3 Chimpanzee Movies

From a couple of articles by Kimberley J. Hockings, et als.: Chimpanzees Share Forbidden Fruit, and Road crossing in chimpanzees: A risky business.

Crossing a Road (movie): Note how the first male out stands watch. AFAIK the 2nd and 3rd are young males: apprentices.

Crop Raiding (movie)

Sharing raided food (movie)

I don't have time to discuss the subject at the moment, but I'm guessing these will be interesting. Compare this "hunter’s anecdotal report" quoted from Guillot, 1956, in Dr. Hockings doctoral thesis Human-chimpanzee coexistence at Bossou, the Republic of Guinea: a chimpanzee perspective:

"I remember one strange encounter I had in the jungle. A troop of chimpanzees was crossing the jungle path ahead of me, an old male, the leader, stood glaring at us from a distance of a few paces. At intervals he intensified his gruntings to hurry up the rest of the troop, cursing the stragglers. The last chimpanzee to cross was a terrified female. Suddenly the big male gave a bound towards her, seized her and shook her and grunted at her something we could not interpret. Whatever it was, it forced her to turn back into the bush. She reappeared a moment later, and now, clinging to her back with both hands and feet, was a grimacing little baby chimpanzee, which in her terror she had abandoned. Then she leaped into the air with her baby in her arms and disappeared among the foliage of the trees. All was now in order, and the old male gave a couple of triumphant grunts, made a gesture as much to say that the path was free for me, and disappeared into the jungle, the last of his troop.”

She calls it "largely anthropomorphic and likely to be somewhat embellished, but serves to highlight the protective nature of the adult male chimpanzee during this high-risk encounter." I wonder how embellished it actually was. Read more!

Neurology and the Soul

I've just found time to read John Wilkin's Is the soul something we should be agnostic about?, as well as two posts he links to: Sean M. Carroll's Physics and the Immortality of the Soul and PZ Myers' Ain't no heaven, ain't no afterlife of any kind, either, say the physicists.

Are you folks kidding me? Or has physics actually discovered and verified an underlying source of determinism while my back was turned? Or is everybody missing at least one part of the big picture? (Or am I imagining things?)

The underlying assumption in all these arguments is that there's no way for something going on in "spirit space" to interact with the real world. Now, I don't claim to be the physicist Sean M. Carroll is, in fact my understanding is amateur and older than decoherence. But my understanding is that, in practical terms, quantum indeterminacy still reigns, at least with regard to even theoretically predicting the outcome of local wave function collapse (or, if you wish, "decoherence").

Consider the situation where an action potential arrives at a synapse, and releases a certain amount of neurotransmitter. The number of molecules of neurotransmitter vary within a small range due "indeterminacy", and the number of receptors for that neurotransmitter that are actually active will also vary, depending on many factors within the cell, many of them also slightly "indeterminate". Thus the actual size and shape of the current resulting from that action potential can vary within small limits. (In fact, even with a fixed number of molecules of neurotransmitter and receptors, there will be some variation in current due to indeterminacy of position of each neurotransmitter molecule while diffusing across the synaptic gap.)

Now, let's suppose that that one action potential is just on the border of causing the receiving neuron to fire an action potential. That is, given the current (heh) condition of the nearby dendritic arbor, the amount of current necessary to cause an action potential to fire is right in the middle of the potential variation (in current) due to indeterminacy.

Does the neuron actually fire? Or does it end up in a state of superposed states of firing and not firing? Well, I think we can state that it fires, that is that decoherence has taken place. Do we actually know the source of all the information involved in the decoherence?

We don't, of course. People who state that decoherence has proven that everything happening on the quantum state is completely deterministic are simply projecting their own prejudice (i.e. religious convictions) on what is still a highly controversial field. There's plenty of room in those little wave function collapses for huge amounts of information to flow into our universe.

We certainly don't know how many of the neurons in our brains actually balance on the head of this pin. For that matter, the calculations that go on in the dendrites to integrate the information from the current flows in the synapses also depend on distributed molecules of receptors, most of which open and close "randomly" depending on quantum processes that contain "indeterminacy".

So, is it possible for:

some sort of blob of spirit energy that takes up residence near our brain, and drives around our body like a soccer mom driving an SUV?

as Sean M. Carroll mocks and PZ Myers quotes? Well, conceivably, if we assume these "spirit" people are using the word "energy" metaphorically. (Which they probably are since they don't understand physics or thermodynamics well enough to use it in a technical sense.)

Of course the blobs of "spirit energy", actually some sort of informational phenomenon, would have to have some way of predicting the outcomes of all their interventions in these decoherences. Perhaps time and information work differently in "spirit space". Perhaps they can "see" the potential outcomes of different combinations of interventions directly, rather than having to compute it with incredibly powerful modeling. In the same way, perhaps, that a man riding a balloon can see the road ahead without having to rely on asking passing strangers about it.

Of course, this is all very interesting, and would make a great "magic system" for a fantasy novel, but is there any evidence, no matter how tenuous, that such a thing might be so?

Actually yes. Compared to other anthropoid species, humans have a third or so higher ratio of glial cells to nerve cells in at least on area of the dorsolateral prefrontal cortex (area 9L):

Based on the nonhuman species mean LS regression, humans displayed a 46% greater density of glial cells per neuron than expected.

[...]

From this prediction, glial density in humans fell within the 95% PIs (observed log glial density = 5.19; predicted = 5.02; upper PI = 5.40, lower PI = 4.63) and represented 32% more glia than expected.^[1]

Perhaps the human brain has evolved, over the last few million years, to be "ridden" by a "blob of spirit energy", and supporting the receipt of information from the blob is what requires the extra glial activity.

Of course, the actual increase isn't all that great, and:

The human frontal cortex displays a higher ratio of glia to neurons than in other anthropoid primates. However, this relative increase in glia conforms to allometric scaling expectations, when taking into consideration the dramatic enlargement of the human brain. We suggest that relatively greater numbers of glia in the human neocortex relate to the energetic costs of maintaining larger dendritic arbors and long-range projecting axons in the context of a large brain.^[1]

So this "evidence" is highly tenuous. But that's very different from saying it would require a new formulation of natural law.

So when PZ Myers says:

The biologists' perspective, which is a little less fundamental, is simply that there is no identifiable 'receiver' localized in the brain (no, not even the pineal gland, as Descartes believed), distributed physiological activity is associated with thought, and injury, disease, and pharmacology can all profoundly influence the mind. Furthermore, the way the brain works involves trans-membrane ion fluxes and synaptic activity — it's all electrochemistry and biochemistry. In addition to that new physics, we'd need a new chemistry to explain how spirit interacts with neurotransmitters or gene expression or protein phosphorylation.

Well, we don't need "new" physics (although we would need to add some stuff to the one we have) and we don't need new chemistry. The receiver is distributed, just like the physiological activity.

Despite what atheists would like to believe, there are still big holes in our scientific understanding of the world; big enough to drive the biggest spirit.

For the moment, I'd recommend agnosticism.


Notes:

1. Chet C. Sherwood, Cheryl D. Stimpson, Mary Ann Raghanti, Derek E. Wildman, Monica Uddin, Lawrence I. Grossman, Morris Goodman, John C. Redmond, Christopher J. Bonar, Joseph M. Erwin, and Patrick R. Hof Evolution of increased glia–neuron ratios in the human frontal cortex PNAS September 12, 2006 vol. 103 no. 37 13606-13611 doi: 10.1073/pnas.0605843103 Read more!

Evolutionary Theory for Creationists

I was recently informed by a creationist that "evolution is a lie!" I went to the trouble of thinking through and writing down my response, so I thought I'd share it with my readers. I created it as a .PDF so clean copies can be printed for creationists who "don't get" the internet. If you want to print it, or save it as a .PDF, click on the word "File" under "Google docs" over at the top left, and select "Print(PDF)".

Evolutionary Theory for Creationists

Can you tell it was written by an agnostic?

This document is entirely original with me, except that the "old saying" I heard somewhere: I don't remember where, I don't know who said it first, and it's something of a paraphrase anyway. With this post I'm putting this document in the public domain as a public service: feel free to copy, modify, and use the result as you please, for profit or not. (Of course, if you claim credit, you'll be "guilty" of plagiarism, but not (AFAIK) theft.) Credit would be nice, but I don't insist on it.

AK Read more!

Thundersnow

Yesterday's occurrence of thundersnow in Chicago had me looking for explanations. Wiki gave a lightweight summary, with just enough technical jargon to make it hard for a typical reader. Subsequent searching lead me to a bunch of good peer-reviewed data on the electrification of thunderstorms, but little of use understanding thundersnow.^{[3] [4] [5] [6]}

I finally found a very recent survey by David M. Schultz and R. James Vavrek,^[1] which while somewhat technical, gave me the insight I was looking for.

Summarizing everything: Thundersnow occurs when the conditions for thunderstorm-type convection are present at the same time as for general snow (in large amounts). This includes the presence of humid air above the freezing point while general temperatures, especially at the ground, are below freezing. A high lapse-rate is also necessary, in order to drive the rapid updraft which creates hail and/or graupel. Substantial electrification requires this.^[3]

We don't yet know for sure how this electrification is caused,^{[1] [2] [3] [4] [5] [6]} but the best guess involves collisions between growing graupel/hail particles and small ice particles.^{[1] [7]}

Some Personal Observation:

My difficulty finding explanations is explained: we don't even know precisely what mechanisms lead to lightning even in thunderstorms, much less thundersnow (which has been much, much less studied). I had always assumed (and you know what that does) that electrification resulted from friction of ice particles with dry air, somehow I had never previously noticed the absence of this mechanism from those considered. Since both simulations and direct experimental measurements of this process would have been easy even in the 19th century, we can presumably rule this mechanism out.

None of the articles intended for general consumption (that I read) explicitly mentioned that we don't know the mechanism for electrification, which would have saved me considerable time trying to find it. (Although the descriptions of the theories and research were well worth the reading.) This points up a general defect in science reporting: the fact that the public is being kept pretty much in the dark regarding how much isn't really known for sure in science.

Schultz, D., & Vavrek, R. (2009). An overview of thundersnow Weather, 64 (10), 274-277 DOI: 10.1002/wea.376

Links:

1  An overview of thundersnow


2  A Climatology of Thundersnow Events over the Contiguous United States Open Access


3  Thunderstorm Electrification (Semi) Open Access


4  The 29 June 2000 Supercell Observed during STEPS. Part II: Lightning and Charge Structure Open Access


5  Relationships between Convective Storm Kinematics, Precipitation, and Lightning Open Access


6  The Electrical Structure of Thunderstorms(Semi) Open Access


7  The Ice Crystal–Graupel Collision Charging Mechanism of Thunderstorm Electrification Open Access Read more!

The Final (so far) Step in Language Evolution

A recently published paper^[1] has impelled me to discuss a favorite theory of mine, involving the actual stages in which our species language skills evolved.  Or rather, the final stage.  The paper itself, Dissociating neural subsystems for grammar by contrasting word order and inflection (by Aaron J. Newmana, Ted Supallab, Peter Hauserc, Elissa L. Newportb, and Daphne Bavelier), reports the investigation of differential brain region usage in interpreting two different types of language:  inflected and positional.

In inflected language, a word's relationship to the rest of the sentence is determined (communicated) through case markers such as inflections (I'm including agglutinating languages in this class).  For instance, the subject of a sentence or clause is identified by different inflection (such as case endings) from the object of a verb or preposition.  By contrast, in a positional language (or construction within a language) this information is communicated by its position in the sentence, clause, or phrase.

What Newmana et al. have shown is that different regions of the brain are activated when a hearer (seer, actually, in this case since they studied American Sign Language) encounters phrases or clauses determined by inflection vs. word order:

To summarize, we exploited a property of American Sign Language, unique among languages thus far studied with neuroimaging, to directly compare the neural systems involved in sentence processing when grammatical information was conveyed through word order as opposed to inflectional morphology.  Critically, this comparison was made within subjects, while tightly controlling syntactic complexity and semantic content.  Reliance on word order (serial position) cues for resolving grammatical dependencies activated a network of areas related to serial working memory.  In contrast, the presence of inflectional morphology increased activation in a broadly distributed bilateral network featuring the inferior frontal gyri, the anterior lateral temporal lobes, and the basal ganglia, which have been implicated in building and analyzing grammatical structure.  These dissociations are in accord with models of language organization in the brain that attribute specific grammatical functions to distinct neural subregions, but are most consistent with those models that attribute these mapping specificities to the particular cognitive resources required to process various types of linguistic cues.^[1]

The Proposed Theory

Now my theory is that the final stage in the evolution of our language skills involve these inflected (and agglutinating) constructions.  Several facts point to this sequence.... (read the rest in the full post)

The simplest form of language is the pidgin, a "simplified language that develops as a means of communication between two or more groups that do not have a language in common".  In its simplest form a pidgin might consist of 2-3 word sentences containing a noun and a verb, with perhaps another noun representing the object of the verb.

A common theory is that many such pidgins develop naturally into creoles, which are usually typified by

• a lack of inflectional morphology (other than at most two or three inflectional affixes),
• a lack of tone on monosyllabic words, and
• a lack of semantically opaque word formation.

(Some exceptions to this standard have been noted.)  This process might take as little as one generation, leading to the widely accepted hypothesis that children come with "hard-wired" expectations of certain features in a language, and, in essence, they look for them hard enough to find them in their parents' pidgin even though it wasn't really there.^{[5] [A1]} 

What I would suggest is that entirely positional languages of this type represented the previous stage of language evolution, with the development of case marking, agreement, and flexible word order as the final evolutionary step.

For any proposed evolutionary step, a selective value must be identified.  In this case, I would propose that, very simply, flexible word order enables substantially improved epic poetry,^{[2] [3]} which in turn enables multi-generational transmission of essential myths, which in their turn can encode selectively valuable historical information.^{[4] [7]}

I'm going to defer discussion of the adaptive value of myths, and even epic, for a moment while we take a look at how languages evolve in the presence of writing.  Although the earlier forms of a language or protolanguage can be inferred from a study of its current structure, most of our information regarding linguistic development comes from written records of some sort, which means that the culture involved had some contact with writing.

Now if writing can carry information across long time periods, it can to some extent replace epic poetry and myth, reducing the need for full flexibility of word order.  This being the case, we should expect the languages of cultures using writing (or in close contact with other cultures that use writing) to show a trend of replacing fully flexible word order constructions with more word-order dependent constructions.  And so it is, especially in that most-studied of language groups, Indo-European ("IE"): 

It has long been noticed that there are trends in language change, such that certain types of development occur often and in unrelated languages.  For instance, English is one of many languages that have formed future markers from a verb of motion.  The development of Indo-European adverbial particles to adpositions, apparently independently in its daughter languages, results from reanalysis of underlying structures and is a very early development of configurational syntax in the language family.^[2]

Thus, we can see a general trend from case-marked (inflected) constructions to systems dependent on word order.  In English this process has been carried almost to completion.  We must note here that the only languages we know about in this group are those of cultures that had, or were in close contact with somebody else who had, writing.  I would predict that any IE languages that remained completely isolated from writing likely retained the fully flexible constructions of the parent language, although until we find them in contact with somebody capable of writing down reasonably large amounts of them we wouldn't know about them, and at that time we would find them already evolving towards more positional constructions.

Since the work of Lord and Parry, it's been recognized (with some debate) that the epic in its original entirely oral form was composed "on the fly" for a specific performance.^[A2]  The actual basic story might stay the same, but each performance was a unique, one-time, composition made up of "formulas", "a formula being 'an expression which is regularly used, under the same metrical conditions, to express a particular essential idea'^[3]". 

The language of epic was thus not an actual spoken dialect but a conventionalised form that developed in a manner typical of orally transmitted poetry and later became a prestigious literary variety.^[2]

We can see, here, that the complete flexibility of word order was a tremendous help in creating formulas to fit any necessary metrical/rhyme pattern.  By the time the Arcado/Cypriot dialect of Proto-Greek was being written down the loss of this flexibility was already under weigh, although the epic traditions in old Ionia (what later came to be called Achaea) may have retained the older form. 

The older IE [Indo-European] system used case to indicate spatial relations, and any accompanying P-word [prepositional and preverbal particles] added meaning without taking over the case function; but both Mycenaean and classical Greek increasingly used prepositional phrases with the preposition governing the noun phrase and determining its case, even though (from a diachronic perspective) it had been the case functions which originally determined what cases a preposition would govern.  In Homer both systems (independent case and configurational syntax) are still present, and [...] a [...] strictly synchronic view of the data is possible if the variation is viewed as the normal outcome of grammaticalisation processes, which typically generate changes which may coexist with the original constructions.  Greek speakers must have been able to recognise and produce both free and syntactically restricted uses of P-words for some time while the reanalysis of the constructions was taking place, just as English speakers can use ‘going to’ in two different syntactic constructions.^[2]

Now, it's important to realize that this shift is exactly the one studied by Newmana et al.  It involves the switch from a system that "increased activation in a broadly distributed bilateral network featuring the inferior frontal gyri, the anterior lateral temporal lobes, and the basal ganglia," to one that "activated a network of areas related to serial working memory."  (Since word-order is an essential part of prepositional (and postpositional) phrases.) 

I would argue that as the presence of writing reduced the dependence on epic for essential long-term cultural memory, languages relaxed into the easier, because older and more thoroughly evolved, positional constructions.  This relaxation, added to the fact that pidgins and (most, if not all) creoles tend to be positional, point to it being the older, original mode.  Indeed, the fact that a well developed temporally serial working memory would have been essential for complex movement in the arboreal environment means that all the building blocks would have been there for many tens of millions of years; the evolution of language simply had to tie to these pre-existing (and mostly pre-adapted) features. 

By contrast, the brain structures and circuits needed for inflected language constructions may well have been brand new, or at least substantially adapted from some pre-existing system for handling complex transformations. 

At this point we need to consider what selective advantage the capacity for epic poetry, and the myth it transmitted, offered our evolving ancestors. 

The Adaptive Value of Myth

Any modern study of myth, IMO, should start with When They Severed Earth from Sky:  How the Human Mind Shapes Myth by Elizabeth Wayland Barber & Paul T. Barber.  Quoting from the first chapter:

[I]f people were so smart--just like us--100,000 years ago, why do the myths they passed down often seem so preposterous to us? And not just to us.  Even ancients like the Greek poet Pindar, who made his living telling such stories ca. 500 B.C., sometimes felt constrained to a disclaimer: "Don't blame me for this tale!" The narrators present these myths as "histories".  Yet how can we seriously believe that Perseus turned people to stone by showing them the snaky-locked head of a monster, or that a man named Herakles (or Hercules) held up the sky for a while, slew a nine-headed water monster, moved rivers around, and carried a three-headed dog up from the land of the dead? Or that a man named Methuselah lived for almost a millennium? That an eagle pecked for years at the liver of a god tied to a mountain, or that mortal men--Beowulf, St. George, Siegfried, and Perseus included--actually fought dragons? And how can one view people like the Greeks or the Egyptians, who each believed simultaneously in three or four sun gods, as having intelligence? Didn't they notice a contradiction there? Why did people in so many cultures spend so much time and attention on these collections of quaint stories that we know of as "myths"?

The problem lies not in differing intelligence but in differing resources for the storage and transmission of data.  Quite simply, before writing, myths had to serve as transmission systems for information deemed important; but because we--now that we have writing--have forgotten how nonliterate people stored and transmitted information and why it was done that way, we have lost track of how to decode the information often densely compressed into these stories, and they appear to us as mostly gibberish. And so we often dismiss them as silly or try to reinterpret them with psychobabble.  As folklorist Adrienne Mayor points out, classicists in particular "tend to read myth as fictional literature, not as natural history" [Mayor 2000b, 192]--not least because humanists typically don't study sciences like geology, palaeontology, and astronomy, and so don't recognize the data.  [my emphasis]

One of the most striking examples they give of long-term preservation of information involves the collapse of Mount Mazama to create Crater Lake in Oregon.  To briefly summarize, a major underground spirit fell in love with a local girl and when his demand for marriage was rejected had a temper tantrum (and battle with the great spirit in the sky) that blew the top off the mountain, resulting in the present caldera lake. 

Geological analysis confirms that there was once a mountain on that spot, and that it erupted violently, spewing around 50 km³ of magma, ash, and lava-bombs until the emptying of its magma chamber caused the caldera walls to collapse inward, forming a pit some 4000 feet deep that later filled with water ([refs]), just as the myth says.  Since the eruption happened almost 7700 years ago ([ref]), this myth must have been carried down for nearly eight millennia.

Our own (typical) assumption, as we read something like the Klamath myth, is that since we do not agree with the Klamath explanation for this fiery occurrence, there is nothing worth looking at scientifically in the story.  But one of our problems as modern observers of myth (or even observers of events such as car accidents) is that people tend to present their observations and their assumed explanations all tangled up together.  On the other hand, if we strip away the explanations proffered but keep and investigate the observations, we can see that the observations in myths are fairly accurate (as far as they go), and at the very least they alert us to something of geological interest that happened in a particular place.  Furthermore, if we take for the moment the Kalamath step of assuming that the Curse of Fire was caused by a wilful being (more of this below), then we can see that the quite logical strategy is to placate that being—with a gift, bribe, or sacrifice—which is exactly what they did in their attempt to prevent or delay future destructive eruptions.  That is, the myth unrolls logically from its own premises—it is not haphazard.  In fact, there are many myths concerning geological events in the Pacific Northwest ([ref]), where until the nineteenth century the population remained stable, that is unreplaced by cultures that had not witnessed the events and therefore did not know what was referred to.^[7]

Note that these mythic memories don't need to be geological: 

An example that can serve to illustrate the historical reality lying behind the mythological narration is provided by the famous combat between Heracles and the Hydra of Lerna.  The analysis of this famous story deserves some attention because it can provide useful insight regarding the origin and factual basis of a myth, as well as other mechanisms of myth-making ([ref]).

The slaying of the Hydra has been one of the myths most widely considered, since antiquity, to rest on natural processes.  The always regenerating many heads of the Hydra have been interpreted as a symbol of the many water-sources feeding the large swamps near Lerna, and the struggle between Hercules and the monster therefore an image of the draining effort.  After finally chopping her main ‘head’, said to be immortal, the hero buried it forever, putting a huge and heavy rock on it.  Kirk (1974), following an interpretation first proposed by Palaephatus, maintains instead that this myth more likely records ancient political events.  In a manner similar to the killing of the Minotaur in the Palace of Knossos, the killing of the Hydra at Lerna, as well as the related myth about the killing of the Nemean lion (the first two labours of Heracles, the Mycenaean hero), seems to contain memories of ancient political events in addition to references about fertility rites.

Strong connections are known to have existed between Lerna until the Early Bronze Age (Lerna III), and the Cretan civilization.  The end of Lerna III was in part evidently due to the invasion of the Indo-European Greeks in c. 2200 BC.  These patriarchal Indo-European-speaking invaders, from whom later the Mycenaeans would originate, marked the end of the Early Bronze Age in many areas of the East Mediterranean.  According to typical Minoan settlement patterns, the political and religious centre and the ‘head’ of the local community, would have been the Palace of Lerna (‘House of Tiles’).  The destruction of the Lernean Palace (2300–2200 BC) is marked by the peculiar singularity, seemingly unique in the whole of Greece, that the Palace was buried by the conquerors under an enormous funerary tumulus ([ref]), considered nevertheless an enigma by archaeologists because it contains no tombs.

This unusual tumulus, deliberately positioned above the ‘head’ of the defeated society, strictly corresponds to the huge mythological rock placed by Heracles above the head of the beast ([ref]).  As such, the facts described by tradition largely coincide with what can be observed on the site.  Even the position of the buried Palace, corresponds to the location of the head of the Hydra, buried in the myth on the side of the road to Elaeus.  The mythological account can therefore be regarded as quasi-historical, recalling an Early Bronze Age phase of the Mycenean conquest of the Greek mainland against the Lernean Minoan related settlement.  The seeming truth behind the myth, and the relevance of the tumulus itself, apparently was already forgotten by the end of the Middle Helladic period (c. eighteenth–seventeenth century BC), as indicated by the fact that the tumulus was then reoccupied by the village after being left untouched for nearly 500 years.  We can thus consider this date as the moment when the local historical memory transmitted by oral tradition became a new myth as transmitted by Hesiod, Ovid, Apollodorus and other ancient writers, because the politico-religious factual story lying behind the myth had been forgotten.[7]

This long-term cultural memory isn't limited to historic events, either.  For example, in the Iliad, the process of sacrifice and sacrificial meal is twice described in almost identical language (1.458-469 and 2.421-432).  The entire description of the process may have been a single formula. 

While we today may see little value in the long-term retention of sacrificial processes, the same technique could have been used for the hunting of animals that are temporarily unavailable, the killing of "monsters" (rare large predators that are making nuisances of themselves), even the manufacture of weapons and other tools requiring materials temporarily unavailable.  Even if the precise process has been distorted in the centuries since its last use, it would have given a creative inventor a major "leg up" in recreating it.

Overall, I think we can regard the long-term cultural memory process of myths as offering a major benefit to the population that possesses it.

Epic as a Carrier of Myth

The final link in the chain is either the easiest or the hardest:  epic poetry as the primary and most effective carrier of myth.  It's generally accepted that poetical systems such as meter, alliteration, assonance, and rhyme, aid in memorizing both complete poems and the poetic formulas used in longer epics.^[3]  There is also evidence that these techniques add to the acceptance of the message by the audience.^[9]  The use of the formulas in epic, in turn, eases the "on-the-fly" composition during performance.  If the story-teller wants to say "next morning", but instead recites "when rosy-fingered dawn the early one appeared", there's much more time for composing the next portion of the performance.  The latter formula would fit metric patterns the former would not.  Because it's a formula, it doesn't have to actually be composed on the fly, rather the story-teller pulls it from his (or perhaps her) mental toolbox based on its "fit" within the metrical pattern and recites it "on autopilot" while thinking about the following formulas.

We have, then, the following logical sequence: 

• Poetic tools (meter, etc.) aid in memorization and audience acceptance,
• composing epic "on the fly" requires a large toolbox of "formulas" with tight requirements to fit into metrical (and other) slots,
• fully flexible word order allows a much larger collection of "formulas",
• the use of inflection allows flexible word order,
• therefore the capacity to use and understand inflected constructions provides the most effective transmission of any story (mythic or otherwise).

Of course, this sequence is hardly "proven", and testing it probably involves some serious challenges given the widespread influence of written material on just about everybody.

Nevertheless, it provides a coherent model for the development of inflection and the associated tools of flexible word order as an evolutionary adaptation, allowing us to perhaps glimpse the evolutionary precursor to our modern language skills.

Appendices:

A1  "... widely accepted hypothesis that children come with "hard-wired" expectations of certain features in a language":  A brief Google search or perusal of the Wiki articles will find many mentions of opposition to this idea.  I'm not going to get into this much, IMO this opposition represents the last-ditch defense of the discredited^[6] "blank slate"^[8] concept of human cognition, and thus falls into the same class with the last-ditch opposition to plate tectonics in the '70's, religious opposition to evolution, and the more specious of attempts to "falsify" the "Greenhouse effect".

(Yes, I know some people will feel their sacred oxen have been gored here, but science is about finding the facts, and IMO twisting the facts to support an outdated Marxist ideology of how human cognition works is just as bad as twisting them to support Biblical literalism.)

A2  "... the epic in its original entirely oral form was composed "on the fly" for a specific performance":  I'm referring here to conditions before any contact with writing had taken place.  Even writing in another culture in close contact with the one under discussion.  Obviously, we can only project what this would have been like, since writing of some sort was necessary to preserve the literature itself, at least until Milman Parry began his studies recording oral performances,^[3]  and of course writing was already present in the culture he studied.  The introduction of writing not only (potentially) replaces some of the essential purpose (value) of epic and other poetry, it permits the permanent preservation of a specific poetic composition, making it available for rote memorization.

It seems likely to me that the appearance of the written Iliad, as well as any other recorded (in writing) performances contemporaneous with it, would have seriously distorted the entire formulaic tradition, potentially distorting our model of what the original, truly pre-literate, epic tradition was like.  Barry Powell has suggested that the Greek alphabet was specifically created to record the work of Homer,^[10] especially the Iliad, and while that may be plausible, I find it more likely that the alphabet was created to record the more typical shorter performances found in the Little Iliad and the other poems of the "Epic Cycle".

These performances would have lasted about 2 hours at full speed; if they were dictated at 1/3 speed an entire dictation session would have required about 6 hours, a good day's work for an aoidos and his scribe.  Based on Parry's research, only the more skilled of aoidoi would have been able to do this.  Alternatively, the inventor of the Greek alphabet might have developed some sort of shorthand allowing him to write at full performance speed.

In the beginning, I suspect that recitals of these dictated poems would have been much less popular than true oral performance:  the most likely scenario is a ship captain or other traveler who carried his written texts with him and performed them in locales where (and when) no true aoidos (or rhapsode) was available.  Or perhaps he was carrying stories popular in the eastern Aegean Sea (i.e. Chios) to the Ionian settlements in the West. 

Once the Greek alphabet was created, and in use (if perhaps only by one man), it seems entirely plausible that a particularly skilled aoidos ("Homer") undertook to create a special masterpiece good for a 20-hour performance.  Thus, the Iliad.  If the same aoidos also dictated the Odyssey, it seems likely that it was many years later.

We know even less about the process by which the recording of Mesopotamian and Babylonian mythologies interacted with the presence of writing.

Newman, A., Supalla, T., Hauser, P., Newport, E., & Bavelier, D. (2010). Dissociating neural subsystems for grammar by contrasting word order and inflection Proceedings of the National Academy of Sciences, 107 (16), 7539-7544 DOI: 10.1073/pnas.1003174107

Links:

1.  Dissociating neural subsystems for grammar by contrasting word order and inflection

2.  Prepositions and preverbs in Hellenistic Greek

3.  The Singer of Tales by Albert Lord

4.  When They Severed Earth from Sky:  How the Human Mind Shapes Myth by Elizabeth Wayland Barber & Paul T. Barber

5.  The language instinct: how the mind creates language (page 21) by Steven Pinker

6.  The fateful hoaxing of Margaret Mead: a historical analysis of her Samoan Research by Derek Freeman

7.  Exploring the nature of myth and its role in science

8.  The Blank Slate by Steven Pinker

9.  Birds of a feather flock conjointly (?): Rhyme as reason in aphorisms

10.  Homer and the origin of the Greek alphabet By Barry B. Powell

Read more!

Animals Without Oxygen

The recent discovery of animals that appear to live entirely without oxygen^[1] has confirmed a scenario of convergent evolution in the development of hydrogenosomes, demonstrating with near certainty that mitochondria have evolved into hydrogenosomes multiple times.  This was already pretty will demonstrated by the discovery of hydrogenosomes with mitochondrial DNA,^{[4] [6] [7]} as well as the fact that they, and mitosomes (similar organelles that do not produce hydrogen) "all share one or more traits in common with mitochondria (Fig. 2), but no traits common to them all, apart from the double membrane and conserved mechanisms of protein import, have been identified so far."^[7] 

These animals are members of the phylum Loricifera, which is (distantly) related to arthropods and other members of the general taxon Ecdysozoa.^[1][5]  Members of this phylum tend to have very complex life cycles (for metazoans), with at least some species having a parthogenic larval stage intervening between stages of adult sexual reproductions.^[5] 

This is an exciting discovery, both in terms of the potential discoveries in energy biochemistry and what it says regarding the overall evolution of the Eukaryotes.

Efforts to pin down the exact "evolutionary tree" of the early Eukaryotes have, more and more, shown a tangled relationship among various proteins (and their coding genes), implicating a large amount of lateral transfer.^[7]  The role of mitochondria has changed during this process.  At one time the various amitochondrial Eukaryotes were regarded as (possibly) descended from the ancestral premitochondrial Eukaryote.  By now, however, it's pretty clear that most (probably all) of these lineages are descended form mitochondrial Eukaryotes.^[7] 

To complicate the picture, a number of (probably distantly related) lineages possess mitochondria that are facultative anaerobes.^[8]  Among these lineages are several animals such as parasitic helminths such as Fasciola hepatica and Ascaris suum.  It seems plausible that the probable hydrogenosomes of these newly discovered Loricifera are descended from such facultatively anaerobic mitochondria.  (Or more precisely, descended from the original mitochondria via such facultatively anaerobic mitochondria.) 

It's interesting to speculate regarding the specific metabolic pathways these species use.  One possibility is that these organelles, despite looking like hydrogenosomes, are actually using sulfate as an electron donor, producing hydrogen sulfide.  Another is that they actually produce hydrogen, which is then used by other organisms for energy, to reduce sulfates to hydrogen sulfide.  Certainly the former would provide more energy for a multicellular creature.  OTOH it would also have (probably) required a longer evolutionary path to reach.  The question I suppose, is whether a simple hydrogen-producing metabolism could have provided enough energy for such a creature. It certainly seems plausible that a sulfate (or sulfite) reducing metabolism could have evolved in a facultative anaerobe, followed by streamlining into an obligate anaerobe.

I'm certainly looking forward to the publication of further research on these animals.

T/H Nick Anthis

Danovaro, R., Dell'Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010). The first metazoa living in permanently anoxic conditions BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-30

1 The first metazoa living in permanently anoxic conditions Open Access (Preliminary PDF)

2 Anaerobic Metazoans: No longer an oxymoron Open Access (Preliminary PDF)

3 Anaerobic animals from an ancient, anoxic ecological niche Open Access (Preliminary PDF)

4 Organelles in Blastocystis that Blur the Distinction between Mitochondria and Hydrogenosomes Open Access

5 An Introduction to Loricifera, Cycliophora, and Micrognathozoa Open Access

6 Degenerate mitochondria Open Access

7 Eukaryotic evolution, changes and challenges

8 Mitochondria as we don’t know them Read more!

I'm Back! (Sort of)

I've been rather quiet lately, with a bunch of projects taking up my time and sending me all over the countryside with little opportunity for the internet, and most of that taken up with a recently completed project, the brag for which you may see at the upper left: I was selected to be a judge for Open Lab 2009, in the neurology division, which was sort of flattering, given that my expertise in the subject is entirely self-taught, mostly from books and technical papers.

I had (AFAIK) only one entry, which wasn't selected, which didn't surprise me. My big posts make extensive use of links (e.g. to explain vocabulary), especially to Wiki, and Open Lab is basically a book, with the selected blog posts printed on real paper. Handling links is presumably a tough issue, and posts that make extensive use of links aren't really all that appropriate.

Which brings me to the next subject of this post, which is blogging itself. (For reasons of time I'm not going to supply links for most of what I say.) Blogging started out (AFAIK) as mostly a way for people to put up links to interesting web pages, perhaps with a few comments. Much of it remains like this, but science blogging has evolved, in part, to something more sophisticated, including explanations of technical issues, and (including here) discussions at relevant tangents.

I was marginally involved in the early days of blogging, being a contributer to HotWired Threads, and one of the original contributers to NewsTrolls. NewsTrolls was an early blog set up by a HotWired Threads contributer called Pasty Drone, as HotWired Threads was winding its way down into obscurity.^[1],  It focused on news items, and had a comments section much as modern blogs do. (This site has since vanished, as have the old Threads on HotWired.)

Even then, I was somewhat skeptical of this format, or rather I didn't see it as being optimum for what I wanted to write. My own purpose, usually, is to make a point based on and relating to peer-reviewed science, while most science blogging today is more a matter of explaining the technical aspects of peer-reviewed science for those who don't understand enough to get it from the paper itself.

However, Blogger makes a great platform for expressing myself without having to code the entire site by hand, so for the moment that's where I'm at.


Links

1.  Educational Blogging by Stephen Downes


Read more!

The Wheel Has Turned (No Spoilers)

The latest book in Robert Jordan's Wheel of Time series, The Gathering Storm has appeared in B&N, although my last understanding is that it wasn't due 'till 11/03. I don't have time for a real review, and by the time I've created one everybody interested will probably have read the book, but herewith a few notes.

For those unfamiliar with the series, I have linked to the Wiki page, but haven't read it. It may not be completely reliable, as the series may be a contentious subject and Wiki sometimes has problems with these. However, it should give you a general idea. If you want to become familiar, I suggest starting with the first book in the series ("Eye of the World") and reading forwards. Don't rely on any sort of summaries. Watch out also for some half-sized books (for children) which split the first few volumes into smaller chunks. A careful perusal of the Tor website or Wiki should allow you to find which is which.

Jordan's posthumous co-writer, Brandon Sanderson, says in the preface, introduction, or whatever (I don't have the book with me as I write) that we should consider this the first 1/3 of the final book of the series ("A Memory of Light"), and I strongly agree.

He also mentions that he has written in his own style, rather than trying to imitate Jordan. I find the writing itself rather similar, however he (IMO) takes a different approach to simultaneity, with different scenes much more separated in time than Jordan. (I may be mistaken about this, I just don't have time to go back and double check. And in any case, this doesn't include the first and last chapters of previous books, whose scenes have always been somewhat out of sync.)

I found this book much more satisfying than the last few, in the sense that many more issues are being resolved than opened. This was to be expected, but I can confirm it.

I'm not going to discuss plot details, or even list which issues have been resolved, but I will say that it's my impression that there are far fewer surprises here than in previous books. That doesn't mean that any issues were resolved in precisely the ways I had anticipated, but that in general the resolution fit within my broader expectations.

I strongly recommend reading it if you're following the series, and I can say that IMO Sanderson is doing a good enough job that we can expect to enjoy the finalization of the series almost as much as if Jordan had done it himself. Read more!

Ardipithecus ramidus Illuminates Human Origins (Science Mag: Open Access)

I'm really short on time, but readers need to know about the October 2 edition of Science Magazine, which: 

presents 11 papers, authored by a diverse international team, describing an early hominid species, Ardipithecus ramidus, and its environment.  These 4.4 million year old hominid fossils sit within a critical early part of human evolution, and cast new and sometimes surprising light on the evolution of human limbs and locomotion, the habitats occupied by early hominids, and the nature of our last common ancestor with chimps.

Science is making access to this extraordinary set of materials FREE (non-subscribers require a simple registration).

I haven't had time to read much of it yet, but what I've seen is very suggestive. Read more!

Carnival of Evolution 16 Is Up

Here. A great line-up, including two from here. Read more!

Encephalon #76 Is Up

Here.

Looks like a great line-up.

BTW, I'm really busy with outside projects right now, so big posts are going to be sort of thin on the ground for a while. Read more!

Energy and the Brain

The questions of how much energy is used by the brain, especially its various parts, and how it's used are important.  For one thing, our understanding of the brain depends strongly on functional magnetic resonance imaging (fMRI), which in turn has a number of built-in assumptions and open questions regarding how blood flow and nutrient concentrations relate to energy usage within the tiny regions (voxels) that it can resolve.^{[7] [8]}  When dividing the brain into "parts" I'm talking not so much about areas or regions of the brain, as the microarchitectural constituents, such as axons, large and small dendrite branches, parts of the synapses on both sides of the synaptic cleft, and even astrocytes and other glial cells.  (There's considerable debate regarding how much and what types of energy transfers take place between glial cells and neurons.^[8]) 

Thus, a very recent paper in Science,^[1] Energy-Efficient Action Potentials in Hippocampal Mossy Fibers (by Henrik Alle, Arnd Roth, and Jörg R. P. Geiger) provides an important resolution to an open question regarding energy usage in unmyelinated axons.  They studied the current flows in axons of the Hippocampal Mossy Fibers, and demonstrated that the axons of these cells likely use about a third of the energy predicted by the standard notion, which is based on work going back to 1952.^{[13] [14]}  The general applicability of this notion has been disputed, however, since at least 1975 based on early data^[11] on unmyelinated axons of different species obtained with radiolabeled K⁺.^[1] 

I'm going to start with the implications of this finding, followed by a discussion of what Alle et al. did and didn't discover, followed by a brief summary of what they did to perform this measurement.

Implications of the Lower Axonal Energy Usage

I've previously discussed the various functional aspects of the brain, in terms of performing the calculations (computations) leading to its function.  These include the general system of action potentials (APs) being fired in neurons, traveling along the axons to the pre-synaptic areas where they stimulate the release of neurotransmitters, which cross the synaptic cleft to stimulate currents in the post-synaptic areas in dendrites of other neurons, which currents in turn produce voltage changes that are transmitted to the soma (neural cell body), the axon hillock, and the Axon Initial Segment (AIS) which are the most common locations for the firing of new APs (primarily the AIS).  I've also discussed the ways in which many calculations can take place beyond the simple determination whether/when to fire an AP, as well as the non-linear ways in which the dendrite behaves as an "active cable", rather than the passive cable used in simpler models of neural activity.

Now, in order to behave as an "active cable", the dendritic membrane has to have some level of on-going current that can be modified in a non-linear fashion in response to voltage changes.  These currents, or rather the ion-pumping activity required to maintain (or recover) the concentration gradients that drive them, cost energy just as do the currents in the synapses and axons.  We have general ideas how much total energy any region of the brain uses during various activities, and the reduction of how much we think the small, local, unmyelinated axons are using means there's more left over for the other functions, including membranes with "active cable" characteristics.  ...

The Results of the Research

Let's start with the easy stuff.  This study was done in the hippocampus, which is one part of the brain out of more than a hundred.  We can't know for sure that similar energy-efficiency holds in any other regions of the brain until similar studies have been made for them.  Similarly, this study was done in rats, and in principle we don't even know if the findings hold true for mice, much less monkeys or humans.  Finally, these findings apply to only one kind of cell in the hippocampus.  In principal it might not hold for the other types of cell even there.

Realistically, however, it's reasonable to assume that what holds in one place holds in all, at least potentially.  Various studies of brain energy have suggested much lower values for axon energy usage,^[11] and we can assume that what evolution has done in one place, it can do in others, assuming some sort of selective incentive to reduce energy expenditure.  And I think we can.  (Ideally, there should be some scattershot studies of other cell types and regions, to verify the general principle.  Hopefully this will offer opportunities for various researchers to get published, now that the cream has been skimmed off the discovery.)

Given the energy incentives for large-brained creatures, it seem likely that this energy efficiency evolved early in the lineages leading to mammals (and likely dinosaurs and birds as well, maybe independently).  However, the rapid early expansion of the brain in Hadrocodium wui, to a point large even for modern mammals,^[15] may represent the first opportunistic use of some mutation allowing for this energy efficiency.  (Studies of monotreme, bird, crocodilian, and other reptilian (and perhaps amphibian, depending on reptilian results) axon current flows are strongly indicated.)

In general, then, unmyelinated axons in mammalian brains can probably be assumed to be as energy-efficient as their needs for high speed will allow.  Further research and modeling will probably give us a good idea what the trade-offs are, this can be expected to be a hot area of research for a while.

Now, let's take a look at what, specifically, was discovered.

I've included links to several discussions of how action potentials work, so I'm not going to try to cover everything here.  Basically, there are several ion flows involved in the action potential in the axon, but primarily they are sodium (Na⁺) and potassium (K⁺), with the Na⁺ concentration much higher outside the cell than inside, thus creating a current when it flows into the cell (I_Na), and the opposite for K⁺ (which currents are abbreviated I_k).  These two currents are in opposite directions, and if they occur simultaneously at any one spot along the axon they will cancel out, while taking up energy.

In the earliest research into such currents, which were done in the giant axon of the squid,^{[13] [14]} there appears to be considerable overlap.  (This type of axon was used because its large size allowed researchers "to insert voltage clamp electrodes inside the lumen of the axon", even at this comparatively primitive stage of the technology.) The assumption was made that this overlap was general, even in mammals, although (as mentioned above) other research on unmyelinated axons suggested otherwise.^[11] 

As it turns out, Alle et al. have discovered that there's much less overlap of currents than previously assumed because the I_K came mostly after the I_Na was complete.  They also determined, through simulations, that

the observed degrees of charge separation are accompanied by comparatively low peak conductance densities, suggesting low numbers of channel proteins per area, which would minimize infrastructural costs for AP conduction.

Thus, not only are APs cheaper in energy costs than has been assumed, but the cost of producing the infrastructure is also lower.

How the Research Was Done

Alle et al. used a technique called patch-clamp recording to measure the currents found in the membrane of rat hippocampal mossy fiber boutons (MFBs).  In patch-clamp recording, a small section of cell membrane is removed with a pipette, in this case from boutons, which are small enlargements of the axon containing the pre-synaptic portion of synapses.  A voltage command was applied that duplicated "a previously-recorded AP wave", and the currents were measured. 

The onset of K⁺ currents (I_K; Fig. 1, B and C, blue traces; n = 8) was significantly delayed compared to that of I_Na (106 ± 5 µs; P < 0.001), similar to results obtained from whole-bouton recordings (Fig. 1D, 115 ± 7 µs; P < 0.001, n = 8; P > 0.5 for patch versus whole-bouton recording).  The resulting small overlap of inward and outward currents [Fig. 1, B (inset) and C] indicated a high Na⁺ efficiency and, accordingly, energy efficiency in hippocampal mossy fibers, contrasting with previous simulations of axonal APs and their underlying currents ([refs]).^[1]

Untangling the technical language, we see that the cell membrane of these particular axons responds to the voltage regime found in the AP with currents that barely overlap.  This is the core finding.

There were also simulations: 

To complement these results by a quantitative assessment of the Na⁺ influx as well as peak Na⁺ and K⁺ conductance densities (G_Na and G_K) underlying an AP propagating along an axon, we performed numerical simulations of APs.  We used conductance functions (Fig. 2A) derived from recorded currents (Fig. 1) in a compartmental model of the mossy fiber ([ref]) to reconstitute propagating APs ([ref to supporting data]).  Simulations resulted in AP waveforms and underlying currents closely resembling recorded APs and currents (Fig. 2B and fig. S1, A to D).  The validity of our approach was further tested with independent predictions of the model, such as I_Na onset potential and AP propagation velocity, which both complied with experimental data (Fig. 2C and fig. S2).^[1]

These demonstrate that the values and timings of the currents involved, when incorporated into simulations, match the observed data.

They also analyzed the energy costs of the activity at the synapse that results from arrival of an AP, estimating that

the cost ratio of the mossy fiber AP itself to the downstream events (Fig. 4) has an upper limit of about 0.15 ([ref to supporting data]), shifting the emphasis of activity-dependent energy demand to downstream processes elicited by transmitter release, as suggested by in vivo work ([refs]).

IOW the APs require less energy, so there's more for other processes.

Alle, H., Roth, A., & Geiger, J. (2009). Energy-Efficient Action Potentials in Hippocampal Mossy Fibers Science, 325 (5946), 1405-1408 DOI: 10.1126/science.1174331

Links:  I've included only the links called out in this leader. Not all of these links are called out in the text.  Many are references taken from the featured paper.  Use the back key if you came via clicking a footnote. 

1.  Energy-Efficient Action Potentials in Hippocampal Mossy Fibers paywall

2.  An Energy Budget for Signaling in the Grey Matter of the Brain Open Access

3.  The neural basis of functional brain imaging signals

4.  The Cost of Cortical Computation Open Access

5.  Hemodynamic Signals Correlate Tightly with Synchronized Gamma Oscillations Free Registration Required

6.  Coupling Between Neuronal Firing, Field Potentials, and fMRI in Human Auditory Cortex Free Registration Required

7.  What we can do and what we cannot do with fMRI

8.  Metabolic and hemodynamic events after changes in neuronal activity:  current hypotheses, theoretical predictions and in vivo NMR experimental findings Open Access Author manuscript

9.  An Energy Budget for the Olfactory Glomerulus Open Access

10.  Functional Trade-Offs in White Matter Axonal Scaling Open Access

11.  Energetic aspects of nerve conduction:  The relationships between heat production, electrical activity and metabolism paywall

12.  Cortical Action Potential Backpropagation Explains Spike Threshold Variability and Rapid-Onset Kinetics Open Access

13.  The Optimum Density of Sodium Channels in an Unmyelinated Nerve paywall

14.  A QUANTITATIVE DESCRIPTION OF MEMBRANE CURRENT AND ITS APPLICATION TO CONDUCTION AND EXCITATION IN NERVE may be open access, slow loading

15.  A New Mammaliaform from the Early Jurassic and Evolution of Mammalian Characteristics Free registration required

Read more!