boiling

1. Standing by the stove the other night, waiting for a kettle of water to boil - as it does, starting from the near-silent rattle through the increasing racket, and the whistle starting, and all the other noises that accompany that moment, I had the distinct feeling that I was hearing the big chromatic crescendo at the end of Prokofiev's great D-minor Toccata, one of my favorite piano pieces. It's not that I was fooled - this was not an auditory deja trompé, but something similar - but I've never felt a piece of familiar music so strongly evoked by some random physical event. It was definitely primed by having listened to that piece something like 10 times in the past week. Now whenever I hear that piece, when it gets to the silence at the end before the crescendo, I will think of a boiling kettle.

2. Horrible problems with the paper I've been working on and hoping to have submitted in a matter of days. A big part of the paper - the way that I interpret the data, basically - is a set of relatively simple contrast perception models which I run through the experiment as tests of different hypotheses. I had calibrated these to a set of human thresholds, which I was never quite comfortable with for various reasons, but that's the way I had done it; as a final touch to a figure, I decide to go and generate thresholds estimates for the 'best' model, to plot against the human data, just to show how similar they are, and when I go to do this, the model starts giving me imaginary numbers, which is bad.

By the time I figured out what was wrong - it wasn't really a problem, I was just not using my code properly - I had decided that calibrating the model to the thresholds for my humans was probably a bad idea, because the way I measured the human thresholds was kind of weird, and I could be sure of simulating these properly, so I should just use some standard thresholds. Why not? Nobody is going to argue with a standard CSF. So I plug a standard in and - and I'm going to note here that every time I do something with this model, I have to go and recompute the simulations, which takes hours - and it all goes haywire. The model that 'works', and that's consistent with all these nice facts that I've lined up and made a nice case out of, still works, but depending on how I implement the change in sensitivity, the alternatives either perform horribly - which you'd think is okay, but really doesn't look plausible, just makes it look like I haven't given them a fair chance - or they come out reasonably similar to the favored model.

So, I have to be fair, at the same time that I don't want everything to fall apart. I am certain that things work the way I think they do, and I'm prepared to be wrong, but if I'm wrong then I don't understand how I'm wrong. And building evidence either way progresses in these multi-hour steps in between which I'm sitting here with a stomach ache because I'm afraid that I'm going to wind up with evidence that my experiment isn't actually that good at discriminating these different models.

The problem seems to be in the low-frequency filters; the lowest frequency filter is basically four points in the Fourier domain, and it happens to take up a disproportionately huge amount of image contrast, so the 'not working' models tend to be uniformly low-pass in the simulation, which I know is not fair, because it's all because of that low frequency channel. So I figured that, since these are 'sustained' stimuli, I would be justified in just taking out the lowest few channels and leaving the top 5 or 6 band-pass channels - one thing here being that I'm not willing to go back and redesign everything to the point where we have low-frequency DC-sensitive channels. But then when I just have the mid-to-high frequency channels, the three models are too similar, which I don't like either, and which I know is just because I'm now allowing the low s.f. to get through. And I also know that this version, even though it has the 'standard' CSF, doesn't really because the lowest channels are shut off. So I turned them back on and changed the gain to the CSF, which I realized I had wrong the first time because....

Anyways, you see what I'm doing - changing more than one thing at a time, and making mistakes because I'm rushing it. This just prolongs everything, because every change, or every attempt to figure out what the effects of a change are, and every mistake, takes many hours to evaluate.

Anyways, high irritation and anxiety.

streamline

double post!? see if i can finish this in 9 minutes.

i finally brought home a hard drive adaptor from the lab so i could copy old files - random stuff - from my mb-dead-old thinkpad. so then i waste an hour or so looking through old text files mostly, going back almost to the start of graduate school (7 years!).

i have older files from older drives, and the further back they go, the more i hate myself; or, the more i hope and pray that i've gotten better. i always write a lot - before i ramped up this dumb journal, i wrote a lot in text or word files that then got thrown in a folder somewhere, so i have piles of examples of my bad writing. not all of it is that bad, really - i like to read myself, i know. some of it is awful, and some of it is embarrassing for showing how wrong i was about something, or naive; and sometimes its revealing because i see that i've been fixated on one issue or another for so many years.

i get done with this and go to have a look at the perceived contrast paper, which i keep saying is almost done, and i realize something: i can save it. i can make it better. i mean, i already think it's a cool paper, but i also have a feeling that no one will be able to read it. but having just waded through a stack of old forgotten pages, and looking at a new stack, i now know what i have to do:

get rid of the complicated figures - three of them, four panels each - and replace with one simple figure with 2 panels. no more of those heatmaps. just plot the function peaks. then, all the model stuff goes to an appendix. anyone who cares already knows all that stuff, or they're the type that likes appendices, so just shunt the calculations off to after the end of the paper. those two steps will hugely streamline the paper, should improve it greatly, make it much more readable. are you brave enough? just when you thought you were done, and you just want to finish it, will you go the extra mile? of course you will!

***QUICKLY***

00:00, no double post!

update march '13

nothing in particular to write about here, just an update on current events:

work
1. blur adapt paper is back in review; i want this one to be over.
2. classification spectrum paper nearing completion; i really like this one.
other work in progress (paper with SM et al, they seem receptive to my suggestions).
3. still need to discuss new experiment with CPT, putting that off; boss suggests writing up a paper on it to figure out which data needs replication the most.
4. started low-level talks with potential collaborators on the migraine-mapping stuff.
5. haven't applied for new jobs yet, NECO seems unlikely to respond.

other
6. reading a new book, "history of tennessee" by James Phelan, written in the 1880's (it's not tacitus, but it's free). he has a habit, sometimes interesting sometimes irritating, of making close analogies between seemingly asymmetric historical events, usually tennessee vs. england, and is fixated on 'anglo saxons'. interesting going at any rate--
7. on piano, mainly trying to master chopin's "minute waltz" over the past few weeks, if i can play it straight through in 2.5 minutes i'll be happy; also on music, greatly enjoying a 2 year old album of french electropop; the songs 'civilization' and 'ohio' are great background when your daydreaming about the colonization of america.
8. this paper on a rogue study using a research botnet to scan pretty much the entire internet is one of the most interesting things i've seen in a while. there's an awesome .gif figure in there, basically showing the earth's rotation in the average number of pingable public IP addresses plotted across the globe.
9. way too much time wasted on reddit, which i only just discovered lucky for me, and playing MH2.
10. i have a horrible, horrible urge to write a longer historical narrative centered around the life of Gideon Morgan. trying my best to resist...

A week later, and I'm still revising that previous post and investigating the identities of various great great etc grandparents. I'm not sure why, but I could guess; but I won't here.

Anyways, in reading about all these Morgans and Boatmans and so on, I've been experiencing a very entertaining picture of the American colonization of Tennessee. As far as I can tell, all of my ancestors around the time of the Civil War and in the preceding generation were in Tennessee or in the border regions with Georgia, Alabama, and Mississippi. So, I am - and I guess I had never really thought of this - as much of a Tennesseean as a person can possibly be, if you qualify 'Tennessee' as the American colonial state, and not as the prior nations of the Cherokee, Chickasaw, and others.

'Colonial state' isn't what you normally hear as a description of a state like Tennessee. 'Pioneer' is usually the term, and certainly that's a good term for the people who were at the very forefront of the colonization, but colonization is absolutely the right word for the phenomenon. And in thinking about it this way, I can't help but understand it through the lens of what I had most recently been reading about: Rome.

Comparisons between Rome and the USA are passe, I know. But that's because the comparisons are usually negative, about degeneration and decadence, but like Matthew White says, that's kind of a recent thing. Earlier Americans were better able to see the parallels between what they were doing and with what the Romans had done in the days of the Republic: enlarging the republic through colonization.

So, I've had in my head the past few days a little comparison and contrast between the two phenomena. The simultaneous similarities and differences are most interesting.

1. The Romans had a single 'home' city. From there, they defeated surrounding tribes and set up new towns on the foundations of the defeated ones, and Romans went out and populated these places, building new cities in the image of Rome; so, Roman culture and language spread across Europe, but it was always tied back to Rome. With the Americans, it was different: there was a string of home cities along the Atlantic coast, from Boston down to Savannah. From these, colonists went west and defeated the local tribes and set up new towns on the foundations of old ones.

2. The initial phase of the Roman Republic, where the Italic and Etruscan tribes were conquered one-by-one, and where the Republic could kinda-sorta be identified with cisalpine Italy, could easily be likened to the pre-Revolutionary American colonial period, where the 13 colonies were consolidated east of the Appalachian mountains. The gradual transition between the Republican and Imperial periods - basically during the 9900's - was also a transition between Rome-as-Italy and Rome-as-Mediterranea. Similar, but much faster, was the transition between pre- and post-revolutionary America; no longer bound by British restrictions to the Eastern Province, the American colonization of the rest of the continent began, and so you have the Continental USA.

3. We're just at the end of that phase now, something like the Nervan dynasty of the 112th century. The borders are more-or-less set, the colonies are all established and mature, and everything is Roman/American within those bounds. But then, there's the third interesting contrast, and a more disturbing one: Roman colonies often, or probably usually, included a mostly indigenous population; Gauls and Belgians and Iberians and Germans and etc. There were enough Romans to make it so that everyone wound up speaking Roman in the end, but the Romans weren't genocidal and didn't practice ethnic cleansing as a rule. Americans, though... our colonies were established almost entirely by the white colonists and their black slaves. The native tribes - the American equivalents of Germans, Belgians, and Gauls were Mohawks, Apache, and Cherokee - had little impact on the colonies; they were absorbed on the fringes at first, and in the end they were exiled and excluded. Like I said up above, most of my ancestors arrived in Tennessee in the first generation or two of colonization, before the ethnic cleansing of the Cherokee and Chickasaw had happened, and while there was clearly a lot of mutual tolerance and intermarriage between the different societies, I don't think I have more than a percent or two of native ancestry. Their effect on the colonies was marginal, and then they were exiled.

I don't think the difference is that Romans were tolerant and Americans weren't. Romans were nasty people in a lot of ways. I think there were two important differences: First, there was a constant and inexhaustible supply of American colonists, coming in from England, Ireland, and elsewhere, whereas the Romans were limited by the numbers they already had in Rome and other big cities. So the Americans had a big positive multiplier to their numbers. Second, and this is more of a guess, there was a negative multiplier on the native Americans because of the century or so of plague that had destroyed their population and set their society in an inordinate degree of chaos; in contrast, the European tribes the Romans contended with hadn't been subjected to any terrible disasters or setbacks, they were just a little behind on the same curve as the Romans. With these two imbalances, the native Americans were overwhelmed too quickly, and so there wasn't time for the two groups to really learn to live together and combine. When differences arose, it was too easy for the whites just to force the Indians to leave, or as was the case earlier on, to exterminate them.

The Romans never could have forced all the Gauls out of France, just to end all the conflicts and yearly revolts and rebellions. The Roman military was strong enough to keep the Gauls from ever winning, but there were too many Gauls to drive out in a death march to Germany, and there wouldn't have been enough Romans to replace them anyways. The scenario just didn't make sense for the Romans, but it did for the Americans. Genocide was a viable alternative on the frontier. And so we have America, and Tennessee, and Me. Humanity is a difficult thing.

RSM

I spent a good part of the past week Googling my ancestry,  trying to fill in the gaps in my grandmother's collected documentation of my mother's side of the family. What's most interesting about doing this is that it gives you a direct route to looking at history; you start with yourself, and trace backwards through people you knew, and people they knew that you didn't, and so on, and before you know it you're learning about the Civil War, or the southern pioneers, or the Revolution.

Looking at it this way, as a continuous route through history, you can almost start to see narratives, although you learn them backwards. Here I'll try to reconstruct one of them forwards: the recent history of my middle name, Morgan - or more specifically, of the legacy of the name Rufus Morgan. In the plot above (invented by me), this is the blue pathway leading directly left from below the center.

Rufus Morgan was born in 1751, in Springfield MA. His father Gideon, also of Springfield, died a year later at the age of 28. Rufus's mother Rachel Kibbe then had his name changed to Gideon Rufus, in memory of his father. Gideon the First's father and grandfather, both named Jonathan, had lived their entire lives in Springfield; his great-grandfather Miles Morgan was one of the founders of the town. The connection between elder and younger Gideon is actually contentious - the internet genealogy consensus maintains that Gideon Rufus's father was Samuel Morgan of Connecticut, who was a descendant of one of Miles Morgan's brothers. However, I am pretty sure the internet is wrong here; I have seen a photo of a document signed by Gideon's mother, where she requested his name be changed in memory of his father. Unless there were two Gideon Rufus Morgans in the area of Springfield, both born around 1751, and one disappeared from history, then I think they are the same, and Gideon came down from Miles.

So, Gideon Rufus was a Minuteman in the Revolutionary War, and after the war he started a career as a civil engineer, involved in the planning of new towns like Saratoga NY. He and his wife Patience Cogswell started their family in Connecticut, and gradually migrated south, through New York down to Staunton, Virginia, where Patience died and Gideon apparently resolved to keep going south with his children into East Tennessee, sometime around 1800. Maybe his father's early death, and his adventures as a Revolutionary War soldier, broke what had been a 150 year bond between that Morgan line and central New England.

As for Gideon II's migration to Tennessee: I'm guessing that they made their trip down the 'Great Wagon Road', along the valleys of the Applachian mountains, passing through Kingsport, and maybe following the Tennessee river from there to Fort Southwest Point. There, in the settlement of Kingston, west of what would become Knoxville, he set up a tavern and trading post, apparently becoming an important local figure in the frontier trade - and conflict - with the Cherokee.

Gideon had many sons:

The oldest, Luther Morgan, went further west and south, and was one of the first generation of white settlers in what became Huntsville, Alabama - his son married into the wealthy family of John Hunt, the city's namesake. He was the grandfather of the Confederate General John Hunt Morgan, famous for his long cavalry raid through Kentucky, Indiana, and Ohio; and great-grandfather of the evolutionary biologist (and Nobelist) Thomas Hunt Morgan.

The second, Gideon Junior, or Gideon Morgan the Third, was a leader of a regiment of Cherokee that allied with the Americans under Andrew Jackson during the Creek War, and that included more famous names like Major Ridge, Path Killer, and John Ross. He married Mary Sevier, the granddaughter of the first governor of Tennessee John Sevier, and a quarter Cherokee on her mother's side; Mary's maternal grandmother was a granddaughter of Oconostota, the leader of the Cherokee who fought and were defeated in the 1780's by the American revolutionaries who were to take Tennessee for themselves. Most of Gideon III's descendants went west to join the exiled Cherokee nation in Oklahoma. I know there was a Gideon Morgan IV who went to join the Cherokee in Oklahoma only after having served the Confederacy in the Civil War, but I don't know the details. There was another son of Gideon III, named Rufus Montezuma, and a daughter named Cherokee America. It looks like that part of the family, the ones with the Cherokee relations, were still in East Tennessee until the 1850's and 1860's, but most had gone to Oklahoma by the 1870's.

The third son was Rufus (II) Morgan, who died in 1826 in Kingston; he was an ancestor of the playwright Tennessee Williams (that link describes the confusion surrounding the identity of Gideon Rufus's father). The fifth (or sixth) was George Washington Morgan, who lived to be 96 years old, dying in the 80's in Nashville. George's son John Tyler Morgan was a Confederate general, and later a US Senator from Tennessee; his Wikipedia entry, I think, clearly indicates that he was the Bad Cousin: he was an influential white supremacist and imperialist who supported violence against blacks, the US war with Spain and the Philippines, and the annexation of Hawaii. One of G.W. Morgan's daughters, a Musidora Morgan, married a Daniel Sayre - their granddaughter was the famous Zelda Sayre, a whole different kind of tragedy.

The fourth son of Gideon Rufus was William Cogswell Morgan. He's the leftmost point on the blue path in the plot at the top of this post; 'WCM'. He went west to Nashville. His wife was Nancy Seawell, born in Nashville in the 1780's, which would make her part of the very first generation (of white people) of my hometown. He was my great-great-great-great grandfather, and I don't know much else about him, except that he died in the 1820's before he was 40 years old, just a few years after his wife died at 33. As far as I know, they had a single son, Lewis Morgan, around 1819.

The record is pretty fuzzy on this part of the story, probably because of William C.'s early death; we don't know where Lewis was born, where his parents died young, where he grew up - Nashville seems the best bet. I don't know who raised Lewis - I could even be wrong on the William C. connection, but I don't think I am. But still, this is the weakest link in the chain, weaker than the Gideon I - Gideon II link. I hope that somewhere in Tennessee, there's some document somewhere that can show clearly who Lewis's father was, but as of now, we just don't have any proof. The alternative is that he came from other Morgans from North Carolina, as I have found several possible Lewis Morgan Srs who were coming into East Tennessee, Alabama, and Georgia at around that time. Lewis Morgan was, in the late 18th century, a popular name. However, none of the dates or marriages fit - the other Lewises were too old or too young, unless we've got his birth date wrong, and they married women other than (and not including) the women we know he married.

At any rate, when the Civil War came, Lewis and his young son Rufus Samuel - as far as I can tell, he was Rufus Samuel the First, and Rufus III - joined up with his cousin John Hunt Morgan's army. I can't find any evidence that either of them took part in Morgan's famous Raid, though family lore has it that Lewis was a part of it, and spent some time imprisoned in Ohio (where Morgan's army finally surrendered). This is one reason to believe in the connection between William and Lewis, because Lewis apparently claimed that General Morgan was an actual cousin. Lewis's first wife was named Sarah Reed - a notebook I have a copy of, made by the daughter of a grandson of Lewis' named Fletcher Morgan, claims that Sarah was half Cherokee - I know nothing else about her. That notebook also insinuates the connection between William and Lewis.

Lewis was apparently murdered sometime soon after the War was over, in northern Alabama somewhere - the story is that he was taking money to a church, when he was robbed at a river crossing and buried in the sand by the thieves. Rufus Samuel ended up back in East Tennessee, where he married in McMinn county and lived to be 77 years old, dying in Chattanooga in 1923, three years after my grandfather, Rufus Samuel Morgan, was born there. I've seen a family picture of the elder Rufus Samuel and his sons. There were a lot of them. One of them was Rufus Samuel II (Rufus IV), who died in a car accident in Ringgold in 1918 at the age of 30 (I know this because it's written on the back of that family picture); another was the aforementioned Fletcher. Another was my grandfather's father, Edward Oliver. Edward Oliver married Anna Lee Wall, worked as a farmhand, a farmer, and later as an bookkeeper in the Chattanooga area, and died in 1963. Anna Lee died nine years later, seven years before I was born.

So now here I am, and in my generation there are three of us with this name Morgan, as a sort of genealogical reliquary - we're all children of my grandfather's two daughters, his only children, so we have different surnames. As near as I can tell, until my grandfather Rufus Samuel Morgan III - Rufus V if we include all namesakes - died, the name of Rufus Morgan had been held by some descendant of Gideon I in every year since 1751. 262 years of Rufus Morgans, from 1751 to 2013. It might continue in some distant line, but to my knowledge it ended with my grandfather. I had never known it had such a long history.

musical optimization

i never write about music, although i listen to and think about and play it a lot. i hereby inaugurate a new journal tag: music. i'll start with a simple observation: Hindemith is the Nelder-Meade algorithm of music. he starts in what seems like a random place, with chaos and dissonance, and gradually winds inward to a tight, crystalline, consonant solution. supposedly he had a System, an algorithm for generating this kind of music, so i think the optimization problem analogy is apt.

now god dammit

i should be working on that blur adaptation paper. i could finish it if i would just put 4-6 hours into it. why am i not doing it? let's ask me.

HAZ, why are you not working on that revision? what is wrong with you? you know what you have to do, so do it. jesus christ. stop procrastinating. you're embarrassing yourself. do it.

do it. do it now. no excuses. there are no excuses. there's nothing more important. do it now.

now

pernicious advice?

"Better is the enemy of good enough."

Supposedly this was the motto of the Soviet Admiral Gorshkov. Voltaire had something similar to say, which Gorshkov was probably paraphrasing, and which translates to something more like "The perfect is the enemy of the good".

My mentor in graduate school often repeated this advice, and now with a few years hindsight, I've decided that this is, for a scientist, an especially bad mantra. It lends itself to 'significance seeking', where you collect results until you observe the effect you're looking for, and then stop collecting. If you've got what you want, why keep looking?

Anyways, I just was thinking about this phrase last night, as so many times before I was looking over a developing set of data with some disappointment at an unexpected turnaround in the meaning of the results; I thought to myself, "better is the enemy of good enough", and then I thought, "what? you haven't even finished the experiment yet!".

Point is, avoid mantras and mottos. If you have a hypothesis to test, do it. Choose your stopping point far in advance, and determine that whatever happens, this will be the test of this hypothesis; if you still aren't convinced one way or another after the test, do another one, but don't go thinking that the first one is invalidated somehow. There is no such thing as "good enough".

how to build a psychophysics experiment

You wouldn't know it from my CV (unless you look at the conference presentations), but I've built dozens of psychophysics experiments in my nearly 10 years in the field. I've developed a routine:

1. First, design the planned trial algorithm; how will the stimulus vary from trial to trial? What kind of responses will be collected, and how will they drive the stimulus variation? Staircases and step sizes, interleaved and latticed. In my mind, I always imagine the algorithm as a gear train driving the stimulus presentation, like the mechanism behind the turning hands on a clock. Here, a model observer is usually set up, if I can figure out what one should look like, to help test the algorithm.

2. With the first step still in progress, set up the actual trial loop and use it to test the basics of the stimulus presentation and internal trial structure, with a dummy response. Usually this part is already there, in a previous experiment, so this step usually consists of taking an old experiment and stripping most of the parts out. The trial loop and its internal structure constitute another gear train, really the interface of the experiment: the stimulus and other intervals and features (sounds, fixation points, ISIs), response intervals and valid buttons, and proper timing etc.

3. The trial algorithm should be settling by now. I start to plug it into the trial loop like this: port over the algorithm, but don't connect it to the stimulus train just yet. Instead, start to work out the finer details of the stimulus presentation with the algorithm in mind. That is, if the algorithm is like a set of gears to transmit variation through the stimulus, we have to make sure that the teeth on the stimulus gear mesh with the teeth on the output gear of the algorithm. And, the input gear to the algorithm has to mesh with the response gear. It's easiest to do this, for me, if I first design the algorithm and set it in place so that I can look at it while I finish the design of the interface.

As the algorithm is being set in place, I'll usually simultaneously start setting up the method for writing the data down. This really constitutes a third little mechanism, an output mechanism outside the big algorithm-trial loop, which records everything about the completed trial up to the response, but before the response moves the algorithm train.

4. Finally, the algorithm and the trial structure get linked together, not without a few mistakes, and the whole machine can be tested. Usually it takes a few debugging runs to find all the gears that have been put on backwards, or connected in the wrong place, or left out completely.

I think that these stages, in this order, are what I have been following for at least five years now, and it seems to work pretty well. There are parts of the skeletons of most of my experiments over the past 3 years that are nearly identical; I think that the for V = 1:Trials statement, and the closeout statements at the end of that loop, have survived through a dozen completely different experiments. The other 99% changes, though some parts are common over many different scripts.

Another thing that's constant is the way I feel when I build these things: I really feel like I'm building a machine. It's the same feeling as when I was a kid and I'd take apart a clock or a motor or a fishing reel and try to put it back together, usually failing because I didn't understand at the beginning, when I took it apart, how it actually worked (I became a scientist, not an engineer). But now, since I'm designing it, I can see where the big wheels contain the little wheels, where there are little clusters of gears connected to other clusters, transmitting motion through the whole thing. I can see how exactly the same thing, the same device underlying the experiment, could be built with gear trains and springs and chains and switches and punched tape (for the random trial order). I should make an illustration one of these days...

Anyways, that's how you do it!

random report

random thoughts after a trip home:

politics:I had the idea that you can view different political philosophies by how they respond to (or acknowledge) a certain axiom, that the state is effectively the ultimate master of all people, that any individual is subject in all ways to the power of the government. Fascists acknowledge the axiom and embrace it, they treat the state as a parent and the people as children, and they endeavor to make the state worthy of this status and authority. Anarchists, while they also acknowledge the axiom, view it as the reason that there can be no state, why the state has to be overthrown and dismantled and prevented from recurring. Anarchists will say that people should be their own masters (or not even that), and that no one should ever make himself master of any other. Socialists are the third group that acknowledge the axiom, but they seek to make the state somehow equivalent with the people - through democratic means - so that while it is still true, it becomes unconcerning, since now the people are their own masters, through the mechanism of the state. American libertarians - and the model American political philosophy that is given lip service but not much actual credit - believe that the state has the potential, which has usually been fulfilled, to take on the role of master of all its subjects, but that it can be contained and controlled like a pack animal. I think that Americans in fact, in their popular political system, actually take on aspects simultaneously of socialism and fascism, believing that the state is a function of democracy at the same time that it is - and I think this is a contradiction with the first property - a benevolent external force that requires respect and adoration. The American left and right both take this attitude, but toward different aspects, although in my systematization they are mostly deluded into thinking that they are model Americans, i.e. libertarians. I guess I am closer to a libertarian than anything else, though if there is some label that applies to a half social anarchist half american libertarian, it would mostly cover me (I like NASA and public healthcare and the NIH).

headache: A really irritating headache on Friday, which I think was partly provoked by jumping jacks in the afternoon and magnified by beer in the evening. Two aspirin either did nothing to help or kept it from getting much worse. Not sure this was a migraine, but I think it was. I could feel it mostly above my right eye, and could actually touch it at the supraorbital foramen. By this I mean that by pressing on this spot, I could modulate the main locus of pain; this is a common sort of property of my headaches. This is just one specific branch of the trigeminal nerve, and except for some slight twinge of pain in my right maxilla, I couldn't find any other specific locus. So, I don't know if this qualifies as 'migraine', or if it's actually some sort of ophthalmic nerve neuritis, but just by scanning a google search of 'migraine and trigeminal nerve', you can see that there is thought to be a strong link between migraine pain and over-excitatory dysfunction of neurons in the trigeminal nucleus, so...

Also, had a nice conversation with my aunt about migraine. So along with my mother and her, she says that my grandmother also had headaches, but not my grandfather, so that must be where it comes from.

work/writing: I realized that the project I'm currently working on would be good to divide into two papers: one on the broader aspects of blur adaptation and the connection to contrast adaptation (which I hope to have data on by the end of this week), and the other on the absence of phase-blur adaptation. The latter might make a good PLoS-1 paper.

endojan

it's the end of january, so why not throw in another entry?

i revamped my priority ranking system yesterday, surprisingly quickly, in the form of a matlab script (the spreadsheet had gotten too complicated, as tasks were completed and added and modified..). right away it showed me that i should do one small job that i had been putting off for months, and so i did it.

it's kind of sad how by forcing structure on my life in such a simple way - write a computer program to sort out a list of the things i have to do - it immediately becomes undeniable that i have to do something. without this little trick, i am apparently lost in a haze, unable to see what is right in front of me. i suspect it is because i am hiding things from myself, and i still do not understand why.

also, tuesday afternoon, i was smacked with an idea and sat down and wrote a story. i satisfied a secret desire today by sending it in to the Nature Futures series. of course, i'm sure a hundred people do this every day, but i couldn't think of a reason not to attempt it - and i decided not to go through a dozen rounds of revising the story, showing it to friends, etc. etc., just because it's so nice not to have to do that for once. anyways, when it's rejected, i'll put it here so we can have it all to ourselves, won't that be nice?

enough. it's time for february.

TKD CSD

So, 4 days ago I dreamed of seeing a scintillating scotoma, and then became vaguely paranoid of how inconvenient it would be to have one on Sunday morning before my black belt test; then, today, after I'm home from the test and from grocery shopping, I for some reason start a conversation with j* about how migraines can be associated with relaxation after stress, and tell her the story of VanValkenburgh's Vacation; and this afternoon, coming in with the groceries, i get distracted for a little while by a foveal afterimage, probably from the sun glinting off a car windshield - but maybe it was something else. Yesterday, or a couple of days ago, I was distracted for maybe a minute by the noisiness of my visual field, having momentarily noticed how snowy everything looked. I think that was Friday...

So finally, about 9pm tonight, in the kitchen about to explain to j* why my shoulder hurts (because I briefly dislocated it by swinging my arm wildly at an odd angle towards an 18-year old), I realize that my foveal vision feels scotoma-like (if there is a word for 'feels like a scotoma', I don't know what it is. Specific feels, like 'rough', or 'bright', or 'salty', have specific, ancient, singular morphemes attached to them, so it's hard to invent a new word for a new feeling, or for one that is rare or obscure enough that it hasn't been named). I pick up a knife and start trying to use the sharp tip, at arm's length, to find a blind spot, but can't find it; the start is always odd, since I think the scotoma is very small and maybe discontinuous, and maybe even not binocular. For whatever reason, I can tell that it's there, but it's often hard to find. Then, as I've mentioned many times here, it seems to disappear; then it reappears.

This one was right field; headache is very slight, I felt it start midway through the aura, as a little jolt of pain, then disappeared. I have to shake my head to feel it; possibly would be a little worse if I hadn't taken an ibuprofen soon after the scotoma was after, though I took it for my shoulder...

So I got another recording with scotmap, which I think is good, but all my code from last summer is written implicitly for a left-field scotoma, and my code is complicated and uncommented, so it will take me a little while to straighten it out and make another good animation to post up here. I do have the data transformed and fitted to the wave model I came up with, and the result is very similar to the last measurement: exactly 3mm/min, starting a few millimeters on the V2 side of the inferior V1/V2 border, 10 or so millimeters from the foveal confluence. This is consistent with my feeling that there is a scotoma, and yet being unable to see it directly; the scotoma begins in V2.

There's something weird at the end, a bunch of data at a much smaller eccentricity; this may be an error, I don't think it's the 'rough spot' that I have mentioned before. Will work it out this week.

Meanwhile, here's a general migraine data plot, relating my estimates of headache intensity on a 10-point scale (notice what a fortunate migraineur I am) to the time elapsed since the previous headache. Most of these ratings are retrospective, based on these journal entries. I see a relationship: more frequent means more intense. The outlier at zero is the night in China last month, where there was no headache at all, which I attributed to the simultaneous alcohol intake with the aura.


In other news, I have failed to make progress this weekend on E*'s presentation.

Also, saw a nice show at the BSO last night: Hindemith, Liszt, and Prokofiev.

year

briefly, because we don't want to dwell on this:

what did we accomplish last year? what did we intend to accomplish?

1a. submitted a fellowship proposal, which was rejected
1b. submitted an R01 proposal, which will be reviewed in 2 weeks (and likely rejected)
3a. submitted 2.5 papers, one published (so we are not zero for 2012), one more accepted, one heavily revised (if all goes well, should be 3+ for 2013)
3b. wrote the classification spectrum paper that is in a holding pattern
4a. completed a binocular rivalry experiment that will make a paper someday, and learned to model binocular rivalry
4b. started a new and improved blur adaptation experiment that is interesting
4c. created a model of my visual cortex that can be fit to my migraine auras
5. wrote a lot in HAZ public journal
6. applied for my first real job
7. learned 14/15 of the bach inventions (9 or 10 of which i didn't already know)
8. trained for my black belt in tkd (testing soon) without getting seriously hurt
9. settled on some new ways of organizing my work (subversion, dropbox, zotero etc etc)

what for this year?
1. find a new job
2a. finally publish the blur adapt paper
2b. submit/publish the classification spectrum paper
2c. write and submit the rivalry paper (short and model-free)
2d. present the new adaptation work and write a paper
3a. learn at least half of the bach sinfonias
3b. learn to sing and play piano at the same time
4a. continue with the journal entries, get back to work-related, less of the self-stuff
4b. start writing journal entries in chinese with some regularity
5a. do the computational experiment in the R01 proposal, funded or not
5b. find somebody to collaborate with on something... hm...
5c. plan some new experiments beyond the proposal stuff

dream aura 2

dreamed last night that a scintillating scotoma was starting; i think i was trying to read, but couldn't see letters, space was distorted as though there were blind spots. i'm wondering if now that i'm familiar with the scotoma experience, the normal dream experience of being unable to resolve text in a dream is now naturally triggering thoughts, and ensuing dream experience, of a migraine aura.

i went to get my laptop so i could start recording the aura, but then i got distracted by downloading a video game, which then autonomously tried to download other games, which made it impossible for me to get back to matlab to run the aura recorder.

after a few minutes, i realized that either i had missed the whole thing, or it had stopped, because there was no scotoma and i couldn't remember seeing any of the big peripheral scintillations. at some point after that, i realized it had all been a dream, and i started wondering whether i actually had a headache or not; then i awoke, and went through the same train of thought again. but happily, no headache.

my tkd black belt test is sunday, and i am slightly nervous that i will get a headache sunday morning; i have a superstitious feeling that i have *caused* the headaches before by thinking too much about being about to have one, when in fact i think i've just subconsciously noticed aspects of prodrome. anyways.

gone, gone..

I need to get back to posting on my research activities, which have not ceased completely believe it or not. Next time, next time.

My grandfather, granddaddy, RSM, died Tuesday night. He was 92, born on the Ides of March in 1920. He was my last grandparent, my mother's father. Her mother, Elizabeth, who I will always say was probably the most important influence on the development of the contents of my mind, died almost 3 years ago at 85. My father's father died in summer of 2001, 89 years old. His mother died in 1998, 84.

My mother's parents were always closer to us, maybe because they were younger than my father's - by a decade - and had a lot more energy left. My father's parents could only tell me stories and talk with me; my mother's parents took me places and taught me things.

Elizabeth gave me books, told me about what she knew and where she'd been, took me to museums and historical sites all over the southeast, taught me to explore cities and the countryside and new towns, and to wonder where we and our ancestors had come from, and where all people and their cities and their civilizations had come from.

Granddaddy took me fishing on the rivers and lakes that he'd fished on since he was a boy - since before they had existed, in the case of those big TVA lakes, I guess. He tried to take me hunting, but I clearly wasn't interested. He took me camping and exploring in forests and mountains. He showed me how to interact with nature, and I don't think he ever knew how much of it stuck with me. I'm not a fisherman, but I know how to fish, and I know how to get around in the woods, and I'm at home in the outdoors. He was also a doctor and an artist. On the outside he was a cynic and a skeptic as pertained to human things, but he was always fascinated with nature, and with the human being and the human mind, and I think he was proud of me for becoming what I am. I know for certain that since I was little I learned to copy his personality, and my mother has commented on it positively and negatively, because he could be harsh and negative. I always wanted to be like him.

It was so strange to see him go, just like it was with Elizabeth, who was always so mobile and active and who spent her last year or so unable to get out of bed. Granddaddy, and I told him this the last time I saw him, was always the strongest person I ever knew, the model of strength, invincible even though I knew he was always getting injured in one way or another, always sick but always too strong for the sickness. But in his last years he lost his house and all of his health, and became thin and pale and weak, and finally he too was stuck in bed, but thankfully only for the last couple of months.

One of the last times I saw him, around Labor Day, I went to pick him up in Dunlap to bring him back to Kingston Springs to stay for a while. He said he wanted to start driving again, as if it were possible, and I think he must have known it wasn't, but also that he knew that to get out and get around was his only way of living, and that otherwise he had nothing left. He talked about his old life, basically the time before Elizabeth died, when he still painted and was still on his own, and had her to take care of and to take care of him. Then she went, and he sold his house and moved from place to place, and I kept thinking he was like a living ghost, and he knew it. I wish he could have lived forever, but nobody does.

So is this the best option we have? Live to be old, and watch as everything is subtracted from you, until you are zero. He had nothing left, he had given it all away or lost it or had it taken from him. I think I will always feel like he lost too much that we could have taken, or that we took things too early. He was more than any of us knew how to deal with, and we didn't know how to deal with his slowly fading away. His nurse called my mother early on Tuesday morning to say he was writhing in bed and laughing, and we all took that as a sign, properly, that he was almost finished. He was so tired, I've never seen anyone so tired...

So sad this week, so sad...

frustration '13

so, this past summer, my boss tells me that he's invited to give a retrospective paper on a particular topic as it pertains to a meeting he's been a regular at for almost 20 years. he asks if i'd be interested in writing it with him, and i honestly said no, i don't know the meeting that well, it's not really my core area, i don't have time now to do a retrospective which means all sorts of reading and research that i don't need to do on old things that nobody cares about anymore, and there are other things i'd rather be doing. he seemed to agree and said okay, we won't do it. then, a week later he tells me he agreed to supply the paper, as if i'd agreed, and so i didn't put up a second protest, except probably for a confused look on my face.

so here we are now, the paper is due, i've written it and spent a few good weeks on it, and i'm satisfied with it. i'm not even going to the meeting to present it. so now he wants to continue making changes and modifications to the structure of the thing, and he wants me to make the presentation for him. this is really frustrating. it's too late to fight it, because the paper is there on the schedule, he's going to present it, and i don't *want* to present it, and if i refuse to make the presentation he's not going to be able to do it himself, and it will just cause a fight and a falling out, which is bad because we're currently on good terms.

this is very frustrating. i'm put, again, in this position of paralysis, where there are several other things that i want to do, or need to get done, and instead i have to do this pointless job instead, and so i wind up doing next to nothing. i'm like a ghostwriter. how is this research? i have papers to revise and resubmit, papers to complete and submit, papers to write and complete, experiments to finish and write up, and instead i'm struggling over this stupid retrospective on a topic that i think is basically irrelevant, and in which my *conclusions* are that that work done on this topic over a 20 year period are basically irrelevant. the paper itself begs the question of why the paper has even been written. i think i made a big mistake in letting myself get put into this assignment.

also

a few other observations from china:

in developed, urbanized places, people live, or aspire to live, in flat, spread-out places (single-family houses in subdivisions, or in the countryside); and they go to work in tall buildings in concentrated, densely-built places.

in developing, urbanizing places, people live, or aspire to live, in tall buildings in densely-built places; and they go to work in flat, spread-out places (factories, construction).

all i noticed was that in china, even in small towns, once you get out of the little villages (where each family has a house of their own), the common people live in tall apartment buildings or highrises, but a lot of them are going to work in huge factory floors, although a lot of them are also going to commercial or service-sector stuff in big multistory buildings. meanwhile in the US, common people (except for young people starting out, or the urban poor, or anyone living in a big city downtown) live in houses surrounded by open space, but they tend to go to work in service sector or commercial business in tall, downtown buildings, although many are also going to work on factory floors. so, it's not a perfect 'economic chiasmus', but still an interesting little contrast.

also, this happened several times: after using the second floor bathroom, i would stand by the window to reassemble my multi-layer winter clothing, looking outside through the blinds. across the street, i would see the front window, at ground-level, of another house, with white curtains drawn. just in front of the window was a little tree with what i think were seed pods hanging from the branches, so that i saw the branches against the window curtain background. each time i saw this scene, i at first would think that the curtain had large-print calligraphic characters printed on it, only to shift immediately to seeing the true depthful scene - deja trompé! even after the shift, there would still be a lingering feeling of 'what are the characters, they are too small to read', which would then quickly disappear as it was obviously a wrong question. it did make me wonder whether or not the same sort of scene had stimulated some artful styles of calligraphy..

dinner aura

(this and the previous post were written as dated, but are posted today, 1-5-13; the times are today's time).

last night, just as we were starting our saturday night banquet, i noticed that everything i was looking at seemed distorted, and then realized that a scotoma was developing, just below and right of fixation. i wasn't able to pay much attention to this one, since i had to eat dinner without looking like a lunatic, but it seemed normal; straightish out to the right of fixation, then arcing downward. there was a period early on where the scotoma was very difficult to find, but i think it was just distributed, or at least not exactly the same in both eyes, but was still there. whereas usually the headache would have started about halfway in, this time there was nothing; maybe a slight sense of headache-like pressure behind the forehead, but no pain. i am guessing this was maybe due to the constant alcohol ingestion? by the time the 10-15 minute mark came around, i had probably had at least 2 shots of baijiu.

absence of a headache was good, since following this i went with jp's father, uncle huang, and uncle wang to get my 'feet washed', which really turned out to mean a full-body massage. a full-body massage while fully dressed in winter getup, sweaters and pants and long underwear. it was nice, though! and lucky no headache, since there was a stage of head-beating.

also, i didn't detect any sort of prodrome. in the morning, i had felt it inordinately difficult to form sentences, and made some strange mistakes in chinese, producing strangely wrong words, which i noticed at the time as out of the ordinary. otherwise, nothing obviously in prediction..

random observations:

(rambling chinese vacation edition):

1. due to jet lag, woke up at about 5:30am yesterday, lay in bed for ~1.5hrs. of course a thousand random thoughts ran through my head, but for a while a lay there watching the augenlicht. long, long ago i noticed how it cycles: against the dark, reddish-black background, a brighter cloud coalesces around the fovea, then fades, then coalesces again. the cycle is somewhere between 5-10 seconds, the cloud is a very low-frequency modulation (maybe ~5degrees across) of the high-frequency noise grain.

what i noticed yesterday was that as the cloud fades, some parts of it seem to 'stick'; this is hard to describe. imagine that the cloud was displayed on a screen, and that its brightest parts, around the peak, were 'clipped'; then, as the could fades, the clipped parts persist, then brighten noticeably, then dissipate as the cycle continues. the impression is similar to a very bright afterimage floating in front of a fixated object, except that my eyes were closed, and i was certainly dark adapted. the clipped portions are sharp-edged, small (half or a quarter degree across), with the spatial appearance of little interconnected droplets of a liquid. i wasn't able to tell if they had the same structure on each cycle, but it seemed that they did.

i cannot guess meaningfully what this is. some sort of pattern formation machinery being stimulated by the structure of the cloud cycle, which has a slower decay constant? it seems familiar, so i might have noticed it at some other time in the past when i found myself lying in bed, unable to go to sleep. when i was in college, that happened a lot, because i would have classes in the morning and force myself to bed, despite wanting to stay up until 2 or 3, and so i'd lay in bed for hours sometimes, waiting to sleep.

i also noticed that i could very clearly see the 'eye crank lines', especially when looking down, whereas usually i can't see them when my eyes are closed.

2. when we finally got out of bed yesterday morning, discovered it was snowing. it eventually stopped snowing and started raining, so the weather yesterday was miserable. still, we drove down south to visit family. we went to visit j*'s father's older sister, who i'd never met before, in a village in another corner of fanchang; her home was like something out of a fairy tale, not so surrounded by garbage and chaos like some of the other villages (which are still nice to visit, don't get me wrong). i had jingping take some pictures. there was a mountain running up directly on the side of the village, with a bamboo forest; spread out away from the mountain and the village was a large expanse of vegetable gardens. we had lunch cooked on a wood stove (and with some electricity). i hope that china is able to keep from totally losing this world as it moves on into the future.. all they really need is to find a way to deal with the garbage.

on the way down there, we drove on a new highway which took us through several tunnels beneath the mountains. at some point, to the right, in the distance, maybe a mile or so distant (in the south of wuhu, there are mountains and there are flat plains, and stark, sudden transitionsn between them), through the snowy, rainy, smoggy haze, i saw a massive building, seemingly in the middle of nowhere. it looked like something in DC; the size of the pentagon, ten or twenty stories wide, sixty stories wide. then, a little further south, a gigantic factory or processing plant, like a refinery or the biggest concrete plant you've ever seen. then, a mountain. i didn't bring the GPS to track where we went this time, but i can probably figure it out from memory. this reminds me of last year, something i never wrote down; on the bus back to shanghai, in the distance i could see a glowing tower, probably a hotel, surrounded by nothing else. it was probably fifty stories high, and surrounded by what looked like a 4th or 5th-tier town. maybe we'll see it again this time, since we're probably taking the same bus back.

also on the wuhu note, i've noticed lots of songbirds here in the subdivision, first time in four winters. maybe whatever drove them away is getting better?

3. dinner at uncle's restaurant. dog meat tastes weird. it was worth a try.

4. still on the roman history kick, been reading Tacitus' history of the 'year of four emperors', on the civil war that commenced with the death of Nero. it really is great reading. in the section on Otho's last stand and suicide, i paused for a while and thought about how all this had happened. i still don't know much about roman history, but i've read livy, so i know something about the beginnings of the republic and how it came to be; and i've read plutarch's lives of marius, sulla, crassus, pompey, and caesar, so i kind of understand how the republic cascaded into the empire.

i thought, the romans had all these lawful institutions for separating power, trading offices more-or-less peacefully and agreeably, avoiding autocracy and civil wars. they kept this up for hundreds of years, but only because to have faltered would have probably meant the end of rome, because there were still so many other powerful players in the vicinity. only after those players - the etruscans, the gauls, carthage - were subjugated, only then could the internal struggles really commence. the rise of the emperors, through the disruptions of marius to caesar, put an end to those struggles by ending all the power sharing. but that meant that once an emperor had failed, the struggles would flare again, and there would be civil war. the situation described - and witnessed first-hand - by Tacitus was the first of several times that this would happen, and it would eventually bring the end of the empire.

so i thought all of that, putting together the pieces that so many others have put together so many times, and then i turned the page, and Tacitus himself begins a digression where he outlines the same reflections on the same reasoning, and again i was impressed at the immediacy of reading the thoughts of a person who lived and died more than 1800 years ago.

5. despite the preceding item on how great Tacitus is, i switched yesterday (at the beginning of the next book of Tacitus, on Vespasian's rebellion) to reading Darwin's 'on expressions of man and animals', or whatever the title is. i've wanted to read this for years, never got around to it until there it was, Free on Ibooks. reading Darwin is great because of the way he makes his thinking so transparent; he explains everything iteratively, first in broad terms, then more and more specific, each time tacking on anecdotes or examples with more and more density. origin of species and the descent of man were written similarly, spiraling down from general statements to specific demonstrations, with examples at every level, but there was less anecdote; here, Darwin is on every page noting a story from some friend or acquaintance, or describing the behavior of his own dogs or farm animals. so, the story is solidy anecdotal, but still convincing, because you can see how he is being led at each stage to a question; if such-and-such is true, we should observe this, and here is an example that we all know, or an anecdote that i'm sure you'll recognize (e.g. how a dog acts when in anticipation of something he likes).

i also like all the talk about "nerve-force". the idea that this nerve-force overflows from the channels of immediate use, into channels of frequent or necessarily convenient use, and only later into less frequently used channels, is important in a lot of his examples. also, his 'principle of antithesis' in explaining some expressions is, i think, an interesting example of something more general than an adaptation aftereffect. for example, the excited dog, when it finds that it will not get what it expects, will look dejected - the 'hot-house face' - with this expression explained as, essentially, the aftereffect of adaptation to an excited manner. i think i will look more into this idea of antithesis in behavior..

words

trying, trying, to get to a black belt in tkd. it's hard, because i am not good at tkd. i have no athletic talent whatsoever, but i try anyways. sometimes it goes well.

so i keep hurting my back over the years, and for the most part it's been less frequent in the past 3, what with the regular exercise. however, i hurt it badly, permanently, last year, after *resting* for a month. not resting actually, but working on a grant proposal, doing nothing but sitting/slouching and reading/writing.

so then, lately, i decided to start doing the sunday afternoon core training class, which is basically variations on sit-ups that you do in rounds, over and over again. it's good. i did it this sunday. the day before, i went to the grocery store, and forgot that we were almost out of rice, so i didn't buy any.

monday night we ate the last of the rice, so tuesday night, on the way home, i went by the grocery and bought two bags, because if you buy two you get a discount. then i went home. this was all on foot or by train. with two 15 pound bags of rice. i didn't perceive a problem.

wednesday night i reached out to lift up the toilet seat, and something in my upper back exploded. so no more tkd for the rest of the week, and it hurt a lot. it's mostly better now, hurts, but i'm not partially immobilized anymore. thursday and friday, along with the back pain, my right arm hurt and my hand was numb. so i'm suspicious that the damage wasn't just to a muscle, but to some part of the spinal machinery, although if so maybe it shouldn't be improving so fast.

i wrote a facebook poem about it:

people who stand
on escalators
cervical spinal nerve eight
the north wind
on cambridge street

in other news, i'm like most americans, preoccupied with guns lately. i don't think anybody has a right to have one, that sums up my opinion. oh well.

going to china tomorrow morning! that will be nice, except i have work to do that i'm not interested in doing but have to do anyways. should be alright.

**
also, this came out a few days ago, didn't know where to put it, it's pretty ordinary:

undirected urges
to assemble words
vaguely resembling
the task at hand

sitting quietly
struggling silently
ignoring tomorrow
avoiding time

congealing thoughts
pooling together
into my hands
out of my mouth

watch and wait
the page to complete
vaguely resembling
the task at hand