Thursday, March 28, 2013


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.

Thursday, March 21, 2013


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!


00:00, no double post!

Wednesday, March 20, 2013

update march '13

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

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.

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...

Thursday, March 07, 2013

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.

Sunday, March 03, 2013


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.