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


How not to do it

This is a long post. It analyzes a paper that recently appeared in Nature. It’s not highly technical but does get into some important analytical subtleties. I often don’t know where to start (or stop) with the critiques of science papers, or what good it will do anyway. But nobody ever really knows what good any given action will do, so here goes. The study topic involves climate change, but climate change is not the focus of either the study or this post. The issues are, rather, mainly ecological and statistical, set in a climate change situation. The study illustrates some serious, and diverse problems.

Before I get to it, a few points:

  1. The job of scientists, and science publishers, is to advance knowledge in a field
  2. The highest profile journals cover the widest range of topics. This gives them the largest and most varied readerships, and accordingly, the greatest responsibilities for getting things right, and for publishing things of the highest importance
  3. I criticize things because of the enormous deficit of critical commentary from scientists on published material, and the failures of peer review. The degree to which the scientific enterprise as a whole just ignores this issue is a very serious indictment upon it
  4. I do it here because I’ve already been down the road–twice in two high profile journals–of doing it through journals’ established procedures (i.e. the peer-reviewed “comment”); the investment of time and energy, given the returns, is just not worth it. I’m not wasting any more of my already limited time and energy playing by rules that don’t appear to me designed to actually resolve serious problems. Life, in the end, boils down to determining who you can and cannot trust and acting accordingly

For those without access to the paper, here are the basics. It’s a transplant study, in which perennial plants are transplanted into new environments to see how they’ll perform. Such studies have, at least, a 100 year history, dating to genetic studies by Bateson, the Carnegie Institute, and others. In this case, the authors focused on four forbs (broad leaved, non-woody plants), occurring in mid-elevation mountain meadows in the Swiss Alps. They wanted to explore the effects of new plant community compositions and T change, alone and together, on three fitness indicators: survival rate, biomass, and fraction flowering. They attempted to simulate having either (1) entire plant communities, or (2) just the four target species, experience sudden temperature (T) increases, by moving them downslope 600 meters. [Of course, a real T change in a montane environment would move responsive taxa up slope, not down.] More specifically, they wanted to know whether competition with new plant taxa–in a new community assemblage–would make any observed effects of T increases worse, relative to those experienced under competition with species they currently co-occur with.

Their Figure 1 illustrates the strategy:

Figure 1: Scenarios for the competition experienced by a focal alpine plant following climate warming. If the focal plant species (green) fails to migrate, it competes either with its current community (yellow) that also fails to migrate (scenario 1) or, at the other extreme, with a novel community (orange) that has migrated upwards from lower elevation (scenario 2). If the focal species migrates upwards to track climate, it competes either with its current community that has also migrated (scenario 3) or, at the other extreme, with a novel community (blue) that has persisted (scenario 4).

Figure 1: Scenarios for the competition experienced by a focal alpine plant following climate warming.
If the focal plant species (green) fails to migrate, it competes either with its current community (yellow) that also fails to migrate (scenario 1) or, at the other extreme, with a novel community (orange) that has migrated upwards from lower elevation (scenario 2). If the focal species migrates upwards to track climate, it competes either with its current community that has also migrated (scenario 3) or, at the other extreme, with a novel community (blue) that has persisted (scenario 4).

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This week’s puzzler

This week’s puzzler comes to us from John Storthwaite in Stonyfield, Minnesota, who has been wondering why there are so many trees blocking his view of the rocks up there.

Suppose you have been given the following problem. A number of objects are located in some given area, say trees in a forest for example, and one wishes to estimate their density D (number per unit area). Distance-based sampling involves estimating D by averaging a sample of squared, point-to-object distances (d), for objects of known integer rank distance (r) from the point. The distances are squared because one is converting from one dimensional measurements (distance) to a two dimensional variable (objects per unit area).

So here’s the puzzler. If you run a line through this arbitrary point, and choose the closest objects (r = 1) on each side of it, what will be the ratio of the squared distances of the two objects and how would you solve this, analytically? Would they be about the same distance away? If not, would there be a predictable relationship between them? The problem can be extended to any number of lines passing through said point, just with correspondingly more pairs of distances to evaluate.

The first questions one should ask here are clear: (1) “Why on earth would anybody want to do that?” and (2) “Is that the type of thing you clowns spend your time on?“. We have answers for those questions. Not necessarily satisfactory answers, but answers nonetheless. Giving an answer, that’s the important thing in life. So, if you know the answer, write it on the back of a $100 bill and send it to…

Anyway, there are two possible solutions here. The first one comes readily if one realizes that the densities within sectors must each be about the same as the overall density, since we assume a homogeneous overall density. But, for a given value of r, the squared distances in each of the two sectors must be, on average, about twice those for the collection of trees overall, because there are only half as many trees in each sector as there are overall. So, e.g. the r = 5th closest trees within each half are on average, 2X the squared distance of the r = 5th closest tree overall.

Knowing this, the relationship between the two r = 1 trees (label them r1.1 and r1.2 having squared distances d1.1 and d1.2) in the two sectors becomes clear. Since one of the two trees (r1.1) must necessarily be the r = 1 tree overall, and the mean squared distance of the two trees must be 2X that of the r = 1 tree, this translates to:

2*d1.1 = (d1.1 + d1.2)/2 and thus,
d1.2 = 3(d1.1),

i.e., one member of the pair will, on average, be exactly three times the squared distance of the other. This result can be confirmed by an entirely independent method involving asymptotic binomial/multinomial probability. That exercise is left, as they say in the ultimate cop-out, to the reader.

This work has highly important implications with respect to a cancer research, and for solutions to poverty, malnutrition, and climate change. It can also help one discern if tree samplers 150-200 years ago were often sampling the closest trees or not.

Funding for this work was provided by the Doris Duke Foundation, the Society for American Baseball Research, the American Bean and Tree Counters Society, the Society for Measuring Things Across From Other Things, and the Philosophy Department at the University of Hullaballo. All rights reserved, all obligations denied. Any re-use, re-broadcast, retransmission, regurgitation or other use of the accounts and descriptions herein, without the express written consent of the closest random stranger on the street, or the closest random stranger on the other side of said street, is strictly prohibited.

Golf course succession

A friend’s property, in the county my parents live in, is surrounded by a nine hole golf course that went out of business several years ago, and is about to be acquired by the US Fish and Wildlife Service. It is undergoing rapid ecological succession to a less managed state since they stopped mowing a few years back. This process is very common with abandoned farm land, but this is the first I’ve looked at a golf course. The place is interesting because the area is naturally wet, being originally part of a very large swamp/wetland complex (the “Great Black Swamp”) that stretched over many counties and caused this area to be the last settled in Ohio. The original vegetation, documented in 1820, was dominated by intermixed treeless wet prairie, and swamp or other northern wetland hardwoods, with standing water over the entire year common. The inherently wet soils might well have affected the course’s success, I don’t know.

Several tree species mentioned in the 1820 GLO land survey notes (see bottom image) are still present, including swamp white oak (Quercus bicolor), american elm (Ulmus americana), pin oak (Q. palustris), green ash (Fraxinus pennsylvanica), hickory (Carya cordiformis), eastern cottonwood (Populus deltoides), and unspecified willows (Salix spp.). Others have clearly come in post-settlement, including black walnut (Juglans nigra), northern catalpa (Catalpa speciosa), weeping willow (Salix babylonica), possibly silver maple (Acer saccharinum), and the completely misplaced jack pine (Pinus banksiana) and eastern redcedar (Juniperus virginiana) (most likely both as yard markers and fairway dividers). How the USFWS will manage the property will be interesting; it may be difficult to recreate the wet prairie habitat given that the natural drainage pattern is now highly altered by ditching and drain tiling.

Wet prairie and hardwood swamp, to farm, to golf course, to...

Wet prairie and hardwood swamp, to farm, to golf course, to…

Goldenrod (Solidago spp), a notorious and obvious late bloomer.

Goldenrod (Solidago spp), a notorious and obvious late bloomer.

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Tree growth analysis issues, again, part two

This picks up from the previous post on Stephenson et al (2014).  Hoping that you’ve looked at the paper, I’ll try to explain why I have concerns about it. It presents a good opportunity to discuss some important analytical issues, biological and mathematical.

I’ll begin with a criticism that relates more to a general concern with scientific publications: the way statements/claims are made in titles and abstracts.  Many scientists will only ever read the abstract of a given article, or even just the title, so it’s extra important to word things carefully there so as not to create the wrong impression.  And since scientific protocol strongly trains for accuracy and brevity in writing, there’s little room for excuses when failing to do so. Their title reads: “Rate of tree carbon accumulation increases continuously with tree size“. That’s an unambiguous, general statement; they’re basically claiming a new, general finding (law?) regarding tree growth rates, world-wide.  Hmmmm. All I will say to that is, better be able to back something like that up, because a lot of people have been looking at tree growth rates for a long time, and some of them are probably going to look pretty closely at it. Or very closely.

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Open discussion

Matt Skaggs had the audacity to ask, and follow up on, a paleobotany/evolution question involving the California flora, which I really should know more about than I do, instead of talking about stupid stuff like football. You can add to that discussion of course (copied below), one that ranges taxonomically from cypresses to sequoias to serpentine-tolerant mustards, and conceptually from Darwin to Wright to Goldschmidt, but I figured I’d better make a post allowing for questions/discussions on miscellaneous topics of interest, for putting up links to interesting articles, and so forth. The abrupt transition from bluegrass song lyrics to the evolutionary origins of serpentine endemics in California is well known to mess with peoples’ senses of flow and thus probably should be avoided. [Editor’s note: the term “bluegrass”, as used above, does not refer to Poa pratensis except in a very historically indirect way–apologies for any taxonomic confusion.]

In other thrilling news, I messed around with some other WordPress “Theme Options” to see if I could get the content and comments to span the screen better, but had no luck and figured I’d better leave well enough alone before I broke something. I was able to force replies to comments to nest to a max of one indentation level to aid the cause however.

Below is copied the discussion by Matt and I, for your literary pleasure. Note that this will likely bring a barrage of comments, so try to get yours in early.

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Fire: The California Rim Fire

USFS 8.17The California Rim Fire in the Tuolumne River Canyon, Stanislaus National Forest, August 17 2013, the day it started. The fire expanded enormously over the next week, into Yosemite NP, was not contained for over two months, and finished as the 3rd largest fire in the California documentary record. Source: US Forest Service, via Tom Clark

Lately I’ve been trying to decide among several possible topical themes to focus on here, which is a challenge since my interests are all over the place.

For several reasons, I’ve decided to finally focus on the issues surrounding wildland fire, using this summer’s Rim Fire in California as the focal point. I couldn’t write about the fire when it happened, which from a news standpoint was fine since, being a national media event, everybody who was anybody (PBS, National Geographic, Time, USA Today, BBC, NY and LA Times, etc.) was busy crawling over each other to see who could dramatize it the most, and because it’s a landscape that’s near and dear to me, for several reasons, now turned to a moonscape in many places. I (and others) saw this coming long ago, and I know what awaits me when I go back in there to continue my research next year.

This event is a potential springboard for the discussion of many issues, including landscape ecology, land management practices, fire/disturbance ecology, remote sensing, climate change effects, and the media portrayal of events and the science behind them.

But for now, and by way of introduction, links to Tom Clark’s posts containing a series of photos and written commentary, here and here, to give you a sense of what happened. And here is great footage of the cockpit-level view of the terrain from a C-130 tanker as it drops a load of fire retardant along a ridge line in the Stanislaus National Forest, as the aircraft’s automatic alert system detects the terrain below. Google and YouTube searches will bring up an enormous amount of information and imagery of the fire if you’re interested.

Carbon dioxide effects on the African savanna

So Bouldin, you ask, are you ever going to post anything on any, you know, actual ecology topics, given the title of the blog, or is it all tree rings and song lyrics all the time?

Well, nothing but a quick link and image here to an article at the Yale Environment 360 page on the effects of CO2 fertilization on landscape-scale vegetation dynamics in the African savanna. I hope to get some time to make some extended comments on the topic, which I find very highly interesting, but at least here’s the link (and there are links to a couple of good papers in the article). In fact I find the various complex relationships between carbon dioxide, water, vegetation, and climate to be one of the most interesting topics in all of ecology, and also one of the more important.

Figure 1 from Bond and Midgley (2012) Phil. Trans. R. Soc. B (2012) 367:601–612 doi:10.1098/rstb.2011.0182

Early effects of fire reduction on California forests

The effects of fire suppression/reduction policies on landscapes of the western United States have been researched extensively.  It is widely known that these policies have greatly changed the nature of the vegetation, and the pre-settlement fire regimes, over very wide areas.  Vegetation in Mediterranean climates (hot and dry in the summer, i.e. California) has generally been altered the most drastically.  However, it has not always been clear how early these changes began.  This is because official government fire suppression policies at state and federal levels did not begin until the 1910-1925 time period (thus well after settlement and Indian removal), and because the magnitudes of pre-settlement Indian burning and pre-1925, non-official fire suppression work, are both pretty unclear.

The following extract from Early Days in Yosemite was written by Galen Clark in 1907, near the end of his life (its original title was: “A Plea for Yosemite“).  Clark lived in Yosemite Valley for many years, beginning in 1856, which was just three years after the Yosemite band of Miwok was driven from its long-time home after hostilities with both white settlers (the “Mariposa War”) and with the Mono Paiute on the east side.  He therefore had about a 50 year, personal perspective on the vegetation changes in the Valley, which is highly valuable.  [He was also elected the first “Guardian” of the Valley, after it was deeded to the State of California in 1864 by President Abraham Lincoln.  According to Yosemite historian Shirley Sargent, Clark was the single most important individual responsible for Yosemite becoming a National Park in 1890, above even John Muir].

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