Exercises: The origin and evolution of life

Summarize Oparin and Haldane's heterotrophic hypothesis on the origin of life, and explain what the Miller-Urey experiment consisted of, what they obtained, and what it demonstrated.

What are stromatolites and which organisms form them? Explain why they are considered one of the oldest pieces of evidence of life on Earth.

Compare the "primordial soup" hypothesis with the panspermia hypothesis: how they agree, how they differ, and what problem the second leaves unresolved.

Explain what coacervates or protobionts are and what "almost living" properties they show (a membrane, exchange with the environment, growth by incorporation), indicating what they lack to be considered cells.

What is the "RNA world" hypothesis? Explain why RNA is a better candidate than DNA to have been the first molecule of life, drawing on its dual function: storing information and catalyzing reactions.

Distinguish between an autotrophic and a heterotrophic organism, and discuss why it is more plausible that the first living things were heterotrophs (using the organic molecules in the environment) rather than photosynthetic.

Describe what the Earth's primitive atmosphere was like according to the classical hypothesis (no oxygen, with $\text{CO}_2$, water vapor, methane and ammonia) and explain the key difference that separates it from the present-day atmosphere.

List three differences between a prokaryotic and a eukaryotic cell, and identify which features of mitochondria (size, double membrane, their own DNA, ribosomes) reveal their bacterial origin.

The diagram represents the endosymbiotic theory of the origin of eukaryotic cells proposed by Lynn Margulis. Explain what occurs between cells 1 and 2 to give rise to cell 3, and cite three pieces of evidence supporting this theory related to mitochondria and chloroplasts.

Place these milestones in the history of life in chronological order and justify the chosen order: appearance of oxygenic photosynthesis, first prokaryotic cells, Cambrian explosion, first eukaryotic cells, land colonization by plants.

About $2\,400$ million years ago, oxygen began to accumulate in the atmosphere (the Great Oxidation Event). Explain which organisms produced it and describe two consequences of this change for life and for Earth's surface.

The Miller-Urey experiment assumed a highly reducing atmosphere that is considered unlikely today. a) Explain what they assumed and what they obtained anyway. b) Discuss why the experiment is still considered a milestone even if the real atmosphere was different: what principle did it demonstrate? c) Indicate which other settings (hydrothermal vents, space) could have supplied the organic molecules.

Carbonaceous meteorites (chondrites) contain amino acids and other organic molecules. Explain what this finding contributes to the study of the origin of life, how it differs from the panspermia hypothesis, and why it demonstrates that organic chemistry is common in the universe.

What is LUCA, the last universal common ancestor? Explain what characteristics are attributed to it (a prokaryotic cell, genetic code, metabolism) and what molecular evidence — the genetic code being practically identical in all living things — supports that we all descend from it.

Compare a mitochondrion and a chloroplast: size, number of membranes, type of DNA and of ribosomes. Discuss, on the basis of this data, why it is believed that the mitochondrion was incorporated into the eukaryotic cell before the chloroplast (which eukaryotes have mitochondria but no chloroplasts?).

Order these steps toward the first cell and justify the chosen order: appearance of a self-replicating molecule, formation of lipid membranes, synthesis of organic monomers, polymerization, and integration of metabolism, inheritance, and an envelope.

In a Precambrian geological borehole, strata between 2700 and 2100 Ma are analyzed. In the lower levels (2700-2400 Ma), abundant banded iron formations (BIFs) with uraninite and detrital pyrite (minerals unstable in the presence of O2) are recorded, alongside cyanobacterial biosignatures. Around 2200 Ma, BIFs almost disappear and the first continental red beds (rich in Fe³⁺ oxides) emerge, while the fossil record shows a drastic drop in the diversity of anaerobic microfossils.

1. a) Justify why there was a lag of hundreds of millions of years between the appearance of the first oxygenic photosynthetic organisms and the effective oxygenation of the free atmosphere.
2. b) A student states: "Oxygen was a toxic waste product that nearly wiped out the biosphere, but without it, complex eukaryotic organisms would never have been energetically viable." Critically evaluate this statement by comparing the energy balance (ATP yield) and the biochemical adaptations required to cope with oxidative stress.

A hydrothermal simulator replicating the Hadean ocean floor has been designed in the lab: alkaline fluids rich in dissolved H2 (pH between 9.0 and 11.0) emerge through mineral microcavities of iron sulfide (FeS) in contact with an acidic primordial ocean (pH between 5.5 and 6.0) saturated with CO2 and dissolved Fe²⁺.

1. a) Justify how the inorganic microporous structure and the pH difference between fluids abiotically reproduce a mechanism analogous to the proton-motive force and cellular oxidative phosphorylation, prior to the existence of enzymes and complex lipid membranes.
2. b) Compare the energetic feasibility of this scenario with the "primordial soup" hypothesis in surface waters, considering the continuity of energy flux and protection against intense ultraviolet radiation and the Late Heavy Bombardment.
3. c) Predict what would happen to the redox potential and the organic synthesis capacity of this hydrothermal system if the external ocean lost its acidity and reached the same alkaline pH as the emerging fluids.

Analyze the following evolutionary information about mammals and dinosaurs:

• During the Mesozoic (about 140 Ma), mammals coexisted with dinosaurs while maintaining a reduced body size (under 5.0 kg), mostly nocturnal habits, and little varied dental morphology, despite already possessing endothermy and hair.

• Non-avian dinosaurs went extinct at the K-Pg boundary (66 Ma ago). Over the following 15 Ma (Paleocene and Eocene), the fossil record shows a morphological explosion in mammals, with the sudden appearance of flying forms (bats), marine forms (first cetaceans), and large herbivores exceeding 1000 kg.

1. a) Explain this temporal contrast using the concepts of "vacant ecological niche" and "adaptive radiation". Why were the advantageous adaptations of mammals not sufficient on their own to trigger their diversification before the K-Pg boundary?
2. b) A classmate claims: "Catastrophes and mass extinctions are the primary engine that creates new species and accelerates the mutation rate". Reasonably refute this statement, clarifying what the actual biological role of mass extinctions in macroevolution is.
3. c) Reasonably predict which current animal group (for example, flightless birds, rodents, or arthropods) would have a higher probability of undergoing an equivalent adaptive radiation if all large terrestrial mammals disappeared today, and what selective pressures would guide their divergence.

A geological research team analyzes 3800 Ma sedimentary rocks from the Isua supracrustal belt (Greenland). Following the study, they obtain the following data:

1. Microscopic graphite inclusions with an anomalous enrichment of the light carbon isotope ($\delta^{13}\text{C} = -30.5\,\text{‰}$), similar to that produced by inorganic carbon-fixing enzymes compared to the abiotic standard value (close to $0.0\,\text{‰}$).

2. Banded and laminated mineral formations with conical morphology that externally resemble stromatolites, but without discernible fossilized cellular remains.

1. a) Justify why carbon isotope fractionation is considered an indirect biosignature of living metabolism and what limitations it presents compared to finding a direct cellular fossil.
2. b) A press report headlines: "Origin of life 3800 Ma ago conclusively proven thanks to Isua fossils". Refute this headline by explaining what purely abiotic geochemical processes can generate laminated structures or isotopic enrichment, and how their falsifiability is tested.
3. c) Design a proposal of two complementary criteria (mineralogical or molecular) that the team should require from these samples before accepting that they unequivocally reflect the presence of primitive living beings.

To test the two main hypotheses on the origin of prebiotic polymerization (surface tidal pools with wet-dry cycles versus deep submarine hydrothermal vents), a team designs two laboratory simulators:

• Reactor A (Surface): Solution of nucleotides subjected to periodic cycles of hydration and desiccation at 60.0 °C under ultraviolet light (short wavelength, representative of the primitive anoxic atmosphere).

• Reactor B (Deep): Continuous gradient of temperature (from 80.0 °C to 20.0 °C) and pH inside microcapillary channels of pyrite and greigite, in complete darkness and submerged in permanent aqueous solution.

1. a) The formation of the phosphodiester bond between nucleotides is a condensation reaction that is thermodynamically unfavorable in dilute aqueous solution ($\Delta G > 0$). Justify how each of the two reactors attempts to resolve or bypass this chemical problem (the so-called "water paradox").
2. b) Predict which reactor will exhibit greater degradation of monomers by photolysis if no protective compound is added, and argue what selective or destructive role UV radiation may have played in the origin of the genetic code.
3. c) If small RNA oligomers with ribozyme activity are successfully synthesized in Reactor B but are unable to escape the mineral microcapillaries, reason whether this confinement is an advantage or an obstacle for the transition toward the first independent protocells.