Quantum Consciousness?

The demarcation problem in science meets New Age tech talk.

What is science and what is not science? The difference is not terribly clear, an issue called the demarcation problem. Is theology a science of the supernatural realm? Is psi research on extrasensory perception science, as it uses scientific methods? Is string theory in physics science, even though its chances of empirical validation seem rather slim?

It isn't very clear. Science tends to be whatever scientists do and view as valid in their expert communities. Whacky ideas may migrate in from fringe areas, (atoms, endosymbiosis, plate tectonics, ulcer-causing bacteria), turning from non-science into science once evidence appears. Conversely, long-hallowed ideas within science may turn out to be complete rubbish, like space-ethers, geocentrism, and the medical humors. There is fringe - mainstream traffic, though it tends to be rather light these days, since mainstream scientists generally know what they are doing.

Unfortunately the fringe areas are enormous, populated by people highly motivated to push pet theories that tend to have some psychological motivator. Psi research is a good example, which responds to our hopeful magical thinking that somehow, some way, even though those darn materialists don't have a drop of imagination in their brains, humans can indeed sense the emotions of others far away, levitate objects, detect water through dousing rods, and see behind playing cards. At least a little, right?

The scientific fringe is part of a broader cultural miasma of misinformation, from Fox news to Herbalife to Koch political subversion to mundane political campaigns and commercial advertisements. We live in a flurry of BS coming at us from all directions, and typically, following the motivation and the funding source is a critical tool to gauge the truthiness of claims. Russia's shameless campaign of lying about Ukraine is perhaps the moment's most egregious and deadly example. So science is far from alone in living in a perilous epistemological swamp. It just tries to do a better job by way of disinterested institutions, public practices, empirical adjudication, and all the other standards that come under the so-called scientific method. Can we deploy such methods on interesting topics, or are they intrinsically confined to uninteresting ones?

The mother of all demarcation nightmares has been creationism. Otherwise known as creation science, or intelligent design. The motivation is obvious: support traditional intuitions (and some scriptural readings) to deny that humans are animals. Credentialed scientists have been deployed, glossy textbooks written, museums established, articles and books written, evidence cherry-picked, school boards subverted, all to push a theory that the scientific community dimissed many decades ago. But given enough science-y paraphernalia, they could make a decent case, at least in the popular media, that they were engaging in science. A spineless political system was reduced to mouthing the mantra that schools should "teach the controversy".

Thankfully that controversy has died down in recent years, and the professional community feels less threatened by cultural bulldozing. Nevertheless, the needle has hardly budged in the population at large, of which 42% believe in creationism outright, and 31% more believe that evolution was guided by god, which is pretty much the opposite of the whole point of evolutionary theory as currently understood. And abroad, the Islamic world is almost uniformly creationist. It is a testament to the strength of psychological intuitions and archetypes, as well as media echo chambers.

Some recent discussions have gotten me interested in another area of motivated science, which is quantum consciousness. Here, it is obvious that our intuition (and a great deal of theology) militates against a materialist view of the brain and mind. The mind-body "problem" has been perennial fodder for philosophy. Could our minds be the subjective product of nerve firings in our brains? No way! Despite the rather obvious empirical parameters that show just that, intuitionally-driven models have always looked elsewhere, invoking souls of various sorts, which typically have the added bonus of immortality, another intuited archetype. The latest version of this is the movement among philosophers to posit a cosmic consciousness (Nagel, Chalmers), which in hand-waving fashion hypothesizes that somehow, consciousness is a basic property of the cosmos, with Jain-ist particles of consciousness in every object, implying that such things as plants, and even rocks, may be conscious. It seems like a total surrender to obfuscation and mysticism, descending from the grandiose premise that, because they have been unable to figure out how it all works, no one else can either. Einstein may be able to get away with such foundational cosmic speculations, but even for him, it took more than handwaving about how no one could explain the speed of light.

One science-y form of this is quantum consciousness, where the mystery of consciousness is creatively linked to the very hard-science-y paradoxes of quantum mechanics to come up with .. something again quite vague, but the idea is that since quantum entanglement can allow instant communication of a sort at great distances, and perform outrageous computations, that this resolves those amazing capacities of our minds. Quantum mechanics has been drafted into numerous pseudoscience fields of this sort, actually.

The specific example of this field that is most advanced, in its quotient of science-y tech-talk and academic paraphernalia, is the Orch-OR theories propounded by Stuart Hameroff and Roger Penrose. Penrose is a Sir, and an eminent physicist and mathematician. Hameroff is a professor of anesthesiology and psychology at the University of Arizona. Their output of papers has been prodigious, and they host an annual conference on the topic, funded by Deepak Chopra's foundations among other interested parties. They are not charlatans, really, but I think they have totally lost the thread in this case. They present a magisterial review of their own theory in 2014.

Penrose starts off by laying the premise of their case- that due to Kurt Gödels' work, the human ability to be certain about things is mathematically impossible, which necessitates a non-conventional solution to consciousness.

"Critical of the viewpoint of ‘strong artificial intelligence’ (‘strong AI’), according to which all mental processes are entirely computational, both books [by Penrose] argued, by appealing to Gödel's theorem and other considerations, that certain aspects of human consciousness, such as understanding, must be beyond the scope of any computational system, i.e. ‘non-computable’. ...  The non-computable ingredient required for human consciousness and understanding, Penrose suggested, would have to lie in an area where our current physical theories are fundamentally incomplete, though of important relevance to the scales that are pertinent to the operation of our brains." 

"As shown by Gödel's theorem, Penrose described how the mental quality of ‘understanding’ cannot be encapsulated by any computational system and must derive from some ‘non-computable’ effect. Moreover, the neurocomputational approach to volition, where algorithmic computation completely determines all thought processes, appears to preclude any possibility for independent causal agency, or free will. Something else is needed. What non-computable factor may occur in the brain?"

Well, the fact is that humans are not that certain about things. Religions may be, but that is an emotional, not a formal, issue. We operate by Bayesian statistics, where new evidence alters our beliefs, which are always tentative and evolving as we gain experience, at least for those who are empirically engaged at all. We are not operating from a tight set of axioms, per the Gödellian system, which we transcend to understand novel or paradoxical truths in some inexplicable way (it only seems that way on LSD!). So this premise seems rather nonsensical, and the whole project starts off on a very sour note. Not only that, but the authors then go on to propose a solution (with quantum qubits migrating in microtubules) that, first, is physically impossible in the brain, and second, doesn't evade Gödel's theory anyhow, being just another form of computation. In Gödel's terms, we are very incomplete systems, whether quantum or not, but seem to get by despite that.

Hameroff's part is to focus on microtubules, which he has identified as the locus of consciousness by way of his studies of anesthesia. In mainstream science, microtubules are cytoskeletal structures, play a central role in orchestrating mitosis and cell shape, and serve as roads for the transport of cargo, which is particularly relevant in neurons, where the distance between the cell nucleus / body and its far projections can be measured in feet. These cells need constant traffic of cargoes over the microtubule network to maintain function.

His proposal is that general anesthetics work by destabilizing microtubules in the brain, or at least their quantum computations. This is itself, apart from its implications in quantum consciousness, a fringe hypothesis. Current thinking in the field is very focused on ion channels and neurotransmitter receptors as the targets, though it has been difficult to pin down the specifics. General anesthetics tend to be membrane-soluble, which leads to hypotheses about their having very broad effects on membranes (not a strong theory on its own anymore) or on proteins embedded in membranes which would naturally bind to hydrophobic chemicals as they do to membrane lipids. It doesn't help one fringe hypothesis to be dependent another one like this, for even if consciousness is not solved soon, the target of anesthesia is likely to be, by normal progress in the mainstream of neuroscience / molecular biology.

One mainstream review states:

"Anesthetics are pharmacological agents that target specific central nervous system receptors. Once they bind to their brain receptors, anesthetics modulate remote brain areas and end up interfering with global neuronal networks, leading to a controlled and reversible loss of consciousness."

It is worth noting that Penrose and Hameroff's review is extensively referenced, with citations to some work that shows, for instance, that microtubules can bind anesthetics. But this was done at such high concentrations, and found among so many other proteins that also bind, that it looks like clutching at straws. They even resort to a little bit of lying, towards the end where they enumerate predictions of their theory:

"Actions of psychoactive drugs, including antidepressants, involve neuronal microtubules. This [prediction] indeed appears to be the case. Fluoxitene (Prozac) acts through microtubules [167]; anesthetics also act through MTs [86]."

The anesthetic cited here is anthracene, which is more a poison and general chemical than an anesthetic. It is not used in medicine at all. There are plenty of chemicals that will knock out frogs (which were the subject here) without telling us much about anesthetics as a specific class. The Prozac reference is highly problematic as well, since Prozac is called an SSRI for a reason. It binds to and inhibits serotonin uptake pumps, and that is thought to be its primary mode of action. If it binds (at again, very high concentrations) to microtubules as cited, that would be a side-effect, not the primary mode of action. Additionally, if microtubule dynamics are altered to some degree by this drug, why do all the other SSRIs with different structures work? The only thing they have in common is their binding and inhibition of the serotonin transporter. This kind of highly selective, indeed misleading, citing is a big red flag, to add to the red flag of psychological motivation.

At the core of the vast enterprise is the propostion that somehow, gravitation, quantum mechanics, and microtubules hosting qubits impinge somehow on their host neurons help their computations escape the Gödellian trap ... and simultaneously constitute atoms of consciousness:

"The Orch-OR [orchestrated objective reduction] scheme adopts DP [Diósi–Penrose objective reduction, which is a version of a quantum gravity theory] as a physical proposal, but it goes further than this by attempting to relate this particular version of OR to the phenomenon of consciousness. Accordingly, the ‘choice’ involved in any quantum state-reduction process would be accompanied by a (miniscule) proto-element of experience, which we refer to as a moment of proto-consciousness, but we do not necessarily refer to this as actual consciousness for reasons to be described."

So a choice made by qubits in this scheme is instantaneous, solving the timing issues that makes free will impossible in a normal materialist theory. It also reflects the Copenhagen interpretation of quantum mechanics where an observer must be invoked to collapse (reduce) the wave function of quantum entities like electrons. The tiny observers apparently add up, in the end, to what we experience as consciousness.

"Consciousness results from discrete physical events; such events have always existed in the universe as non-cognitive, proto-conscious events, these acting as part of precise physical laws not yet fully understood. Biology evolved a mechanism to orchestrate such events and to couple them to neuronal activity, resulting in meaningful, cognitive, conscious moments and thence also to causal control of behavior. These events are proposed specifically to be moments of quantum state reduction (intrinsic quantum “self-measurement”)."

One problem, among very many, is that this sets up another mind-body conundrum. In the religious soul theories, the soul is immaterial, so it is hard to explain how it receives perceptions from the brain and injects its decisions back into that brain, which is at least acknowledged as the conduit for human behavior and sensation, if not its computational processor. Some interface is required, like the pineal gland in the system of Descarte. But in such an interface, how are physical atoms moved by immaterial, supernatural entities? There is no easy way to deal with this, other than waving it away with assertions of pan-soul-ism, where there is no localized interface, and the soul pervades everthing in some magical way.

With the microtubules, the authors claim that they might communicate with each other across the brain via gap junctions, which are small portals leading directly from one cell to another. But not only does normal nerve conduction show little effect from these junctions, indicating that they are typically not highly connected with other cells, but microtubules from one cell do not enter other cells through such junctions, (they stop at the border), so there really can't be a direct network. So the authors back up and say that the microtubules might affect their host nerve function, which then makes the whole theory nearly pointless, since a mere potentiation of normal nerve function gets us back into normal neurobiology and whatever that can accomplish in generating consciousness.

"The most logical strategic site for coherent microtubule Orch OR and consciousness is in post-synaptic dendrites and soma (in which microtubules are uniquely arrayed and stabilized) during integration phases in integrate-and-fire brain neurons. Synaptic inputs could ‘orchestrate’ tubulin states governed by quantum dipoles, leading to tubulin superposition in vast numbers of microtubules all involved quantum-coherently together in a large-scale quantum state, where entanglement and quantum computation takes place during integration. The termination, by OR, of this orchestrated quantum computation at the end of integration phases would select microtubule states which could then influence and regulate axonal firings, thus controlling conscious behavior."

One might also note in passing that the superposition of vast numbers of coherent entangled quantum entities in the brain is judged impossible by experts in the relevant fields. They have been laboring mightily to set up qubit computers in vacuums near absolute zero with handfuls of electrons. The idea that this could be done easily on a massive scale in the liquid, warm brain would cause some surprise and shock.

In the end, despite the intense New Age interest in this kind of speculation, and its extensive scholarly apparatus, it is at the far-out fringe of brain studies. At a regular neuroscience conference, Hameroff attends, but the issue of quantum consciousness is nowhere else in sight. A physicist comes with a stray poster that also invokes quantum computation, but the session devoted to mechanisms of consciousness is cleanly and clearly mainstream. They are not interested. In demarcation terms, Hameroff and colleagues have academic positions and publish their thoughts, but these are not fruitful thoughts, as they use heavily cherry-picked data for support, and sponsor no evident empirical progress in their program, which thus remains an edifice of rather wild speculation.

I am knowledgeable, but not an expert, and to me, it looks like a big snow job more than a serious scientific theory, from premises through the elaborate contents, to the conclusions. At its heart, there is a -magic happens here- kind of quality to the invocations of quantum effects that are supposed to solve non-problems like free will, or significant problems like subjective consciousness that are best left as single problems rather than compounded with significant mysteries from radically separate fields like quantum gravity.

There is also an unwillingness to recognize the great deal of mainstream work that undermines the theory. For instance, consciousness is quite well timed in its occurrence relative to other brain events like perception and willed action. There is no reason to demand instantaneous action / computation when it is well known that consciousness trails perceptions by hundreds of milliseconds, and also trails various types of reflex actions and even the opening phenomena of willed actions by similar amounts. It has a function of global integration and monitoring, rest assured. But intuition is, as usual, a poor guide to what is really going on.

Another issue is the localization of consciousness. Is your liver conscious? Are your toe nails? I don't think so, which speaks to the plausibility of cosmic consciousness theories implying the consciousness of rocks, plants, etc. Indeed, most processes in the brain are unconscious. Yet all neurons have microtubules in profusion, indeed all cells do, so theories connecting their cosmic capabilities with consciousness turn on their specific arrangement or augmentation, which ends up little better, indeed far worse, than mainstream theories about the arrangement, connectivity, and other properties of nerve cells whose relationship to thought is rather more plausible.

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Chaperones Step in to Increase Evolution's Promiscuity

Mutations are usually bad, but can be made less bad with some protein folding help.

Proteins are the central mechanics of life, catalyzing the reactions, lifting the loads, purifying the fluids, and expressing the genes. They are also the most frequent targets of damaging mutations in their encoding genes. Some of these mutations happen outside the amino acid coding regions, in regulatory areas, but the most dramatic ones are typically within the coding region, changing the amino acid sequence.

Such mutations can not only change the function of a protein, but can also change its stability- its ability to fold and stay folded. Random polypeptides typically do not fold in any coherent way, in contrast to biologically evolved proteins, so the ability to fold tightly is weakened by most mutations.

Here is where saviors come into the picture- the chaperones, which are proteins specialized to help other proteins fold. The most massive of these feature a large cave whose internal surface can switch, with consumption of ATP, between hydrophobic and hydrophilic surfaces. It is like sticking your protein inside a jiffy-pop dome that can alternately encourage unfolding and folding in a protected, isolated space, until the protein gets it all together. Remember that the insides of proteins tend to be hydrophobic, and the outsides tend to be hydrophilic, which helps to direct the folding path in normal proteins, in addition to detailed spatial and electrostatic relationships among the amino acids.

Structural aspects of one chaperone, GroES/GroEL, within which other proteins (purple & yellow, in d) other proteins can fold in isolation. As shown in C, the interior can switch, using ATP, between hydrophobic and hydrophilic surfaces, encouraging folding and unfolding, respectively. Thus even without knowing how the protein is supposed to fold, this chaperone can, given enough time and energy, bias the folding pathway towards folding. It also seems to be able to detect that it contains a folded protein, prompting opening of the chamber.

Like stability, solubility is another danger. Proteins that are not sufficiently hydrophilic on their outsides tend to glomb together and create scrambled clots in cells, like we find in brains with dementia. Keeping proteins from aggregating is another job for chaperone proteins, which can pull such proteins apart, and / or tag them for degradation altogether.

A recent paper describes how chaperones can help to buffer organisms from the effects of modestly deleterious mutations, allowing a more diverse landscape of mutations in a population than otherwise possible. This is not a new idea, but the researchers try to put a more quantitative spin on it, and look in novel places for the effects chaperones have.

"For instance, enhancing chaperone capacity through over-expression has been directly shown to promote enzyme evolvability. Chaperones have been found to act both as genotypic and phenotypic capacitors."

Some of the most interesting bits of work concern protein interaction networks. Over the years, biologists have found that the cell full of proteins is a little like the internet, with lots of interactions between various proteins. There are some very dense sub-networks with a few hub proteins that have many partners, and then more peripheral proteins. These hub proteins tend to have a bit more disorder in their protein structure, perhaps because their many interactions require a bit of hydrophobic exposed area for each one (or else a floppy region that hides the interaction area prior to the partner's appearance). So these proteins are particularly dependent on chaperone assistance in folding:

"Upon deletion of [chaperone] SSB, 50% of the hub proteins, but less than 10% of the non-hubs aggregate immediately."

Hub proteins, by the author's analysis, tend to be more frequent "clients" of chaperones such as Hsp90 and Hsp70, and have more disordered regions in their structure.

They also do an interesting survey of the degree of rewiring of such protein networks between the distantly related yeast species, S. cerevisiae and S. pombe, to set up a metric of which proteins have maintained pretty much the same function, vs those whose partnerships have changed the most (i.e. become "rewired"). They then use two metrics of evolutionary change within protein sequences, the non-synonymous vs synonymous mutation rate, and second they devise a new conservative vs non-conservative change metric for mutations that are non-synonymous. This allows them to find that while highly rewired proteins tend to have lower than average non-synonymous mutation rates, befitting their key status in their networks, (i.e. increased purifying selection), they also have higher than average non-conservative amino acid mutations, perhaps as a sign of positive selection at key spots, plus, of course, the assistance that chaperones provide to enable structurally marginal mutants to survive.

"[Chaperone] Hsp90 was found to promote protein evolutionary rates in strong substrates [dependent on Hsp90 assistance for folding] when assessed by dN or ω [metrics of degree of change in protein sequences]."

Such analyses can help us dive ever deeper into the details of evolutionary history, given the vast resources of the genome sequences now available at every turn. In this case, it emphasizes that while each protein, indeed each nucleotide position, is an individual case, we can make some crude generalizations from sequence to function and back again. For the chaperones, it is evident that they are most important for difficult proteins, whether by intrinsic design in the interaction vs independent folding tradeoff, or temporarily after a damaging mutation, which may be resolved back to the original state eventually, or to some new state with new significance for the organism.

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Give a Guy a Hammer ...

Mathematician Max Tegmark thinks the fundamental reality is math. A review of Our Mathematical Universe.

The unknown seems to drive us into conniptions, whether one's habit of thought is theology, science, or formal philosophy. The idea that the fundamental reality of our cosmos might be inexlicable is as foreign to the most advanced scientist as it was to the earliest shaman.

So there we are. Physicists are knocking their heads against several walls such as dark energy, the proper interpretation of quantum mechanics, the union of quantum mechanics and relativity / gravity, and of course, the origin of the universe. They have virtually run out of experimental options, the colliders having become as super as they are realistically going to get. What now?

One can sense this fix from recent years of the magazine Scientific American, which runs ever more fanciful articles about the nature of the universe under the heading of physics. Speculation is running rampant, and the field seems to be gradually leaving the orbit of reason. What is time? What is space? Quantum foam, strings, etc.. All worthy questions, but far too speculative and sketchy to be fed to lay readers.

A recent entrant in the cosmic speculation derby is Max Tegmark with a book about how the universe is all a big mathematical structure. It is an excellent book in most respects, very readable and fair on the known science. Even sensible in a pontifical denouement of social policy. He has the most sterling credentials as an MIT physics professor, cosmologist, and protoge of John Wheeler. I should add that I am no expert in the least respect here, so I am just offering an educated lay perspective on the book and its ideas, as presented.

There are excellent aspects also to his cosmological speculations. For instance, he develops a helpful hierarchy of multiverse categories, this being a book largely about multiverses:

Level 1 multiverse: This is the notion that inflation during the big bang gave rise not only to the region of space we can see, but to much more. How much more? Hard to say, but it could be rather enormous, all within the product of the big bang we date to ~13.8 billion years ago.

Level 2 multiverse: Here the additional notion is added that inflation, the key process that we know of from the big bang, could have been a continuous process, not just producing our universe, but many, indeed an infinite number, of others in a process that is still going on. It adds the idea that these others might have different basic physics- different constants, symmetries, etc. Why this would be is due to the unboundedness of our current theories of what might have gone on. So why not everything possible?

Level 3 multiverse: Hugh Everett came up with an interpretation of quantum mechanics that contradicts the Copenhagen interpretation, and posits that the Schrödinger equation never "collapses". It just spawns other realities where events we think occur randomly actually occur in all possibilities, each in its own reality. This does not imply the multiplication of mass and energy into these other universes, but the superposition of an infinity of different possibilities in the mathematical space of quantum mechanics- the Hilbert space- of which we see only one sample at any moment. So it all looks the same as the Copenhagen collapse interpretation.

Level 4 multiverse: This is Tegmark's special theory, where not only does the level 2 multiverse generate an infinity of universes with different laws from some originating ur-structure, but even the most basic mathematical structure- his ultimate reality- can differ to generate alternate inflation (or non-inflation) regimes, of evey possible type. Indeed, he speculates that every computable mathematical structure exists and generates its own multiverse..es.

To be brief, I can easily understand the level 1 multiverse, and don't have a big problem with the level 3 multiverse of quantum mechanics. The others are a different story. Level 2 seems a cop-out, interpreting a lack of knowledge and specification about the universe as a permissive free-for-all where everything possible occurs. The premise is, as Tegmark notes, that our universe has about 32 numbers from which physicists can, in principle, calculate all physical aspects of our universe (not counting the pending conundrums of dark energy and dark matter, among others). And the values of these numbers are, of course, quite important. Any little change here or there would blow us to smithereens. So how did they get set up?

There are two basic approaches. The traditional way was to say god did it, end of story. A slightly more updated version is to look into the matter scientifically and keep hunting for simplifying and unifying theories, especially using mathematics. This has been the job of physics for several centuries, and seems to have arrived at a sizeable set of irreducible particles and forces, but can't seem to break through to a universal theory. The most modern way is to say that all the possibilities occur in all possible universes, of which there are an infinity, and we find ourselves, naturally, only in the one that lets glorious us happen. Ergo, the level 2 multiverse.

What is the prospect of yet more simplifying and unifying insights into the universe(es)? I have no idea. But the multiverse hypotheses seem to give up prematurely, and to what end? Even with a virtual infinity of universes, the chance that we get one that has 32 numbers, some possibly irrational, and thus almost impossible to get precisely right, ranging over countless orders of magnitude, still seems slim. So I am still rooting for a unifying explanation rather than a ramifying one whose sense is saved only by the anthropic principle. And that is really what we are talking about at this point- a rooting interest in where scientific speculation heads, since no evidence to date decides among these possibilities, and evidence may never do so.

Now we get to the weirdest part of the book- the level 4 multiverse, or Tegmark's theory that reality, at its base, is math, not just that it is described by math. And that all possible mathematical structures give rise to their own multi-multiversi, etc., ad infinitum. This is all more than a little fanciful. And his arguments, forming the core of the book and the armature around which so much else is built, are surprisingly weak.

The beginning premise is that external reality exists, separate from us, and even separate from us as observers. This is not at all hard to accept. After all, the universe had to roil and moil for quite some time before we were here to observe it, so the people who posit reality as a figment of our imaginations, or quantum-wise demand observation as the requirement of reality, do not have much to stand on. Then Tegmark goes on with the rest of his argument, which I abridge:

"If we assume that reality exists independently of humans, then for a description to be complete, it must also we well-defined according to nonhuman entities- aliens or supercomputers, say- that lack any understanding of human concepts."
... 

"This means that it [a master theory of everything] must contain no concepts at all! In other words, it must be a purely mathematical theory, with no explanations or 'postulates' as in quantum textbooks ..." 

"Taken together, this implies the Mathematical Universe Hypothesis, i.e. that the external physical reality described by the ToE [theory of everything] is a mathematical structure." 

"This means that our physical world no only is described by mathematics, but that it is mathematical (a mathematical structure), making us self-aware parts of a giant mathematical object. A mathematical structure is an abstract set of entities with relations between them. The entities have no "baggage": they have no properties whatsoever except those relations."

There, in a nutshell, is his argument. Note the slight of hand of getting from a description of reality to the reality itself. He explains himself later on:

"I'm writing is rather than corresponds to here, because if two structures are equivalent, then there's no meaningful sense in which they are not one and the same, as emphasized by Israeli philosopher Marius Cohen."

I can't say that this is convincing, at least to one untutored in the arts. One can also ask whether the starting premise makes any sense. Why must a universe be describable by any entities at all, human or non-human? It could just exist in some way and for some reason we can not understand or describe. The assumption is that there is a theory of everything, which I would certainly like to see. But I don't think it is a given that such a thing exists, let alone that it needs to have the describability property Tegmark claims for it. It could just as well be undescribable, and filled with the relatively arbitrary properties we actually see.

The one thing such a theory must be is consistent enough internally to produce a reality that has the symmetries and durable properties ("laws", constants, etc.) that we see in our versions of physics. And that, of course, is why mathematics is such a useful tool in physics, not because rocks are equations, but because our reality has, necessarily, the kinds of strucures and consistencies that we can use mathematics to describe. The ultimate theory may end up being a beautifully simple equation one can write on a T-shirt (as Tegmark dreams), but we don't know that yet, and it is very hard to see how that could be, with so many simple mathematical structures already known and tested in this respect. Are strings simple? Probably not.

And why one would want to theorize our reality as being a math structure ... that is admittedly beyond me. Tegmark claims that, among other benefits, this gets rid of an infinite regress issue, as we look for ever more fundamental particles and principles. (Though we have reached an end in particle terms, not being able to divide the electrons and quarks any further.) Having the most fundamental "one" be a total abstraction, and indeed every possible total abstraction in his level 4 multiverse, buys finality at the cost of nonsensicality, little better than the turtles or deities of yore. Specifically, it is Platonism revived, thinking that what is in our minds (where math is, exclusively) is the fabric of the universe, not its map. Indeed, one suspects in the end that this book is another edition in the old-as-humanity tradition of seeing the origins of the cosmos in the mirror.

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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.

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.

• Alternate views on Kagan.
• A contrasting view from the "No, we can't" side.
• Newsflash to libertarians.. government is not, and can not be, voluntary. That would be anarchy.
• Corporations just can't help themselves from cheating on taxes. They are human, after all.
• More Obama heroics ... protecting (some of) the Pacific.
• Martin Wolf on "waking up" to climate change.
• The one PAC to rule them all, but probably not.
• Average Americans are not all that bright, in political and historical terms, sad to say.
• Devolution in Teatopia.
• Some thoughts on economics as a curriculum.

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

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.

• Global warming ... is politically global.
• National Review: To hell with planet Earth.
• The arctic? It's melting, too.
• Yes, the stupid party, and proud of it.
• Truth dawns in Saudi Arabia.
• Tyson and scientism.. we don't discover meaning, we construct it.
• Our electricity system needs a regulatory overhaul.
• As wealth concentrates upward, debt concentrates downward. The poorer you are, the more you need it, the worse the terms, and the more predatory the sharks.
• Anatomy of the financial crisis, in official narratives.
• The story behind the (lack of) cramdown, in 2008.
• Marx was sort of right.. capitalism could use another big war right about now. Or at least intelligent economic policy.
• About all those new jobs... they aren't very good.
• This week in the WSJ, Warmists = Hitler.

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.
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• 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.

Which Came First, Sex or Death?

Bodies to do the dirty work: on the origin of germ cells, somatic cells, and bodies.

Imagine you are a termite colony. The vast majority of termites can not reproduce- they are disposable workers for the good of the whole, while the alates, or winged reproductive caste, are set aside to reproduce new colonies. Your body works the same way ... virtually all its cells are on a one-way trip to death, with only the germ cells, and a vanishingly small proportion of those, giving rise to descendents in a bid for immortality.

Once upon a time, all cells were immortal. That is to say, they had no intrinsic lifespan, and could live as well as reproduce endlessly. Why give that up? A recent paper discusses the ins and outs of germ-somatic cell and tissue separation which happened early in multicellular animal evolution.

There are several theories about why this division of labor would take place. One is simple practicality- that not all cells are in a position to reproduce. Would you like your bone cells to send out new embryos to form babies? Such a democratic system would be a big mess, though plants approach it with their capacity to generate reproductive structures from any active meristem. And anyhow, every cell shares the same genome, so it shouldn't make that much difference which one in a body makes the germ cells, right?

Other theories focus on what a germ tissue can be optimized for, such as going through relatively few rounds of replication, thus minimizing mutation, or being fed by other cells, so that they do not have to do their own metabolism, which is mutagenic, again reducing the rate of mutation. While female germ cells often adhere to the former theory, male germ cells tend not to, being produced in vast profusion, requiring high rates of replication. The authors of a recent paper focus on the latter hypothesis, called the "dirty work" hypothesis; that bodies are devised to do all the dirty work of life, while the germ cells are protected from dangers of many sorts, especially from metabolic damage.

Metabolism is a messy process, spewing free radicals and other damaging chemicals about the cell. Both the production of carbohydrates using solar energy to split water molecules, and the process of using carbohydrates by splitting oxygen and returning CO2 to the air are very high-energy processes, as one can see any time something burns. Metabolic enzymology controls them, but at some point, free radicals have to be made, high-energy electrons need to be shot from one place to another, and there is no perfectly safe way to do this. The mitochondrion is an attempt to keep the danger contained in a membrane-enclosed space, but that is not completely effective either.

The paper is computational one, modelling various ecological strategies connected with this hypothesis.

"We tested the dirty work hypothesis using digital evolution, an approach where digital cells are self-replicating computer programs that evolve in an open-ended fashion and are theoretically capable of performing any computational function. For this study, we consider a world of 400 multicellular organisms (“multicells”) that compete for space, where the rate of reproduction of each multicell depends on the number and rate of computational functions being executed by constituent cells."

Basically, if you impose a mutagenic cost of doing the basic processes of life- gathering food, digesting it, metabolizing it, etc., then it stands to reason that if germ cells are spared these risks in a multicellular colony or organism, they will be able to spread their genomes with less mutagenic risk to future generations. Of course, some mutations are needed. A minimal level is required for adaptation and evolution, and some organisms even ramp up their rates of mutation when under stress, in a somewhat desperate bid for success. But on the whole, evolution has put vast resources and endless optimization into the project of high-fidelity reproduction, because as any Darwinian knows, most mutations are harmful.

So it should not be surprising that multicellular organisms rapidly took advantage of this opportunity to increase fidelity by segregating germ cells away from everything else, and building bodies to do all the so-called dirty work, including sex and thinking- which is, incidentally, very metabolically expensive.

Segregation of germ and non-germ cells, in a virtual evolution program, plotted on the X-axis, vs bands of mutagenicity going downwards from  zero (top) to high levels (bottom). 

The experimenters set various levels of mutagenicity to their virtual life tasks, and found that at intermediate levels, their virtual life forms would segregate non-reproductive cells into a soma with pretty much complete probability. At very low mutagenisis levels, there was no advantage to such segregation, and it did not evolve. At very high levels of mutagenicity, specialization of some cells (i.e. the body) to deal with mutagenic activities was essentially lethal, so such environments were avoided entirely rather than adapted to. Their simulations are clever, if very schematic. But they get the simple point across, that the origin of divided somatic / germ bodies is easily understood as a natural consequence of multicellular evolution.

So what about sex? Many bacteria have some form of sex, exchanging bits of their DNA, despite being single-celled and having only one genome to play with. Therefore sex developed long before death did, in the sense of the programmed death of a somatic body after reproduction, as is common among all animals and plants. No cell lives forever, but those that reproduce by binary division have no clear point of death. In contrast, our bodies, specialized for the complex operations of getting a living in a hostile world up to the point when a new generation can be created and nurtured out of the germ cells, have a very definite, genetically programmed (if only by default) endpoint. The way life spans vary between species of animals, but much less within them, suggests strongly that life span is not an accident, but is part of the developmental program, making way for the new generation on an optimized schedule, for evolutionary, and even cultural, rejuvenation.

As one might imagine, these ideas are related to the selfish gene hypothesis, put forth by George Williams and popularized by Richard Dawkins. Which is that bodies are the robotic (and disposable) entities devised by genes for their propagation. That is a strongly skewed perspective, however, making of the gene an almost conscious, greedy, self-sufficient, anthropomorphised totem, which is more than a little fanciful. Rather, organisms are complex communities with delegated and divided functions, one of which is to keep safe the genetic code that the whole community relies on for high-fidelity propagation. Even if the body and its mind can be viewed as disposable cat's paws for that code, they are the only part of the community that can be cognitively selfish; the gene is just a large molecule.

"The same information-work tradeoff may also have motivated a switch from RNA to DNA as the molecule of heredity. According to the RNA world hypothesis, RNA initially served as both a carrier of genetic material and a catalyst for metabolic work. However, RNA instability may have motivated a shift to DNA genomes and catalytic proteins. This is a type of molecular division of labor, ensuring both high fidelity transmission of hereditary information and the execution of critical chemical work."

• Reagan, evangelicals, and the Klan.
• Enlightenment? Not so fast!
• Just how powerful is their god, anyhow?
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• Kids these days ... can not deal with the 70's.
• Sustainable economics- why GDP is not the right measure, or the right worry.
• Secrecy, corruption and fraud in private equity companies. We are shocked!
• "Yet another example of lazy, both-sides-do-it journalism."
• Otters playing the organ? What next?
• Whose side is Mary Jo White on? Shame on the SEC, as usual.
• Why incompetent men dominate in management ... we are suckers for narcissism and overconfidence.
• "Bank of America runs its business through more than 300 offshore tax-haven subsidiaries. It reported $17.2 billion in accumulated offshore profits in 2012. It would owe $4.3 billion in US taxes if these funds were brought back to the US."