1
Q
Population Dynamics of Infectious Disease
A
2
Q
A
3
Q
Infectious Disease
A
A product of an interaction between two species.
4
Q
The Host
A
A resource for the pathogen, in order for the pathogen to grow and multiply.
5
Q
Disease
A
What is caused by the pathogen in the host, which is affected by various factors, e.g., host age.
6
Q
Pathogens have different life history strategies:
A
E.g., HIV and measles.
7
Q
HIV Life History Strategy
A
There;s a peak in the viremia, then it declines due to cytotoxic T cells (antibodies also play a role), but the viremia never completely goes away. It settles for 8-10 years at a particular stable level. While it’s at a stable level, the virus is still invading, and destroying, CD4 T cells. CD4 T cells then decrease, the viremia increases againa and AIDS occurs.
8
Q
Antiretroviral Therapy
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Can keep the stable viremia levels even lower.
9
Q
Measles Life History
A
The viremia grows after the host is infected. After a week, symptoms develop, and the immune system begins to synthesise antibodies and T cells against the virus. This resolves the viremia, so by 14 weeks, there’s undetectable levels of viremia in the blood. The host is then typically immune to all subsequent infections by measles.
10
Q
Colonisation by HIV
A
the population begins as completely susceptible. A person with the virus appears, then spreads the pathogen from person to person. If someone has the virus, they are counted as infected, so they’re no longer susceptible to the virus. (Though a new strain could emerge).
11
Q
The compartmental model can be used to model HIV, and other viruses with similar life histories:
A
This model uses variables to describe the state of the host. There are only two variables/compartments: Susceptible/S and Infected/I.
12
Q
λ
A
The per capita rate at which hosts from from S to I. I.e., the force (per capita risk) of infection.
13
Q
What happens as y increases?
A
The rate of cahnge of y decreases, as the pathogen uses up its own resources by infecting hosts. This means there is density-dependence.
14
Q
When a pathogen spreads, it creates a population-elevl reduction in resources. What is the term often given to this?
A
Herd immunity (though not for a virus with a life history like HIV’s).
15
Q
What happens until y=1?
A
The spread will continue until everyone is infected. All patches will be colonised eventually.
16
Q
What actually is λ?
A
The likelihood of being infected, if you were susceptible,a nd entered a population. This depends on how many people are already infected, and how likely you are to come into contact with soemone who is infected, so that they could spread it to you, which depends on the type of transmission.
17
Q
λ=
A
By
18
Q
To what is λ proportional?
A
The number of people who are infected. It doesn’t have to be a linear relationship, but the linear part of any more complicated relationship will dominate.
19
Q
B
A
A combination of parameters relating risk of infection to prevalence of infection.
20
Q
When λ= By:
A
dy/dt= By(1-y).
21
Q
What is beta in the case of a directly-transmitted pathogen?
A
You are at risk of acquiring the pathogen from anyone in the population, so beta modifies the likelihood of getting the disease after you’ve bumped into someone.
22
Q
What is beta in the case of a sexually-transmitted infection?
A
Instead of N, it’s the number of sexual partners per year. Beta is the probability of getting the disease from each interaction.
23
Q
Why is biting rate, a, squared?
A
In order to successful completion of the lifecycle, the mosquito must bite, and infect a host. Then the host must be bitten again by another mosquito to transmit the disease to someone else.
24
Q
The graph of y against time:
A
Introduce the infection with a small number of people, the infection gains traction; then infection rate increases rapidly. The pathogen is consuming so many resources that rate of infection slows down again, and plateaus. This shape mimics real pathogens, incl. HIV.
25
Depending on the ttransmission setting, …
… the proportion of people infected by HIV in different parts of the world can vary hugely.
26
Why can HIV colonise hosts so effectively?
It changes its antigens frequently, allowing it to become chronic.
27
TB exhibits high levels of carriage of the disease.
It colonises a host, and often re-emerges when the host is an adult, when it can cause necrosis of the lungs. There is a stable pattern of emergence, when a high proportion of the population is infected.
28
What cells does TB invade?
Macrophages.
29
What does the Herpes Simplex virus do during primary infection?
It enters periphery sensory nerves, and migrates along the axon to sensory nerve ganglia in the CNS, allowing the virus to escape the immune response, and become latent. Gnaglia aren't very active, so this allows it to evade the immune system.
30
Herpesviruses
HSV1 (cold sores), HSV2 (genital herpes), VZV (Varicella Zoster Virus/chicken pox), EBV (Epstein-Barr Virus), CMV, HHV6, HHV7 and HHV8. HSV1 and HSV2 are the simplex viruses.
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VZV, EBV, CMV, HHV6 and HHV7.
Primary infection generally occurs in a sub-clinial infection in early childhood, with subsequent life-long persistence of the infection.
32
What causes herpes viruses to re-emerge?
If the host becomes immunocompromised or stressed.
33
Re-emergence of chivken pox as shingles occurs more often than thought.
1 in 3 people over 60 get shingles.
34
R0: the Basic Reproduction number.
R0= B/µ. The average number of secondary cases generated by a primary case in a totally susceptible population. It's a fundamental measure of the transmission potential of a pathogen in a given setting.
35
When an infected person enters a population, …
… they may not infect anyone, or they may cause a chain of infections. The proportion of infected will only take off when the average number of people infected per case is greater than or equal to 1.
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Population Dynamics of Infectious Disease II
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Measles vs. HIV Life Histories
Unlike HIV, which permanently colonises a host, measles enters a host, then comes out of the host as fast as possoble to infect another host.
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The SIR model adds a 3rd compartment:
R: recovered.
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σ
The inverse of the average duration of infection is the recovery time. E.g., if the infectious period lats 7 days, it whould take 1/7 days to recover.
42
How long is natural immunity to measles known to last?
At least 65 years.
43
Z
The sum of I and R. The proportion of the population not available for infection.
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When has herd immunity been reached?
When rate of infections becomes negative.
45
What is required for the pathogen to spread?
dy/dt must be greater than 0, when z=0. B/σ must be greater than 1.
46
R0 in this context
R0=B/σ, and it has the same interpretation as before.
47
After the infection rate declines, number of infections stays down at 0. Where is this observed?
In small populations.
48
When does the epidemic return?
When people who were immune start to die, and when births occur, so the susceptible population increases again.
49
Measles in Iceland
The isolated island means the susceptible population would build up, until the pathogen was re-introduced when ships arrived. The more frequently ships reintroduced the pathogem the more frequent the epidemics.
50
Before vaccination:
Generally regular biennial epidemics (with small annual epidemics in-between). (Seen typically in larger, interconnected populations.)
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Vaccine Era:
Much lower incidence, and more irregular epidemics. This can be seen in measles epidemics in England and Wales pre- and post-vaccine development.
52
Why weren't the regular cycles exhibited by measles before vaccination a reflection of seasonal patterns of infection?
These weren't annual cycles.
53
Where does µ operate?
On every compartment.
54
Where do births occur?
Only in the susceptible compartment.
55
What causes the dampened oscillations on an SIR model?
Eevnetually enough susceptible people build up for there to be a second epidemic, but there are still fewer susceptible people, so the second epidemic is smaller.
56
What happens to the dampened oscillations in the absence of any other factors?
It settles into another equilibrium. This equilibrium is different because the proportion infected when there's vaccination is very small, but the proportion immune is very high.
57
Why are these dynamics cyclic?
There's a lag between consumption and resource renewal.
58
Pathogens associated with the SIR lifestyle:
Unstable dynamics.
59
Pathogens associated with the SI lifestyle:
Stable dynamics.
60
Endemic
The infection is present at a baseline level in a particular region.
61
Why might oscillations not appear dampened in real life?
Other factors.
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Examples pathogens with SIR models:
Measles, mumps and rubella.
63
Properties of SIR Model Pathogens
Short infectious period. Lifelong immunity.
64
Examples of SI Model Pathogens:
HIV, Herpesviruses and Syphilis.
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Properties of SI Model Pathogens
Lifelong carriage.
66
In both SI and SIR Models, where does the equilibrium point converge?
At the herd immunity threshold: 1 - 1/R0.
67
Eradiction
You don't have to vaccinate everybody; as long as you as the proportion vaccinated exceeds the herd immunity threshold, you can eradicate the disease. p > 1 - 1/R0.
68
Why have we eradicated smallpox while measles still remains one of the leading causes of childhood mortality worldwide?
Differences in R0. The lower the R0 number, the easier it is to vaccinate enough people to exceed the threshold.
69
There's no vaccination available for…
… malaria, RSV, cytomegalovirus, Ebola virus, HIV and hepatitis C.
70
There are only partially-effective vaccines for…
… influenza and tuberculosis.
71
What do measles and influenza have in common?
Hemagglutinin that they use to bind to cells. Antibody binding sites surround the receptor binding site on hemagglutinin.
72
Measles Hemagglutinin
Has a neutralising antibody epitope in the middle of its receptor binding site. Antibodies are made against the epitope.
73
How is the hemagglutinin in influenza different?
The receptor binding site is somewhat protected by loops that hang over it to stop antibodies from getting into the receptor binding site. These loops are able to change.
74
The 2009 Swine Flu Pandemic
The hemagglutinin was very similar to the in the Spanish flu pandemic of 1918.
75
Consequences of a Pathogen Mutating
Someone who is immune is now susceptible. The pathogen is maing the population more susceptible again.
76
A model with lots of strains within it can exhibit a behaviour seen in flu:
There is a sequential dominance of straisn in each season. You can make a vaccine against that strain in a season.
77
Plasmodium falciparum
There are many different antigens, but the strains are co-circulating instead of sequential.
78
Life History Strategies of Infectious Agents
Impact on their population dynamics and our ability to control them.
79
Success of Vaccines
SIR pathogens have been fairly succesfully vaccinated against. For antigenically diverse and SI pathogens, vaccines haven't yet been made.
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81
Climate and Life on Earth Part 1: Understanding Biodiversity.
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83
Biodiversity:
A property of nature that underpins its resilience and adaptive capacity. Diversity of life from level of genes to ecosystems, and applies to all the interactions between the levels.
84
UN Convention on Biological Diversity:
Variability among living organisms from all sources, including, inter alia, terrestrial, marine and other aquatic ecosystems, and the ecological complexes of which they are part; this inlcudes the diversity within species, between species and of ecosystems.
85
With what other terms is biodiversity conflated?
E.g., nature, wildlife, natural capital etc..
86
Why do we need to define biodiversity properly?
In order to avoid false narratives about biodiversity being bad for people, e.g., elephants arid crops, byt are part of a larger ecosystem that benefits people, avoid reducing biodiversity to just one of its components, enable its measurement, determine its role in ecosystem health, function and services, enable monitoring, and for conservation and restoration.
87
Biodiversity is Multidimensional
Changing variation, abundance and rarity. Changing composition across species, genera and even biomes.
88
Species Richness
Often used as a proxy for biodiversity.
89
Variability within and among components:
Richness: numbers of components. Evenness: equitability of components. Heterogeneity: disparity in the form and function of a component.
90
Components that are often quantified:
Taxonomic or phylogenetic species. Ecological functions.
91
Alpha Diversity
The pool of local species, or naother component.
92
Beta Diversity
The turnover of species among sites.
93
Gamma Diversity
The pool of regional species.
94
Where do latitudinal diversity gradients occur?
In marine, terrestrial and freshwater ecosystems in both hemispheres.
95
How many breeding birds in a hectare plot in the UK, Congo and southeastern Peru?
UK: 30-40. Congo: 240. Southeast Peru: 500 birds. This latitudinal diversity gradient is mirrored in other groups.
96
Elevational Diversity Gradients
Also ubiquitous. For most species, there's a peak at mid-elevation.
97
Some Clades in the Tree of Life
Significantly more diverse than others. Rates of speciation also vary across the tree of life.
98
Fish found in Lake Malawi
Up to 1000/800 species of Lake Malwai Cichlid (partly driven by sexual selection), compared to just 5 Tigerfish species.
99
Heliconid vs. Cethosia Butterflies
Many 100s of specie sof Heliconid butterflies in Central and south America, but many fewer specie sof Cethosia butterflies in southeast Asia, despite their similar life-histories.
100
Right-Skew Hollow Curve
Common pattern observed across many biological groups: most higher taxa contain few subordinate taxa, while a few contain many.
101
What causes this right-skew hollow curve?
Uneven rates of speciation and extinction. Lineage-specific traits and historical contingency are important.
102
The Tropics are both a radle and museum of biodiversity:
They contain both young and old diversity.
103
Older Clades
Don't necessarily have more species than younger clades.
104
Over a 30 million-year timeframe, how many species of funarids, cisticolids and mesites evolved?
300+ species of funarids, but only 100 cisticolids, despite being morphologically similar. Only 3 mesites speciated in this time, though they aren't morphlogically similar.
105
Hypotheses for Geographical Variation in Biodiversity
Area, climate stability, more energy/solar radiation, higher ambient temperatures and biodiversity begets biodiversity. These are all at play, but some player greater roles in speciation in some lineages than others.
106
Area:
Large continents in the Southern Hemisphere mean more space (niches) and opportunities for diversification. Large population with lower extinction rates.
107
Climate Stability:
Stable, predictable resources allow for specialisation, and hence, speciation.
108
More Energy/Solar Radiation:
Higher levels of net primary productivity resulting in more resources and niches, hence more oportunity for speciation.
109
Higher Ambient Temperatures:
Faster rates of evolution due to higher mutation rates and faster physiological processes.
110
Biodiversity begets biodiversity:
More species, more complex species interactions (e.g., host-pathogen, predator-prey), more co-evolution and more speciation. More species create different pressures that lead to speciation.
111
Hypotheses for Phylogenetic Variation in Biodiversity:
Combination of stochastic and determinstic factors. Time (now disproven), life-history traits and biogeographical factors.
112
Time
Once thought to be a factor, but phylogenetic trees have revealed no correlation between the age of the lineage and the number of species.
113
Life-History Traits
Predispose some lineages to radiate, e.g., low dispersal-- some species in the tropics have little reason to disperse, so tend to speciate when barriers form.
114
Biogeographical Factors
Isolate populations from one another, and stop or slow gene flow, allowing the process of divergence and speciation to begin.
115
Deterministic Factors
Lineage-specific properties, e.g., morphology.
116
What happened when the Andes rose?
The entire continent of South America shifted from being tilted towards the Pacific to being tilted towards the Atlantic.
117
South America is the most biodiverse continent. Why might this be the case?
Landscape change driving diversification. Poor dispersal ability of many rainforest species amplifies the effects of biogeography.
118
Why is biodiversity important?
for its cultural value (nature has its own rights), material value and security (it creates a healthy, stable environment).
119
Resilience
Capacity of a system to resist, and recover from, perturbation.
120
What facilitates habitat resilience?
Connectivity and biodiversity.
121
Connectivity:
Allows for migration and range shifts to track moving ecological niches as an adaptive response to climate change.
122
How does biodiversity facilitate resilience?
Species richness safeguards evolutionary potential, diversity (taxonomic, phylogenetic and functional) and functional redundancy. Abundance increases resilience.
123
Up to the saturating point, biodiversity increases…
… the efficiency and stability of ecosystem functions.
124
Different ecosystems have different abilities to recover and different vulnerabilities to disturbances.
Some ecosystems are easily disturbed, but recover quickly, e.g., grasslands. Some ecosystems have high resistance, but recover slowly. These are fine; it's only when there's low resistance, and slow recovery that problems occur.
125
Ecosystem Functions
Resource capture, biomass production, nutrient recycling and decomposition.
126
Annual value of ecosystem services for the global economy:
~US$125 trillion.
127
What did paired, global analyses of naturally-regenerating forests demonstrate?
That they store more carbon, have high water availability, prevent erosion more effectively and harbour more species compared to monocultures.
128
Loss of ecosystem services from 1997 to 2011 due to land use change:
$4.3-20 trillion per year.
129
Economic value of the Amazon:
Generates 20 billion tonnes of rain per day to fuel the agricultural economy of ~US$240 billion in South America.
130
Economic value of pollination:
£690 million in the UK alone. £1.25 billion globally.
131
How many billions of tonnes of carbon does the Amazon rainforest store?
25-300 billion tonnes of carbon. Equivalent to 15-20 years of global greenhouse gas emissions.
132
133
Climate and Life on Earth Part 2: Drivers of and Solutions to Biodiversity Loss.
134
135
Functional Diversity
Range, value and distribution of an organism's traits within an ecosystem that influences its function.
136
What do functional traits include?
Leaf size, root depth, nitrogen fixing ability and hunting strategy.
137
At what levels is biodiversity being lost?
Species-level, population-level and ecosystem-level.
138
Global Rate of Species Extinction
10-100x higher than the average rate over the past 10 million years, and is accelerating.
139
IPBES
Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Like the IPCC, but for biodiversity.
140
Mass Extinction
75% of species or group of species must be lost. This has happened in cycads, and is close in amphibians, but no other groups. We're not at that mass extinction yet.
141
How long do species live on Earth normally?
3-11 million years.
142
Local Extinctions
We don't know what we've lost. There's a lag period as local extinctions can lead to global extinctions.
143
Living Planet Index
Based on over 5000 species. Considers terrestrial vertebrate species. Since the 1970s, 73% decline in vertebrate populations. 85% of freshwater species are in decline.
144
How many species of plants and animals will be at risk of extinction by 2100?
0.5-1 million.
145
Vertebrate Declines Across the World:
North America: -39%. Europe and Central Asia: -35%. Asia and the Pacific: -60%. Africa: -76%. Latin America and the Caribbean: -95%.
146
By what % has land and sea protected areas increased since the 1970s?
600%.
147
The Rio Convention
Yet to make improvements at the global level, but has made improvements at the local level.
148
Ecosystem-Level Biodiversity Loss
Loss of wilderness, and biotic homogenisation.
149
Biodiversity Intactness Index (BII):
Average abundance of originally present species across a broad range of species, relative to the abundance in an undisturbed habitat.
150
What's driving this biodiversity loss?
Changes in land and sea use, direct exploitation of organisms, climate change, pollution and invasive alien species. These all interact.
151
Changes in land and sea use:
Humans have altered 75% of land and 66% of marine environments since pre-industrial times.
152
Direct Exploitation of Organisms:
In 2015, a third of marine stocks were being fished at unsustainable levels.
153
Climate Change
Global warming has already impacted almost half of threatened mammals, and 1/4 of birds.
154
Marine Plastic Pollution
Has increased tenfold since 1980, with an average 300-400 million tons of waste dumped annually into the world's waters.
155
Invasive Alien Species
The numbers of alien species per country have risen by about 70% since 1970.
156
Where does the largest impact on biodiversity come from?
Commodity-derived deforestation in the tropics.
157
Other Changes in Land Use:
Wildfires. Forestry. Shifting agriculture. Urbanisation: 80% of the world's populations are expected to live in cities by 2100.
158
Deforestation in the tropics directly affects biodiversity.
Contributes 13% of total greenhouse gas emissions. 50% of Earth's species live in tropical rainforests. ~9 million hectares of forest are lost each year.
159
Rates of Deforestation in Brazil
Declined by 32% last year.
160
Loss of Agricultural Productivity
Deforestation triggers major shifts in rainfall and increased global temperatures. Thus, there is increased conversion of forest to agriculture to compensate.
161
Teleconnections
Global sky rivers.
162
How does deforestation of rainforests affect water availability?
It has decreased water availability in local cities, e.g., Sao Paolo, but also through teleconnections, it has affected precipitation patterns in Ukraine and Russia.
163
How would complete deforestation of Central Africa affect rainfall globally?
It would cause decline sin rainfall in the US Midwest, the Gulf of Mexico, Ukraine and southern Europe.
164
Largest Drivers of Biodiversity Loss on Land and in the Sea:
Commodity-driven deforestation (land), and industrial fishing (sea).
165
Drivers of Tropical Deforestation
Beef (67% of deforestation)> soy (for animal feed, too) > palm oil > timber > paper products.
166
How much aniaml biomass do humans harvest from the seas each year?
~100 mt.
167
What % of major marine stocks are depleted or over-exploited?
75%.
168
Industrial Fishing
Has the greatest impact. 700,000 reported industrial fishing vessels covering > 55% of the oceans.
169
Global Forest Watch and Global Sea Watch
Working to prevent illegal deforestation and fishing.
170
Last year was the hottest on record.
We may have passed the 1.5°C threshold already, though I sincerely hope not.
171
When the environment changes, organsism either…
… change their behaviour (e.g., their phenology), adapt (e.g., cahnge tehri phenotype), move (e.g., niche-tracking, moving north, or upslope) or go extinct.
172
Issues with Organisms' Abilities to Adapt, Move or Change their Behaviour:
Not all co-dependent species change together, leading to mismatches. Some species cannot track their niches or preferred habitats. The rate of phenotypic change cannot keep pace with the rate of environmental change.
173
Phyto- and Zooplankton Blooms
Mismatch in the Southern Ocean, affecting global circulation.
174
Examples of Changes in Phenology
Since the 1960s, many European and North american bird species have been breeding 8-10 days earlier. Since 1970, 70% of Californian butterfly species have advanced first flight by 24 days.
175
Examples of Range Shifts and Niche Tracking
colonisation of the temperate zone by subtropical flora and fauna. Bird ranges and tree lines are shifting upslope in the Himalayas and the Andes. Since 1972, >50% of European birds, butterflies and dragonflies have shifted ranges 20-240km north.
176
4 Reasons Why Species Go Extinct Due to Climate Change:
1. Nowhere to go (e.g., isolated on mountain tops, habitat fragmentation). 2. Spatial and temporal mismatches, e.g., asynchronies between predators and prey. 3. Species enter the range of a novel pathogen or predator. 4. Rate of environmental change is faster than the rate of evolution.
177
Amphibian ranges are niche-tracking, but…
… moving into the range of a fungal pathogen. Rate of evolution of amphibians needs to be 10,000x faster to keep pace with environmental changes.
178
What % of population declines are driven by climate change alone?
~7%.
179
Coral Reef Bleaching
16% of species in the 1997-98 El Nino event. >30% of the Great Barrier Reef was bleached in the 2016-17 El Nino event.
180
Mountain-Restricted Species
67% of Harlequin frogs are extinct due to climate change.
181
With +1.5°C:
4% of mammals would lsoe half their habitat. 70-90% of coral reefs will vanish.
182
With +2°C:
8% of mammals would lsoe half tehir habitat. 99% of coral reefs would vanish.
183
With +3°C:
41% of mammals would lose half their habitats.
184
Exceeding +1.5°C could trigger multiple climate tipping point, such as…
…Loss of mountain glaciers, collapse of the Greenland ice sheet or die off of low-latitude coral reefs.
185
The Problem of Incrementalsim
There always seems to be a more imemdiate problem, but others are looming behind it.
186
The current economic system si actively investing in its own demise, and needs to be transformed.
From 2018 to 2023, 0.2 trillion US$ were used in funding for 'nature', but 1.69 trillion was used for harmful subsidies (going into oil and gas etc.), and 5 trillion was used for private finance for extraction. Extraction of natural resources, harming the biosphere.
187
Environmental Land Management Schemes
Incentivising farmers to care for ecosystems, e.g., by protecting hedgerows.
188
The Extractive Economic Model
An indirect driver of biodiversity loss.
189
The Crisis of Separation
The disconnect between people in industrialised countries and nature.
190
What can governments do to address indirect drivers?
Decarbonise: incentivise renewables, tax fossil fuels. Scale up conservation and restoration. Stop subsidising fossil fuels and exploitation of land and sea. Tax harm to the biosphere. Take a holistic view of nature into account.
191
What can businesses do to address indirect drivers?
Decarbonise, eliminate deforestation, and other destructive practices from supply chains, and invest in nature and renewables.
192
What can individuals do to address indirect drivers?
Diet change, vote for those who care, spread the word and conduct interdisciplinary research.
193
Rights for Nature
Enshrined in the constitutions of countries such as Bolivia, Ecuador and Ireland.
194
When universal basic income was introduced, what did many communities implement?
Ecosystem restoration.
Biology Term 2
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