The Dome Fire

13 December, 2020

This August a fire swept through the Mojave National Preserve in southern California and killed about a million Joshua trees. Let us take a moment to mourn them, along with the ancient giant sequouias that we also lost this year.

(The article has a subheading that mistakenly says “countless ancient redwoods” also died, but the article itself does not claim this, though it has a section on coastal redwoods and the fires affecting them.)

• John Branch, They’re among the world’s oldest living things. The climate crisis is killing them, New York Times, December 2020.

This lavishly illustrated article talks about all three species. I’ll just quote the part on Joshua trees, since they live pretty close to here.

Mojave National Preserve, Calif. — On the August day when fire broke out on Cima Dome in the Mojave National Preserve, the California desert already was making international headlines. The thermometer at nearby Death Valley had reached 130 degrees, the highest temperature reliably recorded on Earth.

As photos of tourists smiling at the thermometer ricocheted around the world — a paradoxical bit of gee-whiz glee on a day portending a dire future — a million Joshua trees were on fire.

Cima Dome is a broad mound, a gentle and symmetrical arc on the vast desert horizon. It is visible from the interstate connecting Los Angeles and Las Vegas. Scientists considered it home to the world’s densest concentration of Joshua trees.

“To the untrained eye or the person not familiar with this region, most wouldn’t even notice it as they go by at 90 m.p.h.,” said Todd Esque, a desert ecologist for the United States Geological Survey. “But for those who do know, this is a huge loss.”

Joshua trees—a yucca, not a tree, named by Mormon settlers—already teeter toward trouble. Their range is shrinking, and they are not well-suited to outrun the quickening pace of climate change. Scientists worry that future visitors will find no Joshua trees in Joshua Tree National Park, the way some worry that Glacier National Park will be devoid of year-round ice.

“It’s a possibility,” Dr. Esque said.

Now wildfires, scarcely a threat historically, are taking out huge swaths at once, aided by climate change and invasive grasses.

The Dome Fire consumed 43,273 acres and killed most of the estimated 1.3 million Joshua trees it burned, according to Mr. Kaiser, the vegetation program manager for Mojave National Preserve.

“Cima Dome was a model for where the Joshua tree could persist for the next 100 years,” Mr. Kaiser said. “It was a beautiful, lush, decadent Joshua tree forest. But they’re wiped out.”

While there are plans to replant the millions of dead with thousands of young Joshua trees, “It’ll never come back like it was,” Mr. Kaiser said. “Not with climate change.”

Joshua trees can grow more than 40 feet tall with spiky, Seussian eccentricity. They typically live about 150 years.

But their range is shrinking faster than the trees can spread to more livable climes—higher in elevation and latitude, generally. The species is thwarted by slow migration (their large seeds, once transported by ground sloths that are now extinct, do not travel far from where they fall) and the overall population appears to be aging. Even at Cima Dome, there were relatively few young Joshua trees.

Those are persistent threats, too. Humans chop down Joshua trees to make room for neighborhoods, roads, even solar farms. And with Joshua trees often sharing the landscape with ranching, invasive grasses are fueling more fires than ever.

While the Dome Fire was shocking in its scope and ferocity, it was not surprising to the scientists who know the area best. “This was just a fire waiting to happen,” said Debra Hughson, chief of science and resource stewardship at Mojave National Preserve.

For more than a century, until 2002, cattle grazed on Cima Dome. Among the legacy of livestock is invasive perennial grasses like red brome. Weirdly, though, those same grasses may have helped the Joshua tree flourish.

Young Joshua trees need a nurse plant to hide under, and the prickly, woody blackbrush—unappetizing to livestock—is a perfect partner. As cattle chomped on grass, leaving vegetation sparse enough to prevent potential fires from spreading, Joshua trees took hold on Cima Dome more than in other places.

“A lot of what we were calling a year ago ‘the largest and densest Joshua Tree forest in the world’ probably didn’t exist in the early part of the 20th century,” Dr. Hughson said.

And after cattle were banned, and the invasive grasses grew uninterrupted, “It was just waiting for a spark,” she said.

The spark came in August, with a lightning strike. With resources stretched because of so many other California fires, the Dome Fire spread uncontrolled. It jumped from Joshua tree to Joshua tree and across park roads and fire lines, fueled by winds that became swirling firenados.

In two days, the blaze had done almost unimaginable damage.

“I was preparing myself for the worst,” Mr. Kaiser said as he toured the burn area. “And it pretty much was the worst.”


US Environmental Policy (Part 1)

8 November, 2020

This blog does not allow discussion of partisan politics. But I can still list some ways in which US environmental policy will change if Biden becomes president.

First and foremost, the US will rejoin the Paris Climate Agreement.

Besides leaving the Paris Climate Agreement, the Trump administration did many other things that didn’t require approval from Congress:

• Nadja Popovich, Livia Albeck-Ripka and Kendra Pierre-Louis, The Trump administration is reversing nearly 100 environmental rules. Here’s the full list, New York Times, 15 October 2020.

Here’s the list. Biden can reverse or halt all these actions without approval from Congress:

Air pollution – completed:

  1. Weakened Obama-era fuel economy and greenhouse gas standards for passenger cars and light trucks.
    E.P.A. and Transportation Department
  2. Revoked California’s ability to set stricter tailpipe emissions standards than the federal government.
    E.P.A.
  3. Withdrew the legal justification for an Obama-era rule that limited mercury emissions from coal power plants.
    E.P.A.
  4. Replaced the Obama-era Clean Power Plan, which would have set strict limits on carbon emissions from coal- and gas-fired power plants, with a new version that would let states set their own rules.
    Executive Order; E.P.A.
  5. Canceled a requirement for oil and gas companies to report methane emissions.
    E.P.A.
  6. Revised and partially repealed an Obama-era rule limiting methane emissions on public lands, including intentional venting and flaring from drilling operations. A federal court struck down the revision in July 2020, calling the Trump administration’s reasoning “wholly inadequate” and mandating enforcement of the original rule. However, the Obama-era rule was later partially struck down in a separate court case, during which the Trump administration declined to defend it.
    Interior Department
  7. Withdrew a Clinton-era rule designed to limit toxic emissions from major industrial polluters, and later proposed codifying the looser standards.
    E.P.A.
  8. Revised a program designed to safeguard communities from increases in pollution from new power plants to make it easier for facilities to avoid emissions regulations.
    E.P.A.
  9. Amended rules that govern how refineries monitor pollution in surrounding communities.
    E.P.A.
  10. Weakened an Obama-era rule meant to reduce air pollution in national parks and wilderness areas.
    E.P.A.
  11. Weakened oversight of some state plans for reducing air pollution in national parks.
    E.P.A.
  12. Relaxed air pollution regulations for a handful of plants that burn waste coal for electricity.
    E.P.A.
  13. Repealed rules meant to reduce leaking and venting of powerful greenhouse gases known as hydrofluorocarbons from large refrigeration and air conditioning systems.
    E.P.A.
  14. Directed agencies to stop using an Obama-era calculation of the social cost of carbon, which rulemakers used to estimate the long-term economic benefits of reducing carbon dioxide emissions.
    Executive Order
  15. Withdrew guidance directing federal agencies to include greenhouse gas emissions in environmental reviews. But several district courts have ruled that emissions must be included in such reviews.
    Executive Order; Council on Environmental Quality
  16. Revoked an Obama executive order that set a goal of cutting the federal government’s greenhouse gas emissions by 40 percent over 10 years.
    Executive Order
  17. Repealed a requirement that state and regional authorities track tailpipe emissions from vehicles on federal highways.
    Transportation Department
  18. Lifted a summertime ban on the use of E15, a gasoline blend made of 15 percent ethanol. (Burning gasoline with a higher concentration of ethanol in hot conditions increases smog.)
    E.P.A.
  19. Changed rules to allow states and the E.P.A. to take longer to develop and approve plans aimed at cutting methane emissions from existing landfills.
    E.P.A.
  20. Withdrew a proposed rule aimed at reducing pollutants, including air pollution, at sewage treatment plants.
    E.P.A.
  21. Relaxed some Obama-era requirements for companies to monitor and repair leaks at oil and gas facilities, including exempting certain low-production wells – a significant source of methane emissions – from the requirements altogether. (Other leak regulations were eliminated.)
    E.P.A.

Air pollution – in progress:

  1. Eliminated Obama-era methane emissions standards for oil and gas facilities and narrowed standards limiting the release of other polluting chemicals known as “volatile organic compounds” to only certain facilities. A federal court temporarily halted the rollback from going into effect after environmental groups and several states filed suit.
    E.P.A.
  2. Proposed revisions to standards for carbon dioxide emissions from new, modified and reconstructed coal power plants, eliminating Obama-era restrictions that, in effect, required them to capture and store carbon dioxide emissions.
    E.P.A.
  3. Began a review of emissions rules for power plant start-ups, shutdowns and malfunctions. One outcome of that review: In February 2020, E.P.A. reversed a requirement that Texas follow emissions rules during certain malfunction events.
    E.P.A.
  4. Proposed a rule limiting the ability of individuals and communities to challenge E.P.A.-issued pollution permits before a panel of agency judges.
    E.P.A.

Drilling and extraction – completed:

  1. Made significant cuts to the borders of two national monuments in Utah and recommended border and resource-management changes to several more.
    Presidential Proclamation; Interior Department
  2. Lifted an Obama-era freeze on new coal leases on public lands. In April 2019, a judge ruled that the Interior Department could not begin selling new leases without completing an environmental review. In February 2020, the agency published an assessment that concluded restarting federal coal leasing would have little environmental impact.
    Executive Order; Interior Department
  3. Finalized a plan to open up part of the Arctic National Wildlife Refuge in Alaska for oil and gas development, a move that overturns six decades of protections for the largest remaining stretch of wilderness in the United States.
    Congress; Interior Department
  4. Approved construction of the Dakota Access pipeline, less than a mile from the Standing Rock Sioux Reservation. (The Obama administration had halted the project, with the Army Corps of Engineers saying it would explore alternative routes.) The pipeline is embroiled in a lengthy legal battle, but has been allowed to continue operating by the Army Corps of Engineers even though a federal court reversed the Corps’ decision to allow the pipeline to run along its current path.
    Executive Order; Army
  5. Rescinded water pollution regulations for fracking on federal and Indian lands.
    Interior Department
  6. Scrapped a proposed rule that required mines to prove they could pay to clean up future pollution.
    E.P.A.
  7. Withdrew a requirement that Gulf oil rig owners prove they can cover the costs of removing rigs once they stop producing.
    Interior Department
  8. Moved the permitting process for certain projects that cross international borders, such as oil pipelines, to the office of the president from the State Department, exempting them from environmental review.
    Executive Order
  9. Changed how the Federal Energy Regulatory Commission considers the indirect effects of greenhouse gas emissions in environmental reviews of pipelines.
    Federal Energy Regulatory Commission
  10. Revoked an Obama-era executive order designed to preserve ocean, coastal and Great Lakes waters in favor of a policy focused on energy production and economic growth.
    Executive Order
  11. Loosened offshore drilling safety regulations implemented by the Obama after following the 2010 Deepwater Horizon explosion and oil spill, including reduced testing requirements for blowout prevention systems.
    Interior Department

Drilling and extraction – in progress

  1. Proposed opening most of America’s coastal waters to offshore oil and gas drilling, but delayed the plan after a federal judge in 2019 ruled that reversing a ban on drilling in the Atlantic and Arctic Oceans was unlawful. Ahead of the 2020 election, Mr. Trump announced he would exempt from drilling coastal areas around Florida, a crucial battleground state, Georgia and South Carolina.
    Interior Department
  2. Repealed an Obama-era rule governing royalties for oil, gas and coal leases on federal lands, which replaced a 1980s rule that critics said allowed companies to underpay the federal government. A federal judge struck down the Trump administration’s repeal, but another court froze the original rule pending litigation.
    Interior Department
  3. Proposed easing the approval process for oil and gas drilling in national forests by curbing the power of the Forest Service to review and approve leases, among other changes.
    Agriculture Department; Interior Department
  4. Withdrew proposed restrictions on mining in Bristol Bay, Alaska, despite concerns over environmental impacts on salmon habitat, including a prominent fishery. The U.S. Army Corps of Engineers has so far denied a permit for a proposed project, known as the Pebble Mine, noting it “could have substantial environmental impacts,” but left the door open for a revised plan.
    E.P.A.; Army
  5. Proposed revising regulations on offshore oil and gas exploration by floating vessels in the Arctic that were developed after a 2013 accident. The Interior Department previously said it was “considering full rescission or revision of this rule.”
    Executive Order; Interior Department
  6. Proposed opening more land for drilling in the Alaska National Petroleum Reserve, a vast swath of public land on the Arctic Ocean. The Obama administration had designated about half of the reserve as a conservation area.
    Interior Department
  7. Finalized a plan to allow logging and road construction in Tongass National Forest, Alaska, by exempting the area from a Clinton-era policy known as the roadless rule, which applied to much of the national forest system.
    Interior Department
  8. Approved the Keystone XL pipeline rejected by President Barack Obama, but a federal judge blocked the project from going forward without an adequate environmental review process. The Supreme Court in July 2020 upheld that ruling, further delaying construction of the pipeline.
    Executive Order; State Department
  9. Approved the use of seismic air guns for gas and oil exploration in the Atlantic Ocean. The Obama administration had denied permits for such surveys, which can kill marine life and disrupt fisheries. However, the Trump administration’s permits to allow seismic surveys expired following a protracted lawsuit, ending the possibility of seismic air gun surveys in the Atlantic in the near term. Companies would need to restart the months-long permitting process.
    National Oceanic and Atmospheric Administration

Infrastructure – completed:

  1. Weakened the National Environmental Policy Act, one of the country’s most significant environmental laws, in order to expedite the approval of public infrastructure projects, such as roads, pipelines and telecommunications networks. The new rules shorten the time frame for completing environmental studies, limit the types of projects subject to review, and no longer require federal agencies to account for a project’s cumulative effects on the environment, such as climate change.
    Council on Environmental Quality
  2. Revoked Obama-era flood standards for federal infrastructure projects that required the government to account for sea level rise and other climate change effects.
    Executive Order
  3. Relaxed the environmental review process for federal infrastructure projects.
    Executive Order
  4. Overturned an Obama-era guidance that ended U.S. government financing for new coal plants overseas except in rare circumstances.
    Executive Order; Treasury Department
  5. Revoked a directive for federal agencies to minimize impacts on water, wildlife, land and other natural resources when approving development projects.
    Executive Order
  6. Revoked an Obama executive order promoting climate resilience in the northern Bering Sea region of Alaska, which withdrew local waters from oil and gas leasing and established a tribal advisory council to consult on local environmental issues.
    Executive Order
  7. Reversed an update to the Bureau of Land Management’s public land-use planning process.
    Congress
  8. Withdrew an Obama-era order to consider climate change in the management of natural resources in national parks.
    National Park Service
  9. Restricted most Interior Department environmental studies to one year in length and a maximum of 150 pages, citing a need to reduce paperwork.
    Interior Department
  10. Withdrew a number of Obama-era Interior Department climate change and conservation policies that the agency said could “burden the development or utilization of domestically produced energy resources.”
    Interior Department
  11. Eliminated the use of an Obama-era planning system designed to minimize harm from oil and gas activity on sensitive landscapes, such as national parks.
    Interior Department
  12. Withdrew Obama-era policies designed to maintain or, ideally, improve natural resources affected by federal projects.
    Interior Department

Infrastructure – in progress:

  1. Proposed plans to speed up the environmental review process for Forest Service projects.
    Agriculture Department

Animals – completed:

  1. Changed the way the Endangered Species Act is applied, making it more difficult to protect wildlife from long-term threats posed by climate change.
    Interior Department; National Oceanic and Atmospheric Administration
  2. Ended the automatic application of full protections for ‘threatened’ plants and animals, the classification one step below ‘endangered’ in the Endangered Species Act.
    Interior Department
  3. Relaxed environmental protections for salmon and smelt in California’s Central Valley in order to free up water for farmers.
    Executive Order; Interior Department
  4. Overturned a ban on the use of lead ammunition and fishing tackle on federal lands.
    Interior Department
  5. Overturned a ban on the hunting of predators in Alaskan wildlife refuges.
    Congress
  6. Reversed an Obama-era rule that barred using bait, such as grease-soaked doughnuts, to lure and kill grizzly bears, among other sport hunting practices that many people consider extreme, on some public lands in Alaska.
    National Park Service; Interior Department
  7. Amended fishing regulations to loosen restrictions on the harvest of a number of species.
    National Oceanic and Atmospheric Administration
  8. Removed restrictions on commercial fishing in a protected marine preserve southeast of Cape Cod that is home to rare corals and a number of endangered sea animals. The Trump administration has suggested changing the management or size of two other marine protected areas in the Pacific Ocean.
    Executive Order; National Oceanic and Atmospheric Administration
  9. Proposed revising limits on the number of endangered marine mammals and sea turtles that can be unintentionally killed or injured with sword-fishing nets on the West Coast. (The Obama-era rules were initially withdrawn by the National Oceanic and Atmospheric Administration, but were later finalized following a court order. The agency has said it plans to revise the limits.)
    National Oceanic and Atmospheric Administration
  10. Loosened fishing restrictions intended to reduce bycatch of Atlantic Bluefin Tuna. Nonprofits have filed a lawsuit challenging the rollback.
    National Oceanic and Atmospheric Administration
  11. Overturned a ban on using parts of migratory birds in handicrafts made by Alaskan Natives.
    Interior Department

Animals – in progress:

  1. Proposed weakening critical habitat protections under the Endangered Species Act by making it easier to exclude certain areas, including for public-works projects, such as schools and hospitals, and for public lands leased to non-government businesses.
    Interior Department
  2. Opened nine million acres of Western land to oil and gas drilling by weakening habitat protections for the sage grouse, an imperiled bird. The Idaho District Court temporarily blocked the measure. The Montana District Court also invalidated the directive, nullifying 440 oil and gas leases, but the ruling is on hold pending appeal.
    Interior Department

Water pollution – completed:

  1. Scaled back pollution protections for certain tributaries and wetlands that were regulated under the Clean Water Act by the Obama administration. (A federal judge in Colorado halted implementation of the rule within the state, but it is in effect elsewhere.)
    E.P.A.; Army
  2. Revoked a rule that prevented coal companies from dumping mining debris into local streams.
    Congress
  3. Weakened a rule that aimed to limit toxic discharge from power plants into public waterways.
    E.P.A.
  4. Weakened a portion of the Clean Water Act to make it easier for federal agencies to issue permits for federal projects over state objections if the projects don’t meet local water quality standards, including for pipelines and other fossil fuel facilities.
    Executive Order; E.P.A. holding areas, which can spill their contents because they lack a protective underlay.
    E.P.A.
  5. Withdrew a proposed rule requiring groundwater protections for certain uranium mines. Recently, the administration’s Nuclear Fuel Working Group proposed opening up 1,500 acres outside the Grand Canyon to nuclear production.
    E.P.A.

Water pollution – in progress:

  1. Proposed doubling the time allowed for utilities to remove lead pipes from water systems with high levels of lead.
    E.P.A.
  2. Attempted to weaken federal rules regulating the disposal and storage of coal ash waste from power plants, but a court determined the original rules were already insufficient to protect the environment. The E.P.A. then proposed a new rule that would allow unlined coal ash ponds, previously deemed unsafe, to continue operating.
    E.P.A.
  3. Proposed a regulation limiting the scope of an Obama-era rule under which companies had to prove that large deposits of recycled coal ash would not harm the environment.
    E.P.A.

Toxic substances and safety – completed:

  1. Rejected a proposed ban on chlorpyrifos, a pesticide linked to developmental disabilities in children. In 2020, the E.P.A. also rejected its own earlier finding that the pesticide can cause serious health problems. (Several states have banned use of the pesticide and its main manufacturer said it would stop producing the product because of shrinking demand.)
    E.P.A.
  2. Narrowed the scope of a 2016 law mandating safety assessments for potentially toxic chemicals like dry-cleaning solvents. The updated rules allowed the E.P.A. to exclude some chemical uses and types of exposure in the review process. In November 2019, a court of appeals ruled the agency must widen its scope to consider full exposure risks, but watchdog groups say the agency has not done so in some assessments.
    E.P.A.
  3. Reversed an Obama-era rule that required braking system upgrades for “high hazard” trains hauling flammable liquids like oil and ethanol.
    Transportation Department
  4. Changed safety rules to allow for rail transport of highly flammable liquefied natural gas.
    Transportation Department

Toxic substances and safety – in progress:

  1. Proposed limiting pesticide application buffer zones that are intended to protect farmworkers and bystanders from accidental exposure.
    E.P.A.
  2. Announced a review of an Obama-era rule lowering coal dust limits in mines. The head of the Mine Safety and Health Administration said there were no immediate plans to change the dust limit but has extended a public comment period until 2022.
    Labor Department

Other – completed:

  1. Repealed an Obama-era regulation that would have nearly doubled the number of light bulbs subject to energy-efficiency standards starting in January 2020. The Energy Department also blocked the next phase of efficiency standards for general-purpose bulbs already subject to regulation.
    Energy Department
  2. Changed a 25-year-old policy to allow coastal replenishment projects to use sand from protected ecosystems.
    Interior Department
  3. Limited funding of environmental and community development projects through corporate settlements of federal lawsuits.
    Justice Department
  4. Stopped payments to the Green Climate Fund, a United Nations program to help poorer countries reduce carbon emissions.
    Executive Order
  5. Reversed restrictions on the sale of plastic water bottles in national parks desgined to cut down on litter, despite a Park Service report that the effort worked.
    Interior Department

Other – in progress:

  1. Proposed limiting the studies used by the E.P.A. for rulemaking to only those that make data publicly available. (Scientists widely criticized the proposal, saying it would effectively block the agency from considering landmark research that relies on confidential health data.)
    E.P.A.
  2. Proposed changes to the way cost-benefit analyses are conducted under the Clean Air Act. Similar rules for the Clean Water Act and other environmental statutes are in development.
    E.P.A.
  3. Proposed freezing efficiency standards for residential furnaces and commercial water heaters designed to reduce energy use.
    Energy Department
  4. Created a product category that would allow some dishwashers to be exempt from energy efficiency standards.
    Energy Department
  5. Initially withdrew, and then delayed, a proposed rule that would inform car owners about fuel-efficient replacement tires.
    Transportation Department

Reducing Bird Deaths Caused by Wind Turbines

3 November, 2020

According to the United States Fish and Wildlife Service, about 300,000 birds were killed by wind turbines in the US in 2015. Another study estimated that wind turbines killed about 500,000 birds and 900,000 bats in the US in 2012.

This sounds bad. But it’s actually tiny compared to some other causes of death! A 2014 paper estimated that power lines kill somewhere between 12 and 64 million birds each year in the US. And another paper estimates that between 1.3 to 4 billion birds are killed by domestic cats each year in the US.

So if you really want to save birds, do something about cats. But it’s interesting to read that there may be an easy way to reduce bird mortality due to wind turbines. Just paint one blade black!

That’s what this laboratory study suggested, back in 2003:

• W. Hodos, Minimization of motion smear: reducing avian collisions with wind turbines, National Renewable Energy Laboratory, NREL/SR-500-33249, August 2003.

Hodos studied the perceptual psychology of birds and recommended field testing. And that’s what these folks did, with a nice hat tip to the Rolling Stones song:

• Roel May, Torgeir Nygård, Ulla Falkdalen, Jens Åström, Øyvind Hamre and Bård G. Stokke, Paint it black: Efficacy of increased wind turbine rotor blade visibility to reduce avian fatalities, Ecology and Evolution 10 (2020), 8927–8935.

With a rather small sample size, they concluded that painting one blade of a wind turbine black reduced the fatality rate by about 70% compared to to the neighboring unpainted turbines. And the treatment had the largest effect on reduction of raptor fatalities.

Audubon Magazine is cautiously optimistic… but the Federal Aviation Authority would need to be persuaded:

The results are promising, says Garry George, director of Audubon’s Clean Energy Initiative, but they’re also preliminary. Eight turbines—half of which were treated with black paint—is not a large sample size, he says, and the researchers found relatively few bird carcasses both before and after painting the blades: A total of 42 dead birds, found at all eight turbines during the study period, were included in the analysis. It’s also not clear if the paint solution achieves the same results across various species of birds. May himself agrees: “Although we found a significant drop in bird collision rates, its efficacy may well be site- and species-specific,” he says. “It is surely not a golden egg solving all bird-collision problems in the world.” He recommended that more turbine operators test the approach around the world to see whether it works in different places and with different bird species.

If it does work, Allison says, painting blades black would be an effective, low-cost solution. But giving birds visual cues with paint isn’t the only solution researchers are testing. More thought is being put into siting, or figuring out where to physically place turbines. By studying nesting areas and common flight paths near potential wind farm locations, Allison says, wind companies can build turbines as far as possible from frequented bird routes. Additionally, wind farms are experimenting with radar, camera, and GPS tech to track birds and automatically shut off turbines as the birds approach. Still, since birds use wind to navigate and soar, there’s inevitably going to be some overlap between the best locations for wind farms and the best migratory pathways for birds.

Researchers are also experimenting with deterrence systems. “When you detect something that you think might be an eagle within a certain distance of a turbine, you emit sounds that will first alert the bird,” Allison says. “If the bird keeps coming, you send a second signal that—you know, the hope is it will persuade the bird to change its flight path.” The turbines will, in essence, scream at birds to stay away, and a report published by AWWI suggests this method could reduce collisions by somewhere between 33 and 53 percent.

Future research might prove that black turbine blades are the wind energy panacea we’ve been waiting for, but for now the idea of seeing painted blades dotted across the landscape is still up in the air in the United States. That’s because painted turbine blades are currently prohibited by Federal Aviation Administration (FAA) regulations, in part due to concern about reduced visibility for aircraft flying at night. “However, we do have a process for considering such changes,” an FAA spokesperson wrote in an email to Audubon—which sounds like they might consider changing their rules.

• Neel Dhanesha, Can painting wind turbine blades black really save birds?, Audubon, 18 September 2020.


Ascendancy vs. Reserve

22 September, 2020

Why is biodiversity ‘good’? To what extent is this sort of goodness even relevant to ecosystems—as opposed to us humans? I’d like to study this mathematically.

To do this, we’d need to extract some answerable questions out of the morass of subtlety and complexity. For example: what role does biodiversity play in the ability of ecosystems to be robust under sudden changes of external conditions? This is already plenty hard to study mathematically, since it requires understanding ‘biodiversity’ and ‘robustness’.

Luckily there has already been a lot of work on the mathematics of biodiversity and its connection to entropy. For example:

• Tom Leinster, Measuring biodiversity, Azimuth, 7 November 2011.

But how does biodiversity help robustness?

There’s been a lot of work on this. This paper has some inspiring passages:

• Robert E. Ulanowicz,, Sally J. Goerner, Bernard Lietaer and Rocio Gomez, Quantifying sustainability: Resilience, efficiency and the return of information theory, Ecological Complexity 6 (2009), 27–36.

I’m not sure the math lives up to their claims, but I like these lines:

In other words, (14) says that the capacity for a system to undergo evolutionary change or self-organization consists of two aspects: It must be capable of exercising sufficient directed power (ascendancy) to maintain its integrity over time. Simultaneously, it must possess a reserve of flexible actions that can be used to meet the exigencies of novel disturbances. According to (14) these two aspects are literally complementary.

The two aspects are ‘ascendancy’, which is something like efficiency or being optimized, and ‘reserve capacity’, which is something like random junk that might come in handy if something unexpected comes up.

You know those gadgets you kept in the back of your kitchen drawer and never needed… until you did? If you’re aiming for ‘ascendancy’ you’d clear out those drawers. But if you keep that stuff, you’ve got more ‘reserve capacity’. They both have their good points. Ideally you want to strike a wise balance. You’ve probably sensed this every time you clean out your house: should I keep this thing because I might need it, or should I get rid of it?

I think it would be great to make these concepts precise. The paper at hand attempts this by taking a matrix of nonnegative numbers T_{i j} to describe flows in an ecological network. They define a kind of entropy for this matrix, very similar in look to Shannon entropy. Then they write this as a sum of two parts: a part closely analogous to mutual information, and a part closely analogous to conditional entropy. This decomposition is standard in information theory. This is their equation (14).

If you want to learn more about the underlying math, click on this picture:

The new idea of these authors is that in the context of an ecological network, the mutual information can be understood as ‘ascendancy’, while the conditional entropy can be understood as ‘reserve capacity’.

I don’t know if I believe this! But I like the general idea of a balance between ascendancy and reserve capacity.

They write:

While the dynamics of this dialectic interaction can be quite subtle and highly complex, one thing is boldly clear—systems with either vanishingly small ascendancy or insignificant reserves are destined to perish before long. A system lacking ascendancy has neither the extent of activity nor the internal organization needed to survive. By contrast, systems that are so tightly constrained and honed to a particular environment appear ‘‘brittle’’ in the sense of Holling (1986) or ‘‘senescent’’ in the sense of Salthe (1993) and are prone to collapse in the face of even minor novel disturbances. Systems that endure—that is, are sustainable—lie somewhere between these extremes. But, where?


Insect Population Crash

25 February, 2018

Scary news from Australia:

• Marc Rigby, Insect population decline leaves Australian scientists scratching for solutions, ABC Far North, 23 February 2018.

I’ll quote the start:

A global crash in insect populations has found its way to Australia, with entomologists across the country reporting lower than average numbers of wild insects.

University of Sydney entomologist Dr. Cameron Webb said researchers around the world widely acknowledge that insect populations are in decline, but are at a loss to determine the cause.

“On one hand it might be the widespread use of insecticides, on the other hand it might be urbanisation and the fact that we’re eliminating some of the plants where it’s really critical that these insects complete their development,” Dr Webb said.

“Add in to the mix climate change and sea level rise and it’s incredibly difficult to predict exactly what it is. It’s left me dumbfounded.”

Entomologist and owner of the Australian Insect Farm, near Innisfail in far north Queensland, Jack Hasenpusch is usually able to collect swarms of wild insects at this time of year.

“I’ve been wondering for the last few years why some of the insects have been dropping off and put it down to lack of rainfall,” Mr. Hasenpusch said.

“This year has really taken the cake with the lack of insects, it’s left me dumbfounded, I can’t figure out what’s going on.”

Mr Hasenpusch said entomologists he had spoken to from Sydney, Brisbane, Perth and even as far away as New Caledonia and Italy all had similar stories.

The Australian Butterfly Sanctuary in Kuranda, west of Cairns, has had difficulty breeding the far north’s iconic Ulysses butterfly for more than two years.

“We’ve had [the problem] checked by scientists, the University of Queensland was involved, Biosecurity Queensland was involved but so far we haven’t found anything unusual in the bodies [of caterpillars] that didn’t survive,” said breeding laboratory supervisor Tina Kupke.

“We’ve had some short successes but always failed in the second generation.”

Ms. Lupke said the problem was not confined to far north Queensland, or even Australia. “Some of our pupae go overseas from some of our breeders here and they’ve all had the same problem,” she said. “And the Melbourne Zoo has been trying for quite a while with the same problems.”

Limited lifecycle prefaces population plummet

Dr. Webb, who primarily researches mosquitoes, said numbers were also in decline across New South Wales this year, which was indicative of the situation in other insect populations.

“We’ve had a really strange summer; it’s been very dry, sometimes it’s been brutally hot but sometimes it’s been cooler than average,” he said.

“Mosquito populations, much like a lot of other insects, rely on the combination of water, humidity and temperature to complete their lifecycle. When you mix around any one of those three components you can really change the local population dynamics.”

All this reminds me of a much more detailed study showing a dramatic insect population decline in Germany over a much longer time period:

• Gretchen Vogel, Where have all the insects gone?, Science, 10 May 2017.

I’ll just quote a bit of this article:

Now, a new set of long-term data is coming to light, this time from a dedicated group of mostly amateur entomologists who have tracked insect abundance at more than 100 nature reserves in western Europe since the 1980s.

Over that time the group, the Krefeld Entomological Society, has seen the yearly insect catches fluctuate, as expected. But in 2013 they spotted something alarming. When they returned to one of their earliest trapping sites from 1989, the total mass of their catch had fallen by nearly 80%. Perhaps it was a particularly bad year, they thought, so they set up the traps again in 2014. The numbers were just as low. Through more direct comparisons, the group—which had preserved thousands of samples over 3 decades—found dramatic declines across more than a dozen other sites.

It also mentions a similar phenomenon in Scotland:

Since 1968, scientists at Rothamsted Research, an agricultural research center in Harpenden, U.K., have operated a system of suction traps—12-meter-long suction tubes pointing skyward. Set up in fields to monitor agricultural pests, the traps capture all manner of insects that happen to fly over them; they are “effectively upside-down Hoovers running 24/7, continually sampling the air for migrating insects,” says James Bell, who heads the Rothamsted Insect Survey.

Between 1970 and 2002, the biomass caught in the traps in southern England did not decline significantly. Catches in southern Scotland, however, declined by more than two-thirds during the same period. Bell notes that overall numbers in Scotland were much higher at the start of the study. “It might be that much of the [insect] abundance in southern England had already been lost” by 1970, he says, after the dramatic postwar changes in agriculture and land use.

Here’s the actual research paper:

• Caspar A. Hallmann, Martin Sorg, Eelke Jongejans, Henk Siepel, Nick Hofland, Heinz Schwan, Werner Stenmans, Andreas Müller, Hubert Sumser, Thomas Hörren, Dave Goulson and Hans de Kroon, More than 75 percent decline over 27 years in total flying insect biomass in protected areas, PLOS One, 18 October 2017.

Abstract. Global declines in insects have sparked wide interest among scientists, politicians, and the general public. Loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. Our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. Here, we used a standardized protocol to measure total insect biomass using Malaise traps, deployed over 27 years in 63 nature protection areas in Germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. Our analysis estimates a seasonal decline of 76%, and mid-summer decline of 82% in flying insect biomass over the 27 years of study. We show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. This yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the European landscape.

It seems we are heading into strange times.


Restoring the North Cascades Ecosystem

13 March, 2017

In 49 hours, the National Park Service will stop taking comments on an important issue: whether to reintroduce grizzly bears into the North Cascades near Seattle. If you leave a comment on their website before then, you can help make this happen! Follow the easy directions here:

http://theoatmeal.com/blog/grizzlies_north_cascades

Please go ahead! Then tell your friends to join in, and give them this link. This can be your good deed for the day.

But if you want more details:

Grizzly bears are traditionally the apex predator in the North Cascades. Without the apex predator, the whole ecosystem is thrown out of balance. I know this from my childhood in northern Virginia, where deer are stripping the forest of all low-hanging greenery with no wolves to control them. With the top predator, the whole ecosystem springs to life and starts humming like a well-tuned engine! For example, when wolves were reintroduced in Yellowstone National Park, it seems that even riverbeds were affected:

There are several plans to restore grizzlies to the North Cascades. On the link I recommended, Matthew Inman supports Alternative C — Incremental Restoration. I’m not an expert on this issue, so I went ahead and supported that. There are actually 4 alternatives on the table:

Alternative A — No Action. They’ll keep doing what they’re already doing. The few grizzlies already there would be protected from poaching, the local population would be advised on how to deal with grizzlies, and the bears would be monitored. All other alternatives will do these things and more.

Alternative B — Ecosystem Evaluation Restoration. Up to 10 grizzly bears will be captured from source populations in northwestern Montana and/or south-central British Columbia and released at a single remote site on Forest Service lands in the North Cascades. This will take 2 years, and then they’ll be monitored for 2 years before deciding what to do next.

Alternative C — Incremental Restoration. 5 to 7 grizzly bears will be captured and released into the North Casades each year over roughly 5 to 10 years, with a goal of establishing an initial population of 25 grizzly bears. Bears would be released at multiple remote sites. They can be relocated or removed if they cause trouble. Alternative C is expected to reach the restoration goal of approximately 200 grizzly bears within 60 to 100 years.

Alternative D — Expedited Restoration. 5 to 7 grizzly bears will be captured and released into the North Casades each year until the population reaches about 200, which is what the area can easily support.

So, pick your own alternative if you like!

By the way, the remaining grizzly bears in the western United States live within six recovery zones:

• the Greater Yellowstone Ecosystem (GYE) in Wyoming and southwest Montana,

• the Northern Continental Divide Ecosystem (NCDE) in northwest Montana,

• the Cabinet-Yaak Ecosystem (CYE) in extreme northwestern Montana and the northern Idaho panhandle,

• the Selkirk Ecosystem (SE) in northern Idaho and northeastern Washington,

• the Bitterroot Ecosystem (BE) in central Idaho and western Montana,

• and the North Cascades Ecosystem (NCE) in northwestern and north-central Washington.

The North Cascades Ecosystem consists of 24,800 square kilometers in Washington, with an additional 10,350 square kilometers in British Columbia. In the US, 90% of this ecosystem is managed by the US Forest Service, the US National Park Service, and the State of Washington, and approximately 41% falls within Forest Service wilderness or the North Cascades National Park Service Complex.

For more, read this:

• National Park Service, Draft Grizzly Bear Restoration Plan / Environmental Impact Statement: North Cascades Ecosystem.

The picture of grizzlies is from this article:

• Ron Judd, Why returning grizzlies to the North Cascades is the right thing to do, Pacific NW Magazine, 23 November 2015.

If you’re worried about reintroducing grizzly bears, read it!

The map is from here:

• Krista Langlois, Grizzlies gain ground, High Country News, 27 August 2014.

Here you’ll see the huge obstacles this project has overcome so far.


The Quagga

13 February, 2016

The quagga was a subspecies of zebra found only in South Africa’s Western Cape region. After the Dutch invaded, they hunted the quagga to extinction. While some were taken to zoos in Europe, breeding programs failed. The last wild quagga died in 1878, and the very last quagga died in an Amsterdam zoo in 1883.

Only one was ever photographed—the mare shown above, in London. Only 23 stuffed and mounted quagga specimens exist. There was one more, but it was destroyed in Königsberg, Germany, during World War II. There is also a mounted head and neck, a foot, 7 complete skeletons, and samples of various tissues.


The quagga was the first extinct animal to have its DNA analyzed. It used to be thought that the quagga was a distinct species from the zebra. After some argument, a genetic study published in 2005 convinced most people that the quagga is a subspecies of the zebra. It showed that the quagga diverged from the other zebra subspecies only between 120,000 and 290,000 years ago, during the Pleistocene.

In 1987, a natural historian named Reinhold Rau started the Quagga Project. He was goal was to breed zebras into quaggas by selecting for quagga-like traits, most notably the lack of stripes on the back half of its body.

The founding population consisted of 19 zebras from Namibia and South Africa, chosen because they had reduced striping on the rear body and legs. The first foal was born in 1988.

By now, members of the Quagga Project believe they have recreated the quagga. Here they are:

Rau-quagga (zebra subspecies)

The new quaggas are called ‘rau–quaggas’ to distinguish them from the original ones. Do they look the same as the originals? It’s hard for me to decide. Old paintings show quite a bit of variability:

This is an 1804 illustration by Samuel Daniell, which served as the basis of a claimed subspecies of quagga, Equus quagga danielli. Perhaps they just have variable coloring.

Why try to resurrect the quagga? Rau is no longer alive, but Eric Harley, a retired professor of chemical pathology at the University of Cape Town, had this to say:

It’s an attempt to try and repair ecological damage that was done a long time ago in some sort of small way. It is also to try and get a representation back of a charismatic animal that used to live in South Africa.

We don’t do genetic engineering, we aren’t cloning, we aren’t doing any particularly clever sort of embryo transfers—it is a very simple project of selective breeding. If it had been a different species the whole project would have been unjustifiable.

The current Quagga Project chairman, Mike Gregor, has this to say:

I think there is controversy with all programmes like this. There is no way that all scientists are going to agree that this is the right way to go. We are a bunch of enthusiastic people trying to do something to replace something that we messed up many years ago.

What we’re not doing is selecting some fancy funny colour variety of zebra, as is taking place in other areas, where funny mutations have taken place with strange colouring which may look amusing but is rather frowned upon in conservation circles.

What we are trying to do is get sufficient animals—ideally get a herd of up to 50 full-blown rau-quaggas in one locality, breeding together, and then we would have a herd we could say at the very least represents the original quagga.

We obviously want to keep them separate from other populations of plains zebra otherwise we simply mix them up again and lose the characteristic appearance.

The quotes are from here:

• Lawrence Bartlett, South Africa revives ‘extinct’ zebra subspecies, Phys.org, 12 February 2016.

This project is an example of ‘resurrection biology’, or ‘de-extinction’:

• Wikipedia, De-extinction.

Needless to say, it’s a controversial idea.


Fires in Indonesia

2 November, 2015

I lived in Singapore for two years, and I go back to work there every summer. I love Southeast Asia, its beautiful landscapes, its friendly people, and its huge biological and cultural diversity. It’s a magical place.

But in 2013 there was a horrible haze from fires in nearby Sumatra. And this year it’s even worse. It makes me want to cry, thinking about how millions of people all over this region are being choked as the rain forest burns.

This part of the world has a dry season from May to October and then a wet season. In the dry season, Indonesian farmers slash down jungle growth, burn it, and plant crops. That is nothing new.

But now, palm oil plantations run by big companies do this on a massive scale. Jungles are disappearing at an astonishing rate. Some of this is illegal, but corrupt government officials are paid to look the other way. Whenever we buy palm oil—in soap, cookies, bread, margarine, detergents, and many other products—we become part of the problem.

This year the fires are worse. One reason is that we’re having an El Niño. That typically means more rain in California—which we desperately need. But it means less rain in Southeast Asia.

This summer it was very dry in Singapore. Then, in September, the haze started. We got used to rarely seeing the sun—only yellow-brown light filtering through the smoke. When it stinks outside, you try to stay indoors.

When I left on September 19th, the PSI index of air pollution had risen above 200, which is ‘very unhealthy’. Singapore had offered troops to help fight the fires, but Indonesia turned down the offer, saying they could handle the situation themselves. That was completely false: thousands of fires were burning out of control in Sumatra, Borneo and other Indonesian islands.

I believe the Indonesian government just didn’t want foreign troops out their land. Satellites could detect the many hot spots where fires were burning. But outrageously, the government refused to say who owned those lands.

A few days after I left, the PSI index in Singapore had shot above 300, which is ‘hazardous’. But in parts of Borneo the PSI had reached 1,986. The only name for that is hell.

By now Indonesia has accepted help from Singapore. Thanks to changing winds, the PSI in Singapore has been slowly dropping throughout October. In the last few days the rainy season has begun. Each time the rain clears the air, Singaporeans can see something beautiful and almost forgotten: a blue sky.

Rain is also helping in Borneo. But the hellish fires continue. There have been over 100,000 individual fires—mostly in Sumatra, Borneo and Papua. In many places, peat in the ground has caught on fire! It’s very hard to put out a peat fire.

If you care about the Earth, this is very disheartening. These fires have been putting over 15 million tons of carbon dioxide into the air per day – more than the whole US economy! And so far this year they’ve put out 1.5 billion tons of CO2. That’s more than Germany’s carbon emissions for the whole year—in fact, even more than Japan’s. How can we make progress on reducing carbon emissions with this going on?

For you and me, the first thing is to stop buying products with palm oil. The problem is largely one of government corruption driven by money from palm oil plantations. But the real heart of the problem lies in Indonesia. Luckily Widodo, the president of this country, may be part of the solution. But the solution will be difficult.

Quoting National Public Radio:

Widodo is Indonesia’s first president with a track record of efficient local governance in running two large cities. Strong action on the haze issue could help fulfill the promise of reform that motivated Indonesian voters to put him in office in October 2014.

The president has deployed thousands of firefighters and accepted international assistance. He has ordered a moratorium on new licenses to use peat land and ordered law enforcers to prosecute people and companies who clear land by burning forests.

“It must be stopped, we mustn’t allow our tropical rainforests to disappear because of monoculture plantations like oil palms,” Widodo said early in his administration.

Land recently burned and planted with palm trees is now under police investigation in Kalimantan [the Indonesian part of Borneo].

The problem of Indonesia’s illegal forest fires is so complex that it’s very hard to say exactly who is responsible for causing it.

Indonesia’s government has blamed both big palm oil companies and small freeholders. Poynton [executive director of the Forest Trust] says the culprits are often mid-sized companies with strong ties to local politicians. He describes them as lawless middlemen who pay local farmers to burn forests and plant oil palms, often on other companies’ concessions.

“There are these sort of low-level, Mafioso-type guys that basically say, ‘You get in there and clear the land, and I’ll then finance you to establish a palm oil plantation,'” he says.

The problem is exacerbated by ingrained government corruption, in which politicians grant land use permits for forests and peat lands to agribusiness in exchange for financial and political support.

“The disaster is not in the fires,” says independent Jakarta-based commentator Wimar Witoelar. “It’s in the way that past Indonesian governments have colluded with big palm oil businesses to make the peat lands a recipe for disaster.”

The quote is from here:

• Anthony Kuhn, As Indonesia’s annual fires rage, plenty of blame but no responsibility.

For how to avoid using palm oil, see for example:

• Lael Goodman, How many products with palm oil do I use in a day?

First, avoid processed foods. That’s smart for other reasons too.

Second, avoid stuff that contains stearic acid, sodium palmitate, sodium laureth sulfate, cetyl alcohol, glyceryl stearate and related compounds—various forms of artificial grease that are often made from palm oil. It takes work to avoid all this stuff, but at least be aware of it. These chemicals are not made in laboratories from pure carbon, hydrogen, oxygen and nitrogen! The raw ingredients often come from palm plantations, huge monocultures that are replacing the wonderful diversity of rainforest life.

For more nuanced suggestions, see the comments below. Right now I’m just so disgusted that I want to avoid palm oil.

For data on the carbon emissions of this and other fires, see:

Global fire emissions data.


1997 was the last really big El Niño.


This shows a man in Malaysia in September. Click on the pictures for more details. The picture at top shows a woman named a woman named Gaye Thavisin in Indonesia—perhaps in Kalimantan, the Indonesian half of Borneo, the third largest island in the world. Here is a bit of her story:

The Jungle River Cruise is run by Kalimantan Tour Destinations a foreign owned company set up by two women pioneering the introduction of ecotourism into a part of Central Kalimantan that to date has virtually no tourism.

Inspired by the untapped potential of Central Kalimantan’s mighty rivers, Gaye Thavisin and Lorna Dowson-Collins converted a traditional Kalimantan barge into a comfortable cruise boat with five double cabins, an inside sitting area and a upper viewing deck, bringing the first jungle cruises to the area.

Originally Lorna Dowson-Collins worked in Central Kalimantan with a local NGO on a sustainable livelihoods programme. The future livelihoods of the local people were under threat as logging left the land devastated with poor soils and no forest to fend from.

Kalimantan was teeming with the potential of her people and their fascinating culture, with beautiful forests of diverse flora and fauna, including the iconic orang-utan, and her mighty rivers providing access to these wonderful treasures.

An idea for a social enterprise emerged , which involved building a boat to journey guests to inaccessible places and provide comfortable accommodation.

Gaye Thavisin, an Australian expatriate, for 4 years operated an attractive, new hotel 36 km out of Palangkaraya in Kalimantan. Gaye was passionate about developing the tourism potential of Central Kalimantan and was also looking at the idea of boats. With her contract at the hotel coming to an end, the Jungle Cruise began to take shape!


Information and Entropy in Biological Systems (Part 5)

30 May, 2015

John Harte of U. C. Berkeley spoke about the maximum entropy method as a method of predicting patterns in ecology. Annette Ostling of the University of Michigan spoke about some competing theories, such as the ‘neutral model’ of biodiversity—a theory that sounds much too simple to be right, yet fits the data surprisingly well!

We managed to get a video of Ostling’s talk, but not Harte’s. Luckily, you can see the slides of both. You can also see a summary of Harte’s book Maximum Entropy and Ecology:

• John Baez, Maximum entropy and ecology, Azimuth, 21 February 2013.

Here are his talk slides and abstract:

• John Harte, Maximum entropy as a foundation for theory building in ecology.

Abstract. Constrained maximization of information entropy (MaxEnt) yields least-biased probability distributions. In statistical physics, this powerful inference method yields classical statistical mechanics/thermodynamics under the constraints imposed by conservation laws. I apply MaxEnt to macroecology, the study of the distribution, abundance, and energetics of species in ecosystems. With constraints derived from ratios of ecological state variables, I show that MaxEnt yields realistic abundance distributions, species-area relationships, spatial aggregation patterns, and body-size distributions over a wide range of taxonomic groups, habitats and spatial scales. I conclude with a brief summary of some of the major opportunities at the frontier of MaxEnt-based macroecological theory.

Here is a video of Ostling’s talk, as well as her slides and some papers she recommended:

• Annette Ostling, The neutral theory of biodiversity and other competitors to maximum entropy.

Abstract: I am a bit of the odd man out in that I will not talk that much about information and entropy, but instead about neutral theory and niche theory in ecology. My interest in coming to this workshop is in part out of an interest in what greater insights we can get into neutral models and stochastic population dynamics in general using entropy and information theory.

I will present the niche and neutral theories of the maintenance of diversity of competing species in ecology, and explain the dynamics included in neutral models in ecology. I will also briefly explain how one can derive a species abundance distribution from neutral models. I will present the view that neutral models have the potential to serve as more process-based null models than previously used in ecology for detecting the signature of niches and habitat filtering. However, tests of neutral theory in ecology have not as of yet been as useful as tests of neutral theory in evolutionary biology, because they leave open the possibility that pattern is influenced by “demographic complexity” rather than niches. I will mention briefly some of the work I’ve been doing to try to construct better tests of neutral theory.

Finally I’ll mention some connections that have been made so far between predictions of entropy theory and predictions of neutral theory in ecology and evolution.

These papers present interesting relations between ecology and statistical mechanics. Check out the nice ‘analogy chart’ in the second one!

• M. G. Bowler, Species abundance distributions, statistical mechanics and the priors of MaxEnt, Theoretical Population Biology 92 (2014), 69–77.

Abstract. The methods of Maximum Entropy have been deployed for some years to address the problem of species abundance distributions. In this approach, it is important to identify the correct weighting factors, or priors, to be applied before maximising the entropy function subject to constraints. The forms of such priors depend not only on the exact problem but can also depend on the way it is set up; priors are determined by the underlying dynamics of the complex system under consideration. The problem is one of statistical mechanics and it is the properties of the system that yield the correct MaxEnt priors, appropriate to the way the problem is framed. Here I calculate, in several different ways, the species abundance distribution resulting when individuals in a community are born and die independently. In
the usual formulation the prior distribution for the number of species over the number of individuals is 1/n; the problem can be reformulated in terms of the distribution of individuals over species classes, with a uniform prior. Results are obtained using master equations for the dynamics and separately through the combinatoric methods of elementary statistical mechanics; the MaxEnt priors then emerge a posteriori. The first object is to establish the log series species abundance distribution as the outcome of per capita guild dynamics. The second is to clarify the true nature and origin of priors in the language of MaxEnt. Finally, I consider how it may come about that the distribution is similar to log series in the event that filled niches dominate species abundance. For the general ecologist, there are two messages. First, that species abundance distributions are determined largely by population sorting through fractional processes (resulting in the 1/n factor) and secondly that useful information is likely to be found only in departures from the log series. For the MaxEnt practitioner, the message is that the prior with respect to which the entropy is to be maximised is determined by the nature of the problem and the way in which it is formulated.

• Guy Sella and Aaron E. Hirsh, The application of statistical physics to evolutionary biology, Proc. Nat. Acad. Sci. 102 (2005), 9541–9546.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.


Biodiversity, Entropy and Thermodynamics

27 October, 2014

 

I’m giving a short 30-minute talk at a workshop on Biological and Bio-Inspired Information Theory at the Banff International Research Institute.

I’ll say more about the workshop later, but here’s my talk, in PDF and video form:

Biodiversity, entropy and thermodynamics.

Most of the people at this workshop study neurobiology and cell signalling, not evolutionary game theory or biodiversity. So, the talk is just a quick intro to some things we’ve seen before here. Starting from scratch, I derive the Lotka–Volterra equation describing how the distribution of organisms of different species changes with time. Then I use it to prove a version of the Second Law of Thermodynamics.

This law says that if there is a ‘dominant distribution’—a distribution of species whose mean fitness is at least as great as that of any population it finds itself amidst—then as time passes, the information any population has ‘left to learn’ always decreases!

Of course reality is more complicated, but this result is a good start.

This was proved by Siavash Shahshahani in 1979. For more, see:

• Lou Jost, Entropy and diversity.

• Marc Harper, The replicator equation as an inference dynamic.

• Marc Harper, Information geometry and evolutionary game theory.

and more recent papers by Harper.