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Researchers generate a reference map of the human epigenome

Helen Knight | MIT News correspondent

The sequencing of the human genome laid the foundation for the study of genetic variation and its links to a wide range of diseases. But the genome itself is only part of the story, as genes can be switched on and off by a range of chemical modifications, known as “epigenetic marks.”

Now, a decade after the human genome was sequenced, the National Institutes of Health’s Roadmap Epigenomics Consortium has created a similar map of the human epigenome.
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New Book: An Irreverent Singularity Funcyclopedia, by Mondo 2000’s R.U. Sirius.

Quoted: “Legendary cyberculture icon (and iconoclast) R.U. Sirius and Jay Cornell have written a delicious funcyclopedia of the Singularity, transhumanism, and radical futurism, just published on January 1.” And: “The book, “Transcendence – The Disinformation Encyclopedia of Transhumanism and the Singularity,” is a collection of alphabetically-ordered short chapters about artificial intelligence, cognitive science, genomics, information technology, nanotechnology, neuroscience, space exploration, synthetic biology, robotics, and virtual worlds. Entries range from Cloning and Cyborg Feminism to Designer Babies and Memory-Editing Drugs.” And: “If you are young and don’t remember the 1980s you should know that, before Wired magazine, the cyberculture magazine Mondo 2000 edited by R.U. Sirius covered dangerous hacking, new media and cyberpunk topics such as virtual reality and smart drugs, with an anarchic and subversive slant. As it often happens the more sedate Wired, a watered-down later version of Mondo 2000, was much more successful and went mainstream.”

Read the article here >https://hacked.com/irreverent-singularity-funcyclopedia-mondo-2000s-r-u-sirius/

The Blockchain is the New Database, Get Ready to Rewrite Everything

Quoted: “If you understand the core innovations around the blockchain idea, you’ll realize that the technology concept behind it is similar to that of a database, except that the way you interact with that database is very different.

The blockchain concept represents a paradigm shift in how software engineers will write software applications in the future, and it is one of the key concepts behind the Bitcoin revolution that need to be well understood. In this post, I’d like to explain 5 of these concepts, and how they interrelate to one another in the context of this new computing paradigm that is unravelling in front of us. They are: the blockchain, decentralized consensus, trusted computing, smart contracts and proof of work / stake. This computing paradigm is important, because it is a catalyst for the creation of decentralized applications, a next-step evolution from distributed computing architectural constructs.

Read the article here > http://startupmanagement.org/2014/12/27/the-blockchain-is-th…verything/

2014 Longevity and Genetics Conference – Keynote Aubrey de Grey

Western Canada’s most futurist-oriented longevity organization, the Lifespan Society of British Columbia, has organized a first-class life extension conference, which will take place later this fall in the heart of downtown Vancouver. The Longevity and Genetics Conference 2014 offers a full-day of expert presentations, made accessible to a general audience, with keynote on the latest developments in biorejuvination by Aubrey de Grey of SENS Research Foundation. The conference will be interactive, with a panel session for audience questions, and VIP options for further interaction with speakers.

Aubrey de Grey

Who will be there? In addition to Aubrey de Grey, there are four other speakers confirmed thus far: Dr. Angela Brooks-Wilson, Head of Cancer Genetics at the Michael Smith Genome Sciences Centre at the BC Cancer Agency, Dr. S. Jay Olshansky, Board of Directors of the American Federation of Aging Research, and co-author of The Quest for Immortality: Science at the Frontiers of Aging, Dr. Clinton Mielke, former Mayo Clinic researcher and founder of the quantified self platform “infino.me”, and lastly, one of futurism’s most experienced and dedicated radical longevity advocates, Benjamin Best, who is currently Director of Research Oversight at the Life Extension Foundation. This conference is a multi-disciplinary event, engaging several points of interest and relevance in the longevity space, from the cellular, genetic science of aging, to the latest epidemiological and even demographic research. You can also expect discussion on personalized medicine and quantified self technologies, as well as big picture, sociological and philosophical, longevity-specific topics.

All around, the 2014 Longevity and Genetics conference, set to take place Saturday November 15, has a lot to offer, as does the host city of Vancouver. A recent study has indicated that a majority of Canadians, 59%, are in favor of life extension technology, with 47% expecting that science and technology will enable living until 120 by 2050. The Lifespan Society of British Columbia is keeping that momentum and enthusiasm alive and growing, and I’m glad they have organized such a high-calliber event. Tickets are currently still available. Learn more about the event and purchase tickets here.

ImageofVancouver
Vancouver B.C.

The Abolition of Medicine as a Goal for Humanity 2.0

What follows is my position piece for London’s FutureFest 2013, the website for which no longer exists.

Medicine is a very ancient practice. In fact, it is so ancient that it may have become obsolete. Medicine aims to restore the mind and body to their natural state relative to an individual’s stage in the life cycle. The idea has been to live as well as possible but also die well when the time came. The sense of what is ‘natural’ was tied to statistically normal ways of living in particular cultures. Past conceptions of health dictated future medical practice. In this respect, medical practitioners may have been wise but they certainly were not progressive.

However, this began to change in the mid-19th century when the great medical experimenter, Claude Bernard, began to champion the idea that medicine should be about the indefinite delaying, if not outright overcoming, of death. Bernard saw organisms as perpetual motion machines in an endless struggle to bring order to an environment that always threatens to consume them. That ‘order’ consists in sustaining the conditions needed to maintain an organism’s indefinite existence. Toward this end, Bernard enthusiastically used animals as living laboratories for testing his various hypotheses.

Historians identify Bernard’s sensibility with the advent of ‘modern medicine’, an increasingly high-tech and aspirational enterprise, dedicated to extending the full panoply of human capacities indefinitely. On this view, scientific training trumps practitioner experience, radically invasive and reconstructive procedures become the norm, and death on a physician’s watch is taken to be the ultimate failure. Humanity 2.0 takes this way of thinking to the next level, which involves the abolition of medicine itself. But what exactly would that mean – and what would replace it?

The short answer is bioengineering, the leading edge of which is ‘synthetic biology’. The molecular revolution in the life sciences, which began in earnest with the discovery of DNA’s function in 1953, came about when scientists trained in physics and chemistry entered biology. What is sometimes called ‘genomic medicine’ now promises to bring an engineer’s eye to improving the human condition without presuming any limits to what might count as optimal performance. In that case, ‘standards’ do not refer to some natural norm of health, but to features of an organism’s design that enable its parts to be ‘interoperable’ in service of its life processes.

In this brave new ‘post-medical’ world, there is always room for improvement and, in that sense, everyone may be seen as ‘underperforming’ if not outright disabled. The prospect suggests a series of questions for both the individual and society: (1) Which dimensions of the human condition are worth extending – and how far should we go? (2) Can we afford to allow everyone a free choice in the matter, given the likely skew of the risky decisions that people might take? (3) How shall these improvements be implemented? While bioengineering is popularly associated with nano-interventions inside the body, of course similarly targeted interventions can be made outside the body, or indeed many bodies, to produce ‘smart habitats’ that channel and reinforce desirable emergent traits and behaviours that may even leave long-term genetic traces.

However these questions are answered, it is clear that people will be encouraged, if not legally required, to learn more about how their minds and bodies work. At the same time, there will no longer be any pressure to place one’s fate in the hands of a physician, who instead will function as a paid consultant on a need-to-know and take-it-or-leave-it basis. People will take greater responsibility for the regular maintenance and upgrading of their minds and bodies – and society will learn to tolerate the diversity of human conditions that will result from this newfound sense of autonomy.

Towards a ‘Right to Science’

In 1906 the great American pragmatist philosopher William James delivered a public lecture entitled, ‘The Moral Equivalent of War’. James imagined a point in the foreseeable future when states would rationally decide against military options to resolve their differences. While he welcomed this prospect, he also believed that the abolition of warfare would remove an important pretext for people to think beyond their own individual survival and toward some greater end, perhaps one that others might end up enjoying more fully. What then might replace war’s altruistic side?

It is telling that the most famous political speech to adopt James’ title was US President Jimmy Carter’s 1977 call for national energy independence in response to the Arab oil embargo. Carter characterised the battle ahead as really about America’s own ignorance and complacency rather than some Middle Eastern foe. While Carter’s critics pounced on his trademark moralism, they should have looked instead to his training as a nuclear scientist. Historically speaking, nothing can beat a science-led agenda to inspire a long-term, focused shift in a population’s default behaviours. Louis Pasteur perhaps first exploited this point by declaring war on the germs that he had shown lay behind not only human and animal disease but also France’s failing wine and silk industries. Moreover, Richard Nixon’s ‘war on cancer’, first declared in 1971, continues to be prosecuted on the terrain of genomic medicine, even though arguably a much greater impact on the human condition could have been achieved by equipping the ongoing ‘war on poverty’ with comparable resources and resoluteness.

Science’s ability to step in as war’s moral equivalent has less to do with whatever personal authority scientists command than with the universal scope of scientific knowledge claims. Even if today’s science is bound to be superseded, its import potentially bears on everyone’s life. Once that point is understood, it is easy to see how each person could be personally invested in advancing the cause of scientific research. In the heyday of the welfare state, that point was generally understood. Thus, in The Gift Relationship, perhaps the most influential work in British social policy of the past fifty years, Richard Titmuss argued, by analogy with voluntary blood donation, that citizens have a duty to participate as research subjects, but not because of the unlikely event that they might directly benefit from their particular experiment. Rather, citizens should participate because they would have already benefitted from experiments involving their fellow citizens and will continue to benefit similarly in the future.

However, this neat fit between science and altruism has been undermined over the past quarter-century on two main fronts. One stems from the legacy of Nazi Germany, where the duty to participate in research was turned into a vehicle to punish undesirables by studying their behaviour under various ‘extreme conditions’. Indicative of the horrific nature of this research is that even today few are willing to discuss any scientifically interesting results that might have come from it. Indeed, the pendulum has swung the other way. Elaborate research ethics codes enforced by professional scientific bodies and university ‘institutional review boards’ protect both scientist and subject in ways that arguably discourage either from having much to do with the other. Even defenders of today’s ethical guidelines generally concede that had such codes been in place over the past two centuries, science would have progressed at a much slower pace.

The other and more current challenge to the idea that citizens have a duty to participate in research comes from the increasing privatisation of science. If a state today were to require citizen participation in drug trials, as it might jury duty or military service, the most likely beneficiary would be a transnational pharmaceutical firm capable of quickly exploiting the findings for profitable products. What may be needed, then, is not a duty but a right to participate in science. This proposal, advanced by Sarah Chan at the University of Manchester’s Institute for Bioethics, looks like a slight shift in legal language. But it is the difference between science appearing as an obligation and an opportunity for the ordinary citizen. In the latter case, one does not simply wait for scientists to invite willing subjects. Rather, potential subjects are invited to organize themselves and lobby the research community with their specific concerns. In our recent book, The Proactionary Imperative, Veronika Lipinska and I propose the concept of ‘hedgenetics’ to capture just this prospect for those who share socially relevant genetic traits. It may mean that scientists no longer exert final control over their research agenda, but the benefit is that they can be assured of steady public support for their work.

Open Source SynBio?

If the controversy over genetically modified organisms (GMOs) tells us something indisputable, it is this: GMO food products from corporations like Monsanto are suspected to endanger health. On the other hand, an individual’s right to genetically modify and even synthesize entire organisms as part of his dietary or medical regimen could someday be a human right.
The suspicion that agri-giant companies do harm by designing crops is legitimate, even if evidence of harmful GMOs is scant to absent. Based on their own priorities and actions, we should have no doubt that self-interested corporations disregard the rights and wellbeing of local producers and consumers. This makes agri-giants producing GMOs harmful and untrustworthy, regardless of whether individual GMO products are actually harmful.
Corporate interference in government of the sort opposed by the Occupy Movement is also connected with the GMO controversy, as the US government is accused of going to great lengths to protect “stakeholders” like Monsanto via the law. This makes the GMO controversy more of a business and political issue rather than a scientific one, as I argued in an essay published at the Institute for Ethics and Emerging Technologies (IEET). Attacks on science and scientists themselves over the GMO controversy are not justified, as the problem lies solely with a tiny handful of businessmen and corrupt politicians.
An emerging area that threatens to become as controversial as GMOs, if the American corporate stranglehold on innovation is allowed to shape its future, is synthetic biology. In his 2014 book, Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life, top synthetic biologist J. Craig Venter offers powerful words supporting a future shaped by ubiquitous synthetic biology in our lives:

“I can imagine designing simple animal forms that provide novel sources of nutrients and pharmaceuticals, customizing human stem cells to regenerate a damaged, old, or sick body. There will also be new ways to enhance the human body as well, such as boosting intelligence, adapting it to new environments such as radiation levels encountered in space, rejuvenating worn-out muscles, and so on”

In his own words, Venter’s vision is no less than “a new phase of evolution” for humanity. It offers what Venter calls the “real prize”: a family of designer bacteria “tailored to deal with pollution or to absorb excess carbon dioxide or even meet future fuel needs”. Greater than this, the existing tools of synthetic biology are transhumanist in nature because they create limitless means for humans to enhance themselves to deal with harsher environments and extend their lifespans.
While there should be little public harm in the eventual ubiquity of the technologies and information required to construct synthetic life, the problems of corporate oligopoly and political lobbying are threatening synthetic biology’s future as much as they threaten other facets of human progress. The best chance for an outcome that will be maximally beneficial for the world relies on synthetic biology taking a radically different direction to GM. That alternative direction, of course, is an open source future for synthetic biology, as called for by Canadian futurist Andrew Hessel and others.
Calling himself a “catalyst for open-source synthetic biology”, Hessel is one of the growing number of experts who reject biotechnology’s excessive use of patents. Nature notes that his Pink Army Cooperative venture relies instead on “freely available software and biological parts that could be combined in innovative ways to create individualized cancer treatments — without the need for massive upfront investments or a thicket of protective patents”.
While offering some support to the necessity of patents, J. Craig Venter more importantly praises the annual International Genetically Engineered Machine (iGEM) competition in his book as a means of encouraging innovation. He specifically names the Registry of Standard Biological Parts, an open source library from which to obtain BioBricks, and describes this as instrumental for synthetic biology innovation. Likened to bricks of Lego that can be snapped together with ease by the builder, BioBricks are prepared standard pieces of genetic code, with which living cells can be newly equipped and operated as microscopic chemical factories. This has enabled students and small companies to reprogram life itself, taking part in new discoveries and innovations that would have otherwise been impossible without the direct supervision of the world’s best-trained teams of biologists.
There is a similar movement towards popular synthetic biology by the name of biohacking, promoted by such experts as Ellen Jorgensen. This compellingly matches the calls for greater autonomy for individuals and small companies in medicine and human enhancement. Unfortunately, despite their potential to greatly empower consumers and farmers, such developments have not yet found resonance with anti-GMO campaigners, whose outright rejection of biotechnology has been described as anti-science and “bio-luddite” by techno-progressives. It is for this reason that emphasizing the excellent potential of biotechnology for feeding and fuelling a world plagued by dwindling resources is important, and a focus on the ills of big business rather than imagined spectres emerging from science itself is vital.
The concerns of anti-GMO activists would be addressed better by offering support to an alternative in the form of “do-it-yourself” biotechnology, rather than rejecting sciences and industries that are already destined to be a fundamental part of humanity’s future. What needs to be made is a case for popular technology, in hope that we can reject the portrayal of all advanced technology as an ally of powerful states and corporations and instead unlock its future as a means of liberation from global exploitation and scarcity.
While there are strong arguments that current leading biotechnology companies feel more secure and perform better when they retain rigidly enforced intellectual property rights, Andrew Hessel rightly points out that the open source future is less about economic facts and figures than about culture. The truth is that there is a massive cultural transition taking place. We can see a growing hostility to patents, and an increasing popular enthusiasm for open source innovation, most promisingly among today’s internet-borne youth.
In describing a cultural transition, Hessel is acknowledging the importance of the emerging body of transnational youth whose only ideology is the claim that information wants to be free, and we find the same culture reflected in the values of organizations like WikiLeaks. Affecting every facet of science and technology, the elite of today’s youth are crying out for a more open, democratic, transparent and consumer-led future at every level.

By Harry J. Bentham - More articles by Harry J. Bentham

Originally published at h+ Magazine on 21 August 2014

The Game Theory of Life

By: Emily Singer — Quanta Magazine

Applying game theory to the behavior of genes provides a new view of natural selection.

In what appears to be the first study of its kind, computer scientists report that an algorithm discovered more than 50 years ago in game theory and now widely used in machine learning is mathematically identical to the equations used to describe the distribution of genes within a population of organisms. Researchers may be able to use the algorithm, which is surprisingly simple and powerful, to better understand how natural selection works and how populations maintain their genetic diversity.

By viewing evolution as a repeated game, in which individual players, in this case genes, try to find a strategy that creates the fittest population, researchers found that evolution values both diversity and fitness.

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GMOs are not the problem, per se

. @hjbentham . @clubofinfo . @dissidentvoice_ .#tech .#gmo .#ethics . @ieet .

Since giving my support to the May 24 march against Monsanto, I have taken the time to review some of the more unusual opinions in the debate over genetically-modified organisms (GMOs). The enthusiasts for technological development as a means of eliminating scarcity and disparity view GMOs favorably. These enthusiasts include Ramez Naam, whose book The Infinite Resource (2013) argues for human ingenuity as a sufficient force to overcome all resources shortages.
On the other end of the spectrum, alarmists like Daniel Estulin and William Engdahl argue that GMOs are actually part of a deliberate plot to burden poor nations and reduce their populations by creating illness and infertility. Such fringe figures in the alter-globalization movement regard big pharmaceutical companies, chemical companies and agri-giants as involved in a conspiracy to create a docile and dependent population. Are the opinions of either Naam or Estulin well-informed, or are they both too sensational?
Most commentators on the GMO controversy, unfortunately, seem to lean towards either the enthusiast or alarmist categories as described. Reason is often lacking on both sides, as people either blindly leap onto the GMO bandwagon as something tantamount to human progress, or they reject all biotechnology as evil by renewing the fallacy that unnatural actions are necessarily bad. The only thing both sides seem to have in common is their resistance to the Malthusian Club of Rome’s insinuations that overpopulation has to be rolled back to save the Earth’s resources.
Ramez Naam persuades us that the fire of human intellect can overcome our limited resources and allow tens of billions of people to exist on our planet without consuming all natural resources. Estulin and Engdahl reject the Club of Rome on the basis that resource limitations do not really exist and the analysis of the Club of Rome is simply aimed at justifying control of the Earth’s resources by the cherished few “elites”.
The truth rests somewhere between what the alarmist fringe critics of GMOs and the techno-progressive enthusiasts are trying to tell us. To be truthful, there is a serious controversy involving GMOs, but it is no outlandish conspiracy in any sense. It is merely an extension of the problem of greed that has burdened mankind for as long as feudal lords or capitalists have been privileged to put their selfish interests above the common good. The problem with GMOs is neither the nature of GM technology, nor something mysterious that takes place in the process of genetic modification. It is the nature of the businesses tasked with running this industry.
Whether or not certain GMOs on the market today actually cause cancer and infertility is irrelevant to the real debate. The problem is that we can guarantee that the companies engineering these organisms do not care if they cause health problems. They are only interested in downplaying or blocking bad news, and putting out constant marketing and good news about themselves. Typical of any fiercely monopolistic firm, this is not an honest relationship with the public, and corresponds to the prevailing belief in profit as the exclusive priority. For their game to be worth playing, they have to put increasing yields, shelf life and resistance to pathogens above anything else when designing crops. They have no choice than to do this, from their perspective, because the alternative is to allow themselves to be outperformed by their rivals.
The fact that corporations put their own profit above health is a systemic issue in the world economy, and it is already known to the majority of consumers. We face it every day. Most of the fast food served by multinational fast food companies is accepted to be unhealthy, so the claim that giant food companies have little interest in our health is not a conspiracy theory. It is only a rational suspicion that the agricultural producers of seeds will also put profit over the long-term health of consumers and the interests of local farmers.
In theory, genetic modification could lead not only to higher yields but healthier food. Unfortunately, the businesses involved only really care about beating competition and becoming the best supplier. This behavior poisons everything, perhaps literally, now that these companies have been entrusted to define the toxicity in crops as a defense against pests. What we can learn from this that the problem is not GMOs per se, but the aggressive greed of the corporations who desire the oligopoly on food production via GM technology.
The public harm caused by giant firms, especially when they practice their ability to lobby the state itself, already runs very deep in most facets of life. The more significant the tools made available to such firms, the greater the potential for harm. Even if specific specimens are not harmful and can be proven completely benign, the fact is that GMOs open up an unacceptable avenue for unprecedented harm and malignant corporate interests invading people’s innards. It is this, rather than the whole science of genetic modification, that should be opposed and protested against.
Genetic modification and synthetic biology do not need to be new instruments of oligopoly and monopoly. There is a benign alternative to foolishly entrusting the mastery and ownership of living organisms to greedy multinational leviathans. We can look into “biohacking”, as popularized by science and technology enthusiasts who favor the empowerment of individuals and small businesses rather than corporations. There is a strong nod in this direction in J. Craig Venter’s book, Life at the Speed of Light (2013), in which he envisages living organisms being quickly customized and modified by lone individuals with the technology of synthetic biology. Such a development would transform society for the better, eliminating any need to trust an unsympathetic and self-interested corporation like Monsanto.
DIY genetic engineering is already possible. DIY means the product will be entirely disinfected from corporate greed, and adhere to your own specifications. They would not be able to put their profit above your health, because they would not get the chance. With this, biohackers can already genetically modify organisms for their own benefit. The extent to which farmers can begin to modify their own crops using comparable technology is not yet clear, but the development nevertheless represents an extraordinary possibility.
What if farmers and consumers could decide genetically modify their own food? In that case, it would not be the profit-oriented poison that is being consumed at so many different levels as a result of corporate greed. Crops would be modified only insofar as the modification will meet the farmer’s own needs, and all the technology for this process could be open-source. This hypothetical struggle for DIY genetic engineering rather than corporate genetic engineering would be comparable to the open-source and piracy battles already raging over digital technology.
Of course, some new hazards could still conceivably emerge from DIY genetic modification, if the technology for it should become ubiquitous. However, the only risk would be from individual farmers rather than unaccountable corporations. This way, we would be moving away from giving irresponsible and vicious companies the ability to threaten health. Instead, we would be moving towards giving back individuals more control over their own diets. Of course, abuse would still occur, but it would not have global consequences or frighten millions of people in the way that current genetic engineering does.
In sum, there is no reason to complain that genetic modification is perilous in its own right. However, there is always peril in giving a great social responsibility to a profit-hungry corporation. In much the same way that large firms have captured the state machinery of our liberal democratic states to serve their greedy interests, we should expect them to be subverting health and the public good for profit.
The complex dilemma over GMOs requires not an anti-scientific or neo-Luddite reaction, but an acknowledgement that intertwined monopolistic, statist and hegemonic ambitions lead to the retardation of technology rather than progress. I have made this very case in an essay at the techno-politics magazine ClubOfINFO, and I consider it to be an important detail to keep in mind as the GMO controversy rages.

By Harry J. Bentham - More articles by Harry J. Bentham

Originally published at Dissident Voice on 23 June 2014