Neuroscience – P2P Foundation https://blog.p2pfoundation.net Researching, documenting and promoting peer to peer practices Thu, 14 Jun 2018 17:26:09 +0000 en-US hourly 1 https://wordpress.org/?v=5.5.15 62076519 Do we need a new myth, or no myth? https://blog.p2pfoundation.net/do-we-need-a-new-myth-or-no-myth/2018/06/21 https://blog.p2pfoundation.net/do-we-need-a-new-myth-or-no-myth/2018/06/21#respond Thu, 21 Jun 2018 09:00:00 +0000 https://blog.p2pfoundation.net/?p=71440 This is the true, biggest challenge I’m facing as a writer and thinker. Myth: Do we need a new one, or do we need to dispense with them altogether? I used to direct theater. I left the theater because I got increasingly dissatisfied with its reliance on stories with clear beginnings, middles, and ends. Aristotle’s... Continue reading

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This is the true, biggest challenge I’m facing as a writer and thinker. Myth: Do we need a new one, or do we need to dispense with them altogether?

I used to direct theater. I left the theater because I got increasingly dissatisfied with its reliance on stories with clear beginnings, middles, and ends. Aristotle’s narrative arc with its rising tension, crisis, and catharsis wasn’t just predictable, but dangerously limiting. Things look bad, but as long as you accept the hero’s solution, everything gets solved and you can go back to sleep. Crisis, climax, and sleep – the much-too-male approach to everything from sex to religion, capitalism to communism.

I left theater for the net, which seemed to offer a more open-ended, connected form of sense-making. So I wrote about that, and the possibilities this opened for everything from economics to society. In my books, I usually tried crashing a set of myths – but then usually offer some alternative at the end. So in my religion book I smashed the myth of apocalypse and salvation, but offered an alternative path toward consensus, progressive collaboration. In another, I exposed the fallacy of hand-me-down truths, but then offered an alternative of collective reality creation. In a graphic novel, I undermined the authority of the storyteller (me) and then have a character hand a pencil to the reader as if through the page. In a book on Judaism, I smashed the idolatry that infected Judaism, but promote a new, provisional mythology of communal sense making. In my books on economics, I crash the cynically devised mythologies of capitalism and corporatism, but offer a new one of circular economics and sharing. In my Team Human podcast, I regularly crash the myth of the survival of the fittest individual, but offer a new evolutionary history of interspecies cooperation.

Better myths, like cultural operating systems, should yield better results. But if they are all myths, are they all ultimately destructive?

Even science falls into the trap. We get an idea – say, that agriculture was a wrong turn – and then “see” evidence that hunter-gatherers worked fewer hours than we did after the invention of agriculture. I have even quoted this ‘fact’ from neuorscientist/sociologist Robert Sapolsky, and others, before realizing it’s based not on science but a story.

People and institutions come to me to help develop a new myth for 21st Century, for digital times. But mythology feels more like the product of a television media environment – imagery and hallucination. The digital media environment is about fact. Memory. It all takes place on memory. That’s why we’re fighting less over who believes what, than what really happened. Where did humans come from? Are things getting better or worse? And the myths are no longer adequate. The stories are not up to the task.

I think Team Human’s job may be to find ways to work together without an overriding mythological construct. We should do something in a new way because it’s just better, on an experiential, practical, or scientific level. Growing food in a certain way – not because it’s connected to Mother Gaia, but because it keeps the soil alive. Not a metaphor. Reality.

If we are destined to think and communicate in myths – if that’s our nature – then we can at least accept that we all use stories to understand the world. Understanding another person means listening to their story – and sharing one’s own – but accepting that both are just stories. Myths are ways of connecting the dots between the moments of human experience. They create a sense of continuity and purpose, even though there may be none. Or myths may help each of us trace a path of cause-and-effect through a maze of reality that is so interconnected it would just overwhelm us to comprehend it in its entirety. We each make our own myth to explain the journey we happened to take. But it’s more of a convenience than a reality. And we can look back on our lives, and come up with a new myth to explain it. The myth is not for someone else, it’s for ourselves.

Of course we can still listen to one another’s perceptions and sense-making – and then gain some empathy for why they’re thinking and acting the way they do – without necessary believing any of it. And, maybe more importantly, without trying to get them to exchange their mythology for ours. Understanding other people’s myths, unconditionally and without being threatened by them, has helped keep me sane during this particularly tumultuous cultural moment.

So what’s Team Human’s job: to come up w a new myth? Or break them all? Whatever we decide, it should be a conscious choice.

This essay started as a monologue on TeamHuman.fm. Please come listen.

Photo by giveawayboy

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Patterns of Commoning: OpenSPIM, A High-Tech Commons for Research and Education https://blog.p2pfoundation.net/patterns-of-commoning-openspim-a-high-tech-commons-for-research-and-education/2017/08/11 https://blog.p2pfoundation.net/patterns-of-commoning-openspim-a-high-tech-commons-for-research-and-education/2017/08/11#comments Fri, 11 Aug 2017 08:00:00 +0000 https://blog.p2pfoundation.net/?p=67063 Jacques Paysan:  Scientific and medical research critically depends on being able to observe very small structures that are invisible to the naked eye. Neuroscientists seeking to find cures for injury-induced paralysis, for example, may want to be able to observe the axons of regenerating neurons on coated nanowires. This kind of experiment often requires extremely... Continue reading

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Jacques Paysan:  Scientific and medical research critically depends on being able to observe very small structures that are invisible to the naked eye. Neuroscientists seeking to find cures for injury-induced paralysis, for example, may want to be able to observe the axons of regenerating neurons on coated nanowires. This kind of experiment often requires extremely high-powered and sophisticated microscopy. While demand for high-end, innovative microscopes is significant, there is only a handful of companies in the world that manufacture such instruments. One reason for this is certainly that the production of high-quality optical equipment in larger scales requires levels of precision and sophistication that are difficult to reproduce. It seems that the smaller the object being observed, the bigger the problems become. The effect of any aberration in the optical system is enlarged along with the desired information. A disturbance of only one thousandth of a millimeter can lead to visible abnormalities. Thus, even with detailed technical knowledge, the manufacturing of high-precision microscopes remains an enormous challenge.

It is therefore a remarkable development that this high-tech domain has recently been invaded by a project, OpenSPIM, in which researchers and engineers are cooperating on all levels under a regime of commons principles. The projects show the power and effectiveness of networked cooperation at the highest levels of scientific research and precision manufacturing.

SPIM is an acronym for “Selective Plane Illumination Microscopy,” which is also known by a more intuitive name, light-sheet microscopy. SPIM differs from other microscopic technologies in how it illuminates observed objects. In conventional instruments, the sample is usually illuminated along the optical axis,1 either through a lens underneath the object or through the microscope objective in the viewing direction. In light-sheet microscopy, however, the illumination light traverses the object like a thin sheet from one side to the other, perpendicular to the optical axis and not from below or above. This unusual configuration gave rise to the technology’s name – selective plane illumination.

This illumination technique was first developed in the beginning of the twentieth century by Richard Zsigmondy and Henry Siedentopf in their so-called Ultramicroscope. When Zsigmondy was awarded the Nobel Prize for Chemistry in 1925, Professor Söderbaum described this instrument quite nicely in his presentation speech:

The idea originated from Zsigmondy and was developed in detail by him in cooperation with Siedentopf, an able optician with the firm of Zeiss. The principle of this instrument is briefly that the intensely illuminated object, the solution to be examined, is observed by means of a microscope from the side, i.e., vertically to the axis of the incident light beam. In this way it is possible to differentiate between particles of such small size that they could not be observed under an ordinary microscope, just as the dust particles suspended in the air in our rooms, which are invisible under ordinary conditions, sometimes become visible when the sun’s rays shine through the window in a definite direction in relation to the observer.2

For understanding the significance of the SPIM principle, it might be helpful to recall some basics of light microscopy. In transmitted light micro­scopy, nontransparent structures become visible because they absorb light and therefore appear darker. In contrast, reflected light microscopy makes objects visible through a reflection or scattering of light, which makes them brighter. Fluorescence microscopy can be regarded as a special case of reflection micro­scopy, where the illumination light is used to cause observable fluorescence of specific structures in the specimen under investigation. Fluorescence micro­scopy has grown dramatically in recent decades, especially with the invention of a variety of new biogenic dyes (e.g., Green Fluorescent Protein (GFP) and its spectral variants), letting researchers now observe processes in living cells, in whole organs, or even in intact living organisms.

The problem with this very powerful approach is the high photon density that is required to cause fluorescence in the sample. During an observation, the sample is exposed to such intense excitation light that dye molecules soon bleach away and the observed samples are damaged or even die. This damage gets particularly severe because the excitation light beam has to travel along the optical axis through the entire specimen; in three-dimensional objects, this destructive flood of photons needs to be repeated for each level of observation.

By using an elegant trick, however, SPIM revolutionizes fluorescence microscopy exactly at this point: The microscope is able to illuminate precisely and exclusively the plane of the object that one wishes to observe. Other parts of the object remain untouched by the intense ray of excitation light, and the points above or below the plane of focus are not even elevated to a glow.

Thus SPIM can actually produce an “optical sectioning” enlargement of thick three-dimensional samples “on the fly.” This is something that traditional “confocal microscopy” can accomplish only through an elaborate point scanning procedure. SPIM avoids this process by illuminating the entire plane of focus, which can now be imaged in milliseconds using high-speed digital cameras. This process also makes it possible to gently observe intact living samples for hours or even days and from multiple perspectives, without destroying the sample. Consequently, SPIM is typically used to observe insect larvae, zebra­fish embryos, the growth of tumors, organoids, and regenerating nerve fibers. Because of its versatility, SPIM has quickly attracted a growing community of enthusiastic followers among researchers interested in noninvasive microscopy on living organisms.

Figure 1: An OpenSPIM image of a 48-hour-old, living zebrafish embryo, in which certain structures like the nervous system and cell nuclei are labeled with the Green Fluorescent Protein (GFP). Photo by openSPIM, under a Creative Commons BY-SA 3.0 license, via OpenSpim.org

Globally, an estimated 100 SPIM systems had been “homebuilt” by this community before ZEISS introduced the first commercial light-sheet microscope in October 2012. Two years later, members of the SPIM community and curious researchers from all over the world converged on Barcelona to attend the First International Lightsheet Fluorescence Microscopy conference, where they eagerly exchanged experiences and ideas for applying and improving SPIM.

Among the speakers at this conference were Ernst Stelzer and Jan Huisken, who are regarded as key inventors of modern SPIM. The reanimation of the old oblique illumination principle known as SPIM in modern research drew upon academic research in which Huisken was significantly involved as a graduate student in Ernst Stelzer’s lab, at the renowned European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. As a postdoctoral researcher at the University of California, San Francisco, Huisken later continued to adapt SPIM to biological applications before returning to Germany to start his own research group at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden (Germany), where he obviously inspired a creative nucleus for further SPIM-related ideas.

It was there where the next breakthrough occurred: “OpenSPIM started, once upon time, at the institute’s canteen where they dreamed up SPIM in a suitcase,” as his colleague Pavel Tomancak tweeted. “It actually exists!” Supported by the international Human Frontiers Scientific Program, the idea was first developed through a wiki,3 which, consistent with the basic ideas of the commons, was published under a Copyleft (CC BY-SA 3.0) license.4 In this wiki, the interested researcher can find a precise list of necessary parts, assembly instructions and video tutorials describing how to build a ready-to-use OpenSPIM instrument in less than one hour, in fourteen discrete steps. From the beginning, the OpenSPIM project committed itself to the principles of open hardware and open software (Pitrone et al. 2013).

Figure 2. OpenSPIM in a suitcase. The camera is seen in the bottom left, the sample chamber in the upper left corner. The box in the center is the laser light-source from which the blue laser is reflected by several mirrors into the sample chamber. Photo by OpenSPIM, under a Creative Commons BY-SA license, 3.0, via OpenSPIM Gallery.

To fully appreciate the achievements of this project, one needs to understand the complex and challenging data-analysis requirements of SPIM microscopy. Depending on its configuration, a SPIM microscope can generate more than 100 megabytes of data per second, potentially during the course of an entire week, all of which must be handled, stored, analyzed and rendered. Simply storing such vast quantities of data, where individual datasets can comprise up to several terabytes, is prohibitively costly for normal computing systems. The system often requires specific software that can work on cloud computing platforms, i.e., high-performance computing on distributed computer networks. Performing such computation at acceptable speeds on individual machines is highly problematic.

Figure 3: The completed OpenSPIM as shown in the open assembly instruction. Photo by OpenSPIM, under a Creative Commons BY-SA license 3.0, via OpenSPIM.org.

Fortunately, the open structure of OpenSPIM provides a solid groundwork for mastering these challenges. For example, OpenSPIM uses only open source Arduino electronic components, and the operation of the system is controlled by the free software µManager. Data analysis and rendering are managed by specialized plugins to the software package Fiji/ImageJ, which is an extensive open source software project for the analysis and processing of scientific image data. Much of the work for those plugins has come from a team led by Pavel Tomancak, a congenial Czech who works at the Max Planck Institute in Dresden. This group is not only renowned as a driving force of the OpenSPIM project, but is highly respected for its missionary zeal in hosting workshops, conferences and academic collaborations to share its knowledge within the growing OpenSPIM community.

Since OpenSPIM started two years ago, the design plans for seven OpenSPIM instruments worldwide have been posted on the wiki.5 The number of unpublished systems is unknown, but more systems are certainly under construction. In any case, global interest in OpenSPIM is remarkable. Curious students and researchers use every possible opportunity to get familiar with the system. Experts say that OpenSPIM does not reach the standards of commercially available or sophisticated home-built systems, but due to its significantly lower costs it is widely accessible to a much broader user community. This makes applications possible, for example, for universities in countries that have very limited research budgets and that could not afford other SPIM systems. Because OpenSPIM is open to all and not proprietary, its usefulness in educational contexts is unparalleled. Anyone who buys a light-sheet microscope can use it, but anyone who assembles an OpenSPIM will also understand it! Beyond that, OpenSPIM also makes research more transparent. Experimental results can be understood and reproduced more easily by peers and thus be verified, which contributes to the integrity and authentication of research results.

Whether OpenSPIM will continue to expand or simply remain an exciting niche project remains to be seen. This will substantially depend on whether or not the SPIM community – including the DIY builders and commercial providers – recognize the value of their ongoing commoning and perceive themselves as active commoners. Will they let their project modifications and improvements continue to flow back to the community and contribute to its flourishing?

If the OpenSPIM platform is seen simply as a launch pad for the proprietary “secret projects” of either businesses or solitary nerds, it is quite possible the project will collapse. The community of OpenSPIM enthusiasts might at some point become exhausted by their voluntary efforts, and find it easier to retreat to their own private, proprietary interests. But there are reasons for optimism: In January 2015, the highly respected journal Nature Methods, which is affiliated with the prominent interdisciplinary scientific journal Nature, selected light-sheet microscopy as “Method of the Year 2014.”6 This will provide strong tailwinds for the OpenSPIM endeavor!

Jacques Paysan photoJacques Paysan (Germany) holds a PhD in Neurobiology, and is a commons fan and SPIM Expert. He lives in the Jagst-Valley in Baden-Württemberg.


Patterns of Commoning, edited by Silke Helfrich and David Bollier, is being serialized in the P2P Foundation blog. Visit the Patterns of Commoning and Commons Strategies Group websites for more resources.

References

1. The optical axis represents a straight line from object to image through the centers of symmetry of all lenses of a microscope.
2. http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1925/press.html
3. www.openspim.org
4. Editors’ note: See the essay on alternative licensing.
5. OpenSPIM should not be confused with customized SPIM systems. Some of the latter are specialized and highly sophisticated systems constructed for specific applications. The costs of such systems can reach hundreds of thousands of euros. In contrast, the costs of an OpenSPIM, depending on its configuration, are typically in the range of tens of thousand euros.
6. http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3251.htm

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The Neurology of Consumer Compulsion https://blog.p2pfoundation.net/neurology-consumer-compulsion/2016/04/09 https://blog.p2pfoundation.net/neurology-consumer-compulsion/2016/04/09#comments Sat, 09 Apr 2016 08:12:57 +0000 https://blog.p2pfoundation.net/?p=55294 In a provocative new essay on the Great Transition Initiative website, neuroscientist Peter Sterling explores “Why We Consume:  Neural Design and Sustainability.”  It is an evolutionary scientist’s argument for how human beings are neurologically wired and what we might do about it. What is the biological substrate for our behaviors as homo economicus and as... Continue reading

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In a provocative new essay on the Great Transition Initiative website, neuroscientist Peter Sterling explores “Why We Consume:  Neural Design and Sustainability.”  It is an evolutionary scientist’s argument for how human beings are neurologically wired and what we might do about it. What is the biological substrate for our behaviors as homo economicus and as social cooperators?  Why do we (over)consume?

Sterling points to such obvious social factors such as our desire for social status and a good self-image, all of it fueled by advertising.  But while these feelings of satisfaction invariably wane, they invariably surge forward again and again: “Something at our neural core continually stimulates acquisitive behavior,” he writes, adding that “we urgently need to identify and manage it.”

Sterling notes that we all have neurological circuits that are periodically bathed in dopamine as a reward for satisfying behaviors. More than a “pleasure center,” these neural responses serve as a reward for human learning and adaptation in a highly varied environment. It is the decline of our highly varied environment that may be responsible for our consumerist obsessions.

“This design [of our neurological circuits] works best in an environment where primary rewards are diverse,” argues Sterling.  “But as capitalist social organization shrinks the diversity of primary rewards to the realm of material consumption, they become predictable and less satisfying. Limited to a few sources of primary reward, we consume them more intensely as the circuit adapts, and eventually they become addictions.”

What insights from brain design might aid the transition to a sustainable civilization? asks Sterling. He answers:

First, we must grasp that humans consume compulsively—insatiably—in large part because our clever circuit for reward learning now encounters too few sources of small surprise. We may rail against the capitalist manipulations that drive consumption from the top down, but that will not satiate our innate, bottom-up drive to consume. Therefore, social policies should follow the precept “Expand satisfactions!” We should re-examine and enumerate the myriad sources that were alienated under capitalism. The list will resemble roughly what we do on vacation: more nature, exercise, sports, crafts, art, music, and sex—of the participatory (non-vicarious) sort.

As a second strategy, Sterling recommends that we recognize that individuals differ in what they regard as their “primary rewards” – but these patterns emerge from the bottom up.  Social policy should recognize this fact: “Start in the classroom, where we now confine large groups of children with diverse innate abilities to ‘attend’ to one topic presented by a ‘teacher’ on behalf of the State. A worse match to the brain circuit for learning can hardly be imagined.”

One of the pleasures of the Great Transition Initiative’s essays are the curated comments that respond to them.  This one has some wonderful responses by Tim Jackson, Fred Magdoff, and Sheldon Krimsky, among others. I especially appreciated David Korten’s insightful elaboration:

Sterling makes periodic references to learning and community and correctly notes that when we humans lived in community in nature, our sources of satisfaction were rich, varied, and consistent with our needs and a right relationship with other humans and the living Earth. Our neural circuits evolved to support learning and life in a living community.

The contrast that Sterling draws between our experience of daily life as participants in Earth’s community of life and our experience of daily existence in the sterile, manufactured, mechanistic, regimented, money-driven setting of consumer society is foundational to a fuller explanation of why we accepted the cultural manipulation and economic restructuring that now threaten our existence.

So our need to experience a fuller spectrum of human satisfactions — and escape the consumerist treadmill — depends upon recovering a richer, less homogenized realm of experience. The commons awaits!

Photo by Iwan Gabovitch

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