Saturday, June 28, 2014

Animals Ain't Got Rhythm, but (Some) Humans Do

Animals ain't got Rhythm, but (some) Humans do.

Do animals have music? Do dogs appreciate piano playing? Typically not. Do even birds, who sing so well, engage in choruses or appreciate songs not their own? Not really. And to hear jays and crows going at it can make one want to run and hide. Insects can carry on very rhythmic thrums of specific kinds, even in choruses, such as the crickets. But the mental bandwidth is such as to prohibit consideration of this monotonous output as music.

Sound is certainly important to virtually all birds and mammals, but the coding is static, not flexible, the meaning very limited. It conveys intense emotion, just not in what we understand typically as music, which includes rhythm as an essential element. So while we regard our own music as quite primal- a direct communication of emotion prior to its elaboration as speech or its perception by other modes- it combines primal emotion with something that is not universal at all: the language of music.

A recent review looked at the capacity of non-humans to learn and appreciate rhythm. It cites "... what biologist Tecumseh Fitch has called “the paradox of rhythm.” As Fitch notes, “Periodicity and entrainment seem to be among the most basic features of living things, yet the human ability (and proclivity) to entrain our motor output to auditory stimuli appears to be very rare.”"
"While the rhesus monkeys (Macaca mulatta) could successfully listen to two metronome clicks and then reproduce the same interval by tapping twice on a key, they had great difficulty learning to tap in synchrony with a metronome of several beats. Specifically, each monkey took over a year of training to learn the metronome task, and when tested, their taps were always a few hundred ms after each metronome click rather than aligned with it."

The author thinks that our evolution of speech was intimately connected to musical and rhythmic ability:
"Specifically, I proposed the “vocal learning and rhythmic synchronization hypothesis” (henceforth, “vocal learning hypothesis”), which suggests that the capacity to synchronize with a musical beat resulted from changes in brain structure driven by the evolution of complex vocal learning. Complex vocal learning is learning to produce complex vocal signals based on auditory experience and sensory feedback. This is a rare trait in nature: most animals (including all nonhuman primates) have a small set of instinctive vocalizations which they can modify in only modest ways in terms of their acoustic patterning."

Parrots provide some comparative evidence for this. They can both learn complex and responsive vocalization, and can keep time with a tempo from a metronome or music, unlike our primate cousins, who are virtually incapable of doing so, even after lengthy training. But parrots do so poorly, (not having music in the wild), so humans remain unique not only in our complexity of music, but in the very basic ability to enjoy and propagate rhythm. The author speculates a bit about the brain anatomy of this, pointing out what are thought to be relevant fiber pathways that are elaborated in humans, but this is all quite schematic to date.

One might hypothesize that for wild animals, keeping rhythm impairs their ability to stay vigilent, one of their highest goals. Entrainment is a sort of hypnosis, which we humans seem to love, along with other mind-altering practices such as drugs of many descriptions. We have given up a measure of individual vigilence in favor of the imaginative and social benefits of daydreaming, music-making, dancing, novel-writing ... many forms of social glue and mental exercise that have higher-level benefits.

  • On beat-deficient humans.
  • Patriots for anarchy.
  • On the importance of ideology in capitalism.
  • Science: truth, or just another ideology?
  • Deregulation is criminogenic.
  • Pushing on a string... in recessions, forget about monetary policy, go fiscal.
  • This week in Das Capital: "The over-work of the employed part of the working class swells the ranks of the reserve, whilst conversely the greater pressure that the latter by its competition exerts on the former, forces these to submit to overwork and to subjugation under the dictates of capital. The condemnation of one part of the working class to enforced idleness by the overwork of the other part, and the converse, become a means of enriching individual capitalists, and accelerates at the same time the production of the industrial reserve army on a scale corresponding with the advance of social accumulation. ... Taking them as a whole, the general movements of wages are exclusively regulated by the expansion and contraction of the industrial reserve army, and these again correspond to the periodic changes of the industrial cycle."
  • Economic graph of the week. It graphs the correlation between political polarization and economic inequality, in the US.

Saturday, June 21, 2014

Yes, We Are The World's Policeman

While humans may be basically and mostly good, we are not good enough for anarchy. A review of Robert Kagan's big-picture review of US foreign policy.

The international system is not a system, it is anarchy. Russia, like a wolf, just took a bite out of Ukraine, and China has recently been taking bites out of the maritime territiories of its neighbors. Whether due to moral progress, American imperialism, or the specter of nuclear war, the last sixty years have been relatively peaceful. There are far more functional democracies around the world, and for that we can be very thankful. There are some forms of international law and some helpful institutions. But in any heated situation, there is a playground kind of hierarchy, where the bigger players do unto the smaller ones unless even bigger ones stop them.

The US has been the biggest for two generations, using its powers for.. well, there certainly is a big debate whether we generally keep the world stable, peaceful and increasingly democratic, or whether we mostly do the reverse through our blundering about, even when our intentions are good, which they often are not, given the intense greed that drives much of the business-government nexus. Iraq is a good example. Be that as it may, we have been the top bully / policeman, and Robert Kagan asks whether we are giving up on this enormous task and turning in an isolationist or "normal" direction, which is to say concerned with our own interests, and not that of the system as a whole, such as it is.

In a lengthy article, Kagan offers a panoramic view of US foreign policy for the last 100 years or so, focusing particularly on the turn that the US took from traditional isolationism from the Revolution through the Depression, towards enormous and invasive world-wide interests after World War 2. Woodrow Wilson turned out to be the true prophet of this later American policy, announcing (if prematurely) that the US is the indispensible nation for keeping the world safe for democracy. Even his mechanism of an international organization was re-animated in the form of the UN, a way for US power to hide, in Augustinian fashion, behind a cloak of international legitimacy: the new world order.

Kagan focuses also on the unique properties of the US that brought this opportunity about- our geographic isolation, and thus lack of immediate threats or entanglements. And our relative disinterest in the particulars of foreign problems, making us a somewhat honest broker. Not mentioned is our overwhelming power, in economic as well as military terms, which put the world at our feet whether they wished or not. It has been an odd imperium.

Kagan's basic point is that the American public (and that lily-livered Obama!) seem to have lost the will to keep up the imperial banner, now that the clarity of the cold war has been lost, and the world becomes ever messier as our various imperial projects of the past (Cuba, Iran, Iraq) keep blowing up in our faces. But not to worry, he assures, imperiums are never perfect, and don't have to be to keep a lid on the more serious trends of instability.

Even if you are not a neocon, however, there is something to be said for the basic point. Because there is no question that the international system needs more structure. The Europeans recognize this, and have been laboring, with very mixed success, on a sort of united states of Europe. And every flareup around the world, where militants and terrorists, generally of an islamist character today, but of other millennial persuasions in the past, seep into weakly governed areas to spread offensive mayhem, reminds us that chaos and anarchy is the worst of all conditions. It is not some libertarian, Galtian paradise. No, it is a dog-eat-dog, zero-sum hell. Voters in Egypt gave a lesson in this, however bitter, by favoring the military's order over an incompetent democracy.

The key is to think about the policeman's role, which is not one of depotism. It is a delicate working around the edges to limit the worst behavior (WMD's, genocide) while building support through community understanding and deference to local sentiments on the vast majority of issues. It is not imperialism, but a more collaborative process where the stakeholders of the international system, by their weight of numbers, led from time to time by the US, and undergirded by the overwhelming force the US can bring to bear, can put boundaries on acceptable behavior of many kinds, but especially on political violence. It ain't a global government, but is better than nothing.

Specifically, it is better than relying on a balanced system of competitive alliances, (the Kissingerian ideal), which never stays in balance and breeds perpetual competition. With the rise of China, we may take the world into such a two-pole system again, which is likely to be unstable. That is why the recent pivot to Asia has been taking place, to convince the smaller powers that the monopolar world has legs for a few decades more.

But there are many problems with the policeman system. If the central policeman presumes too much on its prerogatives, (such as G. W. Bush and Iraq), the legitimacy of the whole system frays, since it only works when the other countries think it serves their interests better to participate and accept US leadership than otherwise (if grudgingly). Secondly, there is a general free-rider problem and indeed a tendecy for the secondary countries to gang up on the leader, just because they can, to score political points, out of spite, etc. South America has been a hotbed of such grievance and bitterness over the last couple of decades, often for the good reason of being the subject of the most retrograde US meddling. The US (or any leader of an implicit police system) makes an easy target. We saw this in the 60's domestically in the US with the groundswell of antipathy to the pigs, the man, the system, etc.

The central reason to save the policeman system is, as Wilson recognized, to make the world safe for democracy. As hackneyed as it sounds, it remains as true today as then. Democracy is not the historically normal form of government nor an easy system of government, as we have found out so sadly in Afghanistan, Iraq, Turkey, Egypt, Hungary, etc.. You don't just hold an election and declare history at an end. Democratic countries have voted themselves into autocracy, and weak ones are preyed on constantly by their more decisive competitiors, both state-ful and state-less. Yet once it takes hold culturally, it is extremely hard to dislodge, making sense of the project of international policing as a temporary way-station to universal democracy and more rationalized, federal-ish world government that is able to tackle the real issues of our time, such as climate heating. If one views democratic government as a better form than others, then having an international system that fosters it consistently under a police-type sponsorship makes a great deal of sense (if the policeman truly does sponsor it, which has been in doubt from time to time). Indeed, the long game vs China as well as vs Russia is a matter of playing for time as they become truly democratic, before the relative power of the US declines out of the policeman role.

End Of Days: I am extinct- the European Houting.

Saturday, June 14, 2014

West Antarctic Ice Sheet: Who Cares?

So the oceans rise by nine feet ... we all will be long dead.

One hears occasionally about the West Antarctic ice sheet "collapse". That seems pretty far off and over-wrought. How can ice sheets collapse? That doesn't make much sense. If an ice sheet is already over the ocean, then its melting wouldn't affect the water level anyhow. So what is the deal?

In this case, the sheet is a large land-based glacier (not an ice shelf, like the Ross ice shelf) whose bottom lies far below sea level by nearly 4,000 feet, though its top rises up over sea level by another mile. This glacier holds about a half million cubic miles of water. Its collapse is going to take maybe 400 years: fast if you are a geologist, but pretty slow for most other people, so it is a bit of a misnomer. Perhaps megamelt might be a better term.

Thwaites glacier forms most of the West Antarctic ice sheet that is shrinking and being undermined.

The problem is that most of the glacier is over land that is far below sea level. Over the last (cold) millennia, it has pushed all the sea water out and stabilized as an enormous glacier. But with climate heating, sea water has begun infiltrating under the glacier, and, with its salt, is going to undermine the whole glacier, melting it far more rapidly than the rest of Antarctica is going to melt in response to rising air temperatures. That is what the observers are talking about.

Cross section view showing how much of the glacier is under sea level and prone to  "collapse".

The researchers in a recent paper describing this situation do two things. They state that based on its recent flow and water loss, that this glacier has already begun collapsing / being undermined by sea water. Secondly, they put together some modelling of the melting process and estimate that even without more global warming, this glacier will unload all its water within 200 to 900 years, contributing on its own about 9 feet to higher global sea levels. Naturally, the rest of the glaciers in the world aren't sitting on their hands either, so it is just one more nail in the coffin of our lovely biosphere as it has been for the last few thousand years since the last ice age. And over the last

It is a classic slow-motion, far away, hidden-under-a-pile-of-ice process, particularly ill-suited to our communal forms of decision-making, i.e. politics. While in terms of geology and evolutionary biology, the melting is going at lighting speed, it is glacial in terms of our day-to-day public policy concerns and decision making. So Barack Obama's heroic regulations of vehicle emissions and power plant emissions are pushing against a vast conspiracy of apathy, inertia, greed, and myopia. They are far too little, far too late, though better than nothing. If CO2 were purple, we would naturally be much, much farther along by now.

Earth's CO2 history, inferred from various fossil and geologic data and models. Present time is on the far left. I have added a teal line at about 500 ppm CO2, which is where we will be in 2050, and which exceeds what Earth has seen for the last ~20 million years (the period marked "N" for Neogene).

And the response really has to be at the level of public policy, nationally and globally. Without a carbon tax or regulated cap, and without natural shortages of fossil fuels (which seem to be in much larger supply than the atmosphere can take), any CO2 that one virtuous tree-hugger spares the atmosphere simply reduces the price of fuels, helping some one else to use more. If renewable energy sources reach economic parity with essentially free fossil fuels, this situation may change. But for now, fossil fuels always win on pure, amoral, economics. Any effective solution has to be common across all users, to address this mounting tragedy of the commons.

And what does morality have to do with it? Why are tree-huggers regarded as virtuous? It is not out of sheer asceticism. It is pertinent to note that the most significant metric & consequence of global heating isn't geology, or climatology, or economics ... it is biology. The problem is not that rocks are getting warmer, or that ocean water is getting acidic. And the problem is not, (mostly), that humans will have to move a few miles inland or start growing crops in Siberia. All that can be accommodated, or has no moral consequence. The real problem is that climate heating is destroying our biosphere with increasing thoroughness, leaving only weeds and jellyfish behind.

We have already done a bang-up job of biological destruction, starting with the megafaunal extinctions of the Pleistocene (courtesy of human hunters). The last couple of centuries have seen a new mass extinction event gathering steam, as humans have commandeered the entire arable biosphere as well as rangelands, ocean productivity, and forests. Then we poisoned everything with DDT, radioactivity, and currently the neonicotinoid insecticides. Now we are placing the final nails, driving up temperatures beyond where they have been in millions of years, and shredding whole ecosystems by acidifying the ocean. It is going to be a doozy of an extinction event, up there with the greatest of all time. What seems to us slow motion is just an instant in the tapestry of life's history on earth- an incredibly destructive one.

When you see iconic species trotted out as examples of saving rare species, like pandas, condors, and tigers, you can be pretty sure that they are the walking dead. Their populations are so small and habitats so vestigal that they have lost genetic & ecological viability. Unless enormous amounts of healthy habitat are set aside, (and air conditioned!), they will go fully extinct sooner or later. One of the basic values of humanity has always been an appreciation for the beauty of nature and a recognition of the bonds we share, from its incredibly varied resources to its spiritual sustanance. We are animals, and we are dust, after all. Another basic value has been to provide for our children and the ensuing generations, which constitutes one the basic drives of life. But if we eat & heat their environment now, what will they have left? Even if we manage to keep our world on an even keel in social terms and refrain from incinerating ourselves in a nuclear war, we will, at the current pace, leave them a pale shadow of the nature that we inherited, and that is a deep and depressing shame.

Saturday, June 7, 2014

Magical multiple sequence alignments

How to use evolutionary sequence alignments to map protein-protein interfaces.

Wonk alert: this is a bioinformatics post of limited interest to lay readers. While researchers have diligently been crystalizing proteins and generating large numbers of structures, the problem of protein structure determination remains, since after getting a single structure, we want to know how a complex of multiple proteins looks, and then how they look in various active states, and on and on. The questions tend to be endless, and the capacity of structure determination methods quite limited despite their amazing advances over the years. RSCB / PDB, the protein structure database, now has about 100,000 structures, of 230,000 protein chains. But many are from obscure species, or from experiments where the same structure was solved many times, with small variations. Most are also static structures, derived under unnatural conditions.

At any rate, researchers are constantly on the lookout for new ways to gain insight into protein structure, be it using fluorescence energy transfer metrology, NMR, photocrosslinking, computational brute force prediction, ... the list is quite long. A recent paper adds another interesting method to this list, which focusses on sites of interaction between proteins, and whose materials are the growing pile of sequences that are streaming out of those ever-more productive DNA sequencers.

The principle behind this method is that evolution is naturally conservative, so one can hunt for sites of protein-protein interaction in the protein's own linear sequences, by noting where individual amino acids change in coordinated ways over evolutionary time. That is to say, if on a protein interface, one partner has an asparagine (+ charge), and the other facing it has an aspartic acid (- charge), if one of them mutates in one lineage of species to the opposite charge, the partner will typically switch as well, under pressure to preserve the strength of the interaction. These are called "covarying residue pairs". Likewise, a spatially bulky amino acid like phenylalanine might covary with a smaller partner like alanine, switching sides in an interaction to keep the interface properly shaped.

This method has been understood and applied previously to interactions within single proteins, which is a more tractable problem. This paper claims to make it a practical method to apply to multiple proteins, as long as you have an enormous amount of sequence information (i.e. as many different related sequences from various species as the segments being compared are long, in amino acids).

Contacts derived from the computational analysis of miscellaneous proteins with solved structures (using what the authors term "Gremlin" scores for amino acid proximity) are shown as yellow, orange, and red lines, extended for clarity. The red connections are ones that in the known structures are over 12Å apart, so the authors suggest that their method shows contacts that depend on flexibiliy or regulatory conditions that are not apparent in the static crystal structures. Part B shows proteins of the Complex I electron transport chain, which are very tightly complexed in the mitochondrial membrane.

The image above shows how well their method detects amino acids in structurally solved complexes that are at interfaces between proteins. It really is quite impressive, though one has to know beforehand that two (or a few) proteins interact for this method to work. It is not something one yet can deploy over a whole genome in blind fashion to find proteins that interact with each other, which would be extremely useful.

To test their method a bit more critically, they predict interacting amino acids for a set of protein pairs with unknown complex structure, though some of the proteins have known individual structures. Mostly this is grist for other researchers and future validation. But they take a few of the pairs whose individual structures are known, (or could be estimated denovo using computational methods), and put them through a static molecular docking protocol, where the virtual structures are fitted together according to their predicted interface. The results shown below make a good deal of sense, (both prima facie, and based on other work on those proteins), and they feel it validates the method.

More complex structures, this time with interfaces predicted entirely by the sequence alignment method, not from prior structural information.

"Taken together, these results suggest that in cases with small conformational change, the docking protocol can recover the entire interface to high accuracy and in cases where binding is accompanied by a large conformational change, the protocol recovers the largest intact and/or unobstructed interface."

The need for large amount of sequence makes this method a bit restricted for the moment, (the researchers used only bacterial proteins), but it is a very clever way to use evolutionary data to gain structural knowledge about complex interactions. It can be appied to stuctures that are otherwise very difficult to study, like membrane proteins, and may eventually provide data on more dynamic interactions that can not be validated by reference to static crystal structures.

  • Molecular machinery, and other PDB posters.
  • Annals of our dying environment ... the Monarch butterfly.
  • Why do we still work? Why is so much work useless? "Suddenly it became possible to see that if there’s a rule, it’s that the more obviously your work benefits others, the less you’re paid for it."
  • This week in the WSJ, Review of another Bonhoeffer bio ... still hunting for an absent god. "It is evident in the conflicted way in which he approached divinity: the awful longing for an absent God, the hunger for the hot touch of an absolute Christ."
  • "Every single state taxes those in the bottom income quintile at a higher rate than those at the top."
  • War on coal? Bring it on.
  • Is reality (and anti-humanism) worth all the trouble? Zizek vs Chomsky.
  • " ... almost everyone who deconverts from religion and declares themselves a nonbeliever does so because of a compelling need to talk about reality."
  • John Oliver on Comcast and our crappy internet.
  • What goes on in hedge funds ... opacity is the business model.
  • US policy on Syria is a disaster from start to finish.
  • Little on Piketty.
  • When libertarians have problems with people with too much money, they...
  • Why do we have economists?
  • Why do we have GDP?
  • They built it ... gilded age loggers raping the land, with fraud and despotism into the bargain.

END OF DAYS: I am critically endangered: the la hotte whistling frog of Haiti.