John P. Harrington and California Native Languages

John P. Harrington is known for taking copious notes on Southern California native languages. In the early twentieth century, many of these languages were already moribund. In at least one case - Tataviam, a Uto-Aztecan language spoken in the Santa Clara River basin which empties into the Pacific between Oxnard and Ventura - Harrington's notes constitute the only attestation the now-extinct language left to posterity.

It always amazes me when languages go extinct, not in isolation in the wilderness, but in the midst of booming humanity. Yes, I understand that the more numerous and economically-overbearing the new language community is (English in this case), the more likely the old language is to go extinct. But it always seems that out of all these people that settled Southern California, more than one would have been interested in recording them before they disappeared into the dust.

Button-Pushing Experiments Disprove Only One Fragile Model of Freewill

Experimental evidence continues accumulating which shows that human motor behavior, and conscious awareness of the decision to perform the behavior, are often preceded by neuronal activity. (Classic Libet experiment described here.) This has sometimes been taken as a disproof of free will. This reasoning is flawed. If we believe "if free will exists, then it applies to all human motor behavior, and all neuronal activity engaged with this motor behavior must be conscious". Therefore, for these experiments to be a disproof, at least two assumptions must be true: 1) the entire chain of events from deciding to act to performing the act must take place within consciousness to be called free will, and 2) this simple motor task model must be generalizeable to all decision-making and motor behavior taking place on all time scales.

To #1: it is possible that the decision is made, relative to the depolarization path of the motor act, "prior" to consciousness. If this is always the case, then epiphenomenalism is the correct description of consciousness, even though we could still have free will, because we can still affect future belief states and motor acts. Consequently it's worth asking if in these models, the "originating" neuron(s) is/are really the originating neuron. Acts of apparent free will merely passing through an unconscious pathway would be even less troublesome to the idea of free will than one originating in unconscious neurons.

Analogously, we cannot choose beliefs - we don't have free will about what we perceive and believe, because perception and belief follow necessarily from sense data and from the model of the universe that exists in our brains. When we encounter sense data, we interpret it immediately as representing something and as being causally related to other things in reality. For example, you cannot see someone smile, and DECIDE consciously whether or not to believe that they are smiling, and whether or not to believe that this means something about their emotional state. But this doesn't mean that we are prisoner to those beliefs and that we cannot influence future perceptions and beliefs. If you cross-check those beliefs, you can engage in behaviors the outcomes of which can differ in obvious
ways that then will allow you to update those beliefs.

At the very least, concluding that experimental results of this sort invalidate the idea of free will, you must carry other assumptions about the nature of consciousness and free will besides just "some objects' motions cannot be predicted from prior states, and those objects have conscious experience which in some way influences those motions". The separability of these two parts of free will - the idea of unpredictable output on the one hand and input from conscious experience on the other - is important. What are the requirements for non-conscious objects with unpredictable output? Are there conscious objects with completely predictable output? Another way of asking is whether things without nervous systems can have free will.

To #2, it's worth asking whether there are classes of decisions that are more or less subject to free will; i.e., how much can we generalize these results? Certainly there are cases where free will can be an illusion, but this falls short of disproving the possibility of free will in general. By all means experimenters should continue asking this question in more settings, although a button-push model wouldn't seem to give the nervous system a chance to shine. My suspicion is that if free will exists in any action it's in long-term executive planning.

It's worth mentioning that it seems strange very strange that our own lack of free will is not obvious to us, given that prediction of the behavior of conspecifics is evolutionarily extremely important. Why the inability to do so exactly, or why the strong appearance that we are the source of action? One speculation is game-theory oriented, that the input-output chain must necessarily be clouded by introducing randomness (which wouldn't really be free will), and our sense of free will falls out of that.

Another attack on the concept is Churchland-like, and questions whether free will isn't just a bad folk idea about human behavior (which I think many enthusiasts of these experiments which agree to). It's worth asking whether belief in something like free will is universal even among non-Western humans - do Solomon Islanders and pygmies have the same belief? - and if so, what it is that predisposes humans to believing this. Do humans with a different conception of agency have different beliefs about this (Aspergers spectrum people)? Finally, do nonhuman animals also believe in free will? I encourage inventive experimentalists to think of a way to support or discredit this hypothesis. If we know different kinds of nervous systems have the same belief we can start understanding what it is we have in common with them that makes us think this.

Signing Off Until Late June

As above. To study for a big test as well as maybe to get some actual original neuroscience research done. Thanks for reading, see you then. -Mike

Epistemology and Encoding Rhetorical Intention in Language

Problems can arise when we misunderstand the rhetorical intentions surrounding informally stated hypotheses, which are certainly not limited to scientific endeavors. A stated hypothesis is a very strange kind of propositional utterance. When we state a hypothesis, we don't know whether it's true but we make the statement as if it were anyway - and we don't consider it to be lying or equivocating either. Why not? It has something to do with your audience knowing why you're uttering a proposition of uncertain truth value, which is exactly why if they don't know your proposition is a hypothesis, there can be problems. For example, Edward Sapir explicitly advanced the Penutian language family as a hypothesis to be investigated, and the theory was quickly adopted as gospel by the linguistic community, much to his distress. Fortunately it has largely been supported by data. It doesn't always work this way, in science or everyday conversation.

Since most languages mark questions and subjunctives explicitly, a fanciful solution would be a hypothesis particle. A simple phoneme would follow any informal statement of a hypothesis (-ba would work), and it would mean this: "I make no assertion about the truth of the proposition preceding this particle, but I want to learn the truth of this proposition, and I invite close scrutiny and criticism of this proposition in service of this goal."

But reflect further about rhetorical intention and truth value in utterances. Our classification of the rhetorical intentions is poor, since we don't recognize classes of utterances which are quite often explicitly encoded. A simple epistemological model of language is that all contentful utterances are commands, either directly to commit an action or to react to provided information, even if that's just for the listener to update his/her model of the world. As such we would expect most utterances will contain signals for rhetorical intention above and beyond the content of the sentence; there is the proposition being uttered, and the intention the utterer has of how the audience should react. Analytic philosophers attempted to approach natural language propositionally although their conclusions were sometimes provincial, hobbled as they sometimes were by an impoverished knowledge of the variety of language structures that existed outside Western Indo-European. Here is a phylogeny of coherent utterances which includes rhetorical intention.


1) COMMAND: "Get out of my house."

Extra-contential rhetorical tag: none.

1.1) Commands are the basic form of language and it is therefore not surprising that the command forms of verbs are usually morphosyntactically as, or more simple than, even the infinitive.


2) CONTENTFUL EXCLAMATION: "A blue hummingbird!"

Extra-contential rhetorical tag: "Recognize this object/event I have verbally pointed to."

2.1) Some languages (e.g. Tagalog, Washoe) do encode this intention explicitly and have focus markers which explicitly declare what the speaker wishes the listener to focus on. These markers occur throughout sentence structures and are not limited to noun-phrase exclamations like the one above.

2.2) Dependent phrase structure is always just another example of recursive phrase structure. That said, shorthand often evolves for parsimony (i.e., "There is a red book on the table" is really just shorthand for, and content-wise exactly the same as, "There is a book that is red on the table".) In languages with copulae like English, superficially there seems to be a distinction between main and dependent phrases only because of phonetic realization (or lack thereof) of recursion, but languages that lack copulae illustrate the principle more clearly.

2.3) There is also an argument that constructions like "there is" or intransitive words equivalent to "exist" are really just reflexive copulae that tie off structural loose ends. Therefore the statement above is equivalent to the proposotion "There is a hummingbird that is blue!" Potential investigation: ergative/absolutive languages with reflexive morphemes are known not to "cross systems", e.g. East Greenlandic, in which using ergative blocks use of the reflexive marker; you can only use one system at a time. So how do the reflexive copular constructions behave in ergative/absolutive languages that have both copulae and reflexivity?


3) DECLARATION: "I am going running at 3pm."

Extra-contential rhetorical tag: "I want you to accept as true the meaning of this proposition, and update your model of the world accordingly."

3.1) Although seemingly the most basic form of utterance, declarative propositions are not even close to the entirety of contentful utterances we make. Still they are zero-grade in all languages that do mark rhetorical intention.


4) YES/NO QUESTION: "Is he very tall?"

Extra-contential rhetorical tag: "I want you to reformulate this utterance as a proposition and then tell me your evaluation of its truth value."

4.1) Questions are usually marked, either by word-order changes, explicit particles (like Japanese -ka) or tone. English has few minimal pairs where tone makes a difference (e.g. permit) and such pairs are related, unlike full tone languages. Still, if the concept of minimal pairs is extended to rhetorical intention, tone is indeed explicitly encoded and certainly distinguishes minimal pairs. ("He is running for governor." "He is running for governor?" These sentences mean different things.)

4.2) Yes/no questions are therefore actually different kinds of utterances than those containing interrogative pronouns. In fact some languages do mark them differently. Latin marked verbs with the suffix -ne only in questions that did not contains interrogative pronouns.

4.3) In all cases that I know of, the verb dominates other parts of speech in taking on question particle - that is, if there's a verb in a sentence and a language has a question particle, the particle attaches to the verb. (Case in point, in Japanese, -ka typically goes on the verb but if a single-noun utterance requesting clarification, the question particle can go on the noun; "He's working in the city," one speaker says, and the other says "Takamatsu-ka,", i.e. "In Takamatsu?"

I have argued previously that verbs and adjectives are both first-order modifiers, but that some first-order modifiers can modify two nouns simultaneously (these are called transitive verbs.) In this view, nouns alone cannot create a proposition since there is no relationship stated between them without verbs. Therefore, it makes sense that the rhetorical marker would be placed on the verb that changes the utterance from a list into a proposition.


5) INTERROGATIVE-PRONOUN-CONTAINING QUESTION: "What is the best restaurant in Portland?"

Extra-contential rhetorical tag: "This is a proposition whose truth value cannot be evaluated since I have deliberately used a placeholder ('what'). I want listeners to reformulate the statement as a proposition but include information that can be plugged into the placeholder slot in such a way as to make the proposition true."

5.1) Interrogative-pronoun containing questions are also usually marked in some way (by word-order, tone, and/or explicit morphemes.)

5.2) Languages often have multiple interrogative pronouns for different types of nominal information, but never to my knowledge are there dedicated adjectival, verbal, or other interrogative words. Interrogative pronouns can be pressed into service for one-off service as verbs and even productively undergo morphosyntactic operations: (Imagine a woman has just been told her twelve year-old son was seen driving to school. "He was what-ing to school?" Nonetheless these kinds of operations on interrogative pronouns are never formalized.)


6) CONTINGENT DECLARATION: "If it rains today, you're on your own."

Extra-contential rhetorical tag: "I have explicitly marked off a proposition whose truth value is influenced by other propositions stated in close proximity and whose truth I may not be certain of, or by the way I obtained the information."

6.1) There are two sub-structures here: one is the typical if-then statement formulation for subordinate clauses we normally think of, but there is also the case of evidential markers most famous among Tupi-Guarani languages. Both systems are ways of explicitly marking the truth-weighting that the listener should give to the proposition so marked.


Though it doesn't merit a separate entry here, it's interesting that hypotheses aren't exactly questions, but they aren't exactly subordinate clauses either (though a hypothesis can be stated as both.) It's my suspicion that humans not engaged in research do not engage in extended hypotheticals - the propositions they are unsure about tend to be simple enough that their hypotheses are all contained in single clauses delineated by if-then markers. For most humans, thoughts complicated enough to require more than one sentence and which are of uncertain truth are merely deception, not hypotheses to be tested.

However if English does follow my humorous suggestion to develop an explicit hypothesis particle and a seventh utterance category, then I should re-state my earlier sentence as "A simple epistemological model of language is that all contentful utterances are commands, either directly to commit an action or to react to provided information, even if that's just for the listener to update his/her model of the world-ba."

The Verb Regularization Rate in English

"The half-life of an irregular verb scales as the square root of its usage frequency: a verb that is 100 times less frequent regularizes 10 times as fast." From Lieberman et al in Nature. An interesting question is to what other morphosyntactic rules this generalizes to, like noun plurals (and to what extent is it influenced by phonetic realization. My guess: not very much.) Pinker and many others knew qualitatively that the less a verb is used, the more likely it is to become regular in a given time period. Now we have the quantitative rule.

Gene Ancestry Visualization Tool?

Most people are familiar with the radial-wheel format of showing the descent of species, like this one:


Image credit Bristol University Department of Chemistry

What would be really cool, and may already exist, which is why I'm posting this, is the same tool existed, except for gene ancestry. (And here is where I make obvious my ignorance of bioinformatics and the descent of genes both.) Genes can often be shown to originate by duplication events. I'm probably being naive about the extent to which the ancestry of genes results from similar events, or can be traced back to common ancestors shared with other genes in the same genome. But unless there was a lateral transfer event, genes all have to have common ancestry with other sequences in the organism, correct?

Ultimately we'd see another radial circle, except with genes radiating out from a common ancestor. The outer surface would be the human genome as it is now. You could place nested concentric circles representing previous phases of the genome (see mock-up below). Yes, I know the "surface" separating primates from non-primates (for example) doesn't represent any qualitative break, and the circle would be pretty lumpy since not all genes or gene families would branch and mutate at the same rates. (Genes I picked are illustrative only.)

Now, there are lots more genes than you could legibly read on a computer-screen-sized wheel, but this is also true for the species-descent wheel, which uses representative organisms. In my dream app, you could select certain gene families or genes with products that catalyzed certain classes or reactions or interacted with other gene products. The point of such a visualization is that you could more easily see when pathways started appearing or becoming more complex. Of course there will have been lots of genes lost in the interim, so we couldn't get a complete picture of what the genome was like at each point in the past. (Going back to the Grand-Daddy autocatalytic RNA would be cool, but unlikely.) If the gene-product features are sufficiently advanced you could even conceivably find "holes" in pathways at ancestral stages where the must have been gene products whose genes are no longer in the genome.

If there are any tools similar to this already out there, I would greatly appreciate a comment. This would be a valuable tool to investigate the evolution of pathways and systems. Especially neurons, of course.

Lewy Body Dementia and Alpha Synuclein as a Lipid Manipulator

In terms of understanding moment-to-moment awareness, cognitive hypofunction disorders with clear genetic contributions are often uninteresting. That is, the problem is usually that the wiring isn't there, or is wrong. The reason this is uninteresting is that if you're interested in what underlies moment-to-moment consciousness, you have to look for properties of the brain that change on the same time-scale, allowing our subjective awareness to represent some of the information in the outside world.

For this reason, pharmacology often presents more research opportunities than disease states, in particular NMDA antagonists and HT2A agonists. But there is a disease state which is notorious for hour-to-hour (or more) fluctuations in cognitive status, dementia with Lewy bodies. As you can see from the linked reference, it's not yet clear whether the disease is a sub-type of Alzheimers, or a distinct condition.

Lewy bodies are alpha-synuclein plus ubiquitin inclusions that appear in neurons specific parts of the brain in disease states; the ubiquitin suggests that these are clumps of protein the neuron is trying to degrade. Their presence is not necessarily indicative that the patient had any of the additional symptoms of Lewy body dementia. Clinical Lewy body dementia is associated with symptoms above and beyond what Alzheimers patients suffer. It also has significant overlap with Parkinson's; specifically, patients exhibit both the motor decline of PD as well as REM sleep disorder. Unlike Alzheimers, onset is not insidious. Unlike either Alzheimers or PD patients and most relevant here, Lewy body dementia patients usually have recurrent visual hallucinations, and are extremely sensitive to dopaminergic- and cholinergic-modifying medications.

When we think of real-time changes to nervous systems, we usually think of information being transmitted in an electrochemically-mediated way by neurotransmitter vesicle diffusion and membrane depolarization. Membrane potentials would also be dramatically and rapidly effected by changes in lipid membrane properties, so I had considered previously whether there were proteins expressed in brain that manipulated or maintained membrane lipid contents. It's interesting that alpha synuclein a) is known to be located on the cell membrane in some fraction, b) is natively unfolded in the cytosol, c) interacts with polyunsaturated fatty acids, d) interacts with membranes correlating with serine phosphyorylation and e) still hasn't been assigned a clear function.

This is why a recent Journal of Molecular Neuroscience paper by Riedel et al at the University of Oldenburg is important. Using an oligodendroglial cell line, they demonstrated the creation of a-synuclein aggregates (in vitro Lewy bodies) both in cells that had a point mutation in a-synuclein predisposing them to aggregate formation, as well as in wild-type cells. This was done by adding DHA (by the way, an omega 3 polyunsaturated fatty acid) and then hydrogen peroxide for oxidative stress. Alpha synuclein aggregates formed both in the mutant cell line as well as in the wild type, though the mutant cells' aggregates were bigger (all compared to non-treated controls).

My hypothesis is that alpha-synuclein is responsible for lipid processing of neuronal membranes to maintain electrochemical constancy, in response to physiologically rapid (minutes to hours) changes in the environment of the cell. In addition to the specific deficits in Lewy body dementia (associated with the brain region where the Lewy bodies appear), this may also explain the rapid fluctuation in cognitive status - cell membranes are unable to respond to a changing electrochemical environment because there's a problem with the protein that controls their lipid content. When alpha-synuclein catches up or the triggering physiological change (pH, solute concentration) reverses to previous levels, the cognitive deficits may disappear.

These findings, though they show an interaction, are therefore causally backwards - here, changes to lipids are initiating aggregation. It could be that once aggregation begins, alpha-synuclein function is off-line, and any new alpha-synuclein produced by the cell gets immediately caught in the tangle and can't perform. (There's evidence that there's more than normal at the membrane in disease states.) Here are future experiments, which in my quick survey of the literature I may have missed: 1) patch clamp recordings of dopamine receptors on cells in culture with loss-of-function mutations or knockouts of alpha synuclein, especially in response to differences in charge, pH, and buffer concentration (to mimic physiologic changes in extracellular fluid). 2) Measurement of individual fatty acid chains in knockout relative to control, in terms of their incorporation into cell membranes.

I'm both excited and nervous because in the coming weeks I will be interacting with patients in the clinic who have this disease, which is why I'm motivated to understand it.