The Ego Tunnel by Thomas Metzinger, 2009

The human brain can be compared to a modern flight simulator in several respects. Like a flight simulator, a consciousness continuously updates an internal model of external reality by using a continuous stream of inputs applied by the sensory organs and employing past experience as a filter. It integrates sensory-input channels into a global model of reality, and it does so in real time. However, there is a difference. The global model of reality constructed by the brain is updated at such great speed and with such reliability that we generally do not experience it as a model. For us, phenomenal reality is not a simulation constructed by our brains; in a direct and experientially untrancendable matter, it is the world we live in. Its virtuality is hidden, where the flight simulator is easily recognized as a flight simulator–it images always seem superficial. 107

Finally, the brain also differs from a flight simulator in that there is no user, no pilot who controls it. The brain is like a total flight simulator, a self modeling airplane that, rather than being flown by a pilot, generates a complex internal image of itself with and its own internal flight simulator. The image is transparent and thus cannot be recognized as an image by the system. Operating under the condition of a naïve-realistic self-misunderstanding, the system interprets the control element in this image is a nonphysical object: the “pilot” is born into a virtual reality with no opportunity to discover this fact. The pilot is the ego. The total flight simulator generates an Ego Tunnel but is completely lost in. 108

 

Amazon Link

Metzinger argues that human consciousness is the result of our brains modeling reality at such high resolution that we are incapable of recognizing it as a mere simulation of reality.  We model the outside world, and it seems real; we don’t recognize that it’s a limited simulation of what’s actually out there.  Without noticing, we accept the simulation as reality itself.

We also model our internal reaction to this simulated “outside” world to such a high degree that it also seems real.  We model our outer world, and we model ourselves as agents within it.

Conscious states could be exactly those states that “meta-represent” themselves while representing something else. This classical idea has logical problems, but the insight itself can perhaps be preserved in an empirically plausible framework. 30-1

Some of the details of the Ego Tunnel model of consciousness were difficult to comprehend, but I was satisfied with just getting the main outline.  I didn’t want to spend hours re-reading and re-reading passages that were tricky, but I may do so in the future upon a complete re-read of the book.  Some of the interviews scattered throughout the book seem to be slightly off-message and I had trouble integrating them with the main thread of the book.

After summarizing his theory, Metzinger moves to topics I find highly interesting; free will, religion and spirituality, the Buddhist doctrine of not-self, and the uniquely human fear of death.  Take a look at the quotes below for a sampling.

Ideas per Page:¹ 4/10 (medium)

Related Books: Waking Up by Sam Harris; Why Buddhism is True by Robert Wright; On Having No Head by Douglas Harding; Straw Dogs by John Gray; The Silence of Animals by John Gray

Recommend to Others: If you are interested in models of consciousness.

Reread Personally:  Maybe, but after other authors on the topic

Quotes:

Modern neuroscience has demonstrated that the content of our conscious experience is not only an internal construct but also an extremely selective way of representing information. This is why it is a tunnel: what we see in here, or what we feel and smell and taste, is only a small fraction of what actually exists out there our conscious model of reality is a low dimensional projection of the inconceivably richer physical reality surrounding and sustaining us. Our sensory organs are limited: they evolve for reasons of survival, not for depicting the enormous wealth and richness of reality in all its unfathomable depth. Therefore, the ongoing process of conscious experience is not so much an image of reality is a tunnel through reality. 6

The ego, as noted, is simply the content of your PSM [phenomenal self-model] at this moment (your bodily sensations, your emotional state, your perceptions, memories, acts of will, thoughts). But it can become the ego only because you are constitutionally unable to realize that all this is just the content of a simulation in your brain. It is not reality itself but an image of reality – and a very special one indeed. The ego is a transparent mental image: you – the physical person as a whole – look right through it. You do not see it. But you see with it. The ego is a tool for controlling and planning your behavior and for understanding the behavior of others. 8

The same general idea holds for more complex states: their phenomenal content is precisely that aspect of a state (say, of happiness plus relaxation) that not only emerges naturally in everyday situations but can also because by a psychoactive substance – or, at least in principle, triggered by an evil neuroscientist experimenting on a living brain in a vat. The problem of consciousness is all about subjective experience, about the structure of our inner life, and not about knowledge of the outer world. 11

Consciousness is a very special phenomenon, because it is part of the world and contains it at the same time.  All our data indicate that consciousness is part of the physical universe and is an evolving biological phenomenon.  Conscious experience, however, is much more than physics plus biology – more than a fantastically complex, dancing pattern of neural firing in your brain. What sets human consciousness apart from other biologically evolved phenomena is that it makes a reality appear within itself. It creates inwardness; the life process has become aware of itself. 15

The apricot-pink of the setting sun is not a property of the evening sky; it is a property of the internal model of the evening sky, a model created by your brain. The evening sky is colorless. The world is not inhabited by colored objects at all. It is just as your physics teacher in high school told you: out there, in front of your eyes, there is just an ocean of electromagnetic radiation, a wide and ranging mixture of different wavelengths. Most of them are invisible to you and can never become part of your conscious model of reality. What is really happening is that the visual system in your brain is drilling a tunnel through this inconceivably rich physical environment and in the process is painting the tunnel walls in various shades of color. Phenomenal color. Appearance. For your conscious eyes only. 20

Our conscious experience of the world is systematically externalized because the brain constantly creates the experience that I am present in the world outside my brain. 23

Just like the water droplets that form a real cloud, some elements leave the aggregate at any given moment, while others join. Consciousness is a large-scale, unified phenomenon emerging from a myriad of physical micro-events. As long as a sufficiently high degree of internal correlation and causal coupling allows this island of dancing micro-events in your brain to emerge, you live in a single reality. A single, unified world appears to you. 30

If this idea is true, the brain state creating your conscious perception of the book in your hand right now must have two logical parts: one portraying the book and one continuously representing the state itself. One part point of the world, and one part itself. Conscious states could be exactly those states that “meta-represent” themselves while representing something else. This classical idea has logical problems, but the insight itself can perhaps be preserved in an empirically plausible framework. 30-1

Just as swiftly and effortlessly, the book-model is bound with other models, such as the models of your hands and of the desk, and seamlessly integrated into your overall conscious space of experience. Because it has been optimized over millions of years, this mechanism is so fast and so reliable that you never noticed its existence. It makes your brain invisible to itself. You are only in contact with its content; you never see the representation as such; therefore, you have the illusion of being directly in contact with the world. And that is how you become a naïve realist, a person who thinks she is in touch with an observer-independent reality. 42-3

We are unable to attend to the construction process that generates the model of the book in our brains. As a matter of fact, attention often seems to do exactly the opposite: by stabilizing the sensory object, we make it even more real. 44

In between 430 and 650 nm, human beings can discriminate more than 150 different wavelengths, for different subjective shades, of color. But if asked to re-identify single colors with a high degree of accuracy, they can do so for fewer than 15. The same is true for other sensory experiences.… Technically, this means we do not possess introspective identity criteria for many of the simplest states of consciousness. Our perceptual memory is extremely limited. You can see and experience the difference between green number 24 and green number 25 if you see both at the same time, but you are unable consciously to represent the sameness of green number 25 overtime. 49, 50

note that when you learn a difficult task for the first time, such as tying your shoes or riding a bicycle, your practicing is always conscious.… whenever the system is confronted with a novel or challenging stimulus, its global workspaces activated and represented in consciousness. This is also the point when you become aware of the process. 56

Those things in the evolution of consciousness that are old, ultrafast, and extremely reliable – such as the qualities of sensory experience – are transparent; abstract conscious thought is not. From an evolutionary perspective this is very new, quite unreliable (as we all know), and so slow that we can actually observe it going on in our brains. In conscious reasoning, we witness the formation of thoughts; some processing stages are available for introspective attention. Therefore, we know that our thoughts are not given but made. 61-2

What do we gain by saying that the neuronal correlate of consciousness is a particular metastable state of a very complex, highly dynamic, nonstationary distributed system – a state characterized by sequences of ever-changing patterns of precisely synchronized oscillations? Further research will lead to more detailed descriptions of such states – but these will likely be abstract, mathematical descriptions of state vectors. Eventually, advanced analytics methods may reveal the semantic content, the actual meaning of such state vectors, and it may be possible to minute manipulate the states and thereby alter the contents of consciousness, thus providing causal evidence for the relation between neuronal activity and the contents of phenomenal awareness. However, this is probably about as close as we can come, in our attempts to identify the neuronal correlates of consciousness. 69-70 [quoting Wolf Singer]

Monkeys can even learn to control a brain-machine interface that lets them grasp objects with a robot arm controlled by certain parts of their brain. 80

In its origins, the “soul” may have been not a metaphysical notion but simply a phenomenological one: the content of the phenomenal ego activated by the human brain during out of body experiences. 85-6

The history of philosophy has shown that technological metaphors had considerable limitations; nevertheless, virtual reality is a useful one. Nature’s virtual reality is conscious experience – a real-time world-model that can be viewed as a permanently running online simulation, allowing organisms to act and interact. 104

But the simple fact remains: you are never in direct contact with your own body. What you feel in the rubber-hand illusion, what AZ feels, or what Philip feels when his left arm is “plugged in” is exactly the same as what you feel when you attended the sensation of your hand holding this book right now which is the feeling of pressure and resistance when you lean back in your chair. What you experience is not reality but virtual reality, a possibility. Strictly speaking, and on the level of conscious experience alone, you live your life in a virtual body and not in a real one. 114

… Schizophrenics sometimes lose the sense of agency and executive consciousness entirely and feel themselves to be remote-controlled puppets. 121

From a scientific, third-person perspective, our inner experience a strong autonomy may look increasingly like that it has been all along: an appearance only. At the same time, we will learn to admire the elegance and the robustness with which nature built only those things into the reality tunnel that organisms needed to know, rather than burdening them with a flood of information about the workings of their brains. We will come to see the subjective experience of free will as an ingenious narrow computational tool. Not only does it create an internal user-interface that allows the organism to control and adapt its behavior, but it is also a necessary condition for social interaction and cultural evolution. 129

A lucid dream is a global simulation of a world in which we suddenly become aware that it is indeed just a simulation. It is a tunnel whose inhabitant begins to realize that he or she actually operates in a tunnel all the time. 140

[Researchers] have created an artificial starfish that gradually develops an explicit internal self-model. Therefore-like it machine uses actuation-sensation relationships to infer indirectly its own structure and then uses this self-model to generate forward locomotion. When part of its leg is removed, the machine adapts its self-model and generates alternative gaits – it learns to limp. 189

But let’s not evade the deeper question. Is there a case for phenomenological pessimism? The concept may be defined as the thesis that the variety of phenomenal experience generated by the human brain is not a treasure but a burden: averaged over a lifetime, the balance between joy and suffering is weighted toward the latter in almost all of its bearers. From Buddha to Schopenhauer, there is a long philosophical tradition positing, essentially, that life is not worth living. 199

We are driven to seek pleasure and joy, to avoid pain and depression. The hedonic treadmill is the motor that nature invented to keep the organism running. We can recognize the structure in ourselves, but we will never be able to escape it. We are the structure. 199

In fact, according to the naturalistic worldview, there are no ends. Strictly speaking, there are not even means – evolution just happened. 200

We are Ego Machines, but we do not have selves. We cannot leave the Ego Tunnel, because there is nobody who could leave. The Ego and its Tunnel are representational phenomena: they are just one of many possible ways in which conscious beings can model reality. Ultimately, subjective experience is a biological data format, a highly specific mode of presenting information about the world, and the ego is merely a complex physical event – an activation pattern in your central nervous system. 208

The self is not a thing but a process. 208

Metaphorically, the central claim of this book is that as you were reading these last several paragraphs, you – the organism as a whole – were continually mistaking yourself for the content of the self-model currently activated by your brain. 209

Mortality, for us, is not only an objective fact but a subjective fact, an open wound in our phenomenal self-model. We have a deep, inbuilt existential conflict, and we seem to be the first creatures on this planet to experience it consciously. Many of us, in fact, spend our lives trying to avoid experiencing it. Maybe this feature of our self-model is what makes is inherently religious.  We are this process of trying to become whole again, to somehow reconcile what we know with what we feel should not be so. 210-1

Whereas spirituality might be defined as seeing what is—as letting go of the search for emotional security—religious faith can be seen as an attempt to cling to that search by redesigning the Ego Tunnel.   Religious belief is an attempt to endow your life with deeper meaning and embedded in a positive meta-context – it is the deeply human attempt to finally feel at home. 211

But everything we know points to a conclusion that is simple but hard to come to terms with: evolution simply happened – foreightless, by chance, without goal. There is nobody to despise or rebel against – not even ourselves. And this is not some bizarre form of neural philosophical nihilism but rather a point of intellectual honesty and great spiritual depth. 212

A dozen of those volunteers rated the psilocybin experience as being the single most spiritually significant experience of his or her life, and an additional 38% rated it to be among the top five most spiritually significant experiences. More than two-thirds of the volunteers rated the experience with psilocybin to be either the single most meaningful experience of his or her life or among the top five most meaningful experiences. 226

It’s important to remember that for thousands of years people of all cultures have used psychoactive substances to induce special states of consciousness: not merely religious ecstasy, relaxed cheerfulness, or heightened awareness but also simple, stupid intoxication. 230

Philosophers can help by initiating and structuring the debates and illuminating the logical structure of ethical arguments and the history of the problems to be discussed. 238

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1 A measure of the number of new or distinct ideas per page. 10/10 would be conceptually dense, like a textbook. 1/10 would be almost completely fluff.

 

 

 

The Shock Doctrine by Naomi Klein, 2007

Amazon Link

Klein documents the global spread of neoliberalism from the end of the Second World War through 2006, when the book was published. Backed by the United States, as well as the World Bank and IMF, neoliberalism was pushed upon South America, Poland, Russia, South Africa, Lebanon, and Iraq following severe shocks, including war, inflation, drastic political change, and natural disaster.  Similar policies appeared in the United States following 9-11 and hurricane Katrina.  Klein describes the neoliberal plan as having three core components:

First, governments must remove all rules and regulations standing in the way of the accumulation of profits. Second, they should sell off any assets they own that corporations could be running at a profit. And third, they should dramatically cut back funding of social programs. —56

In general, Klein argues, people would dismiss these types of pro-corporate/pro-austerity programs out of hand under normal circumstance; the elites who push these measures are opportunists who use (and sometimes deliberately cause or prolong) shocks in order to promote policies that would never be accepted in a “typical” political or economic atmosphere.

Sadly, there are hundreds of pages documenting horrible political, economic, and environmental shocks, resulting in all manner of misery.  Many of these were, Klein argues, fueled, deliberately exacerbated, or allowed to fester in order to implant or cement neoliberal policy.

Klein certainly documents many shocks followed by moves toward neoliberal economic policy, but I’m not so sure she’s on to some particularly new dynamic. It seems more likely that elites are pursuing power as they always have.  But perhaps the form it’s taking has been uniquely shaped by current economic system in a globalized world.

In a perverse way, what pisses me off the most in this book are not the blatant horrors (i.e., the US supporting an Argentine regime that tortured and murdered) but the more subtle government-corporate alliances.  There are many people involved who were not murders or torturers, but nevertheless stole a great amount from society.  But they remained members of the elite! They walked around as though they were respectable.  Some examples:

The president of Argentina’s central bank announced that the state would absorb the debts of large multinational and domestic firms that had, like Chile’s piranhas, borrowed themselves to the verge of bankruptcy. The tidy arrangement meant that these companies continued to own their assets and profits, but the public had to pay off between $15 and $20 billion of their debts; among the companies to receive this generous treatment were Ford Motor Argentina, Chase Manhattan, Citibank, IBM and Mercedes-Benz. –158

… Argentina’s entire early – 90s shock therapy program was written in secret by J.P. Morgan and Citibank, two of Argentina’s largest private creditors. In the course of a lawsuit against the Argentine government, the noted historian Alejandro almost got Noah uncovered a jaw-dropping 1,400 – page document written by the two US banks for Cavallo in which “the policies carried out by the government from ‘92 on are drawn up… The privatization of utilities, the labor law reform, the privatization of the pension system. It’s all laid out with great attention to detail… –167

How can that kind of thing happen? How can these people not be laughed out of the office when they make that type of suggestion? “Yes—we get to keep all the money, and they take all the debt.” Sound familiar? It’s the same bullshit that happened during the financial bailout after the 2007 crisis.  It’s infuriating. Everyone knows it’s beyond the pale to capture and torture political opponents. Why doesn’t that apply to outsourcing all of your risk to the populace while you reap huge rewards?

A more accurate term for a system that erases the boundaries between big government and big business is not liberal, conservative, or capitalist, but corporatist. Its main characteristics are huge transfers of public wealth to private hands, often accompanied by exploding debt, an ever-widening chasm in between the dazzling rich in the disposable poor and an aggressive nationalism that justifies bottomless spending on security. –15

Especially within the US, this is the type of situation I am most worried and frustrated about.  But I’m not sure that corporatism (especially in the US) is caused by neoliberalism.  It seem more like a special case of corruption, a failure of the rule of law, instead of the result of disaster capitalism per se.

In particular, the corruption and corporatism that has entered the military was shocking to me.  The scale of it is truly disconcerting:

At the start of the occupation, there were an estimated 10,000 private soldiers in Iraq, already far more than during the first Gulf War. Three years later, a report by the US Government accountability office found that there were 48,000 private soldiers, from around the world, deployed in Iraq.  Mercenaries represented the largest contingent of soldiers after the US military–more than all the other members of the “coalition of the willing” combined –378

Of course Klein didn’t have the hindsight that we do in 2017, but her choice to hold up Venezuela as an example of an alternative economy obviously seems absurd and purely ideological, given the state of Venezuela’s government and economy.

She also points to countries of South America bartering to fill their needs (Cuba sending doctors in exchange for oil, for example) as a model for escaping or improving upon a neoliberal model, but barter (as opposed to a credit/debit/finance/cash system) is the last resort for economic exchange (see David Graber’s Debt—The First 5,000 Years).

And then, for the cherry on top, she discusses Hamas filling a governmental void in an ambivalent light, as if she’s suggesting that they’re a workable alternative to neoliberalism, instead of an extortionist, terrorist group.

Finally, Klein discusses shock therapy itself, describing the procedure as it was used when it was being developed in the medical dark ages, and using the therapy as it was practiced before evidence-based medicine, as a metaphor for the shock doctrine.

This brought electroshock therapy full circle to its earliest incarnation as an exorcism technique. The first recorded use of medical electrocution was biased with doctor practicing in the 1700s. Believing that mental illness was caused by the devil, he had a patient hold onto a wire that he powered with a static electricity machine: one jolt of electricity was given for each demon. The patient was then pronounce cured. 112

This is very unfortunate, because it discredits this shock therapy and paints it as a barbaric and ineffective intervention for mental illness.  However, in the modern-day shock therapy is a safe and effective treatment for major depression, that is administered to patients in a human and controlled manner.  Shock therapy has already been stigmatized by its portrayal in films like One Flew Over the Cuckoo’s Nest, and it’s sad that the treatment is still getting this type of coverage as late as 2007 (see Shrinks by Jeffery A. Lieberman).

Ideas per Page:¹ 3/10 (lower, lots of supporting data for her thesis, but all largely within a similar paradigm)

Related Books:  ??

Recommend to Others: If you are looking for an openly biased (not a criticism) work on the topic, perhaps.  Don’t’ know enough about the topic to really say.  Also watch the youtube documentary of the same name.

Reread Personally:  No

Quotes:

Where leftists promised freedom for workers from bosses, citizens from dictatorship, countries from colonialism, Friedman promised “individual freedom,” a project that elevated atomized citizens about any collective enterprise and liberated them to express their absolute free will through their consumer choices. 52

In March 1972, in the midst of Letelier’s tense negotiations with ITT, Jack Anderson, a syndicated newspaper columnist, published an explosive series of articles based on documents that showed that the telephone company had secretly plotted with the CIA and the State Department to block Allende from being inaugurated two years earlier. 65

After several false starts, the opportunity came in October 1965, when General Suharto, backed by the CIA, began the process of seizing power and eradicating the left. The CIA had been quietly compiling a list of the country’s leading leftists, a document that fell into Suharto’s hands, while the Pentagon helped out by supplying extra weapons and field radios so Indonesian forces could communicate in the remotest parts of the archipelago. 67 [the same horrific massacre documented in “The Act Of Killing” and “The Look of Silence”]

Mercedes-Benz (a subsidiary of DaimlerChrysler) is facing a similar investigation stemming from allegations that the company collaborated with the military during the 1970s to purge one of its plants of union leaders, allegedly giving names and addresses of 16 workers who were later disappeared, fourteen of them permanently. 109

It was in this loaded context that Amnesty International developed its doctrine of strict impartiality: its financing would come exclusively from members, and it would remain rigorously “independent of any government, political faction, ideology, economic interest or religious creed.”  … Since human rights violations were a universal evil, wrong in and of themselves, it was not necessary to determine why abuses were taking place but to document them as meticulously and credibly as possible. 118 – 9

… Torture is an indicator species of a regime that is engaged in a deeply anti-– democratic project, even if that regime happens to have come to power through elections. 125

The remainder of the national debt was mostly spent on interest payments, as well as shady bailouts for private firms in 1982, just before Argentina has dictatorship collapsed, the who did it one last favor for the corporate sector. Domingo Cavallo, president of Argentina’s central bank, announced that the state would absorb the debts of large multinational and domestic firms that had, like Chile’s piranhas, borrow themselves to the verge of bankruptcy the tidy arrangement meant that these companies continued to own their assets and profits, but the public had to pay off between $15 and $20 billion of their debts; among the companies to receive this generous treatment were Ford Motor Argentina, Chase Manhattan, Citibank, IBM and Mercedes-Benz. 158

Sooka said… “ I would do it completely differently. I would look at the systems of apartheid – I would look at the question of land, I would certainly look at the role of multinationals, I would look at the role of the mining industry very, very closely because I think that’s the real sickness of South Africa… I would look at the systematic effects of the policies of apartheid, and I would devote only one hearing to torture because I think when you focus on torture and you don’t look at what it was serving, that’s when you start to do a real revision of the history.” 211

…he [Yeltsin] issued a decree 1400, announcing that the Constitution was abolished in parliament dissolved. Two days later, a special session of Parliament voted 636 – 2 to impeach Yeltsin for this outrageous act (the equivalent of the US president unilaterally dissolving Congress” .… Clinton continued to back him, and Congress voted to give Yeltsin $2.5 billion in aid.  227

When Yeltsin abolished the Soviet Union, the “loaded gun” that had forced the development of the original [Marshall] plan was disarmed. Without it, capitalism was suddenly free to lapse into its most savage form, not just in Russia but around the world. With the Soviet collapse, the free market now had a global monopoly, which meant all the “distortions” that had been interfering with its perfect equilibrium were no longer required.  …. Those normal European countries (with their strong social safety nets, workers protections, powerful trade unions and socialized healthcare) emerged as a compromise between communism and capitalism. Now that there was no need for compromise, all those moderating social policies were under siege in Western Europe… 253

In South Korea, the IMF subversion of democracy was even more overt. There, the end of the IMF negotiations coincided with scheduled presidential elections in which two of the candidates were running on anti-IMF platforms. In an extraordinary act of interference with the sovereign nation’s political process, the IMF refused to release the money until it had commitments from all four main candidates that they would stick to the new rules if they want. With the country effectively held at Ransom, the IMF was triumphant: each candidate pledged his support in writing. 270

Beneath the jargon, it was simply an attempt to bring the revolution in outsourcing and branding that he [Rumsfeld] had been part of in the corporate world into the heart of the US military. 284

Anyone can be blocked from flying, denied an entry visa to the US or even arrested and named as an “enemy combatants” based on evidence from these dubious technologies-a blurry image identified through facial recognition software, a misspelled name, a misunderstood snippet of a conversation. If “enemy combatants” are not US citizens, they will probably never even know what it was that convicted them because the Bush administration has stripped them of habeas corpus, the right to see the evidence in court, as well as the right to a fair trial in a vigorous defense 304

In other words, you have corporatism: big business and big government combining their formidable powers to regulate and control the citizenry. 307

Wherever it has emerged over the past thirty-five years, from Santiago to Moscow to Beijing to Bush’s Washington, the alliance between a small corporate elite and a right-wing government has been written off as some sort of aberration – Mafia capitalism, oligarchy capitalism and now, under Bush, “crony capitalism.” But it’s not an aberration; it is where the entire Chicago school Crusade – with its triple obsessions – privatization, deregulation and union-busting – has been leading. 316

When the war moved inside the jails, the military was so short on trained interrogators and Arabic translators that it couldn’t get information out of its new prisoners. Desperate for more interrogators and translators, it turned to the defense contractor CACI International Inc.… whose workers did not need to meet the rigorous training and security clearances required of government employees, [it] was it easy as ordering new office supplies; dozens of new interrogators arrived in a flash. 378-9

In July 2006, Boeing, the inspector general for Iraq reconstruction, issued a report on “lessons learned” from the various contractor debacles. It concluded that the problem stemmed from insufficient plan and call for the creation of a “a deployable reserve Corps of contracting personnel who are trained to execute rapid relief and reconstruction contracting during contingency operations” and to “pre–qualify a diverse pool of contractors with expertise and specialized reconstruction areas” – in other words, the standing contractor army. In his 2007 state of the union address, Bush championed the idea, announcing the creation of a brand-new civilian reserve Corps. “Such a core would function much like our military reserve. It would ease the burden on the Armed Forces by allowing us to hire civilians with critical skills to serve on missions abroad in America needs them,” he said. 381

The emergence of this parallel privatized infrastructure reaches far beyond policing. When the contractor infrastructure built up during the Bush years is looked at as a whole, what is seen as a fully articulated state within a state that is as muscular and capable as the actual state is frail and feeble. This corporate shadow state has been built almost exclusively with public resources (90% of Blackwater’s revenues come from state contracts), including the training of its staff (overwhelmingly former civil servants, politicians and soldiers”). Yet the vast infrastructure is all privately owned and controlled. The citizens who have funded it have absolutely no claim to this parallel economy or its resources. 417

The actual state, meanwhile, has lost the ability to perform its core functions without the help of contractors. Its own equipment is out of date and the best experts have flooded the private sector. When Katrina hit, FEMA had to hire a contractor to award contracts to contractors similarly, when it came time to update the Army manual on the rules for dealing with contractors, the Army contracted out the job to one of its major contractors, and PRI – it no longer had the no-how in-house. 417

Perhaps part of the reason why so many of our elites, both political and corporate, are so sanguine about climate change is that they are confident they will be able to buy their way out of the worst of it. This may also partially explain why so many Bush supporters are Christian and-timers. It’s not just that they need to believe there is an escape hatch from the world they are creating. It’s that the rapture is a parable for what they are building down here… 419

In Venezuela, Chavez has made the co–ops a top political priority, giving them first refusal on government contracts and offering them economic incentives to trade with one another. By 2006, there were roughly 100,000 cooperatives in the country, employing more than 700,000 workers. Many are pieces of state infrastructure – tollbooths, highway maintenance, health clinics – handed over to the communities to run. 455

So Bolivia provides gas at stable discounted prices; Venezuela offers heavily subsidized oil to poorer countries and share his expertise in developing reserves; and Cuba sends thousands of doctors to deliver free healthcare all over the continent, while training students from other countries at its medical schools.… The major benefit is that ALBA is essentially a barter system, in which countries decide for themselves what any given commodity or server service is worth, rather than letting traders in New York, Chicago or London set the prices for them. 456

To the outside world, Solidere was the shining symbol of Lebanon’s postwar rebirth, but for many Lebanese and has always been a kind of holograph. Outside the ultramodern downtown core, much of Beirut lacked basic infrastructure, from electricity to public transit, and the bullet holes inflicted during the Civil War were never repaired on the façades of many buildings. It was in those neglected slums surrounding the gleaming center that has the law built its loyal base, rigging up generators and transmitters, organizing trash removal, providing security – becoming the much vilified “state within a state.” 461

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1 A measure of the number of new or distinct ideas introduced per page. 10/10 would be conceptually dense, like a textbook. 1/10 would be almost completely fluff.

 

 

 

SPOILERS Review: The Last Jedi

I think it’s difficult to assign a grade to The Last Jedi, because the quality of various plot threads differs dramatically. For me, The Force Awakens was a joy to watch (even if it was a carbon copy of A New Hope). The Last Jedi had so many glaring problems that it was difficult to sit back and simply enjoy the ride.

I’d like to focus on three categories; the weakest parts of the film, what was missing, and what I found to be excellent.

The opening sequence which sets the stage for the rest of the film is quite weak.  First, the stakes are rather low. The Empire is chasing a rebel ship (First Order, Resistance, whatever) which we’ve seen a thousand times, but we have no reason to really be worried, or even interested– only lame characters are getting killed, and this is basically the status quo of the Star Wars universe. Second, the idea of an extended, relatively slow, linear chase between starships is absurd, because the Empire has such an immense fleet that it would be trivial for them to coordinate with other craft and have them make lightspeed jumps into the path of the escaping rebel vessel.  So the core driving force of the plot arc is ridiculous within the Star Wars universe, and  limps out of the gate.

The Rose-Finn story arc is the most glaring mistake. It eats up considerable screen time, yet does not forward plot or character development, and has the shit-ass comic vibe of the prequels.  Rose is a poorly developed character (What skills does she have? What is her personality?).  Finn, who was an insecure, goodhearted, and just-brave-enough guy in Awakens, is now a bumbling idiot who relies on oversized rabbits to get him from one plot point to the next. Benicio Del Toro’s considerable acting talent is completely wasted on a character who’s a minor part of a pointless digression.

There are so many gags in the casino environment; the true hacker is a parody Frenchman, BB-8 shoots coins at enemies, they make a loud, obvious landing on a “pivotal” mission to save their friends. Contrast this with the realistic, lived-in world of Rogue One, when the protagonists meet the blind force-adept character. Notice how the frames of Rogue are not overloaded with shitty CGI, slapstick humor, and forgettable characters.

The duel between Finn and Phasma falls totally flat.  No one cares about Phasma– she’s not a part of this film’s plotline in any way. She is only thrown in because she is an action figure. Contrast her death with that of Boba Fett. His death was quick and minor, in accordance to his importance to the main plot arc. But he still matters more to the audience because he is fucking awesome, not a “chrome dome”.

Del Toro’s betrayal of Finn and Rose is similarly meaningless. Why would they expect a hacker-for-higher, who they met in a prison cell, to exhibit loyalty? Contrast this to Lando’s betrayal of Han Solo in Empire. We care about Han; he and Lando have a history together. The betrayal affects the plot and all of the main characters.

This betrayal occurs between Rose and Del Toro, two characters we don’t give a shit about, and it literally affects nothing because Pink Hair has a plan that takes care of the rebels regardless of Finn and Rose’s actions. Nobody cares–not the audience, not the other characters.

I could go on for pages, but let me just mention a few more awful things: Leia floats through space when she is dead; BB-8 can do anything now; Poe is one-dimensional, Luke plotting to murder his nephew is completely out of character, as is brushing off his shoulder to taunt Kylo; Maz Cantina flying around killing people while face-timing.

I also felt there were some major elements missing from this episode. There is no romance between Finn and Rey, or Kylo and Rey.  In my mind this seemed to be a big part of The Force Awakens, especially near the ending.  I was also disappointed that we didn’t learn more about the Knights of Ren/Snoke’s background (instead we had to follow Rose and Finn through an Episode One detour).  I was also a little disappointed that they didn’t recut the film to feature Leia’s on-screen death.  Now her death will just be part of the opening crawl in the next film, or mentioned as an off-camera event. If only there had been an appropriate time for character to die, like when she was floating lifeless through cold vacuum of space…

There were some truly amazing elements. I loved the communication between Kylo and Rey via the force.  Their relationship, and the relationship between the dark and light side of the force, is at the heart of this trilogy. What a fun way to illustrate that balance, between characters we actually care about.

I also love how Luke and Kylo both felt that the Jedi and the Sith had run their course and needed to be replaced with some new paradigm. Kylo, Rey, and Luke are all searching for meaning, and balance, and a way forward, and are looking to forge unsteady alliances. It’s compelling. Kylo and Rey’s performances are excellent, and Luke’s performance is good, especially given some of the bullshit he had to do.  He somehow kept the character slightly dignified.

The scene in Snoke’s throne room is one of my favorite sequences in the entire saga. It was unpredictable, well acted, pivotal to the plot, and visually stunning. I feel that it surpassed any action sequence in another other Star Wars film.

Overall, the sequences surrounding the Sith and the Jedi range from good to fantastic. The other components of the film, range—to quote Norm McDonald—from shit to fucking shit.

Nevertheless, I want to see the film again. I hope JJ Abrams is able to salvage this trilogy in the next film.

Diabetes and Me

Introduction

There is a strong genetic component to Type One Diabetes (T1D), as evidenced by twin and familial studies. In monozygotic twins (identical twins, with the same genome), if one twin gets T1D, there is more than a 65 % chance that the other twin will get it by the age of 60 (1). If you are a sibling of a T1D patient, you are at higher risk for developing T1D than members of the general population; there is a 6% probability for siblings, compared to 0.4% among the white US population (2).

Importantly, the presence of T1D is not completely genetically determined; rather, your genetic makeup increases your susceptibility. This is obvious upon examining the monozygotic twin studies mentioned above; if T1D was fully genetic then you would expect 100% of monozygotic twins to be (or not be) diabetic, but this is not the case. Therefore, environmental factors must also play a role. Additionally, cases of T1D in western societies have doubled in the past 20 years, a rate of change presumably too quick to be caused by genetics alone.

Type One Diabetes is a polygenetic disease, meaning that many different genes affect the probability of contracting the condition. This contrasts with diseases such as cystic fibrosis, which manifest from mutations in a single gene and inheritance of the disease follows Mendelian genetics. Genes that increase one’s risk of developing T1D are called susceptibility genes. Researchers have identified over 40 different susceptibility genes for T1D, with a range of risk (3). Susceptibility genes that confer the highest risk are found on chromosome six, and are part of the major histocompatibility complex II (MHC II a.k.a. human leukocyte antigen II (HLA-II)). An estimated 50% of the genetic risk for T1D can be attributed to HLA locus (4).

The MHC II is involved in the immune response against bacteria and viruses. It is a protein complex embedded within the cellular membrane of specific cell types and is involved in displaying antigens (peptides derived from proteins inside the cell). Antigens that are derived from invading bacterial or viral proteins are displayed on MHC II complexes. This allows the immune system to target infected cells for destruction. MHC II also displays self-antigens (peptides derived from its own genome). This acts as a quality control so that the immune system doesn’t destroy your own cells. In autoimmune diseases, self-antigens, MHC complexes, and/or some other aspect of the immune system does not function properly, so the immune system destroys normal, healthy body tissues.  In T1D, immune cells destroy the pancreatic β cells. The immune response that is elicited against β cells is a complex topic which I plan to address in a future write-up. The MHC II genotype that confers the highest risk for T1D is DR3/4-DQ8 (DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302). Given the importance of this genotype in T1D susceptibility, the rest of this article will be dedicated to trying to understand it.

 

What is DR3/4-DQ8?

The DR3/4-DQ8 genotype refers to specific types of MHC II complexes[1] displayed on specific cell surfaces. There are five types of MHC II complexes that can be displayed: DO, DM, DR, DQ, and DP. These complexes differ in their amino acid sequence (mainly at the peptide (antigen) binding site), and have been classified by serotyping. MHC II complexes are composed of two polypeptides (alpha (α) and beta (β)) that combine to form a heterodimer (two different polypeptides that come together to form a complex).

Therefore, the genotype of an MHC II complex depends on two genes, the α and β, which come together to form DO, DM, DR, DQ, and DP complexes. Given that there are five different types of MHC II complexes—each containing an alpha and beta peptide—and humans are diploid (contain two copies of each gene), the variation in MHC II complexes comes from twenty different genes. The DNA sequence varies among individuals for these genes, leading to different alleles for the MHC II complexes. These alleles are indicated by the number following the letter designation (i.e. DR3, DQ8). There can be thousands of different alleles within the HLA encoding region of chromosome six. Indeed, the HLA region is the most diverse region observed in the human genome, with over  six thousand alleles (5).

Figure 1. MHC class II complexes are embedded in the membranes of antigen presenting cells. They are composed of two proteins (alpha and beta) that form an antigen binding site. Each polypeptide (corresponding to a single gene) has intracellular and transmembrane domains, as well as two extracellular domains. The B1 and A1 extracellular domains form the site where processed antigens are presented (the peptide binding site).

 

So let’s take a closer look at the DR3/4-DQ8 genotype: DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302.

MHC II complexes are identified by the first two letters (DR and DQ for the above genotype).

Because each complex is composed of an alpha and beta there should be a B or A designation after the two-letter code. Above we see that DR does not have an alpha (A) gene described—this is because the DRA1 is non-variant (no alleles), so people don’t bother writing it.

The “/” designates the second set of alleles (from the other chromosome—remember, humans are diploid).

Some will refer to DRB1*0301-DQA1*0501-DQB1*0201 as DR3-DQA1*0501-DQB1*0201 or just DR3 or DQB1*0201.

Similarly, DRB1*04-DQA1*0301-DQB1*0302 can be called DR4-DQA1*0301-DQB1*0302 or DR4 or DQB1*0302 or DQ8.

Presumably, some abbreviate these genotypes to just DR3 or DR4 (or DQ8). Often the DR3/4-DQ8 genotype is referred to as “heterozygous”. This is because the individual has two different alleles for DR (i.e. DR3 and DR4, where homozygous would be DR3/DR3 or DR4/DR4).

The DQB1*0302 allele is often referred to as DQ8 and is linked to DR4.  Presumably, if you are DR4 than you are automatically DQ8 (as I have suggested above).

 

Figure 2. Chromosome 6 pair representing the gene organization for a DR3/4-DQ8 individual. The genes are transcribed and translated to form the protein complexes below (Figure 3).

Figure 3. Representation of the complexes expressed in a DR3/4-DQ8 cell. Alleles specific to the DR and DQ MHC II complexes increase susceptibility to T1D. These susceptibility alleles are often referred to as DR3 and DR4 (or DQ8). Some hypothesize that the heterozygous individuals can form chimera DQ complexes that have atypical antigen specificity.

 

DR3/4-DQ8—What’s the risk?

Of people who have T1D, approximately 40% have the DR3/4-DQ8 genotype, as compared to 2.4% of the general population (2). If a child is DR3/4-DQ8, the risk of developing diabetes is between 1 in 15 and 1 in 25, as compared to 1 in 300 for the general population (though by which age of diagnosis this risk is calculated at is unclear to me)(6). Patients with this genotype typically present disease phenotypes at an early age (within childhood). It’s likely that if you were diagnosed with T1D after childhood you probably do not have this genotype. However, having part of this genotype can increase susceptibility—95% of patients have DR3 or DR4 alleles, compared to ~40% of the U.S. white population (7).

Being recently diagnosed with T1D and having genotyping data from 23andme, I wanted to know if I could learn anything about my own genetic susceptibility. It looks like 23andme used to provide information on T1D susceptibility but probably got rid of it after issues with the FDA.

However, 23andMe genotypes many positions which are not included in susceptibly reports. This data can be accessed through the “browse raw data” tab, downloaded, and fed into other programs like Promethease to get more info. The quickest way to determine if an individual is DR3/4-DQ8 is to genotype two positions of the MHC-II locus: rs7454108 and rs2040410 (8). Presumably, this is because alleles are linked, so if you know the genotype at one position you can be reasonably confident of the sequence at neighboring positions (haplotypes). If rs7454108 is C/T then you are DR4 (8). 23andme doesn’t genotype rs2040410 but you can use a proxy SNP: rs2187668 (9). If rs2187668 is A/G or A/A you are DR3 (8). If you have both (DR3 and DR4) then you are DR3/4-DQ8 (8). These statements are summarized in an algorithm represented in Figure 4.  Disclaimer: this algorithm may not be correct, please consult the corresponding references for further information, and please let me know if I missed something.

The Barker et al. paper that describes these two SNPs (8) has no discussion on using these SNPs for identifying if an individual is homozygous for DR3 or DR4. However, I propose that these SNPs can be used to predict homozygosity for two reasons.

First, of 1,191 DR3/4-DQ8-positive individuals in the T1DGC, 94% were AG/CT (rs2040410/rs7454108) and 4.6% were AA/CT.

Second, DR3/4-DQ8-positive individuals in the British cohort were 87.4% AG/CT and 10% AA/CT, and in the DAISY all positive individuals were AG/CT.

In these cohorts, the CT genotype was always present for DR4 individuals, but the DR3 genotype was either AG or AA. An AA genotype at rs2040410 would predict homozygosity, but this is not the case in some of these cohorts (i.e. 10% DR3/4-DQ8 positive individuals were AA/CT in the British cohort).

Therefore, rs2040410 is not that great for predicting DR3 homozygosity. But the provided algorithm uses a proxy SNP (rs2187668) which seems to be better for predicting homozygosity (10).

Figure 4. A. Algorithm for determining DR3/4-DQ8 genotype from 23andme data. This chart is largely based off (8). The authors demonstrated that these two SNPs can be used to identify DR3/4-DQ8 individuals. However, they use rs2040410 for DR3, whereas this algorithm uses rs2187668. This is because 23andme doesn’t genotype rs2040410, but rs2187668 is a proxy SNP for rs2040410 (9). The percentage of individuals with this genotype is reported below (SNPedia, European ancestry). SNPedia uses the compliment for rs2187668 (i.e. if 23andme reports C/C than use G/G (as used here)). The heterozygous genotype is CT/AG (rs7454108/rs2187668). If the genotype is A/G for rs2187668 but not C/T for rs7454108 then the individual is DR3/X (~20%), and if rs7454108 is C/T but not A/G for rs2187668 then the individual is DR4/X (~25%), where X is some other DR allele (not DR3 or DR4). B. SNP sequence and corresponding alleles. Percentage of population taken from SNPedia. DRX is some other DR allele.

 

Interpreting the risk of individual alleles is complicated because HLA-II alleles seem to play a protective role. There are at least three alleles that seem to play a protective role against T1D: DQB1*0602, DRB1*0403, and DRB1*1401 (11). However, 23andMe does not genotype these positions and/or there is no information regarding these SNPs on SNPedia. Consequently, this leaves any protective role of SNPs out of the above algorithm.

After about ten months on the wait list, I finally met with a genetics counselor to discuss the genetics of T1D and the chance of my potential off-spring being DR3/4-DQ8. I learned, from a clinical perspective, the genetics of T1D is still very far in the research realm and therefore little can be said about the risk of the disease for my potential off-spring.

In her 20 years of being a genetics counselor, at a well-known university hospital, she has not once seen a T1D patient to discuss the genetics behind the disease. I told her about the SNPs from GWAS studies and she seemed unimpressed. She informed me that GWAS studies have not provided anything to genetic councilors yet, and she seemed suspect about the prospect.

Indeed, since one of the first publications on GWAS in 2007, I cannot find a clear example of it being applied in the clinic. However, this is still a very young field in scientific terms, and I imagine the results of GWAS will start to materialize within the years to come (if not in the clinic at least in the lab).

Nonetheless, I learned from my 23andme data that I am DR3/DRX, and that I inherited my DR3 allele from my father (he is also DR3/DRX, whereas my mother is DRX/DRX). My wife is DR4/DRX. If I understand correctly, this would mean that the probability of our off-spring being DR3/DR4 is 25%. This seems quite high.

 

References

1. Redondo, M.J., Jeffrey, J., Fain, P.R., Eisenbarth, G.S. and Orban, T. (2008) Concordance for islet autoimmunity among monozygotic twins. N Engl J Med, 359, 2849-2850.
2. Steck, A.K. and Rewers, M.J. (2011) Genetics of type 1 diabetes. Clin Chem, 57, 176-185.
3. Barrett, J.C., Clayton, D.G., Concannon, P., Akolkar, B., Cooper, J.D., Erlich, H.A., Julier, C., Morahan, G., Nerup, J., Nierras, C. et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet, 41, 703-707.
4. Mehers, K.L. and Gillespie, K.M. (2008) The genetic basis for type 1 diabetes. Br Med Bull, 88, 115-129.
5. Noble, J.A. and Erlich, H.A. (2012) Genetics of type 1 diabetes. Cold Spring Harb Perspect Med, 2, a007732.
6. Rewers, M., Bugawan, T.L., Norris, J.M., Blair, A., Beaty, B., Hoffman, M., McDuffie, R.S., Jr., Hamman, R.F., Klingensmith, G., Eisenbarth, G.S. et al. (1996) Newborn screening for HLA markers associated with IDDM: diabetes autoimmunity study in the young (DAISY). Diabetologia, 39, 807-812.
7. Steck, A.K., Armstrong, T.K., Babu, S.R., Eisenbarth, G.S. and Type 1 Diabetes Genetics, C. (2011) Stepwise or linear decrease in penetrance of type 1 diabetes with lower-risk HLA genotypes over the past 40 years. Diabetes, 60, 1045-1049.
8. Barker, J.M., Triolo, T.M., Aly, T.A., Baschal, E.E., Babu, S.R., Kretowski, A., Rewers, M.J. and Eisenbarth, G.S. (2008) Two single nucleotide polymorphisms identify the highest-risk diabetes HLA genotype: potential for rapid screening. Diabetes, 57, 3152-3155.
9. Romanos, J. and Wijmenga, C. (2009) Comment on: Barker et al. (2008) Two single nucleotide polymorphisms identify the highest-risk diabetes HLA genotype: Diabetes 57:3152-3155, 2008. Diabetes, 58, e1; author reply e2.
10. Monsuur, A.J., de Bakker, P.I., Zhernakova, A., Pinto, D., Verduijn, W., Romanos, J., Auricchio, R., Lopez, A., van Heel, D.A., Crusius, J.B. et al. (2008) Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PLoS One, 3, e2270.
11. Baker, P.R., 2nd and Steck, A.K. (2011) The past, present, and future of genetic associations in type 1 diabetes. Curr Diab Rep, 11, 445-453.

 

[1] Writing “MHC II complexes” is redundant, as the C in MHC stands for complex, but I want to emphasize the fact that there is more than one MHC II and it’s not clear to me how to pluralize MHC II. Also using the phrase “MHC II molecules” can be confusing as a MHC II complex is composed of two protein molecules that come together to form a MHC complex.