer annual submissions from their faculty.
Possibly the most critical concern is that many important scientific journals are published by academic societies which host additional activities and benefits to the scientific community. The profits from a society’s publishing division allows for the development of membership programs, conferences, and other benefits. With a loss of publishing income, member groups will have to make up revenue elsewhere, likely from the pocket books of the members themselves.
The Federal Government’s Conflicting Approach
As already mentioned, the United States federal government has provided mandates for research funded by taxpayer money to be published in an openly accessible way. For example, the National Institutes of Health requires all of their funded research to be listed with the government-hosted PubMed Central. However, just recently on December 16, 2011, a bill was introduced in the House of Representatives called the “Research Works Act,” which proposes to restrict the existing mandate of network dissemination of published work — without the publisher’s prior consent.
Certainly this a tantalizing development, which one might cynically think that the publishers have something to do with it … and, one might be right: The Association of American Publishers announced strong support for the legislation. A thorough review of this complex debate was offered a couple of weeks ago by The Chronicle of Higher Education , and it is interesting to note that many academic publishers, like MIT Press and Oxford University Press, have already expressed their opposition to the AAP’s position and are clearly trying to distance themselves from the anti-open-access side of the debate.
The primary point from the publishers is that although federal funds certainly initiate some of the research work, it is only through the independent professional efforts of the publishers providing peer-review, analysis, editing, and the final development of the work in a format that is desired by the community, that the research work can even be presented for others to access. And this independent presentation should not be controlled by the government on a case-by-case basis.
Making OA revered
With all of the issues facing scientific publishers to deal with the inevitable advancement of Open Access, it will still largely be up to the scientific authors themselves to make the transition to sustainable OA complete. In the culture of academic scientific research, recognition is still critical as the old mantra of “publish or perish” still drives many young post-docs and non-tenured faculty. Listing twenty articles with unknown journals might not provide the needed prestige as one killer article in the top journal in the field.
Scientists are still getting a handle on what OA resources are available today, and, although many may strongly support their work to be freely available, there still comes a necessarily selfish point where one’s own career and security is paramount, and selecting the right journal for submission becomes vital. A detailed survey from 2006 of researchers was reviewed by Alma Swan  describing the current state of mind of authors in their selections of journals and what their concerns and ideas are toward Open Access. Of particular note, many researchers still are not aware of the available OA resources in their field, as they likely remain focused on the publications they “grew up with” during their own education. With the current generation of new scientists, it will then be up to the OA publishers to bring their journals to distinction both in the view of their respective scientific communities and in the eyes of the individual scientists working in the field.
Dynamic Patterns Research has developed a concise reference list for reaching open access scientific knowledge, and tries to highlight the most important resources currently available. This reference will evolve as major changes occur in the availability of resources. Not only will DPR be utilizing these resources frequently, but we hope that it will provide an exciting portal for our readers into some of the top scientific advances happening today.
Update: February 17, 2012 A significant group of professional mathematicians are taking a stand against a major publisher. It seems like a key issue is the fact that many professional scientists are providing critical editorial services for the publishing houses — as volunteers — while the publisher’s profits are increasing at significant rates.
“Mathematicians Organize Boycott of a Publisher” :: New York Times :: February 13, 2012 :: READ