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

A massive mess of old tree data

I’m going to start focusing more on science topics here, as time allows. I’ll start by focusing for a while on some forest ecology topics that I’ve been working on, and/or which are closely related to them.

I’m working on some forest dynamics questions involving historical, landscape scale forest conditions and associated fire patterns. I just got done assembling a tree demography database of about 130,000 trees collected in about 1700 plots, in the early 20th century, on the Eldorado and Stanislaus National Forests (ENF, SNF), the two National Forests that occupy the mid- to upper-elevations on the relatively gradual western slope of the central Sierra Nevada. The data were collected primarily between 1911 and 1923 as censuses of large plots (by today’s standards, each ~2 or 4 acres) as part of the first USFS timber inventories, when it was still trying to figure out just what it had on its hands, and how it would manage it over time. An enormous amount of work was involved in this effort, but only a small part of these data has apparently survived.

The data are “demographic” in that the diameter and taxon were recorded for most trees, making them useful for a number of analytical purposes in landscape, community and population ecology. They come from two datasets that I discovered between 1997 and 2001, one in the ENF headquarters building, and the other in the National Archives facility in San Bruno CA. For each, I photocopied the data at that time, and had some of it entered into a database, hoping that I would eventually get time to analyze them. For the ENF data, this was a fortunate decision, because the ENF, as I later learned, has managed in the mean time to lose the entire data set, most likely along with a bunch of other valuable stuff that was in the office housing it. I thus now have the only known backup. Anyway, that time finally came, but the data were in such a mess that I first had to spend about three months checking and cleaning them before they could be analyzed. The data will soon be submitted as a data paper to the journal Ecology, it being one of the very few journals that has adopted this new paper format. In a data paper, one simply presents and describes a data set deemed to be of value to the general scientific community. There is in fact a further mountain of data and other information beyond these, but whether they’ll ever see the light of publication is uncertain.

An example first page of one of many old field reports and data summaries involved

An example first page of one of many old field reports and data summaries involved

We, and others, are interested in these data for estimating landscape scale forest conditions before they were heavily altered by humans via changed natural fire regimes, logging, and grazing (primarily). These changes began in earnest after about 1850, and have generally increased with time. This knowledge can help inform some important current questions involving forest restoration and general ecosystem stability, including fire and hydrologic regimes, timber production potential, biological diversity, and some spin off topics like carbon dynamics. They can directly address some claims that have been made recently regarding the pre-settlement fire regimes in California and elsewhere, in certain papers.

The data assembly was much slower and more aggravating than expected–I won’t go into it but I’ll never do it again–but the analysis is, and will be, very interesting for quite some time, as much can be done with it. Some of the summary or explanatory documentation associated with the data is entirely fascinating, as is some of the other old literature and data that I’ve been reading over as part of the project. In fact I’m easily distracted into reading more of it than is often strictly necessary, but so doing has reminded me that a qualitative, verbal description can be of much greater value than actual data, scientific situation depending. Possibly the most interesting and important aspect to this is the degree to which really important information has been either lost, completely forgotten about, or never discovered to begin with. This is not trivial–I’m talking about a really large amount of detailed data and extensive, detailed summary documentation. Early views and discussions regarding fire and forest management, and the course these should take in CA, are extensive and very revealing, as we now look back 100 years later on the effects of important decisions made then. There are also lessons in federal archiving and record keeping.

I’ll be posting various things as time allows, including discussions of methods and approaches in this type of research. I’m also applying for a grant to cover the cost of free pizza at the end, although to be honest I’ve not had great success on same in the past. You might be surprised at the application numbers and success rates on that kind of thing.

“Fearfully wild, with a blaze of quick electric light in his dark eye”

Never in several lifetimes of dreams and visions will I ever tire of reading the works of this man.

Visalia is the name of a small town embowered in oaks upon the Tulare Plain in Middle California, where we made our camp one May evening of 1864. Professor Whitney, our chief, the State Geologist, had sent us out for a summer’s campaign in the High Sierras, under the lead of Professor William H. Brewer, who was more sceptical than I as to the result of the mission.

Several times during the previous winter Mr. Hoffman and I, while on duty at the Mariposa gold-mines, had climbed to the top of Mount Bullion, and gained, in those clear January days, a distinct view of the High Sierra, ranging from the Mount Lyell group many miles south to a vast pile of white peaks, which, from our estimate, should lie near the heads of the King’s and Kaweah rivers. Of their great height I was fully persuaded; and Professor Whitney, on the strength of these few observations, commissioned us to explore and survey the new Alps.

We numbered five in camp:—Professor Brewer; Mr. Charles F. Hoffman, chief topographer; Mr. James T. Gardiner, assistant surveyor; myself, assistant geologist; and our man-of-all-work, to whom science already owes its debts.

When we got together our outfit of mules and equipments of all kinds, Brewer was going to reengage, as general aid, a certain Dane, Jan Hoesch, who, besides being a faultless mule-packer, was a rapid and successful financier, having twice, when the field-purse was low and remittances delayed, enriched us by what he called “dealing bottom stock” in his little evening games with the honest miners. Not ungrateful for that, I, however, detested the fellow with great cordiality. “If I don’t take him, will you be responsible for packing mules and for daily bread?” said Brewer to me, the morning of our departure from Oakland. “I will.” “Then we’ll take your man Cotter; only, when the pack-saddles roll under the mules’ bellies, I shall light my pipe and go botanizing. Sabe?”

So my friend, Richard Cotter, came into the service, and the accomplished but filthy Jan opened a poker and rum shop on one of the San Francisco wharves, where he still mixes drinks and puts up jobs of “bottom stock.” Secretly I longed for him as we came down the Pacheco Pass, the packs having loosened with provoking frequency.

The animals of our small exploring party were upon a footing of easy social equality with us. All were excellent except mine. The choice of Hobson (whom I take to have been the youngest member of some company) falling naturally to me, I came to be possessed of the only hopeless animal in the band. Old Slum, a dignified roan mustang of a certain age, with the decorum of years and a conspicuous economy of force retained not a few of the affectations of youth, such as snorting theatrically and shying, though with absolute safety to the rider, Professor Brewer. Hoffman’s mount was a young half-breed, full of fire and gentleness. The mare Bess, my friend Gardiner’s pet, was a light-bay creature, as full of spring and perception as her sex and species may be. A rare mule, Cate, carried Cotter. Nell and Jim, two old geological mules, branded with Mexican hieroglyphics from head to tail, were bearers of the loads.

My Buckskin was incorrigibly bad. To begin with, his anatomy was desultory and incoherent, the maximum of physical effort bringing about a slow, shambling gait quite unendurable. He was further cursed with a brain wanting the elements of logic, as evinced by such non sequiturs as shying insanely at wisps of hay, and stampeding beyond control when I tried to tie him to a load of grain. My sole amusement with Buckskin grew out of a psychological peculiarity of his, namely, the unusual slowness with which waves of sensation were propelled inward toward the brain from remote parts of his periphery. A dig of the spurs administered in the flank passed unnoticed for a period of time varying from twelve to thirteen seconds, till the protoplasm of the brain received the percussive wave; then, with a suddenness which I never wholly got over, he would dash into a trot, nearly tripping himself up with his own astonishment.

A stroke of good fortune completed our outfit and my happiness by bringing to Visalia a Spaniard who was under some manner of financial cloud. His horse was offered for sale, and quickly bought for me by Professor Brewer. We named him Kaweah, after the river and its Indian tribe. He was young, strong, fleet, elegant, a pattern of fine modelling in every part of his bay body and fine black legs; every way good, only fearfully wild, with a blaze of quick electric light in his dark eye.

Shortly after sunrise one fresh morning we made a point of putting the packs on very securely, and, getting into our saddles, rode out toward the Sierras. The group of farms surrounding Visalia is gathered within a belt through which several natural, and many more artificial, channels of the Kaweah flow. Groves of large, dark-foliaged oaks follow this irrigated zone; the roads, nearly always in shadow, are flanked by small ranch-houses, fenced in with rank jungles of weeds and rows of decrepit pickets.

Our backs were now turned to this farm-belt, the road leading us out upon the open plain in our first full sight of the Sierras. Grand and cool swelled up the forest; sharp and rugged rose the wave of white peaks, their vast fields of snow rolling over the summit in broad, shining masses. Sunshine, exuberant vegetation, brilliant plant life, occupied our attention hour after hour until the middle of the second day. At last, after climbing a long, weary ascent, we rode out of the dazzling light of the foot-hills into a region of dense woodland, the road winding through avenues of pines so tall that the late evening light only came down to us in scattered rays. Under the deep shade of these trees we found an air pure and gratefully cool.

Passing from the glare of the open country into the dusky forest, one seems to enter a door and ride into a vast covered hall. The whole sensation is of being roofed and enclosed. You are never tired of gazing down long vistas, where, in stately groups, stand tall shafts of pine. Columns they are, each with its own characteristic tinting and finish, yet all standing together with the air of relationship and harmony. Feathery branches, trimmed with living green, wave through the upper air, opening broken glimpses of the far blue, and catching on their polished surfaces reflections of the sun. Broad streams of light pour in, gilding purple trunks and falling in bright pathways along an undulating floor. Here and there are wide, open spaces, around which the trees group themselves in majestic ranks.

Our eyes often ranged upward, the long shafts leading the vision up to green, lighted spires, and on to the clouds. All that is dark and cool and grave in color, the beauty of blue umbrageous distance, all the sudden brilliance of strong local lights tinted upon green boughs or red and fluted shafts, surround us in ever-changing combination as we ride along these winding roadways of the Sierra.

We had marched a few hours over high, rolling, wooded ridges, when in the late afternoon we reached the brow of an eminence and began to descend. Looking over the tops of the trees beneath us, we saw a mountain basin fifteen hundred feet deep surrounded by a rim of pine-covered hills. An even, unbroken wood covered these sweeping slopes down to the very bottom, and in the midst, open to the sun, lay a circular green meadow, about a mile in diameter.

As we descended, side wood-tracks, marked by the deep ruts of timber wagons, joined our road on either side, and in the course of an hour we reached the basin and saw the distant roofs of Thomas’s Saw-Mill Ranch. We crossed the level disc of meadow, fording a clear, cold mountain stream, flowing, as the best brooks do, over clean, white granite sand, and near the northern margin of the valley, upon a slight eminence, in the edge of a magnificent forest, pitched our camp.

The hills to the westward already cast down a sombre shadow, which fell over the eastern hills and across the meadow, dividing the basin half in golden and half in azure green. The tall young grass was living with purple and white flowers. This exquisite carpet sweeps up over the bases of the hills in green undulations, and strays far into the forest in irregular fields. A little brooklet passed close by our camp and flowed down the smooth green glacis which led from our little eminence to the meadow. Above us towered pines two hundred and fifty feet high, their straight, fluted trunks smooth and without a branch for a hundred feet. Above that, and on to the very tops, the green branches stretched out and interwove, until they spread a broad, leafy canopy from column to column.

Professor Brewer determined to make this camp a home for the week during which we were to explore and study all about the neighborhood. We were on a great granite spur, sixty miles from east to west by twenty miles wide, which lies between the Kaweah and King’s River cañons. Rising in bold sweeps from the plain, this ridge joins the Sierra summit in the midst of a high group. Experience had taught us that the cañons are impassable by animals for any great distance; so the plan of campaign was to find a way up over the rocky crest of the spur as far as mules could go.

In the little excursions from this camp, which were made usually on horseback, we became acquainted with the forest, and got a good knowledge of the topography of a considerable region. On the heights above King’s Cañon are some singularly fine assemblies of trees. Cotter and I had ridden all one morning northeast from camp under the shadowy roof of forest, catching but occasional glimpses out over the plateau, until at last we emerged upon the bare surface of a ridge of granite, and came to the brink of a sharp precipice. Rocky crags lifted just east of us. The hour devoted to climbing them proved well spent.

A single little family of alpine firs growing in a niche in the granite surface, and partly sheltered by a rock, made the only shadow, and just shielded us from the intense light as we lay down by their roots. North and south, as far as the eye could reach, heaved the broad, green waves of plateau, swelling and merging through endless modulation of slope and form.

Conspicuous upon the horizon, about due east of us, was a tall, pyramidal mass of granite, trimmed with buttresses which radiated down from its crest, each one ornamented with fantastic spires of rock. Between the buttresses lay stripes of snow, banding the pale granite peak from crown to base. Upon the north side it fell off, grandly precipitous, into the deep upper cañon of King’s River. This gorge, after uniting a number of immense rocky amphitheatres, is carved deeply into the granite two and three thousand feet. In a slightly curved line from the summit it cuts westward through the plateau, its walls, for the most part, descending in sharp, bare slopes, or lines of ragged débris, the resting-place of processions of pines. We ourselves were upon the brink of the south wall; three thousand feet below us lay the valley, a narrow, winding ribbon of green, in which, here and there, gleamed still reaches of the river. Wherever the bottom widened to a quarter or half a mile, green meadows and extensive groves occupied the level region. Upon every niche and crevice of the walls, up and down sweeping curves of easier descent, were grouped black companies of trees.

The behavior of the forest is observed most interestingly from these elevated points above the general face of the table-land. All over the gentle undulations of the more level country sweeps an unbroken covering of trees. Reaching the edge of the cañon precipices, they stand out in bold groups upon the brink, and climb all over the more ragged and broken surfaces of granite. Only the most smooth and abrupt precipices are bare. Here and there a little shelf of a foot or two in width, cracked into the face of the bluff, gives foothold to a family of pines, who twist their roots into its crevices and thrive. With no soil from which the roots may drink up moisture and absorb the slowly dissolved mineral particles, they live by breathing alone, moist vapors from the river below and the elements of the atmosphere affording them the substance of life.

The Indian system

Just about as prescient, and early, of a description of the California wildland fire and forest development problem as you will find:

As regards the growth of young timber—save only among the heavy redwood forests—the number of young trees which within the last decade or two has sprung up, is very great. All the open pine forests, back of the coast, are becoming rapidly stocked with young trees, and much of the open grazing land is rapidly being converted into brush or becoming covered with young saplings—generally Douglas spruce [Douglas-fir] or yellow [ponderosa] pine.

The cause of this increase is unquestionably the cessation of the old Indian practice (formerly general) of running fires through the country to keep it open to facilitate hunting, or in driving game before the flames into enclosures set with snares. Under this system about half the ground was burned over each year, in alternate halves; thereby the open lands were kept free of brush and all growth of young trees was checked in the forests. The older, well matured trees, however, suffered very little, as so little undergrowth could mature between one fire and another, that sufficient heat was not developed to hurt older trees, fairly covered with bark and with limbs some distance above the ground. In fact, the Indian system became in some sense a method of forest preservation, and to it we undoubtedly owe the noble forests which were transmitted to our hands.

We may acknowledge this debt to the red man, although his methods may no longer be available in a growing country studded if only sparsely with improvements. The Indian’s method may not have been an ideal one, but it was a better one in his day and generation than our lack of all method is in ours.

The very growth of young trees, left uncared for as at present, must be to those with the good of the forest at heart, a source of concern rather than of satisfaction. With forest fires running—often twenty in a county at one time—and public sentiment dormant to the extent that, save where individual property is at stake, few take the trouble to put out even such incipient fires as might be killed with little effort, there can be no question but that in the growth of young trees lies the certain guarantee of total extermination of much of our best forest land, within a few years, unless some effectual methods of protection are inaugurated.

Thirty years ago fires ran yearly through the woods, but forest conflagrations were unknown; the large trees standing sparsely scattered, say five to ten to the acre, were unable to transmit fire, and there was little on the ground to burn. Now thousands of young trees fill the open spaces, and a fire started not only destroys the young trees but the patriarchs of the forest also.

As yet the evil has attained no very serious proportions; but so surely as the young growth is permitted and fires not kept out entirely (which will be found a simply impossible matter) fires will occur, which will sweep everything in their path out of existence.

The longer the matter is left to find its own solution the more difficult and expensive of application remedial measures will become. As a means of protection against fires, one effectual method, and only one, suggests itself—the isolation of such forests as it may be deemed essential to preserve, into blocks of moderate area, separated by strips of waste land, wide enough to insure no spread of fire from one belt to another. This done, the forests may be left to grow up densely, if desired, without fear of extensive damage.

Topographical conditions would generally suggest the location of these waste strips. Ridge summits and canon bottoms (especially the former) are natural barriers to fire, being only crossed with difficulty by flames, when free of brush and litter. The lines of watershed on spurs are generally sparsely timbered, and could be easily maintained free of undergrowth, even if not denuded of their trees. As regards the strips which have been designated as waste, they might in many cases be capable of sodding or being maintained in grass, producing range and pasture, and for the rest, the authorized use of fire by duly commissioned persons, duly provided with adequate means of checking the spread of flames, might suggest itself as the simplest, cheapest, and most efficient method.

Of course these proposals only have reference to the public lands, private holdings must remain subject to private management, and such forests as now are held in private hands must survive or perish, as the owner elects. In any event, private holdings, when lying within the lines of districts which it might be wished to treat on the basis proposed, will always cause complication. If anything is to be done at all, it is time to do it now, while the Government owns whole districts free from settlers, and consequently, in this respect, at least, need have nothing but the public interest to consider.

First Biennial Report of the California State Board of Forestry, 1886-1888

“A systematic record of great biological value”

Paul Sears was an early plant ecologist who did a lot of good work at the University of Nebraska and previously at Ohio State, Nebraska being the nexus of American plant ecology in the early 20th century. He was I believe, the first president of the Ecological Society of America. He was also one of the very first ecologists–of what is now a legion–to estimate landscape scale forest taxonomic composition at pre-settlement time, using the bearing/witness tree record contained within the early federal land survey. Here he takes a humorous swipe at the geometric wisdom inherent in the survey design. Ya can’t put a rectangular grid on a round planet fer cryin’ out loud, but hey, thanks for recording all those trees! 🙂

Surveying of Ohio was begun in July, 1786, under The Geographer of the United States, Thomas Hutchins, employing for the first time his device of sections one mile square. This empirical device was hailed as a great American invention, although the State of Ohio has since been found to possess a curved surface in common with the rest of the earth. All corners which lay within the forest were located with reference to nearby trees, the species of which were noted. These corners becoming permanent, the net result of Hutchins’ plan has been the preservation of a systematic record of such great biological value as to redeem its geometrical shortcomings.

A little background might be useful. Ohio was the first state surveyed under the federal land survey, all previous states being surveyed in all manner of ways by various entities under various authorities and quality control procedures, i.e. without a comprehensive and systematic plan. By law enacted in 1785–the very first congress–a hugely important law affecting how the public domain would be disposed of, all states added to the country from that point forward were to be surveyed under a systematic, regular survey design with very specific instructions regarding how to proceed (Thomas Jefferson being a driving force behind this). Ohio, being the first such state added, in 1803, also served as the test state, where various survey designs were tried out before deciding on the one that, with minor modifications, has been followed the last 200 years in the 30 federal land survey states.

To my knowledge no other branch of ecology has the quality of historic data sets dating to +/- pre-settlement times, i.e. before all the heavy impacts occurred, and most certainly not over such an enormous geographic extent. In fact, I don’t think it’s even close. We’re very lucky in that regard, and we have people like Thomas Jefferson, with his sense of mathematical order and intense interest in all things natural and landscape, for it.

Sears, Paul B. 1925. The Natural Vegetation of Ohio: I, A Map of the Virgin Forest

Around Yosemite walls and through Yosemite forests

So, I’ve been entering bearing tree data collected by land surveyors inside what is now Yosemite National Park, for work on estimating historic forest conditions in the Sierra Nevada. Bearing trees were designed to “bear witness” to the location of on-the-ground survey markers, in case something should happen to them, and several pieces of information on them were recorded in the field notes (previous post here). So up comes the next Township on the list: Township 2 South, Range 21 East, Mt. Diablo Meridian, or T2SR21E MDM in surveyors’ shorthand, an area now inside YNP, surveyed under authority of the General Land Office (GLO) in 1880, 10 years before YNP came into existence.

An original (1880) YNP bearing tree, in 2005, with blaze partially exposed.

An original (1880) YNP bearing tree, in 2005, with blaze partially exposed.

Well, damned if that isn’t a pretty good place to run into the man, Clarence King, and thereby to slow down the scientific progress on which society so utterly depends. Once I start reading King’s writings it’s all over in terms of getting things done. He’s done it to me before, and he will do it again.

Continue reading

“Our eyes often ranged upward”

At last, after climbing a long, weary ascent, we rode out of the dazzling light of the foot-hills into a region of dense woodland, the road winding through avenues of pines so tall that the late evening light only came down to us in scattered rays. Under the deep shade of these trees we found an air pure and gratefully cool. Passing from the glare of the open country into the dusky forest, one seems to enter a door and ride into a vast covered hall. The whole sensation is of being roofed and enclosed. You are never tired of gazing down long vistas, where, in stately groups, stand tall shafts of pine. Columns they are, each with its own characteristic tinting and finish, yet all standing together with the air of relationship and harmony. Feathery branches, trimmed with living green, wave through the upper air, opening broken glimpses of the far blue, and catching on their polished surfaces reflections of the sun. Broad streams of light pour in, gilding purple trunks and falling in bright pathways along an undulating floor. Here and there are wide, open spaces, around which the trees group themselves in majestic ranks.

Our eyes often ranged upward, the long shafts leading the vision up to green, lighted spires, and on to the clouds. All that is dark and cool and grave in color, the beauty of blue umbrageous distance, all the sudden brilliance of strong local lights tinted upon green boughs or red and fluted shafts, surround us in ever-changing combination as we ride along these winding roadways of the Sierra.

Clarence King,
Mountaineering in the Sierra Nevada

Hardy-Weinberg genetic equilibrium and species composition of the American pre-settlement forest landscape

This post is about how binomial probability models can, and cannot, be applied for inference in a couple of very unrelated biological contexts. The issue has (once again) made popular media headlines recently, been the focus of talk shows, etc., and so I thought it would be a good time to join in the discussions. We should, after all, always focus our attention wherever other large masses of people have focused theirs, particularly on the internet. No need to depart from the herd.

Binomial models give the coefficients/probabilities for all possible outcomes when repeated trials are performed of an event that has two possible outcomes that occur with known probabilities. The classic example is flipping a coin; each flip has two possible outcomes of h = t = 0.5, and if you flip it, say twice (two trials), you get 1:2:1 as binomial coefficients for the three possible outcomes of (1) hh = two heads, (2) ht = one head and one tail, or (3) tt = two tails, which gives corresponding probabilities of {hh, ht, tt} = {0.25, 0.50, 0.25}. These probabilities are given by the three terms of (h + t)^2, where the exponent 2 gives the number of trials. The number of possible outcomes after all trials is always one greater than the number of trials, with the order of the outcomes being irrelevant. Simple and easy to understand. The direct extension of this concept is found in multinomial models, in which more than two possible outcomes for each trial exist; the concept is identical, there are just more total probabilities to compute. Throwing a pair of dice would be a classic example.

The most well-known application of binomial probability in biology is probably Hardy-Weinberg equilibrium (HWeq) analysis in population genetics, due to the fact that chromosome segregation (in diploids) always gives a dichotomous result, each chromosome of each pair having an equal probability of occurrence in the haploid gametes. The binomial coefficients then apply to the expected gamete combinations (i.e. genotypes) in the diploid offspring, under conditions of random mating, no selection acting on the gene (and on closely linked genes), and no migration in or out of the defined population.

Continue reading

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.

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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