The hour is getting late

There must be some kind of way out of here
Said the joker to the thief
There’s too much confusion–
I can’t get no relief

Businessmen, they drink my wine
Plowmen dig my earth
None of them up and down the line
Have any idea what it’s worth

No reason to get excited
The thief he kindly spoke
There are many here among us
Who feel that life is but a joke

But you and I we’ve been through that
And this is not our fate
So let us not talk falsely now
The hour is getting late

Bob Dylan, All Along the Watchtower

You might like the gypsy life

There is nothing in my head today
Nothing awful there to ponder, or confuse me
Go ahead in what you have to say
And I will listen as I listen to the news

I know the whole truth there is horrible
It’s better if you take a little at a time
Too much and you are not portable
Not enough and you’ll be making happy rhymes

You might like the gypsy life
You judge your progress by the phases of the moon
Get your compass and your sharpest knife
‘Cause people will love you when they know you’re leaving soon

There is nothing in my head today
I’ll cross the river people, as I cross my heart
The pigeon bridges are a place to stay
I will go under as I try to do my part

You might like the gypsy life
You judge your progress by the phases of the moon
Get your compass and your sharpest knife
‘Cause people will love you when they know you’re leaving soon

John Gorka, The Gypsy Life
Antje Duvekot’s beautiful version

Bayesian Bad Boys

There are many things I don’t understand regarding how various folks do things, and here’s a good example. It falls, to my mind, within what Brian McGill at the Dynamic Ecology blog last year called “statistical machismo”: the use of statistical methods that are more complicated than necessary in order to appear advanced or sophisticated, when these are either unnecessary (but trendy), or worse, clearly not the best choice for the problem at hand. “Cutting edge”, their practitioners like to think of them, but I’ve got no problem in calling them sophistry that stems from a lack of real statistical understanding, combined with a willingness to do whatever will maximize the chances of getting published, of which there rarely seems to be a shortage.

I’ve had, for some time, a growing suspicion that much of the use of Bayesian statistical methods in science falls pretty squarely in this category. That of course doesn’t mean I’m right, especially since I do not fully understand everything about modern Bayesian methods, but I get the basic ideas, and the following example is a good illustration of why I think that way. It relates to my recent cogitations on the design of a general, model-based partitioning (clustering) algorithm for a common type of categorical data: data in which each sample is represented by only a small fraction of the total number of categories. In such cases, clear associations between the various categories is far from obvious.

I started thinking about the issue in relation to the estimation of forest tree community types in some widespread and very important historical tree data sets, where each sample contains individuals from, at most, only two to four tree taxa (usually, species), when there may be upwards of 10 to 30 such taxa in the population over some large landscape area (earlier post on this topic here) However, the issue has by far its greatest application in the field of population genetics, specifically w.r.t. the goal of identifying cryptic population structure–that is identifiable groups of individuals who are breeding primarily or entirely among themselves (“demes”), leading to allele and genotype frequencies that vary characteristically from deme to deme, demes which are not otherwise readily identifiable by external phenotypic characters. These are groups involved in the first step on the road to “incipient species”, to use Darwin’s phrase. The similarity with the tree data is that at each gene locus for any given diploid individual–which represents our sample–you have only two alleles, even though many such may occur in some larger, defined population.

In 2000, Pritchard et al. published what would have to be considered a landmark study, given that it’s been cited nearly 14,000 times since. This comes out to about 2.5 citations per day; I wouldn’t have guessed that so many popgen papers were even published at that kind of rate. The paper introduces a method and program (“STRUCTURE”) for the above-stated task, one based on Bayesian techniques, using Markov Chain Monte Carlo (MCMC), which is an iterative method for estimating parameters of the posterior distribution when no analytical techniques, or approximations thereof, are available. Furthermore, the paper has spawned several spin-off papers introducing various modifications, but all based on the same basic Bayesian/MCMC approach. And each of those has gotten hundreds to thousands of citations as well.

I freely admit that I am an unabashed maximum likelihood (ML) type of thinker when it comes to statistical inference and model selection. I’m far from convinced that Bayesianism offers any clear, definitive advantage over ML methods, while appearing to be saddled with some complex, time-consuming and uncertain estimation techniques (like MCMC), which is most definitely a disadvantage. To my view, Bayesianism as a whole might well fall within Brian’s machismo category, at least as employed in current practice, if not in its fundamental tenets. I very much doubt that many people who use it do so for any reason other than that a lot of others are using it, and so they just go with the flow, thinking all is kosher. Scientists do that a lot, at least until they develop their own understanding of the issues.

As I was thinking through the problem, it seemed to me pretty clear that, although a strict analytical solution was indeed not possible, one based on a ML approach, as heavily guided by expectations from binomial/multinomial probability and divisive clustering, was the way to go. Indeed, I can’t see any other logical and algorithmically efficient way to go about solving this type of problem. The underlying goal and assumptions remain the same as Pritchard et al’s, namely to find groups that approximate Hardy-Weinberg equilibrium, and which therefore represent approximately randomly mating groups. And there is also still a “Monte Carlo” procedure involved, but it’s quite different: always guided by a definite strategy, and much less intense and random than in the Bayesian/MCMC approach. As far as I can tell, nobody’s taken this approach (although I just found an Iowa State student’s dissertation from last year that might), and I don’t know why. I thought it was recognized that defaulting to a uniform (i.e. uninformative) prior probability distribution–because you really have no idea otherwise, or worse, when the idea of some “prior distribution” doesn’t even make sense to begin with–and you have quite a few parameters to estimate, that MCMC algorithms can be very slow to converge (if at all), and to do so to potentially unstable estimates at that. But that’s exactly what the authors did, and there are other limitations of the approach also, such as having to constrain the total number of possible demes to begin with–presumably because the algorithm would choke on the number of possible solutions otherwise.

These are the kinds of things I run into far more often than is desirable, and which generate a certain mix of confusion, frustration and depression. If I keep working on this topic–which I find fascinating and which, being statistical, generalizes to different fields, but which I really don’t have time for–I’ll post more details about the two approaches. The fan mail has been clamoring for posts on this topic. Or ask questions if you’re entirely desperate for something to do while waiting for the Final Four to go at it.

You would not think

Albert Einstein, disguised as Robin Hood–
Keeps his memories in a trunk
He passed this way, about an hour ago
With his friend, some jealous monk

He looked immaculately frightful
As he bummed a cigarette
Then he went off, sniffing drainpipes,
And reciting the alphabet

And you would not think, just to look at him
But he was famous, long ago
For playing the electric violin
On Desolation Row

Bob Dylan, Desolation Row

Meant to be sung

We sailed up a river, wide as the sea
We slept on the bank, on leaves of a banyan tree
And all of these spirit voices rule the night

Some stories are magical, meant to be sung
Songs from the mouth of the river, when the world was young
And all of these spirit voices rule the night

The candlelight flickers, the falcon calls
A lime-green lizard scuttles down the cabin wall
And all of these spirit voices…

Sing rain water, sea water, river water, holy water
Wrap this child in mercy; heal her–heaven’s only daughter
And all of these spirit voices rule the night

The lord of the earthquake, my trembling bed
The spider resumes the rhythm of its golden thread
And all of these spirit voices rule the night
And all of these spirit voices rule the night
And all of these spirit voices rule the night

Paul Simon, Spirit Voices

That is worth some money

This is a lonely life
Sorrow is everywhere you turn
And that is worth something when you think about it
That is worth some money
That is worth something when you think about it
That is worth some money

We are standing in the sunlight
The early morning sunlight
In the harbor church of St. Cecilia
To praise a soul’s returning to the earth
To the Rose of Jericho and the bougainvillea

This is the only life
Now that is worth something when you think about it
That is worth some money
That is worth something when you think about it
That is worth some money

Paul Simon


Been reading history lately, a long lingering interest.

Specifically, the history of the encounters of Europeans, and then Americans following 1783, with the various native tribes of North America, a vast, complex, and highly interesting (and important) topic. I’ve dipped into this from time to time, mostly with respect to the far western states, especially California and Nevada, but the crucial time period for the United States generally, i.e. when national attitudes and policies were first being formed, occurred in the few decades following the Treaty of Paris. All the major issues came to the front immediately, when the Northwest Territory was officially declared part of the United States, in 1787, via the Northwest Ordinance. This area was “northwest”, relative to the defining western boundary of a fair chunk of the country at the time–the Ohio River—and encompassed the large area between the Ohio and Mississippi Rivers, including the all the Great Lakes other than Lake Ontario.

There’s a vast literature on European–Native relations, and some tremendous reading therein, but I’ve yet to see any concise statement as pointed and indicting as this one. It is the (reported) official response to a group of American Commissioners, by a group of tribes formally at war with the United States–the first American war after the Revolution, declared by President Washington just about a year into his first term, in 1790. Lasting until 1794, it produced some highly noteworthy events and people. The events including what was, by far, the most severe defeat ever suffered by the American military at the hands of native peoples (including the infamous Little Bighorn), which occurred two years previous, at a remote wilderness site on what is now the Indiana-Ohio border about half way between Cincinnati and Fort Wayne. Along with a prolonged series of attacks on settlers, this drove the vast majority of the settlers from the area, and left the natives in undisputed control of the Territory. The people produced included two of the most powerful Native American leaders ever known–Little Turtle and Tecumseh, as well as a future president, William Henry Harrison.

The context of their response (below) is as follows. The American Commissioners had argued that, via the Treaty of Paris, all lands formerly claimed by the British (and by the French before 1763), north of the Ohio River and south of the Canadian boundary, had formally been transferred to US control. Upshot: the native tribes were expected/requested to cede control of the area, to the United States, for a stipulated sum of money. Having just defeated two American armies, including completely destroying one, and having formed a confederacy of affiliated tribes exceeding the power of even the infamous Iroquois confederacy, we can imagine what their response to this was. The exchange occurred “at the foot of the rapids” of the Maumee River, in what is now Maumee Ohio, a suburb of Toledo. Maumee is a derivation of Miami, a leading tribe in the confederation that included several large and significant tribes, including Pottawattamies, Ottawas, Chippewas, Shawnees, Wyandots, Delawares, Kickapoos and some others. The Commissioners had also argued there were now numerous settlers in the NW Territory, such that Indian control was just not feasible.

Money to us is of no value, and to most of us, unknown. And, as no consideration whatever can induce us to sell the lands on which we get sustenance for our women and children, we hope we may be allowed to point out a mode by which your settlers may be very easily removed, and peace thereby obtained. We know [as the Commissioners had stated] that these settlers are poor, or they would never have ventured to live in a country which has been in continual trouble ever since they crossed the Ohio. Divide, therefore, this large sum of money which you have offered us, among these people. Give to each, also, a portion of what you say you would give to us annually, over and above this very large sum of money; and, as we are persuaded, they would most readily accept it in lieu of the land you sold them. If you add, also, the great sum of money you must expend in raising and paying armies, with a view to force us to yield to you our country, you will certainly have more than sufficient for the purpose of repaying these settlers for all their labor and their improvements.

You have talked to us about concessions. It appears strange that you should expect any from us, who have only been defending our rights against your invasions. We want peace. Restore to us our country, and we shall be enemies no longer. You make one concession to us by offering us your money, and another, by having agreed to do us justice, after having long and injuriously withheld it; we mean, in the acknowledgment you now make, that the King of England never did, and never had a right to give you our country, by the treaty of peace. And you want to make this act of justice a part of your concessions; and you seem to expect that because you have at last acknowledged our independence, we should for such favor surrender to you our country. You have talked, also, a great deal about pre-emption, and your exclusive right to purchase Indian lands, as ceded to you by the King at the treaty of peace. We never made any agreement with this King, nor with any other nation, that we would give to either the exclusive right of purchasing our lands; and we declare to you that we consider ourselves free to make any bargain or cession of lands whenever, or to whomsoever, we please. If the White people, as you say, made a treaty that none of them but the King should purchase of us, and that he had given that right to the United States, it is an affair that concerns you and him, and not us. We have never parted with such power.

We desire you to consider that our only demand is the peaceable possession of a small part of our once great country. Look back and review the lands from whence we have been driven to this spot. We can retreat no further, because the country behind hardly affords food for its inhabitants; and we have, therefore, to leave our bones in this small place to which we are now confined. We shall be persuaded that you mean to do us justice when you agree that the Ohio [river] shall remain the boundary line between us. If you will not consent thereto, our meeting would be altogether unnecessary. This is the great point which we hoped would have been explained before you left your homes, as our message, last fall, was principally directed to obtain that information.

Done at the Foot of the Maumee Rapids, the 10th day of August, 1793.


Source, (p. 38)

Winter time

A fair bit of the whitish water emanated from the sky yesterday. So, decided to head out with the old camera and see what I could see. Well, lots of the usual, but certainly more beautiful, and in at least one case, some somewhat unexpected goings on in the neighborhood.

The old lighthouse–and I do mean old–is still there:

The ice machine, thank goodness, is operating:

White house, white fence, white, white white:

Continue reading

I hear them all

I hear the crying of the hungry
In the deserts where they’re wandering
Hear them crying out for Heaven’s own
Benevolence upon them
Hear destructive power prevailing
I hear fools falsely hailing
To the crooked words of tyrants when they call
I hear them all
I hear them all
I hear them all

I hear the sound of tearing pages
And the roar of burning paper
All the crimes in acquisition
Turn to air and ash and vapor
In the rattle of the shackles
Far beyond emancipators
Where the lowliest, they gather in their stalls
I hear them all
I hear them all
I hear them all

I hear the drilling of the armies
And the firing of their vollies
As the shots ring out relentless
With absurdity and folly
Though the smoke is thick with anguish
And the body counts are endless
Songs of peace will rise, above the cannonballs
I hear them all
I hear them all
I hear them all

So, while you sit and whistle Dixie
With your money and your power
I can hear the flowers a-growing
In the rubble of the towers
I hear leaders quit their lyin’
I hear babies quit their cryin’
I hear soldiers quit their dyin’, one and all
I hear them all
I hear them all
I hear them all

I hear a tender word from Zion
I hear Noah’s waterfall
Hear the gentle lamb of Judah
Sleeping at the feet of Buddha
And the prophets from Elijah
To the old Paiute Wovoka
Take their places at the table when they’re called
I hear them all
I hear them all
I hear them all

Old Crow Medicine Show and David Rawlings

Needless to say, this one goes into the set list, pronto. It’s all C, G, and D shapes with an E minor here and there (D, A and E at capo 2, key of D). Done as only Old Crow can.

Aesculus glabra!

Ezekiel Elliott, Ohio State

Ezekiel Elliott, Ohio State, breaks through the line in Ohio State’s NCAA football championship game victory over Oregon Monday night, capping an improbable run to the title in the first year of the college football playoff. Photo by Kirby Lee, USA TODAY sports

Awesome Buckeyes, just plain awesome.
Enough said.

Christmas, on the run

Hey has anybody seen Eddie lately?
I haven’t seen him since the weather turned cold
He had just found a couple of coats for his daughters–
He said they were five and six years old

He’d said he might hop a freight back toward Memphis
Get them in school, find work, cut his hair
He knows in his sleep the best spots on the mighty river
Craves the power of it; loves the air

Merry Christmas everybody
Merry Christmas everyone
Merry Chrismas to you squirrels and pigeons
Merry Christmas on the run

He believes his older sister is still in Utah
He’d give anything to see her again
Been fifteen years since he left the foster home at fourteen
With his dreams, a compass and a gun

Had never believed the stupid story of Santa
Nor the one about a mom and dad
He’s mute regarding trust and love; agnostic
But has a hundred definitions of sad

Christmas Eve, out beyond, in the random
Under bridges, or in the open air
Edges of trainyards, beyond the watchmen
Vacant houses, park benches, city squares

Merry Christmas everybody
Merry Christmas everyone
Merry Chrismas to you stray cats and dogs
Merry Christmas, you gypsies on the run

Merry Christmas to the the scared, the broken, and the lonely
Merry Christmas to the trees, the clouds and the sun
Merry Christmas everybody
Merry Christmas everyone

Peace on earth, good-will to men


Here’s a beauty, my favorite for the season, courtesy of Henry W. Longfellow, with music by John Gorka. Can it really be almost 25 years since John recorded this for Windham Hill? There’s also this excellent cover by John Elrod that I just found.

Christmas Bells, John Gorka

I heard the bells on Christmas Day
Their old, familiar carols play,
And wild and sweet
The words repeat
Of peace on earth, good-will to men!
Peace on earth, good-will to men!

And in despair I bowed my head;
“There is no peace on earth,” I said;
“For hate is strong,
And mocks the song
Of peace on earth, good-will to men!”
Peace on earth, good-will to men!”

Then pealed the bells more loud and deep:
“God is not dead, nor doth He sleep;
The Wrong shall fail,
The Right prevail,
With peace on earth, good-will to men.”
Peace on earth, good-will to men.”

Abridged, Henry W. Longfellow, 1864

Well, how ’bout that

The blog known as “RealClimate” has put up a couple of posts on its first ten years this week, here and here. Surprisingly, they state that they’ve “done well” and honor themselves for their ability to do what others couldn’t or wouldn’t 10 yrs back. Well, this is good stuff indeed.

In the interest of public education I’ll be providing a little additional insight when time and energy allow. Just a little, say 4/10 = 40% or so maybe.