"Trying to define the undefinable": are taxonomists too focused on species?

A recent article in the New Yorker includes a good overview of why identifying species can be problematic:  

"You Name It: Carl Linnaeus and the effort to label all of life" by Kathryn Schulz, August 21, 2023 

Extended quote from article:

"What Linnaeus sought to do was organize nature according to its fundamental, intrinsic divisions--to carve it at the joints, in Plato's famous formulation.  But what he actually did, for the most part, was impose artificial categories on the natural world for the convenience of scientists.

This is not a retroactive assessment; Linnaeus himself knew full well the limitations of his classification method.  To achieve a system completely in accordance with nature was, he wrote, "the first and last wish of botanists."  But the more closely you looked at her bounty the more difficult that prospect became--so, in the meantime, "artificial systems are absolutely necessary."

In philosophy, this tension between intrinsic and imposed categories takes the form of a debate between nominalism and realism.  Realists believe that nature is full of real and discrete categories, from 'amphibian" to "zinc," and that the job of the scientist is to discern them accurately.  Nominalists believe that nature lacks clearly defined categories, and that we simply impose those distinctions upon it--creating, as it were, the illusion of joints where none really exist.  

This is not just the position of post-truth relativists.  "I look at the term 'species' as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other": that is Charles Darwin, in the second  chapter of "On the Origin of Species."  That book, of course, trumpeted to the world a very large problem with the entire notion of a species.  According to evolutionary theory, species are constantly changing--emerging, diverging, going extinct.

The very concept of a species is in radical flux, too, with more than twenty competing definitions in circulation.  Choosing a definition is not just a matter of what goes in the dictionary under "species"; which one you use will determine how you divide up nature, such that a group of creatures that would be regarded as a species by one standard might not merit the label by another.  

All this confusion comes, as Darwin wrote, "from trying to define the undefinable."  Yet committed realists continue to promulgate more and more definitions, in the belief that one of them will map perfectly onto some intrinsic and stable feature of nature.  Darwin called that idea "laughable," a word that captures the impossibility but not the gravity of arbitrarily imposing categories on living beings.

Xeriscaping or Zero-scaping?

 Xeriscaping is a low-water user landscaping practice in the desert Southwest.  Typically gravel or rock is used as the major groundcover, with desert-adapted plants interspersed.  Herbicides are generally used to control unsightly weeds in the gravel areas. 

Zero-scaping is when landowners skip all of the landscaping and just use herbicides to maintain dirt lots.  Unsurprisingly, the result is often phenomenally ugly.  However, this technique is extremely popular.  Why?

Herbicide-maintained zero-scaping.  The property is listed on one of the popular home-rental websites, so it has to look "presentable"!

Property line contrast.  The owner on the right has elected to let their grass grow tall, creating habitat for wildflowers and pollinators.  They usually mow it once or twice a year.

Close-up of herbicide area.  Not what I would call "presentable".

Another property owner trying to make their yard look nice.  The lush growth on the right shows what they are fighting against.

Some zero-scaping is counter-productive.  Here coir logs were used to try to control erosion.  The slope may even have been seeded.  But the over-zealous (or under-caring) landscaping company tasked with controlling weeds on the property has been very thorough in killing everything.  The result is continuing erosion into the waterway.

 

Are Pollinators Necessary for Food Production?

Pollinator enthusiasts claim that "1 in 3 bites of food are dependent on pollinators", but the reality is that many crops have been bred to self-pollinate.  For example, soybeans produce bean-like flowers, and many wild beans do require insect pollinators, but soybean flowers never open; they self-pollinate.  

In the wild, 70-90% of flowering plant species (angiosperms) do require an animal (usually an insect, bird, or mammal) to move pollen from one flower to another. Source. Only a few species have evolved to become self-reliant or to rely on wind.  But in human agriculture, we've selected for species that "breed true", which often means selecting for self-pollination. 

Many flowering agricultural crops would appear to need pollinators, but don't.  Or at most the pollination is optional: it doesn't hurt for insects to visit the flowers, and sometimes they help to fertilize and hence set more fruit, but they aren't strictly needed.  Although about three-quarters of crops benefit in some way from animal pollination, only about 10 % depend fully on pollinators to produce the seeds or fruits we consume, and they collectively account for only 2 % of global agricultural production. Source.

I created this table to show the AZ crops that require pollinators.

Data from Our World in Data: https://ourworldindata.org/pollinator-dependence

More information: https://en.wikipedia.org/wiki/List_of_crop_plants_pollinated_by_bees

Biodiversity in the United States

Summary

NatureServe's Map of Biodiversity Importance (MoBI) is actually 4 main maps and 53 supporting maps.

The four maps showcase different aspects of biodiversity in the United States using Geographic Information System (GIS) technology. The maps are all based on data from NatureServe, which aims to assess the status and distribution of biodiversity across the United States. Each map uses a different metric to measure biodiversity and provides valuable insights into different facets of the complex and multifaceted concept of biodiversity. These maps can be used to inform conservation efforts and guide land use decisions to protect and preserve biodiversity in different regions of the United States. However, it is important to note that each map provides a limited view of biodiversity, and a comprehensive understanding of biodiversity requires consideration of multiple factors and metrics.

For example, it is difficult to determine which map shows the highest biodiversity in Arizona because each map uses a different definition of biodiversity. Map #1 shows the richness of imperiled species in the United States, but does not provide a total biodiversity count. The highest value in Arizona for this map is 11. Map #2 shows the summed range-size rarity of imperiled species in the United States, which measures the presence of imperiled species with small ranges, but does not necessarily capture total biodiversity. Maps #3 and #4 focus on areas of under-protected biodiversity importance of imperiled species and may not be as useful in determining total biodiversity.  It would be helpful to have a map that shows the total biodiversity of an ecoregion, which is not captured by any of these maps.

More resources

MoBI ESRI Overview

 Story map 

YouTube The Map of Biodiversity Importance | Dr. Healy Hamilton's Presentation at 2020 Esri UC

Detailed notes on each map

Map #1: Richness of Imperiled Species in the United States

1) Richness of Imperiled Species in the United States: link

a. High values identify areas where more imperiled species are most likely to occur.

b. Richness values are simply a tally of the number of species with habitat overlapping a cell.

c. Values range from 0 to 31, but the color ramp maxes out at 11.  

a. Highest value in AZ is 11.

b. Tenneessee has highest value upstream of Chattanooga and Knoxville along the Clinch river in the Cumberland river valley.

d. This is the prettiest map and easiest to interpret.

e. Most of the Sonoran desert has 0 imperiled species?  What about Pygmy owls?Sandhills east of Carlsbad only have 1 imperiled species (lesser prairie chicken).  What about lizards?  What about rare plants?

Map #2: Summed Range-size Rarity of Imperiled Species in the United States

2) Summed Range-size Rarity of Imperiled Species in the United States:  link

a. High values identify areas where species with very small ranges (and thus fewer places where they can be conserved) are likely to occur; the presence of multiple imperiled species contributes to higher scores.

b. Range-size rarity for each species is the inverse of the total area mapped as habitat. Summed range-size rarity is the sum of the range-size rarity values for all species with habitat that overlaps a cell.

c. The range for RSR values in cells containing species habitat is 0.0000002784 to 1.44584. A single species can have a value as high as 1.020335, which means just one 990-m cell contains all habitat for that species.  The RSR score for a species with habitat in two 990-m cells is 0.510167. 

d. This map is probably most important for conservation, and because its harder to interpret maybe is easier to use…less questions!

 Map #3: Protection-weighted Range-size Rarity of Imperiled Species in the United States

3) Protection-weighted Range-size Rarity of Imperiled Species in the United States: Link

a. High values identify areas where more unprotected, restricted-range species are likely to occur.  

b. Weighted based on how much of range is in protected areas.

c.  Each species was assigned a PWRSR score equal to the product of range-size rarity and the percent of habitat that is unprotected. The PWRSR raster sums these scores for all species with habitat that overlaps a cell.

d. Note:  Data based on USGS "GAP" analysis.  "Protected areas" include Wilderness and National Monument (GAP 1 and 2), but not Federal lands open to extraction like National Forests and BLM (GAP 3). 

Map #4: Areas of Unprotected Biodiversity Importance of Imperiled Species in the United States 

4)  Areas of Unprotected Biodiversity Importance of Imperiled Species in the United States: link

a. Values of “1” identify areas where under-protected and range-restricted species are most likely to occur, including areas where the presence of multiple imperiled species contributes to higher scores

b. This is the same as #3 above, but with a cutoff value to make the map black and white.

c. AUBIs (Areas of unprotected biodiversity importance)

AI Developments... and Predictions

 I've been watching the AI developments... and the bloggers writing about the AI "foom".

• Scott Alexander on the feeling of being on the verge of AI Apocalypse.
• Scott Alexander on the new Janus-faced AI simulators, a weird new breed of alien intelligence we didn't expect.
• Erik Hoel on why we shouldn't be cavalier about the potential impact of super-intelligent AI.  (Item 4 of 9 on the page).

But in my opinion, the new AI chatbots may replace Google's current search, but they will stop far short of replacing anything but the most mundane human jobs. 

Its so hilarious that people are worried about artificial intelligence when we haven't even made a robot that can flip hamburgers yet!  Wake up and smell the grease:  the real world is complicated and messy.  We can't even replace the jobs that everyone, even the people currently working them, want replaced.  I don't think we're going to be replacing professionals anytime soon.

Just look at driverless cars.  Driving is a great example of something you'd think computers would be good at.... if you'd never driven a car in the real world!  Computers are great at driving cars in video games, but the real world is messy.  That's the Real World problem.

The second problem is even bigger: the messiness of the human social world!   Even if driverless cars were better than human drivers, that's not good enough.  We expect computers to be perfect.  If a company sells me a car and I wreck it, I'm responsible.  But if the company sells me a driverless car that crashes, the company is responsible.    

For every task that matters we want a human to be responsible.  Even if they solve the Real World problem with bigger and better AIs, the Responsibility problem will always prevent human replacement.  Imagine if my boss could replace me with a computer: he would then be 100% liable for any mistakes the computer made!  Is that the kind of liability any Pointy Haired Boss wants??  As long as he has real humans working for him, there's always someone to share the responsibility.  

Example: imagine something that's even simpler than driving a car: flying a passenger airplane!  I'm sure autopilot could fly an airplane as well as a human.  But would anyone want to fly on an airplane with no human pilot?  We'll always have the human pilots, even if the autopilot does more and more of the routine work.

Humans are social creatures.  The humans who think AI will rule the world must be living inside a computer world.  Its interesting that, as more and more of our world is computerized, we hear more and more from the people living inside the computer world.  But its not the real world!

In These Cheatgrass-Infested Hills

Matthew Miller, The Nature Conservancy writer/editor, has written a beautiful article about coming to grips with beautiful yet non-native landscapes.

In my opinion, there are too many conservationists lost in a dream of pure "native" nature, unable to see the flawed-but-still-beautiful world around them.  I empathize with his struggle to learn to love degraded places, even the hard-to-love places that are infested with cheatgrass.  

Trying to widen our circle of appreciation to include even nasty invasives helps us appreciate the natural in the unnatural: the native pollinators that use invasive wildflowers, the native birds that nest in invasive trees. 

To quote Princess Mononoke, our task now is "to see with eyes unclouded by hate."

Climate Prediction Skill

The US Climate Prediction Center issues forecasts beyond the normal National Weather Service's 10-14 day window.  They provide weekly and monthly forecasts out to 3 months.  Given the timeframe and the fact that their forecasts cover the entire contintental US, its not surprising that the forecasts are often wrong.  But how wrong?  And is their skill improving over time?

I analyzed their 3 month temperature and precipitation forecast skill using data provided on their "Gridded Seasonal Verifications" webpage.  

Note that skill is measured on a scale from -50 to 100, where -50 would be a forecast that was exactly wrong in every area, 0 would be a prediction that did no better than chance, and 100 is a prediction that was exactly right in every area.  

They provide data starting in 1995.  Since that time in the mid 1990's, linear trendlines show that their forecast skill has slightly improved for both Temperature and Precipitation.  Precipitation skill started out lower, but has almost doubled (from 10 to 20) while Temperature skill started higher but has not increased as much (from 22 to 28).

However, the last 10 years have not been as successful:

Since 2012, neither Precipitation nor Temperature skill have increased.  In fact, mean temperature forecast skill has decreased markedly since 2018.  Before that, Temperature skill had been doing quite well in the period 2014-2018.  It is not clear what changed in 2018.  A similar transition may be happening with Precipitation, where the period 2019-2022 saw consistently good predictions, but since the beginning of 2023 the forecast skill has fallen off a cliff.

With increased use of machine learning, it seems likely that long-term weather forecast skill should increase.  However, complex chaotic weather patterns are most impactful to climate predictions in the 1-3 month time frame, so this area of weather/climate prediction may continue to have lower than hoped for success.  

Rare Plants and High Quality Ecosystems Mapped in Washington State

 The new HDMS mapper from WNHP shows rare plants as well as Ecological Integrity Assessments (EIAs) for a wide range of ecosystems.

For example, here are the rare plant areas East of Renton:

And here are the natural ecosystems with an "A" rating:

Science & Technology - 2022 Year in Review

AI

 2022 was the big year for Artificial Intelligence, the year when AI became a household word.  The image generators were first, like Dall-E, but by the end of the year the latest GPT release (Chat-GPT) had taken over.  

Overview of some of the big AI releases:  link

Space

Big milestones in space included the successful first images from the James Webb Space Telescope (JWST), showing individual stars inside galaxies at the very beginning of time.  Link to images from JWST.

The DART asteroid-impact missions was a success!  Video reviews here and here.  

And sadly, the Planetary Society's crowd-funded solar sail, Lightsail 2, crashed back into the Earth's atmosphere after 3 years sailing on sunlight.  Link.

Environment

While its hard to pick the top environmental story, the fact that Earth warmed at an all-time record pace created climate disruptions everywhere.  

On the positive side, researchers have created a form of ultra-white paint that can reflect more energy than is absorbs.  Buildings coated with this paint would have a natural cooling ability that could reduce ambient temperatures and reduce energy required for AC.  I'm very hopeful that this can become cost effective and widely used in desert cities.  Link.

Plant-Pollinator Interactions in Yavapai County, AZ

 Introduction

Pollinators visit plants seeking nectar and/or pollen. Pollinators include insects (e.g. butterflies, moths, beetles, bees, wasps, flies), bats, and birds. In any geographic region, native and non-native pollinators visit native and non-native plants.

Pollinators may be specialists and/or generalists who visit plants for different reasons. For example, some pollinators specialize on the pollen of certain plant species such that they visit only certain plants to harvest pollen from them. These pollen-seeking specialists may be nectar-seeking generalists to the extent that they indiscriminately harvest nectar from any plant species.

Pollinator-plant interactions are a subject of ongoing study. In North America alone there are more than 3,600 bee species. Ecologists document pollinator-plant interactions to understand which pollinators visit which plant species and why.

Methods

We use iNaturalist—a citizen science computer application—to document our observations of pollinators and plants in the places we visit. We have five years of non-systematic observation data from Yavapai County, AZ that we use for our analysis. We looked at which plant species are most frequently visited by pollinators across different taxa. This will help us better understand which local plant species are popular amongst pollinators.

We annotated five years of pollinator observation records from Yavapai County, AZ with the scientific name of the plant species each pollinator is visiting. Our database includes a total of 265 distinct counts of pollinator-plant interactions (note this is different from the number of observations).

Here is a link to our current plant-pollinator interactions in iNat.

There are some notable issues that exist with our data:

·        We did not systematically collect the data. We did not employ ecological sampling methods, we did not sample data at regular intervals of time, and we did not take measures to ensure we systematically sought observations of pollinators across distinct plant taxa in unbiased ways. Therefore, our dataset contains bias.

·        We are analyzing our dataset for fun. Since the data contain unintentional bias, we do not intend for the results of our analysis to be reliable for landscape or species management decisions.

·        Our data contain blank fields (unknowns) at the level of insect taxon family, genus, and species. Because we cannot fill in the blanks with reliable data, we conduct our analysis at the level of insect taxon (e.g. insect family, genus, or species).

·        Our database’s plant records contain plant taxa information at the level of genus and species.

See this post for more thoughts on the limitations of this type of analysis.

Total insect taxa associated with plant genera

 

Count of distinct insect taxa associated with the top ten plant genera by month

This graph reflects the top ten plant genera ranked according to the counts of distinct insect taxa associated with them. In our database, we have data for many more plant genera than those shown.

The top ten plant genera include Asclepias, Baccharis, Ceanothus, Cirsium, Dalea, Ericameria, Helianthus, Hymenothrix, Machaeranthera, and Opuntia. 

There may be more associations between distinct insect taxa and plant genera during the summer months of June, July, and August but they are not reflected in this graph because we didn’t observe them due to extreme heat and/or monsoon rains.

This project and data analysis were a collaboration between Conor Flynn and Alexandra Permar.