Saturday, June 30, 2012

Job creating supply side trickle down

Let's take a look at the right wing economic mantras.

A recent cartoon struck me with a very simple statement. The K chronicles had a line "Rich people are rich because they save their money." Simple, obvious, yet profound. If we want to push the economy towards saving, then giving more money to the rich would be the way to do it. But if we want the opposite, we need to do the opposite.

The current crisis is at core a lack of demand. Credit has been pulled from businesses, homeowners, credit card holders. Wealth has fallen. Everyone is scrimping, saving more, and spending less, and the aggregate result is less economic activity- at least less than we could have if everyone were usefully employed and fairly paid.

The economy hangs on the balance of saving versus spending. If it were booming, we would want to encourage saving. But as it is crawling, we want to encourage more spending and less saving. The current low interest rates are part of the equation, but the more important part is missing- the spending that should be coming from government. The stimulus helped, but has petered out, while state and local governments have heavily retrenched and are spending less.

In the stimulus, legislators asked whom to give the money to. Would it be directly spent on public goods like infrastructure and energy sustainability? Would it go to individuals, and if so, which ones? Would it go to the rich or the poor? Washington came up with an unholy mix of payroll tax cuts, going to the lower and middle class, an extension of the Bush tax cuts, going to the rich, and some infrastructure spending and state support.

Going by the above, the Bush tax cut extension was entirely useless, hardly contributing to spending and demand. But aren't its targets the "job creators", and isn't giving them money bolstering the "supply-side" of the US economy, from whence higher pay and other benefits "trickle down"? This is the Reagan revolution in a nutshell, giving us three decades that dramatically reshaped economic inequality, towards the guilded age heights we now enjoy.

Back when inflation was an issue, reweighting the economy towards supply (i.e. away from demand) made some sense. Though why that involved giving money to the rich, instead of, say, cutting military spending and funding research, isn't clear at all. In today's environment, however, it is sheer madness, and we don't hear the line used very often anymore. "Job creators" has taken its place in the mouths of Republicans.

Republicans want job creators to feel comfortable and confident, not put-upon and protested against. They should be coddled by a reversion to feudal rights to run roughshod over the environment, over their employees, and into the public purse. Oh, and fawning treatment by the media would be nice too!

But who creates jobs and why? Most are just created by ongoing businesses in response to economic prospects. Anything the government can do to improve those prospects, by way of Keynesian spending, is going to raise employment and help get us off the deflationary / zero interest rate floor. Raising or lowering taxes on individual rich people will have no effect. If such a business needs money, they go to banks to borrow some- which is even more dependent on future economic prospects.

The other class of jobs is created by entrepreneurs- those hallowed innovators always threatening to "go Galt", in the minds of Republicans, if they face just one more environmental regulation or raised tax bill, perhaps decamping to Mexico, where they can find virtually stateless regions to do business in! More seriously, entrepreneurs are an important element of US innovation and success, but their critical decisions come long before they hire accountants to moan about the difference between marginal tax rates of 31% or 35%. That is not what sent the Steves to their garage to build the Apple I.

The inspiration of socially significant business success is only partly money, and then only in the most vague and uncountable way. Entrepreneurs need efficient monetary rewards to keep their dreams alive and building, (if successful), but other motivations and resources clearly are equally important, like the cultural influence they can have through their work, the education they and their colleagues have gotten from mostly state-sponsored institutions through their lives, and the sheer enjoyment of building a temple to themselves in the form of, in this case, Apple Computer, worshipped throughout the world.

The most fatal bar to entrepreneurial innovtion is generally the anticompetitive barriers and corruption sponsored by existing businesses. Who wants to license hairdressers? Not hairdressing entrepreneurs, but established hairdressers. Who wants to raise tarriffs against imports of sugar? Concentrated interests who use the state to further their own ends. It is not the state in general that is bad for entrepreneurs, but the state made captive to incumbent interests, expressed in bureaucracy, red tape, and corruption. If Republicans were interested in bringing those costs to light and eliminating them, they would be doing the country a service. But of course most of their funding (and Democratic funding as well) comes from precisely such incumbent interests.

Lastly, and most importantly, the trickle-down theory has long been a self-serving staple of Republican thought, if not rhetoric. Apparently, giving more money to the rich benefits society generally. How much more? Well, it is hard to tell where this process is supposed to end! As argued above, nothing could be more destructive in the demand-deficient environment we find ourselves in now, where encouraging people (i.e. the rich) to save is really the last thing we should be doing.

But it isn't true more generally either. The rich are thought to invest their savings. But what forms do these investments really take, and how socially productive are they? Much of it takes the form of government bonds, which lays the question of how such savings are employed right back onto the government. Most of the rest goes into the markets- bonds, stocks, real estate, hedge funds, etc. But buying such shares is difficult to truly call investing, since the businesses long since issued their shares and got their money (see the Facebook IPO), and one's purchase neither helps neither them nor anyone else hire more workers. These markets provide liquidity, buttressed by ongoing speculation by those rich enough to gamble in the prospects of the various companies, just as they might gamble on horses.

The listed companies can use their market valuation to issue more shares, or sell themselves, or buy other companies, but at this point, the individual investor is not doing anything for economic growth. If, say, Apple's stock rises to absurd heights due to market speculation, above what is warranted by fundamental parameters like its price/earnings ratio and dividend yield, then what have the investors jointly accomplished? They may have given the company the firepower to buy other companies, or to give themselves bigger bonuses. But all this is in the hands of the company's management, which may not hire any more workers or do anything economically productive with their high stock price at all. By far most of this wealth goes to other speculators who sell their shares at the proper time, rather the improper time (and then in all probability deposit them as government bonds). The transmission to economic growth is vanishingly tenuous, far more a symptom than a cause.

The spectacle of Bill Gates and his fortune should disabuse anyone of the trickle-down theory of pampering the "job creators". His percieved highest use for his money, after having crushed countless small companies and subjected us all to truly atrocious software, is not incubating startups and leading the next tech revolution, but giving it away on philanthropic projects such as disease relief in Africa. Laudible indeed, but it shows the ultimate poverty of accumulating money to absurd levels in private hands, for the sake of economic efficiency and prosperity. Much better if that money were in the hands of regular consumers driving normal demand for economic and other cultural goods, or, let it be said indeed, in the hands of the government in its role as provider of the public goods such as education.

  • In the class war, we've lost.
  • Krugman reviews it all again, for the umpteenth time.
  • Skidelsky on leisure, consumption, inequality, and modern capitalism."That road leads to a division of society into a minority of producers, professionals, supervisors, and financial speculators on one side, and a majority of drones and unemployables on the other."
  • Lakoff on Obama's weak economic framing- it isn't enough to be right.
  • Apple, abusing its employees both here and there.
  • For Greece, there is no way out. Not only do they need complete debt forgiveness, but also rebalanced trade flows with (or continuing bailouts/gifts from) the rest of Europe.. read Germany.
  • Kaplan on Pakistan. But from what I hear, Switzerland has mountains & languages, too.
  • Enough waiting for the Fed- they don't have the answer anyhow.
  • Big banks- who needs 'em?
  • Climate catastrophe, annals of appalling"... the World Bank has been investing heavily in coal-fired power production"
  • The Texas Republican platform reads as follows: "We oppose the teaching of Higher Order Thinking Skills (HOTS) (values clarification), critical thinking skills and similar programs that are simply a relabeling of Outcome-Based Education (OBE) (mastery learning) which focus on behavior modification and have the purpose of challenging the student’s fixed beliefs and undermining parental authority."
  • Economics quotes of the week, from Joe Stiglitz:
"But the crisis showed to everyone what economic research had long revealed—the argument was a sham. What was called incentive pay was anything but that: pay was high when performance was high, but pay was still high when performance was low. Only the name changed. When performance was low, the name changed to 'retention pay.'"
"What we’ve achieved is a state too constrained to provide the public goods—investments in infrastructure, technology, and education—that would make for a vibrant economy and too weak to engage in the redistribution that is needed to create a fair society. But we have a state that is still large enough and distorted enough that it can provide a bounty of gifts to the wealthy. The advocates of a small state in the financial sector were happy that the government had the money to rescue them in 2008—and bailouts have in fact been part of capitalism for centuries."

"The narrative that you describe [of capitalism] ignores the extent to which a lot of the inequalities in the United States are not the result of creative activity but of exploitive activity. And if you look at the people at the top, what is so striking is that the people who’ve made the most important creative contributions are not there."

Saturday, June 23, 2012

We are at fault

Humans caused megafauna extinction in Australia.

As we weigh just how badly we intend to destroy the biosphere over the next few decades and centuries, a glance back at pre-history tells of some past indiscretions already on the books. The megafauna of Africa co-evolved with humans, and perhaps got to know their murderous ways in time to avoid them, at least enough to survive in part up to the present time in some spectacular examples- elephants, hippos, giraffes. Other continents had easily as dramatic a cast of megafauna, from giant sloths, lions, mastodons, to giant kangaroos, and moas. But on other continents, they lacked behavioral experience of humans and perhaps immune or other defenses, and disappeared rapidly after humans arrived.

The story has been documented on a correlation basis all over the world, from major continental invasions (North America and the Martin overkill hypothesis) to every island ever inhabited by humans. The magafauna of the Galapagos (i.e. its tortoises) are hanging on by a thread and only by conscious human reversal of our otherwise rapacious ways. The causes of extinction of mammoths in particular remains controversial, but I would bet far and away on humans being the ultimate cause- at least preventing their persistence in the refugia where they took shelter during previous warm periods.

A recent paper nails down the case of Australia in quite a bit more detail, showing the extremely close coincidence in time between the arrival of humans and various changes in the local ecology, including megafauna extinction. The researchers searched through layers of a prehistoric swamp for pollen, spores, charcoal, and carbon dates, to come up with a broad picture of the area.
"Australia's megafauna included twenty or more genera of giant marsupials, monotremes, birds, and reptiles, which were extinct by 40k years ago, soon after people colonized Australia"
A key part of the analysis is the spores of Sporormiella, a fungus that specializes on herbivore dung, serving as an index of herbivory by large animals. Unfortunately, they provide their graphs in two pieces, and to make them fit better, I rotated them flat. They track several ecological markers from 129k to 3k years ago.
Pollen abundance and other characteristics, by depth, from a pre-historic swamp in Australia, showing changes throughout, especially around the arrival of humans about 40k years ago (light gray vertical highlight on both graphs).
Green- rainforest flowering plants
Dark green- rainforest conifers and other gymnosperms
Red- Sclerophyll taxa= scrubby savannah- eucalypts, acacias, banksias, 
Yellow- Poaceae = grasses
Brown- Sporormiella indicate large herbivore presence.
Gray- charcoal from wild fires.

One can readily see that conditions dried out a bit at 70k years ago, well before humans arrived, reducing the rainforest angiosperm count. Sporormiella counts went up all the way until humans arrived at ~ 41k years ago. At that same time, pollen from grasses rises dramatically, as does charcoal. Rainforest pollen declines progressively, replaced by pollen from scrubby savannah plants.

The significance of this data set is in part that it corresponds to waht was climatically a quiet time. All that happened was that some humans learned how to build a boat to float across the Sunda Straight to Australia. The North American megafauna extinction is mixed up with the end of the ice age, but here in Australia, the climate was stable, so it easier to assign these widespread and dramatic landscape changes to the one thing that did change- the arrival of humans. It is highly reminiscent of how native Americans managed the prairies- by burning them frequently, finally banishing even scrubby plants in favor of all grasses all the time.

So, humans have been wreaking large-scale landscape damage and extinction for a very long time. We live in an impoverished world with only a glimmer of consciousness of what we have lost. The first European settlers in the Americas had unimagined bounty at their doorstep, which they then went on to systematically destroy in a typical tragedy of the commons. Fisheries are doing the same worldwide. But consciousness isn't enough, we need collective action.

"I have suggested to the monetary advisory committee for the FOMC that it is past time to try another tack: lower the payment for NOT extending credit. The power of monetary policy is to alter behavior in the world of credit. The 25-basis point payment, along with extremely low money market rates, enables banks to earn 1/4 percent a year from the Fed for doing nothing."

Saturday, June 16, 2012

Aristotle would be amazed

An exceedingly brief review of De Anima, or, On the Soul.

As an amateur philosopher, it behoves to do some spade work in the vineyards of the ancients. So I picked up an edition of Aristotle, and was intrigued.

First, it gradually becomes apparent that Aristotle has something different in mind than we do with the word "soul". He is an inveterate biologist, and is interested in that which animates the organism. So in his day the very basic question of what separates the quick from the dead was, as it were, a very live question. What is the function of breathing? What is the nature of sensation, which must also cease upon death? What characterizes all living things- breathing (no), locomotion (no), vision or other higher sensations (no), touch (maybe), need for food (yes).

His proto-Darwinian thought is incredibly tantalizing, though typically tangled up with theology.
"The acts in which it [life] manifests itself are reproduction and the use of food- reproduction, I say, because for any living thing that has reached is normal development and whch is unmutilated, and whose mode of generation is not spontaneous, the most natural act is the production of another like itself, an animal producing an animal, a plant a plant, in order that, as far as nature allows, it may partake in the eternal and divine. That is the goal towards which all things strive, that for the sake of which they do whatsoever their nature renders possible."

Theology nowadays has of course been driven off the field from many of these questions. Its soul is a shadow of its former self- some sticky residue of intuition that consciousness could not possibly come from the same mechanisms that so evidently perform all the other wonders of life.

At any rate, one can readily tell that Aristotle would be delighted beyond words to see the knowledge we have today, so long in coming after his labored speculations. Indeed, only in the last 250 years have we markedly advanced beyond the ancients in the necessary knowledge (principally chemistry and evolution) to answer most of his speculations.

And speculations they were ... and endless hairsplitting and repetition that is, frankly, painful to read. He is frequently conversing with Plato, that mystic philosopher, and so has to trot out various commonly held theories of the day.
"Thinking, loving, and hating are affections not of mind, but of that which has mind, so far as it has it. That is why, when this vehicle decays, memory and love cease; they are activities not of mind, but of the composite which has perished; mind is, no doubt, something more divine and impassible."
"Some hold that the soul is divisible, and that one part thinks, another desires. If, then, its nature admits of its being divided, waht can it be that holds the parts together? Surely not the body; on the contrary it seems rather to be the soul that holds the body together; at any rate when the soul departs the body disintegrates and decays. If, then, there is something else which makes the soul one, this unifying agency would have the best right to the name of soiuld, and we shall have to repeat for it the question: Is *it one or multipartite? If it is one, why not at once admit that 'the soul' is one? If it has parts, once more the questikon must be put: What holds *its parts together, and so ad infinitum?"
"Mind is itself thinkable in exactly the same way as its objects are. For (a) in the case of objects which involve no matter, what thinks and what is thought are identical. (b) In the case of those which contain matter each of the objects of thought is only potentially present. It follows that while *they will not have mind in them (for mind is a potentiality of them only in so far as they are capable of being disengaged from matter) mind may yet be thinkable." -translation by J. A. Smith 

This gives you an idea of the language, which clearly comes from a time before modern editing. In many places, one has a distinct sense of disjoint-ness; that something has been lost in the lengthy chain of transmission from the author. Someone may have fallen asleep! Yet, there is also a glimmer of sense here, in that the nature of the mind is open to some kind of analysis, even though Aristotle couches the idea in a pile of nonsense about thoughts and minds being identical when abstract, a sort of identity theory of computational simulation.

It is fascinating to experience a person from such a long-ago epoch, deploying his formidable intelligence on problems that were incredibly obdurate. And it is a scandal that his wooly speculations would be the standard of intellect for the next nearly 2000 years.

  • Republican unworthiness to hold national office, continued.
  • Unworthiness and vitriol, continued..
  • Chronicle of addiction: "And the jungle drums start to pound."
  • Free range continues his tale. "And wait until you hear this tale my friends because it is beyond Afghan crazy; it’s Pakistan crazy and the only level of crazy above that involves extraterrestrials."
  • Labor exploitation in IT.
  • US median family net worth dropped by almost half during this little depression.
  • Robert Reich: income = spending; lack of income = depression.
  • JP Morgan is a hedge fund, on the taxpayer's dime.
  • Inequality's relation to the crisis. Trickle up leads to an unproductive rentier class.
"According to the pro-inequality theorists, these growing surpluses [of concentrated corporate and private wealth] should have led to a boom in productive investment. Instead, they ended up fuelling commodity speculation, financial engineering and hostile corporate raids, activity geared more to transferring existing rather than creating new wealth and reinforcing the shift towards greater inequality."

Saturday, June 9, 2012

Free speech ≠ Coerced listening

A comment on Citizen's United.

A recent article about the Citizen's United case and associated machinations at the Supreme Court got me thinking about free speech. When the decision first came out, I was somewhat sympathetic because, gosh, who could be against free speech? Does the government really have a justification for censoring advertisements and other media around an election?

But I realized that this is really a false framing. The constitutional right we have is to speak freely. Just like I am doing now.. you are reading completely free speech, published freely (indeed for free!) and are reading it voluntarily (I hope).

Campaign advertising, indeed all advertising, is an entirely different proposition. When we sit down to watch TV, for instance, we are attracted by one experience, say a dramatic show with smart characters and exciting stories. That is what we are volunteering to watch. But through the magic of modern capitalism, at the same time we are force-fed quite another experience- the advertisement.

We neither want to watch this other content, nor are enthusiastic about its domineering psychological effects, which are carefully engineered to invade the most heavily fortified mental citadel. We may record our shows and fast-forward through the ads, but they still leave their imprint, political or otherwise.

This is what the PACs, campaigns, 527's, think tanks, etc. are buying into with their dollars- an ecosystem of involuntary forced listening & watching which has nothing to do with free speech, but rather with the power of forcing others to listen to one's free speech. The money buys the power, not the free speech. The equation of money with speech could indeed not be more pernicious, and to see our Supreme Court fail to make this distinction is a true mark of its right-wingery.

What would a better system look like? The US has since before its founding always had mass media, and Benjamin Franklin well knew the power of owning one's own printing press. Now everyone has a printing press, and no one has the time to read everything or judge what is worth listening to. We continue to need editors, gatekeepers, and curators of the media landscape to sift the wheat from the chaff. In the world of books, the user-curated Amazon model has been wonderful, and similar real-time mechanisms through social networking services are, well, works in progress.

What we don't need is to enshrine the practice of force-feeding innocent citizens with toxic propaganda as some kind of constitutional right, because it isn't, neither for the victim nor the perpetrator. We have the spectrum now on the internet on many platforms to give everyone their own bullhorn and printing press to express free speech freely. The Democratic party can have its message go out 24/7 to anyone who wants to listen. What they don't have any constitutional right to is to force their message down anyone's eyeballs via advertising.

So, one model is to ban advertising entirely, at least for political uses, and leave political discussions to other venues like books, magazines, editorial pages, and news media, of which there are plenty. Ron Paul is a good example of someone getting his message out and thriving on virtually no advertising. That means banning robocalls too, incidentally. Talk about unwanted, coerced communication! Such a policy would also spare our politicians a great deal of expense, and dampen their corrupting arms race for money.

But I think our political system needs something more- more political speech, not less. More venues for civic engagement and political communication, just not coerced listening. We as communities have a strong role in regulating these political platforms / megaphones in ways that open them to diverse and civically useful views.

I have proposed a voucher system for media and political financing, where citizens have a new form of currency specially set aside for those purposes, insuring that they get equal votes in their provision.

Without being quite so ambitious, great improvements could be made in the media environment by promoting the public interest more systematically. The fact that most newspapers in the US are local monopolies presents one opportunity. They are typically owned by some conglomerate that milks their markets as best they can, holds uniformly Republican-friendly views, and has no responsibility to the public for their editorial policies or lack thereof.

Such newspapers easily fulfill the same kind of scarcity condition that has been found to justify neutral content regulation of broadcasters with their constrained spectrum licenses (back when we cared!). Thus they can and should be regulated in terms of their news and editorial content along the lines of promoting diversity and promoting expression from the local community. This might require, for instance, creating a public editorial board that runs the editorial content and is a non-partisan, independently elected office.

Publishers (and politicians) could still be free to publish anything they like in other forms- leaflets, articles, books, and competing newspapers and weeklies. But if one newspaper becomes an effective local monopoly, it would be deemed a public utility for the purposes of editorial content, and be run as a public-interest entity, much like PBS.

Of course this is a very tricky issue, promoting the public interest while keeping the state's hands off any direct controls, while keeping a strong interpretation of freedom of speech and press. But the point should be obvious- promoting maximally useful and diverse speech on the public stage rather than translating financial power into a megaphone that drowns out all else.

"It is clear that the system is failing and that means we have a choice. The problem is that we first have to identify that we have that choice. ...
 While for a few decades the neo-liberals were able to persuade us that there deregulation of labour and financial markets was delivering massive wealth to us all, it is difficult to mount that case now. The evidence is compelling – the neo-liberal model is fatally flawed. So we have a choice. The problem is that the choices we have are clouded by the snowstorm of lies that the elites bombard us with every day. The Irish yes vote is an extraordinary example of that."

Saturday, June 2, 2012

A pore at the core of nerve action

A voltage-regulated ion channel protein studied in all its quivering atomic detail.

One of my earliest interests in biology was the nature of membrane proteins- how they could conduct ions back and forth across the membrane, thereby giving us energy as well as mental activity. One of the most obscure mysteries in the field was the dauntingly-named voltage-gated channel.

Nerves don't conduct electricity the way wires do. They are messy and biological, after all. Their conduction is far slower, but at the same time continuously refreshed as the signal moves along. The mechanism starts with a nerve membrane that is poised with an excess of sodium (Na+) on the outside, and an excess of potassium (K+) on the inside. This is the product of a pump (the Na/K exchange pump) that is always working away, sort of like the sump pump of the nerve cell.

The ion distribution is such that the resting state of nerve cells as well as most other cells is slightly charged, at -70 mVolts. If you open up the membrane to K+ ions only, this potential moves to -90 mV, and if you open the membrane to Na+ ions only, it moves to +100 mV. So the Na+ imbalance is significantly higher than the K+ imbalance.

The magic happens when a faint electical impulse comes along from upstream, and is felt by the special proteins mentioned above- channels (proteins that let ions through passively) that are gated by voltage- i.e. turned on when they feel a slight tingle. First, Na+ voltage-gated channels open, and dramatically let Na+ into the cell, which reverses the membrane polarity (the nerve fires, or spikes) to +40 mV. Then they close, and a different protein- the voltage-gated K+ channel- opens after feeling this positive charge. This restores local order, bringing the voltage back down to -70 mV. Indeed it brings the voltage slightly beyond, (called hyperpolarization), which prevents nerve impulses from going backwards, forming the so-called refractory period.

Action potential, in gory detail. The signal is travelling to the left, and some of the gating (Na+ and K+) on different protein channels is shown in seqeuence. The Na+ gates open when their "gating threshold" is reached, here at -55 mV. They close when the voltage rises further to +30 mV, when the K+ gates open.

A recent paper described in atomic detail how the K+ channels work, responding to a voltage change across the membrane they sit in, by shifting their shape in a complex way that alternately opens or closes their central pore, which is itself selective for K+ ions. How a protein channel can even be selective for K+ vs Na+ ions with their identical charge and similar shape is, incidentally, another highly interesting tale of protein structure & chemistry.

Author's cartoon model of the K+ channel's open state, with the critical S4 helix popped up and the channel opened, seen from the side in cut-away. K+ ions are in green, and the four channel subunits are shown on the right from a top view, with the voltage-sensitive modules in blue/red and the central pore in tan.
Author's cartoon model of the K+ channel's closed state. The S4 helix has descended and the regulatory domains have moved slightly away from the pore.

The key to this protein's dynamics is a part of its structure (helix S4, shown above as a purple rod) that has numerous positive charges on arginine and lysine amino acids along its length. This helix has been studied for some time, and its charges have been called the "gating charge", or "voltage sensor", following electrophysiological studies in bare membranes that showed that this segment of the protein, even in the absence of ions, accounts for some charge movement when one imposes an electic field, presumably being some important part of the protein that is itself charged and moves physically in response to an imposed voltage. A crystal structure has also been out for a few years, showing the static structure of this protein in open conformation.

The new paper is a tour-de-force of computation, taking these structural studies to the next dynamic level through atomic-level simulation of key parts of the protein over times up to 230 microseconds. Molecular dynamics is a well-developed field, though rarely deployed to protein-size chemicals, since the computational demands are so high. It resembles other kinds of compulational simulation, like aereodynamic airplane part simulation, weather simulation, climate simulation, etc., though it is very much on the more rigorous end of the spectrum, since basically all the relevant variables are understood.

In essence, it models each atom with its various chemical bonding, quantum mechanical, van der Waals, hydrophibic, and electrical characteristics, plus the jiggling of Brownian motion, to calculate by brute force a known chemical structure evolving through time. The method is commonly used by drug companies to "dock" drug candidates with their protein targets to see whether they might be effective lock-and-key matches. for instance.

In this case, the researchers started with known structures of the open channel, and imposed a simulated electrical field as would occur across the membrane the channel resides in to close it. They offer several movies of their simulations, two of which I link below, and believe have open access.

Starting frame from simulation, with open pore.
Ending frame from simulation, with closed pore, and red helices jutted down.

The pore of the channel is in blue at center, and begins in the open configuration. The voltage sensing domains are symmetrically arranged outside, linked by the critical red helix S4, which is the main voltage sensor. If you advance the movie rapidly by hand, you can note more easily the transition from open to closed. At the movie's native rate, the stochasitic Brownian motion overwhelms the closing movement, but is certainly interesting for that sake to show how proteins work in detail.

Another simulation frame, closeup of the sensor helix S4 from the side, in popped-up condition.

Above is a side view, of the voltage sensing S4 helix and its domain, but not the channel it regulates. The linked movie is a composite of two simulations, one from open to closed, then the reverse, from closed back to open. The colored bar at the bottom of the movie shows the charge being applied, which switches halfway through from red (more negative inside; hyperpolarization) to blue (more positive inside; depolarization). The rate is not uniform in the video, but the time elapsed is marked. Note how the critical arginine side chains (positively charged, with blue branched ends) work their way stepwise down the stable green helix by interacting with negatively charged partners.

As the researchers state, using the abbreviations R for amino acid arginine and K for lysine, both positively charged: "The S4 helix-bearing gating charge residues R1, R2, R3, R4 and K5- is the main VSD [Voltage Sensitive Domain]  moving part. S4 translated ~15Å overall across the membrane in sequential steps while rotating ~120°, moving in a groove formed by the largely stationary S1 ro S3a helices."

The S4 helix links to the pore in a couple of ways, first through its end, joining to a linker colored above in yellow, which tugs the inside end of the pore. Secondly, the four protein blobs that hold the S4 helices rotate around a bit in response to the S4 helix movement (evident in the first video sequence), in a way that helps the rest of the pore either open or close, in a sort of origami dynamic.

There is much more going on here than can be briefly related, but this gives you a taste for the main points, the explanatory power, and indeed the beauty of such a detailed analysis of an important biological structure.

"The obvious measure of the failure of this approach has been that the IMF has not decreased world poverty. In fact, the overwhelming evidence is that these programs increase poverty and hardship rather than the other way around. The IMF has a long-history of damaging the poorest nations."
  • Economics image of the week- we continue falling behind where we could be: