Severe analytical problems in dendroclimatology, part fifteen

I’m going to give this topic another explanatory shot with some different graphics, because many still don’t grasp the serious problems inherent in trying to signal and noise from tree ring size. The most advanced method for attempting this is called Regional Curve Standardization, or RCS, in which ring size is averaged over a set of sampled trees, according to the rings’ biological age (i.e. ring number, counting from tree center), and then dividing each individual series by this average. I include five time series graphs, successively containing more information, to try to illustrate the problem. I don’t know that I can make it any clearer than this.

First, shown below are the hypothetical series of 11 trees sampled at a single sampling location.

Each black line shows the annual ring area progression for each of 11 trees having origin dates spaced exactly 10 years apart (the bold line is just the oldest tree of the group). By using ring area as the metric we automatically remove part of the non-climatic trend, which is the purely geometric (inverse quadratic) effect from each series. Any remaining variation is then entirely biological and it exhibits a very standard tree growth pattern, one in which growth rate increases to a maximum value reached relatively early life (here, around age 80 or so) and then declines more slowly toward a stable asymptote, which I fix at 1.0. Each tree’s trajectory occurs in a constant climate over the 300-400 year period measured.

The next figure adds two components:

First, the blue line represents a constantly increasing climatic parameter over time, say temperature, expressed as a ratio of its effect on ring size at year 0. Thus, at year 400, the cumulative climatic effect on ring area, regardless of biological age, is exactly 3-fold of its year zero value (scale at right). The second addition is the series of red lines, which simply represent those same 11 trees’ growth trajectories growing under this climate trend. The climatic effect on growth is a super simple linear ramp in all cases–I am not invoking any kind of problematic, complex growth response (e.g. “divergence”), or any other complication. Thus, by definition, if we divide the two corresponding ring series for each tree, we get exactly the blue line, in all cases.

In the third figure:

I add a green line–this is the estimated RCS curve, computed the standard way (by aligning each tree according to its biological age and then averaging the ring sizes over all trees). This RCS curve is thus the estimated non-climatic ring size variation, which we accordingly remove from each tree by dividing the red growth series by it. Finally, we average the resulting 11 index series, over each of the 400 years, giving the stated goal: the estimated climatic time series.

It is at first glance entirely clear that the green RCS curve does not even come close to matching any of the black curves representing the true non-climatic variation…which it must. According to standard dendroclimatological practice we would now divide the 11 red curves by this green RCS curve–which is thereby guaranteed not to return the true climatic signal. So what will it return?

It returns the orange line shown above. No that’s not a mistake: it will return an estimated climatic trend of zero.

And this is the entire point–the supposedly most advanced tree ring detrending method is fully incapable of returning the real climatic trend when one exists. Note that I’m keeping everything very simple here–this result does not depend on: (1) either the direction or magnitude of the true trend, or (2) the magnitude, or shape, of the non-climatic trend in the sampled trees (including no such whatsoever). That is, this type or magnitude of result is not specific to the situation I set up. The problem can be reduced, but never eliminated, by increasing the variance in tree ages in the sample. But since standard field sampling practice is to sample the oldest possible trees at a site, this is very rare, a fact which the data of the International Tree Ring Database (ITRDB) shows clearly–which is ironic given that Keith Briffa and Ed Cook mentioned the importance of exactly this issue in a white paper available at the ITRDB site.

Lastly, suppose now that the last usable year for all ring series occurred a few decades ago. This will occur, for example, due to many ITRDB field samples being collected decades ago now, or for any perceived problems in the climate-to-ring response calibration function, which is must be stable and dependable (notably, the “divergence” effect, in which linear relationships between climate and ring size break down, badly). What will be the result of eliminating, say, the last five decades of data, and replace them with instrumental data? Well, you will then get exactly this:

Look familiar? Does that look like anything remotely approaching success to you? Again, I have not even broached other possibly confounding problems, such as co-varying growth determinants (e.g. increasing CO2- or N-fertilization, changing soil moistures, or inter-tree competition), nor non-linear responses in the calibration function, nor any of the thorny issues in large-scale sampling strategies, reconstructions and their corresponding data analysis methods. Those things would all exacerbate the problem, not improve it. It’s a total analytical mess–beginning and end of story.

I can’t make it any clearer than this. And yes I have the R code that generated these data if you want to see it.

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I’ve Been Converted

Some Easter slide guitar, courtesy of one of the true masters thereof, Kelly Joe Phelps.

Well I know, yeah I know…that I’ve been converted…
Now do you?

You’ve got to know sir
That I’ve made me a change
That I’m not afraid to call my Savior’s name
Well I know…that I’ve been converted now…
Do you?

Kelly Joe Phelps, I’ve Been Converted

There may still be some time

I just closed my eyes again–
Climbed aboard the Dream Weaver train
Trying to take away my worries of today
And leave tomorrow behind

Fly me high through the starry skies
Take me to an astral plane
Across the highways of fantasy
Help me to forget today’s pain

Though the dawn may be coming soon
There may still be some time
Fly me away to the bright side of the moon
And meet me on the other side

Gary Wright, Dream Weaver

Harlan

I don’t know his name for sure but I think somebody said “Hi Harlan”” to him from their car stopped at an intersection. He is well known in those parts.

I’ve seen him for months on the streets, and since I’ve been here less than a year, I’d guess he’s been there much longer. He looks to be in his 60s, and walks with a single crutch at all times, such that your can hear him coming even when you don’t see him. He accosts almost every passer-by with a much garbled “Could you spare a dollar, I’m trying to get something to eat”. He seems to be reasonably successful, based on the number of people I see stopped with him, and as far as I can tell, he actually uses the money for food, not alcohol (a big issue with street beggars). He has, for all I can tell, not a soul in this world to count on for anything. I have no idea where he stays at night.

When I first saw him last summer he acted as described above. I had not seen him throughout the winter, yesterday being the first time I’d ventured out on the streets in that area. Harlan was still begging but now also yelling intermittently–incoherent phrases aimed at nobody in particular, and with gusto.

It was still chilly out, but I found a nice spot in the afternoon sun and set down my guitar and amp and plugged in and set up. I could hear Harlan coming down the sidewalk, and he pointed at my stuff and mumbled something incoherent that appeared to involve some danger of being arrested by the cops or something, I’m not sure. I replied “OK man” and continued with what I was doing, and Harlan moved on.

There was hardly anybody on the streets but it was downright comfortable for the first time in months so I started playing, for the practice if nothing else. I soon noticed a guy off to my right 10 yards, smoking a cigarette and listening. A few minutes later he came up and said he had no money with him but if he did he’d give me some, because I sounded great, quite similar to Pat Metheney. He was a bassist; he knew music and paid me other generous compliments. I replied no problem man, being compared favorably to Pat Metheny is worth more to me than dollar or two. He left but came back soon with two friends, threw in a tip and we all talked briefly about guitar favorites: Leo Kottke, Ry Cooder, and Chris Smither in particular. I convinced them that yes, they really should see Chris when he comes to town in May. And Leo Kottke’s song “I Yell at Traffic” came to my mind.

I resumed playing and a little later, Harlan came around the corner, yelling, stopped for a minute, and then sat down on some restaurant steps a few feet away. He stopped yelling and muttering to himself. He just say there, listening. Sensing this, I broke into a slow and deliberate rendition of arguably the most beautiful song I know, Bob Dylan’s Visions of Johanna, a waltz which I do in the key of A. Harlan continued to sit and gaze into the distance, in the warm sun and listen, the sound reverberating through the street. And then through another piece, before getting up and continuing his march. Hopefully, a few minutes of beauty and solace in an otherwise desperate existence.

If I see him again, I’m going to do it again, except that I’m going to try to play the best thing my fingers will generate.

Experts only

So, the IPCC has produced a special report on the issue of limiting the global temperature increase to 1.5 degrees C. This report is still open for comments for another 13 days…if you are an “expert” in the IPCC’s eyes. And what if you are not? Well if you’re American, you could still have commented, for a 30 day period that ended last week (Feb. 8), through a commenting system run by the United States Global Change Research Program (USGCRP)…assuming you actually knew about it.  And that latter issue is the topic of this post.

All IPCC report drafts are open to expert review, internationally, through a system the IPCC operates. In that system, you apply to be a reviewer by submitting your name and qualifications, which basically involves stating your expertise, including your degree and a list of up to five publications that demonstrate it. Then IPCC-associated folks say yes or no to your request.

But IPCC reports are also open to comments by national governments. The United States of course does so, the USGCRP administering this process.  But unlike the IPCC process, the USGCRP solicits comments from… anybody.  The notifications for these comment periods are required by law to be posted in the Federal Register, and the notice also appears on a USGCRP web page (corresponding links here and here; screenshots for the two below).
Fed Register

usgcrp2

At least for this report, the USGCRP also posted four Twitter notices, on January 16, 24, 29 and February 5, all identical.  Why they waited six days before the first notice I don’t know. Below is the Jan. 24 notice.

usgcrp1

You still have to register, but in that process you just select the category from a drop-down list that best describes your status, in one of five broad categories, screenshot below:
USGCRP Registration screen

I now encourage you to read the Federal Register notice linked to above. Notice exactly what it says. Specifically, even though the process is open to everyone, the entire notice, including the title (“Call for Expert Reviewers…”) is framed in the language of “expert” reviewer, the crux of which reads as follows:

As part of the U.S. Government Review, starting on 8 January 2018, experts wishing to contribute to the U.S. Government review are encouraged to register via the USGCRP Review and Comment System (https://review.globalchange.gov/?)… The USGCRP coordination office will compile U.S. expert comments and submit to the IPCC, on behalf of the Department of State, by the prescribed deadline. U.S. experts have the opportunity to submit properly formatted comments via the USGCRP Review and Comment System (https://review.globalchange.gov/?) from 8 January to 8 February 2018. To be considered for inclusion in the U.S. Government submission, comments must be received by 8 February 2018.

Experts may choose to provide comments directly through the IPCC’s Expert Review process, which occurs in parallel with the U.S. Government Review. Registration opened on 15 December 2017, and runs through 18 February 2018: https://www.ipcc.ch/?apps/?comments/?sr15/?sod/?register.php

The Government and Expert Review of the IPCC Special Report on Global Warming of 1.5 °C ends February 25, 2018.

Do you see any indication anywhere in any of it, that indicates that the commenting process is in fact open to the general citizens of the United States? I don’t. This is in fact only apparent when you actually go to the USGCRP Review and Comment page, and attempt to register, per the screen shot above. To say nothing of the fact that experts using the IPCC’s review system have 90 days to comment whereas those using the USGCRP’s have only 30.

OK, so then one day ~two weeks ago I was wasting my time and energy, which is to say I was reading Twitter comments, and I noticed a climate scientist, Katharine Hayhoe relay a message inviting “colleagues” to comment on the IPCC report (original comment here). In response, a climate activist, Steve Bloom, asked her directly (paraphrasing) “And what about people like me?”, meaning non-academics (and non-experts to the IPCC).

This conversation immediately went downhill, but the bottom line in this context is that Hayhoe either (1) had no idea that all Americans still had nearly another two weeks or so to comment on the report, or (2) she did know but didn’t tell him. I have no evidence for believing the latter, and so the logical conclusion is the former. I didn’t see the exchange until a few days later, but when I did I jumped in to alert everyone that yes indeed, any American citizen could still comment for another week or so. I also directly criticized Hayhoe for not knowing this, given that she was a lead author on a chapter of another report, the National Climate Assessment #4 that just went through the USGCRP review process. But after seeing how the USGCRP phrases their official notices (and Tweets) regarding their review process, I can surely see why she might not have known.

Hayhoe, who won the AGU’s “Climate Communication” award four years ago (with its $10,000 prize) made no response whatsoever to my comments—she simply blocked me on Twitter, meaning I can no longer read any of her comments there. No acknowledgement of the USGCRP process, no apology to Bloom, nothing. Her main comment in the process was to tell Bloom not to talk disrespectfully to climate scientists, adding that he’d been warned before, screen shot below.
Hayhoe Twitter comments
Steve Bloom–no, no response from him either. The only person to comment at all on what I said was Richard Betts, a UK climate scientist who stated that it was interesting to learn that the United States allowed all citizens to comment on IPCC reports. Maybe the United States, unlike the IPCC, understands that having something important to say, is not limited to “experts”, whatever the latter entails exactly. Volumes could be written on that topic alone, but that’s not for the here and now.

So, this is just one example of the kind of thing we’re dealing with in the whole climate change public outreach circus, or tragedy, whichever it is. But it’s one thing if it’s just an entertaining circus, and another thing altogether if your so-called “climate communicators” can’t communicate crucial facts about the public interaction process.

One hundred years of NHL hockey; some analysis

This post has been updated, with corrected data and modified discussion, as detailed in the text.

Does anything say “100 Years of the National Hockey League” like say, a Tampa Bay vs Vegas matchup.  Montreal, Toronto, Ottawa?  Please; bunch of party crashers them.

In case you missed it, National Hockey League play is, today, exactly 100 years old. On December 19, 1917 the first two games in the new league had the Toronto Arenas at the Montreal Wanderers, and the Montreal Canadiens at the Ottawa Senators. This limited slate was due in large part to those being the only four teams in the league.  It turns out that the Wanderers got their first and only win in franchise history, which lasted just six games. They got past the Arenas in the common hockey score of 10-9. The Arenas, conversely, went on–along with the Canadiens–to become one of the two most storied franchises in NHL history: today’s Toronto Maple Leafs. The Senators’ first incarnation lasted until 1934, and after a 58 year absence came the second (and current) version in 1992.

So anyway, there’s hype and hoopla happening, and also discussions of the greatest seasons, teams, players, etc. As for me, I thought it would be great fun to crunch 90 years of team-season numbers to see what they indicated about team records, actual versus expected. Two minutes for tripping, and without even inhaling anything.

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You would not think, just to look at him…

So yesterday I was riding the bus, which I only do when I need to tote both my guitar and amp downtown. The two-plus miles is just a little too far for the ~60 pound carry, especially given an injured shoulder and wrist, and sidewalks that are a mess from a foot of snow last week.

A couple of stops  after boarding, on steps a guy with a very tattered beige coat, like something that might have been involved in say, some street fights, or use as a dog’s bed. He was dragging a heavy-looking plastic bag full recyclables, and sat down next to me.

“Play the guitar, eh?”
“Yeah” says I.
“What kind of stuff you like?”
“Acoustic 12…a lot of Bob Dylan, but also John Gorka, Chris Smither, Greg Brown, the Dead, some Zeppelin…some of my own stuff too.”

In the five minutes before he got off, he told me the abridged version of how he once played a lot, both guitar and keyboards, apparently as a professional musician, including a lot of local shows at various venues, with a band was busy and popular, mostly back in the 1980s and 90s I gathered. He said he made good money at it and even shared the bill with some well-known bands/acts, such as Mitch Ryder, Steppenwolf, and (I think) Dave Alvin’s band (The Blasters?).   About how Ryder once got quite upset with him, when his band was supposed to be opening his show but he was instead drunk in a local bar, having completely forgotten about it.  His band mates had to track him down, and the resulting delay caused Ryder to open for him, instead of vice-versa. He smiled at the memory.

I asked him if he was still performing or playing. He talked for a couple of minutes–about how that’s all gone now. He lives on disability and food stamps, supplemented I guess, by whatever he gets from collecting and hauling recyclables via foot and bus, and street begging, which he said he makes some money at.

“Yeah, I could…but damn alcohol…” he said.

As he got up to get off, I invited him to bring his guitar and we could jam together on the street. He said that would be cool, and would do so. There wasn’t time to get his name or number.  Hope I see him again.

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

 

WAR, Pythagoras, Poisson and Skellam

Getting into some issues only makes you wish that you hadn’t, when you realize how messed up they are, at a fundamental level.

Here’s a great example involving statistical analysis, as applied to win/loss (“WL”) records of sports teams, the base concept of which is that it’s possible to estimate what a team’s WL record “should” have been, based on the number of goals/runs/points that it scored, and allowed, over a defined number of games (typically, a full season or more). This blog post by Bill James partially motivates my thoughts here.

Just where and when this basic idea originated I’m not 100 percent sure, but it appears to have been James, three to four decades ago, under the name “Pythagorean Expectation” (PE). Bill James, if you don’t know, is the originator, and/or popularizer, of a number of statistical methods or approaches applied to baseball data, which launched the so-called “SABR-metric” baseball analysis movement (SABR = Society for American Baseball Research). He is basically that movement’s founder.

In the linked post above, James uses the recent American League MVP votes for Jose Altuve and Aaron Judge, to make some great points regarding the merit of WAR (Wins Above Replacement), arguably the most popular of the many SABR-metric variables. The legitimacy of WAR is an involved topic on which much virtual ink has been spilled, but is not my focus here; in brief, it tries to estimate the contribution each player makes to his team’s WL record. In the article, James takes pointed exception to how WAR is used (by some, who argue based upon it, that the two players were basically about equally valuable in 2017). In the actual MVP vote, Altuve won by a landslide, and James agrees with the voters’ judgement (pun intended): WAR is flawed in evaluating true player worth in this context. Note that numerous problems have been identified with WAR, but James is bringing a new and serious one, and from a position of authority.

One of James’ main arguments involves inappropriate use of the PE, specifically that the “expected” number of wins by a team is quite irrelevant–it’s the *actual* number that matters when assessing any given player’s contribution to it. For the 2017 season, the PE estimates that Judge’s team, the New York Yankers, “should” have gone 101-61, instead of their actual 91-71, and thus in turn, every Yanker player is getting some additional proportion of those ten extra, imaginary wins, added to his seasonal WAR estimate. For Altuve’s team, the Houston Astros, that’s not an issue because their actual and PE WL records were identical (both 101-61). The WAR-mongers, and most self identified SABR-metricians for that matter, automatically then conclude that a team like this year’s Yanks were “unlucky”: they should have won 101 games, but doggone lady luck was against ’em in distributing their runs scored (and allowed) across their 162 games…such that they only won 91 instead. Other league teams balance the overall ledger by being luck beneficiaries–if not outright pretenders. There are major problems with this whole mode of thought, some of which James rips in his essay, correctly IMO.

But one additional major problem here is that James started the PE craze to begin with, and neither he, nor anybody else who have subsequently either modified or used it, seems to understand the problems inherent in that metric. James instead addresses issues in the application of the PE as input to the metric (WAR) that he takes issue with, not the legitimacy of the PE itself. Well, there are in fact several issues with the PE, ones that collectively illustrate important issues in statistical philosophy and practice. If you’re going to criticize, start at the root, not the branches.

The issue is one of statistical methodology, and the name of the metric is itself a big clue–it was chosen because the PE formula is similar to the Pythagorean theorem of geometry: A^2 + B^2 = C^2, where A, B and C are the three sides of a right triangle. The original (James) PE equation was: W = S^2 / (S^2 + A^2), where W = winning percentage, S = total runs scored and A = total runs allowed, summed over all the teams in a league, over one or more seasons. That is, it supposedly mimicked the ratio of squared lengths between one side, and the hypotenuse, of a right triangle. Just how James came to this structural form, and parameter values, I don’t know and likely very few besides James himself do; presumably the details are in one of his annual Baseball Abstracts from 1977 to 1988, since he doesn’t discuss the issue that I can see, in either of his “Historical Baseball Abstract” books. Perhaps he thought that runs scored and allowed were fully independent of each other, orthogonal, like the two sides of a right triangle. I don’t know.

It seems to me very likely that James derived his equation via fitting various curves to some empirical data set, although it is possible he was operating from some (unknown) theoretical basis. Others who followed him, and supposedly “improved” the metric’s accuracy definitely fitted curves to data, since all parameters (exponents) were lowered to values (e.g. 1.81) for which no theoretical basis is even possible to conceive of: show me the theoretical basis for anything that scales up/down according to the ratio of a sum of parts, and one component thereof, by the power of 1.81. The current PE incarnation (claimed as the definitive word on the matter by some) has the exponents themselves as variables, dependent on the so-called “run environment”, the total number of runs scored and allowed, per game. Thus, the exponents for any given season are estimated by R^0.285, where R is the average number of runs scored per game (both teams) over all games of a season.

Even assuming that James did in fact try to base his PE on theory somehow, he didn’t do it right, and that’s a big problem, because there is in fact a very definite theoretical basis for exactly this type of problem…but one never followed, and apparently never even recognized, by SABR-metricians. At least I’ve seen no discussion of it anywhere, and I’ve read my share of baseball analytics essays. Instead, it’s an example of the curve-fitting mentality that is utterly ubiquitous among them. (I have seen some theoretically driven analytics in baseball, but mostly as applied to ball velocity and trajectory off the bat, as predicted from e.g., bat and ball elasticity, temperature, launch angle, and etc, and also the analysis of bat breakage, a big problem a few years back. And these were by Alan Nathan, an actual physicist).

Much of science, especially non-experimental science, involves estimating relationships from empirical data. And there’s good reason for that–most natural systems are complex, and often, one simply does not know, quantitatively and apriori, the fundamental operating relationships upon which to build a theory, much less how those interact with each other in complex ways at the time and space scales of interest. Therefore one tries instead to estimate those relationships by fitting models to empirical data–often some type of regression model, but not necessarily. It goes without saying that since the system is complex, you can only hope to detect some part of the full signal from the noise, often just one component of it. It’s an inverse, or inferential, approach to understanding a system, as opposed to forward modeling driven by theory; these are the two opposing approaches to understanding a system.

On those (rare) occasions when you do have a system amenable to theoretical analysis…well you dang well better do so. Geneticists know this: they don’t ignore binomial/multinomial models, in favor of curve fitting, to estimate likely nuclear transmission genetic processes in diploid population genetics and inheritance. That would be entirely stupid, given that we know for sure that diploid chromosomes conform to a binomial process during meiosis the vast majority of the time. We understand the underlying driving process–it’s simple and ubiquitous.

The binomial must be about the simplest possible stochastic model…but the Poisson isn’t too far behind. The Poisson predicts the expected distribution of the occurrence of discrete events in a set of sample units, given knowledge of the average occurrence rate determined over the full set thereof. It is in fact exactly the appropriate model for predicting the per-game distribution of runs/goals scored (and allowed), in sports such as baseball, hockey, golf, soccer, lacrosse, etc. (i.e. sports in which scoring is integer-valued and all scoring events are positive and of equal value).

To start with, the Poisson model can test a wider variety of hypotheses. The PE can only predict a team’s WL record, whereas the Poisson can test whether or not a team’s actual runs scored (and allowed) distribution, follows expectation. To the extent that they do follow is corresponding evidence of true randomness generating the variance in scores across games. This in turn means that the run scoring (or allowing) process is stationary, i.e., it is governed by an unchanging set of drivers. Conversely, if the observed distributions differ significantly from expectation, that’s corresponding evidence that those drivers are not stationary, meaning that teams’ inherent ability to score (and/or allow) runs is dynamic–they change over time (i.e. between games). That’s an important piece of knowledge in and of itself.

But the primary question of interest here involves the WL record and its relationship to runs scored and allowed. If a team’s runs scored and allowed both closely follow Poisson expectations–then prediction of the WL record follows from theory. Specifically, the distribution of differences in two Poisson distributions follows the Skellam distribution, described by the British statistician J.G. Skellam in the 1950s, as part of his extensive work on point processes. That is, the Skellam directly predicts the WL record whenever the Poisson assumptions are satisfied. However, even if a team’s run distribution deviates significantly from Poisson expectation, it is still possible to accurately estimate the expected WL record, by simply resampling–drawing randomly several thousand times from the observed distributions–allowing computers to do what they’re really good at. [Note that in low scoring sports like hockey and baseball, many ties will be predicted, and sports differ greatly in how they break ties at the end of regulation play. The National Hockey League and Major League Baseball vary greatly in this respect, especially now that NHL ties can be decided by shoot-out, which is a completely different process than regulation play. In either case, it’s necessary to identify games that are tied at the end of regulation.]

If instead you take an empirical data set and fit some equation to those data–any equation, no matter how good the fit–you run the risk of committing a very big error indeed, one of the biggest you can in fact make. Specifically, if the data do in fact deviate from Poisson expectation, i.e. non-stationary processes are operating, you will mistake your data-fitted model for the true expectation–the baseline reference point from which to assess random variation. Show me a bigger error that you can make then that one–it will affect every conclusion you subsequently come to. So, if you want to assess how “lucky” a team was with its WL record, relative to runs scored and allowed, don’t do that. And don’t get me started on use of the term “luck” in SABR-metrics, when what they really mean is chance, or stochastic, variation. The conflation of such terms in sports that very clearly involve heavy doses of both skill and chance, is a fairly flagrant violation of the whole point of language. James is quite right in pointing this out.

I was originally hoping to get into some data analysis to demonstrate the above points but that will have to wait–the underlying statistical concepts needed to be discussed first and that’s all I have time for right now. Rest assured that it’s not hard to analyze the relevant data in R (but it can be a time-consuming pain to obtain and properly format it).

I would also like to remind everyone to try to lay off high fastballs, keep your stick on the ice, and stay tuned to this channel for further fascinating discussions of all kinds.  Remember that Tuesdays are dollar dog night, but also that we discontinued 10 cent beer night 40 years ago, given the results.

Everything is broken

Broken bottles, broken plates
Broken switches, broken gates
Broken dishes, broken parts
Streets are filled with broken hearts
Broken words never meant to be spoken
Everything is broken

Broken cutters, broken saws
Broken buckles, broken laws
Broken bodies, broken bones
Broken voices on broken phones

Broken hands on broken ploughs
Broken treaties, broken vows
Broken pipes, broken tools
People bending broken rules
Hound dog howling, bullfrog croaking
Everything is broken

Bob Dylan, 1989

What was it, roughly, that we were thinking there, if anything? Part two.

So, there was a high school class reunion a few months back, and it’s World Series time again, so now seems a good time for an overdue, second episode of our series of the above title. In episode one, I explored an incident involving sub-optimal decision making in high school so I think I’ll just continue on that theme here.

I saw a number of old classmates, and teammates, at the reunion. I think class reunions are great. They can cause one to reflect on really important topics, such as the passage of time, or the nature of life’s changes. Or to even deeper things. Explosives for example. Just what “loud” really entails. The nature of stupidity.

It seems that I had become aware that personal fireworks were legal in the next county, and had thus traveled the 40 miles to obtain a few dozen “M-80” fireworks, ostensibly for use during the Fourth of July. It also seems that sometime later, my friend Steve and I found ourselves parked in front of our friend Doug Brown’s house after dark, with said bag of M-80s and a lighter. Now, an M-80, we’d been told, contained the equivalent gunpowder of a quarter stick of dynamite, which I thought was pretty impressive but did no actual testing of. If one of these things goes off on, say, someone’s front porch, it would not typically go unnoticed, and that concept did seem, to us, worthy of some testing at that particular time.

It additionally seems that I was the driver and Doug’s house was off to our left. The plan, which I think we put a solid 30 seconds of thought into, was that we would launch one of these onto Doug’s porch–about maybe 75 ft away–while seated in the vehicle, so as to effect a prompt getaway. We came up with a fair and efficient division of labor in which Steve would light the fuse and hand the thing to me–I would then fire it toward the porch and immediately hit the gas, making ourselves rapidly scarce. It was a great plan as far as I was concerned: all I had to do was throw and floor it, whereas Steve had the equivalent of six to eight sticks of dynamite in a bag on his lap, with an open flame in his hand. This struck me as equitable, given that I was providing the vehicle and the right arm.

So…what’s the baseball connection here, you may wonder. Well, I played shortstop in high school, whereas Steve didn’t, and so it was logical that I should do whatever throwing was involved. Shortstop is a fun position, because you get to sprint to chase down ground balls, and then watch the first baseman sprint to chase down the throw you just sailed some distance beyond him. Now, 70-80 feet is a lot shorter than a typical throw from shortstop to first base…but an M-80 is also a lot lighter than a baseball. So I knew I should put some mustard on it to insure getting it at least somewhere near the porch. Being quite experienced at firing balls into the adjacent woods from deep short, I wasn’t too worried about it. If the M-80 banged off the front of the house first or whatever, no big deal, I mean assuming nobody opened the front door at the wrong instant.

Now may be a good time to remind ourselves of the importance of taking all potentially relevant variables into consideration–apriori even–in events like these. And do we think enough about the tangible value of trial runs? Probably some room for improvement there too.

Anyway, Steve successfully got said firework lit without blowing us up, and the ensuing exchange to me was also flawless. With right arm extended and a good five seconds or so to work with, I eyed Doug’s porch and applied my best Nolan Ryan fastball to the explosive. Now, I think it’s fair to say that (1) the average person is just not that aware of exactly where one’s car door meets one’s car roof, (2) that I qualify as quite average in that context, and (3) that that specific location took on above average significance, in that particular situation. In short, when my hand was just about to send said explosive device on it’s planned trajectory, said hand was inadvertently applied, with considerable force, to said vehicular location, and separated from said device, thereby placing the latter on a trajectory not nearly as likely to achieve the original objective. This in turn would necessitate a rapid adjustment in plan and action, not to mention vocalization.

This is more or less a science blog, and I ask you, are many topics more fascinating, really, than the physics of acoustics under confinement? Maybe heredity–I find that interesting too. Also, involuntary reflexes, impromptu vocalizations: good stuff. How about hand-eye coordination under duress? Personal safety and survival? Blood?
Bodily dismemberment? All topics worthy of consideration when you get down to it. Let’s explore some of these for just a moment.

Acoustic physics, let’s take. As we know, Newton’s First Law of Loud, states “Any acoustically active device, placed under spatial confinement, will manifest even more of its acoustic characteristics, in fact quite a lot more than you’d think just from theory alone”. Take spatial relationships: just how much room for rapid bodily movement is there, really, in the front passenger seat of a typical car? How can humans maximize movement efficiency in response to active, explosive devices experiencing random trajectories?

Now back to our story. To cut to the chase, upon hand-car impact, our active device–the one under current discussion–experienced a rather sudden change of x coordinate velocity–one markedly away from Doug’s front porch, opposite that really, which is to say in the general direction of one Steve. More specifically, toward Steve’s male-specific, hereditarily significant anatomy. And there it landed, for a brief moment. Although entirely stunned, and with my hand feeling possibly broken, I was still able to collect myself, breathe a sigh of relief and comment on just how fortunate we were, really, that said M-80 had not taken an alternate trajectory and landed instead, in or near the bag of 30 or so other M-80s, within the confines of our vehicle, in which we too were present, due to our plan, in the street in front of our friend Doug Brown’s house. Steve also reflected for a bit on this fortunate state and concurred that such an outcome would have been potentially problematic on several counts, not the least of which was just how autopsies and identifications based on scattered body parts are conducted.

The preceding is not in fact what transpired at that moment.

Rather, Steve executed what I think to this day is the most rapid series of body movements I’ve ever seen from a human being, with the possible exception of the time I scrambled up and over a rock to find my neck about three feet directly in front of the head of a large rattlesnake. Conscious thought was not part of the process. M-80s had fuse times of roughly six to seven seconds, going strictly from memory. I’d guestimate that at this point, about four of those remained. As I recall it, there were, in order (1) an involuntary yell, (2) a ceiling-constrained jump upward, and (3) a failed attempt to flick the thing, by a backhand motion, away from where it resided. This process took maybe two seconds, maximum, and led to another entirely frantic attempt–panicked would work–which succeeded in flinging the thing down towards Steve’s feet. This, very fortunately, was not where the bag of other M-80s had been placed, and additionally, it’s one thing to have your feet blown off but quite another to have your evolutionary lineage ended.

Down there our device detonated, with a flash, maybe 1 to 1.5 seconds later.

What M-80 detonations lack in duration and beauty of light display they make up for in sheer decibels; they aren’t fireworks so much as small bombs. This was the most unbelievably loud thing I’d ever heard, and that includes seeing Ted Nugent in the old concrete and steel Toledo Sports Arena (also with Steve). It was concussive. Steve told me he basically could not hear for several days. The car was immediately filled with an acrid cloud of sulfurous smoke. My hand felt very possibly broken. I could neither hear nor see, and my first thought was “We gotta get out of here right NOW, before Doug comes out and sees this”. Or even worse, his dad, with a possible call to the police. But even in the best of circumstances, it’s not easy to go straight from Nolan Ryan to Mario Andretti, quickly. I could not see without sticking my head out the window, which I did until the breeze created cleared out the cab. I’m not sure that Steve knew exactly what had happened or even where he was, but didn’t have time to investigate. I was pretty sure he was alive and that would have to be good enough for the moment.

I think the evening’s festivities were concluded with this event, although I wouldn’t necessarily place money on that either. If Doug is reading, I’d like to formally apologize for the rubber patch laid in front of his house and any subsequent effect on property values that may have resulted.

Thanks for reading and please stay tuned for the next episode, in which we’ll explore how surprisingly inconvenient cul-de-sacs can be in certain circumstances, and/or other fascinating topics.

Our Lady of Tectonic Process

The following excerpt is a description of what is now the Los Angeles CA area. Note the title of the work, at bottom. The Portola/Crespi expedition is considered the first land-based, Caucasian exploration of what is now the State of California. So…just who were the people these Native Americans referred to, where indeed did they come from, and what route did they take to get there? And how long did they stay? And were the fair- and red-haired children Crespi mentions as having observed, their children?

July 28 [1769]
We set out at six o’clock in the morning from this grand plain and watering place of Santiago, following the same northwestward course of these last days’ marches, keeping on over this same plain, skirting the range on our right (to the north)…The scouts returned last night and said they came upon a full-flowing river a league and a half away…Its course comes out of the mountain range that must lie about two or three leagues away from us, from northeast to southwest…This river bed is very much lined with trees: white cottonwoods, willows, sycamores and other kinds we don’t recognize. By what we’ve seen from the sands along its banks, this river must plainly carry very large floods, and we had some trouble crossing it even now, in the depth of the dry season and dog days. There will be no crossing it in the rainy season…

We made camp close to the river here, and we have felt three strong earthquakes within less than an hour today at noon. The first and most violent must have lasted the length of a Creed, the other two less than a Hail Mary; a great shaking of the ground however was felt during all three. This is a most beautiful spot–with a great amount of soil and water, and this beautiful river going as it does, through the midst of the wide and far-ranging plain here–for founding a mission…

The heathens of this village here, who have been spending the whole day with us, brought and showed us nine cutlasses without hafts, along with four or five eyeless matting needles and a thick spike about half a yard long, all of which, they gave us to understand, had been given to them upcountry, toward the north, by some people there like ourselves, and we also understood there to be Fathers like ourselves. Whether this means they have a connection with New Mexico or the Apaches we cannot tell, or, whether some nation may have intruded upcountry toward the northward whither they were pointing.

Cover Image of Henry Wagner’s book Juan Rodriguez Cabrillo,
California Historical Society

July 29
We set out at two o’clock in the afternoon from here at the famous, large, pleasant and full-flowing River of the Sweetest Name of Jesus of the Earthquakes, crossing its bed with difficulty because of its swiftness…

July 31
On going about two leagues we came across another stream with some running water, which must carry very large floods in season because of the great deal of sand it has on its banks. We came upon such a vast number of rose bushes that a large hundredweight could have been made up with the flowers that we saw open and blooming. From horseback I plucked more than four dozen of them that came into my hands. The grapevines are countless in number, some of them large with very large clusters. We twice came upon woods so dense that it was necessary for the soldiers to clear a way to get through the various sorts of trees, willows, grapevines, cumin, holythistles, and many other kinds of tall weeds, such that it is a vastly pleasant site to see. There are vast numbers of antelopes on this plain…tracks of very large animals are seen…they say that in the mountain range running along on the north, there are a great many bears.

August 2
Our Captain and the scouts reported that about half a league or more from this spot…to the west, they came upon volcanoes of pitch coming out of the ground like springs of water. It boils up molten (and there must have been about forty of these springs, and perhaps many more, they said), and the water runs off one way and the pitch another. They reported…seeing very large swamplands of it, enough they said to have caulked many ships with…we christened them The Volcanoes of Pitch of Porciuncula. We all felt four quakes at dawn today; since we began hearing them at the Sweet Name of Jesus river, there have been fourteen, very persistent and strong though not long-lasting, and we attribute these continual earthquakes to the pitch volcanoes here.

August 6
They told us that upcountry–pointing northeastward–there were people like us–pointing to the soldiers–with guns, swords, and horses–pointing to our mounts–and there were three Fathers like ourselves (pointing to our habits); that two or three of themselves had been there; that it was reached in thirteen days’ travel from sunrise to sunset, and there was sea close by, and many large animals, which from their commentary and gestures, we thought must have been buffaloes; and that a great many people from there had come on horseback to their country, and had returned. Whether this is New Mexico or not, who can say?

Brown, A.K., ed. 2001. A Description of Distant Roads, Original Journals of the First Expedition into California, 1769-1770, by Juan Crespi

On a mission on Independence Day

Independence Day, anniversary no. 241 is upon us, a holiday surely on the short list of important ones in the United States. There’s no end to the philosophical and political ideas that can be, and have been, expounded upon. But as for me, I’m thinking about connections inspired by the research and personal reading I’ve been doing lately. Bear with me grizzlies, while I attempt to connect genetic research on rare California plants to American history.

I started graduate school in genetics, not ecology, and that field has always been the most fascinating to me. I’m in fact currently working on a topic that bridges the two fields, referred to as genetic biocontrol, the aim of which is to use genetic methods to reduce fitness, and hence population sizes, of harmful or otherwise unwanted species. So, I was sad to learn in a recent special issue devoted to the work of Dr. Leslie Gottlieb of UC Davis, on polyploid genetics, that he had passed away five years ago. The major focal taxon of Gottlieb’s work was the genus Clarkia, and I had some good conversations with him when I was doing restoration and propagation work on a very rare Clarkia (C. lingulata) endemic to the Merced River canyon, the main river flowing into, and through, Yosemite Valley. This is a famous species in plant genetics, cited in textbooks as an example of instantaneous speciation (see here and here), derived from it’s progenitor, Clarkia biloba. Clarkia lingulata is found in only two populations near the junction of the South Fork Merced with its main stem, a few miles west of the western boundary of Yosemite National Park.

Said River of Mercy is not merciful this year though, or any time at high water, should you happen to be in it. It is uncontrolled, and at high water rages through a steep, boulder filled death sieve as it leaves Yosemite Valley and heads for the San Joaquin. I still remember well the day that a woman, with her three kids, fell asleep at the wheel after driving all night, and drove off the road and into the river at daybreak, just above this location, drowning them all. When I was kayaking, the Merced was the only river that ever scared me off the river, although part of that was due to being solo and exhausted, which is a full-on recipe for disaster. There is also some very interesting history regarding Clarkia lingulata‘s location, one involving the cause of the American discovery of Yosemite Valley in 1851, but I won’t go into that here.

In one of our discussions, Les discussed some aspects of another rare Clarkia species he was working with, Clarkia franciscana. The species is so named because it is found only in the immediate area of the San Francisco Presidio–and this makes for a segue from genetics to history, involving the SF Presidio, Spain, Mexico and the United States, Upper (or New) California, and July of 1776.

The history of what is now the state of California has, I think, to rank as one of the most interesting of any in the world, and especially so from 1846 to 1850. Just a week before the momentous event in Philadelphia, a small group of Spanish Franciscans, with a small military escort, arrived from the Carmel River area (just south of present Monterey, CA), to extend the Spanish Upper California dominion northward by establishing their third presidio (military base and/or fort, the first two being at San Diego and Monterey in 1769/1770), and with it another mission of course. These establishments were significant because both were to carry the name of the order’s founder, Saint Francis of Assisi.

On June 27 1776, this group came upon a small creek draining the peninsular hills east (toward San Francisco Bay), which they named Dolores, and decided that this would serve as the future mission site. On June 29 they established an altar and consecrated the site, and then began looking for a strategic location for the presidio and fort, which they located on a high bluff commanding the narrow entrance to the bay (the “Golden Gate”), just to the water side of what is now the southern anchorage of the Golden Gate Bridge.

A depiction of Mission Dolores circa 1893 by Edward Borein

At this point, books worth of material could be inserted discussing the Spanish (and after 1822, Mexican) discovery, settlement and management of Upper California, and with jaw fairly agape at both the process and the end result (circa 1848), for much of it. And we, with the benefit of 20/20 hindsight, wouldn’t be the first to do so either–the Russians, the British, and especially the Americans, of that time, did so also. It’s documented in various writings, which are for me at least, entirely fascinating. Some of it seems to defy logic. If anyone could write an authoritative book titled “Imperial expansion: how not to do it”, it would have to be the Spanish and/or Mexicans.

To say that things went downhill for the Spanish from 1776 to 1848 would be the understatement of the century. Twenty-one missions were established in Upper California during the “mission period” from 1769 to the American conquest in 1846, but for various reasons including Russian presence starting around 1805, only two north of Mission Dolores (Missions San Rafael and Solano), and both of those quite late in the game. The events in Philadelphia five days after consecration of the Mission San Francisco de Assis (= Dolores) site, caused the Spanish to pull back on several intended plans in northwestern New Spain, now the western United States, including expansion north of San Francisco Bay and another plan for a series of missions in the interior lands east and south of it.

Mission Dolores circa 1842 by Henry Miller

One argument has it that in so doing the Spanish were hoping to marshall their energies to re-claim parts of Spanish Florida lost initially to the French, and hence to the British after 1763, thinking that the Revolutionary War might offer their best chance to do so. But this plan, along with apparently about everything the Spanish and Mexicans did from 1800-1850, backfired. Not only did they not increase Spanish Florida, they quickly lost what they already had. This was followed later (1822) by the entire loss of New Spain, i.e. Mexican independence. The fracturing of the once vast Spanish empire then continued as the Mexicans in turn quickly lost Texas to independence, whose annexation by the United States about a decade later thus led to the Mexican-American war. In amazingly short order therein, they then managed to not only not reclaim Texan territory, but instead to astoundingly quickly lose both California and New Mexico. This was followed in less than a year by surrender, and with it the additional loss of what are now roughly the states of Utah, Nevada and Arizona. The total area is a large and very valuable chunk of real estate, by any standard.

I’m no historian, though I read my fair share, but compared to the serious difficulties and drain of two wars with the British spanning 40 years, and the even more extended and often ferocious wars with various Native American tribes, this sudden acquisition of a vast, important territory without much of a fight stands out. James Marshall discovered gold in the tail race of John Sutter’s sawmill east of what is now Sacramento just about two weeks before the Treaty of Guadalupe-Hidalgo officially ceded all this territory to the United States. That this should happen to a people who had historically been obsessed and sometimes deluded by various fantastic stories regarding that material, kind of says it all. Marshall and Sutter tried to keep the discovery secret for a couple of months but that was a lost cause, and they likely knew it–it was a virtual certainty that the gold veins and placer deposits that ran up and down half the Sierra Nevada, and elsewhere, would be found in almost no time by those about to pour unobstructed into what was now the United States. And so they poured. And the rest as they say…

I will knock–just like before

I’m the latest apparition
Cutting slices in the night
I come through without permission
Moving in and out of human sight

I’m the tapping on your shoulder
I’m the raven in the storm
I’ll take shelter in your rafters
I’ll be the shiver when you’re warm

I’m the gold in California
I’m the wealth in Mexico
Like the vultures in the valley–
I will wait for you to go

I’m the gypsy in your pocket
I’m the horseman in your dreams
I’m the reason dogs are barking
I’m the hand that stops the scream

I’m the baby’s cry that isn’t
I am the distant relative
I’m the scratching in the ceiling
I am advice you shouldn’t give

I’m the ghost of a traveling salesman
My foot will be there in your door
Though I can walk through walls and windows
I will knock–just like before

Raven in the Storm, John Gorka