Sonoran Desert Tortoise - Follow Up

In my previous post "Sonoran Desert Tortoise Population Status", I argued that a decline in the ratio of tortoise observations to total iNaturalist observations indicated a possible decline in the actual population of tortoises.  

However, that conclusion rests on the assumption that opportunistic "citizen science" observers have not changed their preferences in photographing other animals.  This could happen if people became less interested in tortoises, or if they became more interested in other taxa.  

Part 1: Trends in Other Taxa

I analyzed various other well-represented taxa in the iNat data to look for possible trends in observer preferences.  Specifically, I looked at all Research Grade (RG) iNat observations of amphibians, reptiles, insects, birds, and plants in the study area: 

Data table with total RG amphibian, reptile, insect, bird, and plant observations in the study area each year.

These are large taxa made up of many species and I expected that the ratio of observations would remain relatively consistent. 

Count of observations by taxa 2013-2024

Observations of all taxa have increased over the last 10 years, but some appear to have increased more than others. I divided the count of each taxa's observations by total observations to investigate proportional changes in the ratio of various taxa:

Ratio of various taxa to total observations 2013-2024

The ratio of various taxa has changed over time.  Specifically, the ratio of plant observations to total observations doubled in 2017.  I don't think this could be due to an actual increase in the number of plants in AZ.  

Instead, I think this must be an indication of a changed bias toward plants, perhaps due to specific iNat users who focus on plants, or a general trend toward more plant-focused observers on iNat.  Plants, because they don't run away, are arguably the easiest organisms to photograph; it could be that as iNat has grown there are now more casual users biased toward photographing easier to observe organisms.  

Regardless of why iNat users are observing proportionally more plants, this appears to be a source of bias that should be corrected in my analysis.    

To correct for the large increase in plant observations, I compared various taxa to total non-plant observations: 

Ratio of various taxa to total non-plant ("total2") observations 2013-2024

This shows a fairly consistent observation ratios for the major animal taxa over the last 10 years.  While there is some year to year variability, there are no long term trends, except reptiles.  Reptiles in general are photographed 71% as often in 2024 compared to 2013. Most of this drop occurred from 2015-2017, with no major changes since then.  It is not clear why reptiles as a group declined in representation.  There are other reptile species of conservation concern besides tortoises and it is possible that reptiles actually are declining, or there could be other sources of observer bias in the data, similar to the trend in plant observations above.

Except for reptiles, all taxa ratios stayed within approximately +/- 15%:

Table: percent change in ratios of various taxa since 2013 and 2017.

Part 2: Another Look at the Tortoise Trend

The analysis in Part 1 led to a refinement in the total observation count used to create ratios, and helped set a baseline for expected change in ratios over the last 10 years.  I used this information to reassess the observed decline in ratio of tortoise observations.  

Tortoise observations were compared to various taxa and to total non-plant observations:

Percent change in the ratio of tortoises to various taxa and to total non-plant ("total2") observations 2013-2024

The ratio of tortoise observations has decreased since 2013 for all 4 animal taxa investigated, and for total non-plant observations.  The decline is remarkably consistent for amphibians, birds, and total non-plant observations ("total2"), and fairly consistent for insects.  The ratio of tortoise to reptile observations tends to fluctuate over time, while maintaining the same overall negative trend.

While most animal taxa ratios show less than 15% change from baseline (Part 1), tortoises are observed 66-84% (mean 72%) in 2024 compared to 2017, and 35-57% (mean 43%) in 2024 compared to 2013:

Table: percent change of tortoise observations to various taxa and to total non-plant observations.

Conclusions

Tortoises show large declines compared to various representative animal taxa and compared to all non-plant observations.  This is the same result I found in my original blog post when I compared tortoises to all observations.  

The result was not affected by removing a potential source of user bias, showing that the original result is robust to some observational biases.  Of course, there will always be more sources of bias that could be analyzed and corrected for.  However, the fact that correcting for one source of bias didn't change the result makes me somewhat more confident that this result is directionally correct.

Conversely, the fact that I did find a large source of observer bias makes me wonder whether there are other large biases in iNat observation trends.  Without analyzing all sources of bias (why did reptiles change in 2017?) these results must remain clouded by potential uncertainties.  

The result was also not affected by which taxa I compared tortoises with, showing that the original result is robust to choice of comparison.  Tortoises appear to be declining, whether they are compared to all observations, all animals, amphibians, reptiles, insects, or birds.  While it is possible that one or more of these taxa are affected by observational bias, the fact that they all point in the same direction makes me more confident that this result is directionally correct and reflects an actual downward population trend.

Sonoran Desert Tortoise Population Status

 Abstract

Population trend data for species under consideration for federal protection is often limited. This study evaluated Sonoran desert tortoise (Gopherus morafkai) population trends in Arizona using iNaturalist citizen science data. We analyzed 1,402 research-grade tortoise observations and normalized them against total observations in the area to account for sampling bias. While both tortoise observations and total observations increased since the early 2010s, the ratio of tortoise to total observations declined consistently from 0.12% to 0.08% between 2017-2025. This decreasing ratio suggests either shifting observer preferences or declining tortoise encounter rates, potentially indicating population decline. These results provide concerning evidence of negative population trends for this species of conservation concern and demonstrate the utility of citizen science data for monitoring species lacking formal survey programs.

Introduction

Sonoran desert tortoise (Gopherus morafkai) live in the Sonoran desert of Arizona and northern Mexico.  A closely related species in California and Nevada, the Mojave desert tortoise (Gopherus agassizii), is Federally protected as a Threatened species under the Endangered Species Act (ESA).  The Sonoran desert tortoise is listed by AZ as a Species of Greatest Conservation Need (SGCN) and was proposed for protection under the ESA but determined "Not Warranted" in 2022.  On June 4, 2025 wildlife groups filed suit in federal court challenging that determination.  

It is difficult to find current population trend data for species that may warrant listing under the ESA, so I attempted to do so using publicly available iNaturalist data.  iNaturalist is a public repository of photographic observations of species.  

Methods

I filtered iNat for Research Grade observation of Sonoran desert tortoises in AZ and found 1,402 observations. I considered limiting the analysis to only live tortoises, but eventually decided to use all research grade observations due to the difficulty filtering. Only ~3% (44 observations) were annotated as dead , and only ~1% (12 observations) were annotated as scat.  

I created an Area of Interest (AOI) bounding box around the tortoise data to search for total RG observations.  There were a total of 1.2 million RG observations in the Sonoran desert of southern AZ.

RG tortoise observations in AZ with bounding box showing AOI.  

More tortoises are observed in places where there are more people to observe them.  Because iNat data is based on opportunitistic data collection, it is liable to biases based on where people live as well as how many people use iNat.  To attempt to correct for this, trend analyses can normalize the count of tortoise observations as a ratio of total observations in the AOI.


Data

Data table of AOI with Total RG Observations, Total Observations, RG:Total Observations Ratio, RG Tortoise Observations, and RG Tortoise: RG Total observations.

Results

Total RG observations in the AZ Sonoran desert have been increasingly consistently since the early 2010s.

Count of total RG observations in the AOI per year.

Tortoise observations have increased since 2013, with some notable dips in 2020 and 2023. It is possible that these dips are due to weather-related impacts to tortoise population, but they could also be due to differences in number of observations.  

Count of tortoise observations per year.

By comparing tortoise observations to total observations, a normalized ratio can be derived. This ratio decreases over time. There is a step change decrease in 2017, which could be a real population decrease or could be due to the huge increase in popularity of iNat in 2017.  However, even if only looking at 2017 -2025, there is still a long term decrease in the ratio of tortoise observations, from around 0.12% to 0.08% of total observations. 

Ratio of tortoise observations to RG observations. 

Discussion

The decreasing ratio of tortoise observations indicates that either people are trending to preferentially observe other species more than tortoises, or that tortoises are making up a smaller percentage of the animals people encounter.  

Despite limitations of citizen science data, these results provide concerning evidence of negative population trends for this species of conservation concern and highlight the utility of iNaturalist data for monitoring species that lack formal survey programs.

An Alzheimer's Bet Based on Biology

Alzheimer's research has been accused of being hijacked by a misleading hypothesis that only survives to enrich drug companies.  The amyloid hypothesis has been extensively critiqued, including by this essay on the blog Astral Codex Ten that looked at problems with the original paper that started (by some accounts) 30 years of misguided research.  

In response to a call for counter-arguments, David Schneider-Joseph, presented a compelling argument in favor of the amyloid hypothesis.  He even went so far as to propose a bet; that a drug targeting amyloid would achieve at least a 75% slowdown in Alzheimer's in the next 12 years.

I wouldn’t take David’s proposed bet, because I’m sure some company will find a way to gerrymander clinical endpoints to get to 75% “slowdown”.  Probably with a drug that has horrible side effects and costs north of $100,000/year.  

I would bet on the following:  the leading* therapy in 12 years will not be one whose sole intended mechanism involves amyloid production or clearance, e.g. monoclonal antibodies, small molecules, or gene editing that work directly on amyloid.  

    * “Leading” means some combination of efficacious and most widely used.

This is the important sense in which the amyloid hypothesis is wrong: it may be “correct” in some narrow biochemical sense, but it is a dead end.

In a way this is an easy bet on the status quo continuing indefinitely, because the current drugs used to treat Alzheimer's do not target amyloid.  However, I’m also bullish on emerging therapies such as creatine, lithium, calcium channels, and mitochondrial therapies including far infrared, ketones, and other ways to generally affect metabolism and autophagy/mitophagy.  Some of these might be shown to improve clearance of amyloid, but the amyloid hypothesis is not necessary or very helpful in the development of these “general" therapies.  

My prediction is based on a general model of how biology works.  Simple infectious and traumatic medical conditions seem most amenable to targeted therapies, while general conditions like mental illness, cancer, and Alzheimer’s are so complicated and depend on so many general health processes that targeted therapies tend to miss the mark.  

Ideally, we would pursue both lines of treatment, but our pharma system is biased toward patentable targeted treatments to the exclusion of all else.  The “Amyloid Mafia” is shorthand for this trend in Alzheimer’s research.  

However, even given the funding disparity between amyloid research and other treatments, non-amyloid treatments are arguably already more efficacious.  As a good Bayesian, I predict this will continue, and so this seems like a safe bet to me!

Quotes from On the Border with Crook

 The past is another country, but in this book it seems like a different planet.  I hadn't been interested in Cowboys & Indians but this military travelogue is a natural history and ethnography of another world.  I've been looking for a good book that describes the endemic historical ecosystems of the Western US and found it in this story of a military officer who followed famous General Crook from one Indian War to another during the 1870's.  

Apparently this book is known as one of the Top Ten books of the Wild West, with stories of when Tucson was a Spanish town, Arizona was Apache territory, and the great plains were full of buffalo.  The writer is thoughtful and observant, and in another or later life might have been an anthropologist.  In reality, he was directly responsible for forcibly removing native peoples from their ancestral lands and the ending of their unbroken lifeways.  But he writes with respect and admiration, and this firsthand account reveals complexities of the American Indian wars that are lost in our modern moralizing view of that time period.

Perhaps it is best to let him speak for himself; these extended quotations offer a window into another world:

P 146: mixing ecology and narrative

The Tonto Basin was well supplied with deer and other wild animals, as well as with mescal, Spanish bayonet, acorn-bearing oak, walnuts, and other favorite foods of the Apaches, while the higher levels of the Mogollon and the other ranges were at one and the same time pleasant abiding-places during the heats of summer, and ramparts of protection against the sudden incursion of an enemy. I have already spoken of the wealth of flowers to be seen in these high places; I can only add that throughout our march across the Mogollon range some eleven days in time-we saw spread out before us a carpet of colors which would rival the best examples of the looms of Turkey or Persia.

Approaching the western edge of the plateau, we entered the country occupied by the Tonto Apaches, the fiercest band of this wild and apparently incorrigible family. We were riding along in a very lovely stretch of pine forest one sunny afternoon, admiring the wealth of timber which would one day be made tributary to the world's commerce, looking down upon the ever-varying colors of the wild flowers which spangled the ground for leagues (because in these forests upon the summits of all of Arizona's great mountain ranges there is never any underbrush, as is the case in countries where there is a greater amount of humidity in the atmosphere), and ever and anon exchanging expressions of pleasure and wonder at the vista spread out beneath us in the immense Basin to the left and front, bounded by the lofty ridges of the Sierra Ancha and the Matitzal; each one was talking pleasantly to his neighbor, and as it happened the road we were pursuing-to call it road where human being had never before passed— was so even and clear that we were riding five and six abreast, General Crook, Lieutenant Ross, Captain Brent, Mr. Thomas Moore, and myself a short distance in advance of the cavalry, and the pack-train whose tinkling bells sounded lazily among the trees-and were all delighted to be able to go into camp in such a romantic spot-when " whiz! whiz!" sounded the arrows of a small party of Tontos who had been watching our advance and determined to try the effects of a brisk attack, not knowing that we were merely the advance of a larger command.

P 127

All sorts of signals are made for the information of other parties of Apaches. At times, it is an inscription or pictograph incised in the smooth bark of a sycamore; at others, a tracing upon a smooth-faced rock under a ledge which will protect it from the elements; or it may be a knot tied in the tall sacaton or in the filaments of the yucca; or one or more stones placed in the crotch of a limb, or a sapling laid against another tree, or a piece of buckskin carelessly laid over a branch.  All these, placed as agreed upon, afford signals to members of their own band, and only Apaches or savages with perceptions as keen would detect their presence.

The Apache was a hard foe to subdue, not because he was full of wiles and tricks and experienced in all that pertains to the art of war, but because he had so few artificial wants and depended almost absolutely upon what his great mother-Nature stood ready to supply. Starting out upon the war-path, he wore scarcely any clothing save a pair of buckskin moccasins reaching to mid-thigh and held to the waist by a string of the same mate-rial; a piece of muslin encircling the loins and dangling down behind about to the calves of the legs, a war-hat of buckskin surmounted by hawk and eagle plumage, a rifle (the necessary ammunition in belt) or a bow, with the quiver filled with arrows reputed to be poisonous, a blanket thrown over the shoulders, a watertight wicker jug to serve as a canteen, and perhaps a small amount of "jerked" meat, or else of " pinole" or parched corn-meal.

That is all, excepting his sacred relics and " medicine,"

P 125

Unlike the Indians of the Plains, east of the Rocky Mountains, the Apache rarely become good horsemen, trusting rather to their own muscles for advancing upon or escaping from an enemy in the mountainous and desert country with which they, the Apaches, are so perfectly familiar. Horses, mules, and donkeys, when captured, were rarely held longer than the time when they were needed to be eaten; the Apache preferred the meat of these animals to that of the cow, sheep, or goat, although all the last-named were eaten. Pork and fish were objects of the deepest repugnance to both men and women; within the past twenty years-since the Apaches have been enrolled as scouts and police at the agencies-this aversion to bacon at least has been to a great extent overcome; but no Apache would touch fish until Geronimo and the men with him were incarcerated at Fort Pick-ens, Florida, when they were persuaded to eat the pompano and other delicious fishes to be found in Pensacola Bay.

P 177

Man's inhumanity to man is an awful thing. His inhumanity to God's beautiful trees is scarcely inferior to it. Trees are nearly human; they used to console man with their oracles, and I must confess my regret that the Christian dispensation has so changed the opinions of the world that the soughing of the evening wind through their branches is no longer a message of hope or a solace to sorrow.

P 158

Prescott has the distinction of being thoroughly American. Prescott was not merely picturesque in location and dainty in appearance, with all its houses neatly painted and surrounded with paling fences and supplied with windows after the American style-it was a village transplanted bodily from the centre of the Delaware, the Mohawk, or the Connecticut valley. Its inhabitants were Americans; American men had brought American wives out with them from their old homes in the far East, and these American wives had not forgotten the lessons of elegance and thrift learned in childhood. Everything about the houses recalled the scenes familiar to the dweller in the country near Pittsburgh or other busy community. The houses were built in American style; the doors were American doors and fastened with American bolts and locks, opened by American knobs, and not closed by letting a heavy cottonwood log fall against them.

P276

What with the cold threatening to freeze us, the explosions of the lodges sending the poles whirling through the air, and the leaden attentions which the enemy was once more sending in with deadly aim, our situation was by no means agreeable, and I may claim that the notes jotted down in my journal from which this narrative is condensed were taken under peculiar embarrassments.

"Crazy Horse's" village was bountifully provided with all that a savage could desire, and much besides that a white man would not disdain to class among the comforts of life:

There was no great quantity of baled furs, which, no doubt, had been sent in to some of the posts or agencies to be traded off for the ammunition on hand, but there were many loose robes of buffalo, elk, bear, and beaver; many of these skins were of extra fine quality. Some of the buffalo robes were wondrously embroidered with porcupine quills and elaborately decorated with painted symbolism. One immense elk skin was found as large as two and a half army blankets; it was nicely tanned and elaborately ornamented. The couches in all the lodges were made of these valuable furs and peltries. Every squaw and every buck was provided with a good-sized valise of tanned buffalo, deer, elk, or pony hide, gaudily painted, and filled with fine clothes, those of the squaws being heavily embroidered with bead-work. Each family had similar trunks for carrying kitchen utensils and the various kinds of herbs that the plains' tribes prized so highly. There were war-bonnets, strikingly beautiful in appearance, formed of a head-band of red cloth or of beaver fur, from which depended another piece of red cloth which reached to the ground when the wearer was mounted, and covered him and the pony he rode. There was & crown of eagle feathers, and similar plumage was affixed to the tail-piece. Bells, ribbons, and other gew-gaws were also attached....

P. 310: Battle of the Rosebud

By daylight of the next day, June 17, 1876, we were marching down the Rosebud.  The Crow scouts with whom I was had gone but a short distance when shots were heard down the valley to the north, followed by the ululation proclaiming from the hill-tops that the enemy was in force and that we were in for a fight. Shot after shot followed on the left, and by the time that two of the Crows reached us, one of them severely wounded and both crying, "Sioux! Sioux!" it was plain that something out of the common was to be expected.

p. 380: "Horse Meat March"

We marched comparatively little the next day, not more than twenty-four miles, going into camp in a sheltered ravine on the South Fork of the Grand River, within sight of the Slim Buttes, and in a position which supplied all the fuel needed, the first seen for more than ninety miles, but so soaked with water that all we could do with it was to raise a smoke. It rained without intermission all day and all night, but we had found wood, and our spirits rose with the discovery; then, our scouts had killed five antelope, whose flesh was distributed among the command, the sick in hospital being served first. Plums and bull berries almost ripe were appearing in plenty, and gathered in quantity to be boiled and eaten with horse-meat. Men were getting pretty well exhausted, and each mile of the march saw squads of stragglers, something which we had not seen before; the rain was so unintermittent, the mud so sticky, the air so damp, that with the absence of food and warmth, men lost courage, and not a few of the officers did the same thing. Horses had to be abandoned in great numbers, but the best of them were killed to supply meat, which with the bull berries and water had become almost our only certain food, eked out by an occasional slice of antelope or jack rabbit.

The 8th of September was General Crook's birthday; fifteen or sixteen of the officers had come to congratulate him at his fire under the cover of a projecting rock, which kept off a considerable part of the downpour of rain; it was rather a forlorn birthday party, nothing to eat, nothing to drink, no chance to dry clothes, and nothing for which to be thankful except that we had found wood, which was a great blessing. Sagebrush, once so despised, was now welcomed whenever it made its appearance, as it began to do from this on; it at least supplied the means of making a small fire, and provided the one thing which under all circumstances the soldier should have, if possible. Exhausted by fatiguing marches through mud and rain, without sufficient or proper food, our soldiers reached bivouac each night, to find only a rivulet of doubtful water to quench their thirst, and then went supperless to bed.

In all the hardships, in all the privations of the humblest soldier, General Crook freely shared; there was no mess in the whole column which suffered as much as did that of which General Crook was a member; for four days before any other mess had been so reduced we had been eating the meat of played-out cavalry horses, and at the date of which I am now writing all the food within reach was horsemeat, water, and enough bacon to grease the pan in which the former was to be fried. Crackers, sugar, and coffee had been exhausted, and we had no addition to our bill of fare beyond an occasional plateful of wild onions gathered alongside of the trail. An antelope had been killed by one of the orderlies attached to the headquarters, and the remains of this were hoarded with care for emergencies.

Cheyenne names

Thunder Cloud

Blown Away

Singing Bear

Fast Thunder

Black Mouse

Shuts the Door

Horse Comes Last

Arapahoe names

Sleeping Wolf

Red Beaver

Sitting Bul

Yellow Owl

Singing Beaver

Eco Sound

 

Sounds spectrographs (e.g. Merlin sound ID) usually show frequencies up to 8 or 10 kHz, but some humans have the ability to hear up to 20 kHz. Most bird song, and indeed most sounds humans care about are less than 10 kHz - usually much less. For example, middle C on a piano is 440 Hz and the highest note on a piano is just above 4 kHz. 

 So what do humans hear above 10 kHz? Some crickets make sound in the 10-20 kHz range, and some rodent squeak distress calls are audible there too. The hiss of water or air from a pinprick hole can be in this range, but it’s not clear humans would need to evolve to hear that. 

So far, I think the most likely sound in this range is the whine of mosquito wings - maybe we evolved to swat mosquitoes? 

 Also, slowed bird song sounds reeeeaaalllly cool! The 2nd to last audio file on this web page is a good example: https://donaldkroodsma.com/?page_id=49

lang eliot also has a recording that is pitch-lower the recording about one octave, to bring the notes into a frequency range that is, at least generally speaking, more appealing to our human musical preferences (note that the vast majority of human-created melodic instruments produce dominant tones that are lower in pitch than the majority of bird songs). https://musicofnature.com/celestial-music/ 

 lang Eliot current project: app that employs advanced algorithms to lower the pitch of bird songs in real time, thereby making them audible during walks in nature. https://hearbirdsagain.org/

What's up with iNat in Japan?

I recently listened to a fascinating podcast about the naturalist community in Japan, specifically about their interest in entomology. However, when I look at iNaturalist statistics for Japan, there appear to be very few observations/observers/identifiers given the population and level of development. 

This figure shows the number of Observations, Observers, and Identifiers versus per capita GDP for select countries that have similar populations. Japan (red X) is way below the trend lines for all 3 metrics.  Mexico (green asterisk) is way above trend.

Interestingly, South Korea (blue triangle) clusters with Japan, although South Korea has a population that is less than 1/2 that of Japan.

Japan clusters with the Philippines and Egypt based on population.  Interestingly, the trend lines for iNat statistics and total population are not as consistent as per capita GDP.  (China is excluded from the chart above and the one below because its population is an outlier compared to the other countries.)

This chart shows total GDP versus Observations, Observers, and Identifiers.  Japan is a clear outlier in the bottom right corner with a high GDP but low iNat statistics.

Conclusions

In this dataset, the strongest r value was Observers versus per capita GDP.  The second highest was Identifiers versus Total GDP.  The lowest was Observers versus Total Population.  This is consistent with the hypothesis that level of development (as measured by GDP) is the strongest predictor of iNat usage. 

For an interactive version of these charts on Tableau Public, use this link: https://public.tableau.com/app/profile/alexandra.permar/viz/iNatCountryComparison/

The DRIP Model: Not Drought nor Deluge

How to find green growing plants in Arizona, a state famous for its long droughts and intermittent, but torrential, rains?  Previously I reviewed the available public models for drought, NDVI, and rainfall, and concluded that rainfall was most useful.  However, the most important factor for plant growth is regular consistent rain.  Not drought, but also not deluge.  I hypothesized that a consistent "drip" of at least 1/4 inch of rain each week would yield the best plant growth, and I created a GIS model to map this.  

Methods

Download data files from NOAA: https://water.noaa.gov/resources/downloads/precip/stageIV/2025/03/04/

Methods: https://water.noaa.gov/about/precipitation-data-access 

lots more info at the bottom link for PDF: NWPS Products and User Guide

GeoTIFF The new QPE GeoTIFFs generated from the NCEP Stage IV data are multi-band GeoTIFF. The bands they contain are: 

● Band 1 - Observation - Last 24 hours of QPE spanning 12Z to 12Z in inches 

● Band 2 - PRISM normals - PRISM normals in inches (see Appendix A- Normal Precipitation) 

● Band 3 - Departure from normal - The departure from normal in inches 

● Band 4 - Percent of normal - The percent of normal

I only use Band 1, for the previous week, not 24 hours.

I download the data using a Power Automate FTP query for: concat('https://water.noaa.gov/resources/downloads/precip/ ', variables('Date2'),  '/nws_precip_', 'last 7-days_', variables('CurrentDate'), '_conus.tif')

In GIS, I Clip rasters to extent and calculate threshold (0.25") for each week:

Then I use Cell Statistics to add all threshold files for a several month period.

Results

10/13-12/01, each week gets 1 point for rain over 0.25"

Northern CA, and areas NE of AZ received more regular precipitation. This beginning of the water year period is important for early germination of desert winter annuals that can lead to "superbloom" springs.  Because most desert areas in AZ did not get much precipitation, the indications were not good for 2025 spring.

12/8 to 3/5, each week gets 1 point for rain over 0.25"

The highest mountains in UT and CO got regular precipitation, as did northern CA. NM did not continue wetter than AZ.  This winter period is important for desert spring ephemeral flowers.  While some areas of the Mojave did get rain, there was basically no rain in the Sonoran desert during this period. 

iNat Isn't Slowing Down in Arizona

The iNaturalist website collects species observations from people all over the world.  It started in 2008 and grew slowly at first and then entered a period of rapid growth in 2017.  As a consequence, the number of species recorded on the website is constantly increasing, passing 300,000 in 2020.  The website is currently adding more than 50 million observations a year. This raises an interesting biodiversity question: how long can the number of species keep increasing?  Another way of stating the question: how many species are there?

Biodiversity scientists use species accumulation curves to estimate the total number of species in a given area.  As they investigate a new study site, they record new species and the date/time the species was observed.  For most sites, the number of new species increases rapidly as scientists describe common species; the number of new species slows as scientists search for more and more rare species.  Graphing the number of species over time should reveal a logarithmic curve.  Based on the equation for that curve, scientists can estimate the asymptote - the number of species the curve will eventually reach given enough time.  This allows scientists to estimate the total number even if they don't finish counting all of the species.

This slowing down does seem to be happening for total species count on iNat.  For example, the 2024 Year in Review showed 50 million observations over the year, and about 1,000 new species (not previously observed and posted to iNat) per month.  

From iNat 2024 Year in Review

In contrast, back in May 2019 more than 6,000 new species were added.  It appears that 2019-2020 was the peak for adding new species, and even as more new users have joined iNat, fewer and fewer new species are being observed.  

These charts show running totals, with new additions colored, so that the logarithmic curve is more visible in Newly Added Species:

From 2024 Year in Review

There were fewer observations and many fewer users in 2019-2020, than now, but the rate of newly added species was much greater.  This appears to indicate that it is getting harder and harder to find new species to add to iNat.  Observable species on iNat are those that can be distinguished with photographic evidence, usually limited to smartphone cameras.  So this estimate does not include microbial life, and probably excludes most microscopic life.  

Its possible that unobserved species are mostly in the middle of remote wilderness areas and that is why fewer and fewer are being observed.  But many of the new species are from the US and Europe - there's still lots to explore!

For example, in Arizona the species accumulation curve is still effectively linear, with about 700 new species each year.  No signs of slowing down here!

The same is true of smaller areas within AZ, for example the Prescott National Forest averages 186 new species observed each year.  

I considered whether the new species could be due to rare birds and insects showing up for the first time.  I also analyzed new plant taxa on Coconino National Forest.  Plants are well-studied and the forest has been extensively surveyed, so it seems unlikely that new species would be discovered yearly.  But, according to the iNat data, not only are new species being continuously discovered, there is no detectable slow down in the rate of discovery!

I'm not sure what conclusions to draw from this analysis.  The standard conclusion would be that we haven't sampled enough species yet to begin to see the rate of new species discoveries slowing down.  This implies that the total number of species is quite a bit greater than the number that have been recorded so far on iNat.  

Another interpretation could be that the actual number of species isn't constant.  In other words, there could be new plants showing up each year on the Coconino.  This could be due to new invasive species, shifting distributions of native species.  It could also be impacted by taxonomist naming conventions; the number of species in even well-explored areas could increase as botanists work to name and describe the huge floristic diversity of the world.

There is still a lot of biodiversity to explore, even in our backyards!

Acid-Base Balance: Foods and Supplements

I previously wrote about the role lactic acid can play in disease.  This raised the question of whether foods and supplements can buffer metabolic acidity.  If so, which foods or supplements are most beneficial?  Does pH correlate to the effect on the acid-base balance of the body?

This is important because:

• Chronic acid load can deplete alkalinizing minerals, leading to e.g. calcium bone loss.
• Long Covid may be caused by metabolic acidosis: https://researchaidnetworks.org/hypothesis-summary/

After researching this, I concluded that a food's pH does not directly correlate with its impact on overall acid base balance.  Potential Renal Acid Load (PRAL) is determined by mineral and protein composition, not its inherent acidity.  

For example:

• Lemons taste acidic due to citric acid, but have a negative PRAL (alkaline-forming) because they're rich in potassium and other compounds that generate bicarbonate when metabolized
• Animal proteins may not taste acidic but have a high positive PRAL (acid-forming) due to sulfur-containing amino acids that get metabolized to sulfuric acid.

The key biochemical factors that determine a food's PRAL include:

1. Protein content (especially sulfur amino acids) - metabolized to produce acids
2. Mineral content: 
1. Potassium, calcium, magnesium - metabolized to produce bicarbonate (alkaline)
2. Phosphorus, chloride - contribute to acid load
3. Organic acid content - intermediates in the citric acid cycle (Krebs cycle), their oxidation generates bicarbonate. Each molecule of malate or citrate metabolized can generate multiple bicarbonate molecules.

Details

The pH of urine is influenced by the body's metabolic acid load and the kidney's ability to regulate hydrogen ion (H⁺) excretion.  The kidneys play a crucial role in maintaining acid-base balance by adjusting the amount of hydrogen ions eliminated or retained.  When the body experiences a metabolic acid load, the kidneys respond by increasing H⁺ excretion. This lowers urine pH, reflecting the increased acid load on the body.  However, positive cations can also stimulate renal acid-base regulation, leading to increased hydrogen ion excretion (and bicarbonate (HCO₃⁻) regeneration).  This results in a decrease in urine pH, even as the body experiences a reduced metabolic acid load.

Cations can also activate enzymes that convert metabolic acids to bicarbonate.  The more positively charged the cation, the more efficiently it can displace hydrogen ions.

Organic acid conjugation to cations enhances alkalinization.  For example, citrate enters the citric acid cycle directly and generates multiple bicarbonate (HCO₃⁻) upon oxidation.

Table of Common Supplements and Food Additives; their pH and effect on acid-base balance.  

This data shows how solution pH and PRAL effects don't always correlate. For example, while KCl has a neutral pH in solution, it has a slightly negative PRAL due to the potassium content. However, extreme pH (either acid or base) can correlate with PRAL effect.

Categories of Supplements

1. Neutral pH, Alkalizing Effect: 
1. Potassium citrate
2. Calcium lactate
3. Potassium gluconate
4. These demonstrate the pH vs. physiological effect paradox
2. Mineral-Organic Complexes: 
1. Magnesium citrate and malate show slightly acidic pH but strong alkalizing effects
2. Zinc citrate has less alkalizing effect despite similar pH
3. Simple Salts: 
1. KCl shows neutral pH with mild alkalizing effect
2. NaCl shows neutral pH and neutral physiological effect
4. Strong Acids/Bases: 
1. HCl, KOH, NaOH show correlation between pH and physiological effect
2. These are exceptions to the general trend of pH not predicting physiological impact

Alkalinizing Potential Ranking

The formula for PRAL (mEq/100g) is: PRAL = 0.49 × protein (g) + 0.037 × phosphorus (mg) - 0.021 × potassium (mg) - 0.026 × magnesium (mg) - 0.013 × calcium (mg).  

Negative PRAL indicates an alkalizing effect on the body.

Example:  mice

Mice diets were compared using Dietary Cation Anion Balance (DCAB), a similar metric to PRAL.  DCAB is calculated by adding the weighted amount of acidifying anions and alkalizing cations in the diet. 

It has been shown in many species that the dietary cation anion balance (DCAB) influences acid base homeostasis and urine pH.  With the DCAB, the resulting urinary pH can be predicted with species-specific equations. 

DCAB [mmol/kg DM] = 49.9 · Ca + 82.3 · Mg + 43.5 · Na + 25.6 · K − 59.0 · P − 62.4 · S − 28.2 · Cl; mineral content in g/kg DM.  (Negative DCAB indicates an acidifying effect on the body.)

The paper found that a negative DCAB results in metabolic acidosis, and "Fed long-term, this can contribute to the reduction of bone mineral density due to a PTH-mediated increase in renal calcium excretion. Metabolic acidosis also induces renal phosphorus excretion, resulting in hypophosphatemia."

Citation: https://www.mdpi.com/2076-2615/11/3/702 

Böswald, L.F.; Matzek, D.; Kienzle, E.; Popper, B. Influence of Strain and Diet on Urinary pH in Laboratory Mice. Animals 2021, 11, 702. https://doi.org/10.3390/ani11030702

Example:  human athletes

Alkaline water has demonstrated its effectiveness as an alkalizing agent in the treatment of metabolic acidosis in both animal and human research. Past studies have shown that daily intake of 2.5–4 L of alkaline water for 3~6 weeks has significant impacts on anaerobic performance and acid–base balance in athletes.  This study showed that alkaline water co-ingested with glutamine led to decreased stress markers in athletes.  Masterjohn hypothesizes that glutamine is converted to glutamate to buffer lactic acid in muscles, and that decreasing PRAL contributes to more available glutamine for other metabolic functions..  

Citation: https://www.mdpi.com/2072-6643/16/3/454

Lu, T.-L.; He, C.-S.; Suzuki, K.; Lu, C.-C.; Wang, C.-Y.; Fang, S.-H. Concurrent Ingestion of Alkaline Water and L-Glutamine Enhanced Salivary α-Amylase Activity and Testosterone Concentration in Boxing Athletes. Nutrients 2024, 16, 454. https://doi.org/10.3390/nu16030454

Thanks to Claude Sonnet for back-and-forth conversation, and for creating the table and figure above.  

More Forest Thinning Science

1. You need Water for Ecohydrology

I previously wrote about the effects of thinning Southwestern ponderosa pine forests on forest hydrology.  AE Brown et al (Journal of Hydrology, 2005) summarized the last 50 years of hydrology research around the world on exactly this question.  Their conclusion was that yes, thinning increases water availability by decreasing evapotranspiration (ET).  However, at drier sites there is less of a difference.

In the figure above, the difference between the grass and forest curves represents the change in mean annual water yield for 100% conversion of one vegetation type to the other.  Partial conversion (i.e. thinning) was shown to have a proportional partial response.  The lack of difference between grass and forest in drier climates (below 500mm or 20 inches precipitation/year) indicates that most ET is actually just evaporation in these areas.  Therefore, because transpiration does not play a large role, reducing transpiration via thinning would not be expected to generate a large increase in water availability.

2. Don't Miss the Forest for the Trees

This classic forestry study found that thinning ponderosa forests increased growth of the remaining trees, but decreased total wood production.  In other words, the increase in vigor didn't compensate for the decrease in trees.  This even includes the decrease in disease (bark beetles) in thinned forests. So the question becomes, do you want a healthier forest or more wood?  

Data is from the The Level-of-Growing-Stock (LOGS) study on thinning ponderosa pine forests in the US West: A long-term collaborative experiment in density management.  A 2020 follow up provides a summary review of this study that started in 1962.  The The AZ portion of the study was conducted at Fort Valley experimental Forest just north of Flagstaff.   PDF with much more info is available from https://www.fs.usda.gov/rm/pubs/rmrs_p055.pdf.