Geobiology

Geobiology20: Short questions and report guidelines

Exam components

GEOBIOLOGY20 includes short questions for the basso. Then, there is an oral part that adjusts the vote. The practical part involves a report where you must describe the activities learned during lab lessons. Fill this report before the oral test and send it to Giovanni at least 1 week in advance.

The evolution and mutual influence of lithosphere and biosphere on Earth

What is the structure of our Earth?

The lithosphere is composed of:

• Continental crust: 35 km mean thickness, granitic rocks.
• Oceanic crust: 5-12 km mean thickness, basaltic rocks.
• Upper mantle: More rigid and colder than the deep mantle. The uppermost part of the upper mantle with the crust above makes the lithosphere (up to about 100 km).

The lithosphere is made of numerous plates (7 main) moving at 1-10 cm/year (nail growth rate). The lithosphere is changing during geological time, which explains a lot in the atmosphere, such as volcanic eruptions causing an increase of CO₂.

Under the lithosphere, there is the asthenosphere: between approx. 100 and 400 km deep, capable of slow flow, especially at 100-200 km. Under the asthenosphere, we have the lower mantle.

Plates are always moving, defining the position of continents and oceans through geologic time. The continents' distribution and the variability of sun radiation are the most important controls on the climate, oceanography, and atmospheric phenomena on Earth. All of them influence the biota. Life on Earth has its paths of biological evolution. The biota may influence the physical properties of the planet Earth at different spatial scales.

Formation and early Earth

4.6 Ga the Earth formed because of the birth of the Sun; this led to a gravitational collapse of a part of a molecular cloud, protoplanetary disk of dense gas, and dust rotating around the Sun. The largest particles can form rock and planetesimals, recognized as rocky (asteroids) and iced (comets) planetesimals.

4.6 Ga: During the Hadean, there was no life, a primitive atmosphere (rich in He, H). At 4.5 Ga a protoplanetary impact occurred, and the atmosphere was less molten. Another protoplanetary (Theia) impact happened against the early Earth, creating the Moon. Melting everything together led to the loss of the first atmosphere.

At 4.2 Ga, volcanoes added different types of elements to the atmosphere such as CO₂, NH₃ till no life. By 3.9 Ga, during the Archean, there was still no life, but evidence of meteorite bombing ended with the formation of a new atmosphere with water vapor and sulfides.

Appearance of life

By 3.8 Ga, the first water appeared as the Earth cooled under 100°C. We have the appearance of life and water. Life, as unicellular organisms, appeared in the depths of the oceanic water due to radiation on the surface. Life can be represented into this typical tree: bacteria, archaea, and eucarya. Two elements in green: plants and cyanobacteria, played an important role in life.

Archaea and cyanobacteria

Archaea are primitive unicellular autotrophs. Presently living in extreme environments, they use energy from chemical reactions on inorganic compounds to live, known as chemosynthesis.

The first evidence of life on Earth is stromatolites (rocky bodies, relief created by seafloor from cyanobacteria). We find them alive in Australia in low tides and the Bahamas in subtidal regions. They are photosynthetic, so in the reaction of photosynthesis, the byproduct is oxygen. Layers richer in organic parts alternate with inorganic layers (the dark are organic-rich and the white is sand-rich).

2.5 Ga after oxygen production of photosynthesis, cyanobacteria produced more and more oxygen, but it was not sufficient for the deep sea, which remains anoxic. The O₂ is not enough yet to accumulate in the atmosphere, because it is consumed for the oxidation of CH₄ and metals. Then we have the oxyrevolution: with an increase in atmosphere and water oxygen levels, which oxidizes everything leading to the formation of Banded Iron Formations (BIF): alternate layers of iron.

Proterozoic and Phanerozoic

2.5 Ga marks the end of the Archean (Eon) because we have the oxygen revolution with the formation of the ozone layer caused by UV radiation.

Proterozoic: Ancient life.

Phanerozoic: Evident life.

Origin of eukaryotic cells

2 Ga is the origin of the eukaryotic cell. The appearance of the first unicellular eukaryotes: acritarchs are organic-walled microfossils with a central cavity. This represents the various stages of the life cycle of algae and are similar to dinoflagellates (the ancestral to them).

Fossils and their significance

Fossil (obtained by digging) = a relic, remnant, or representation of an organism or its activity occurring in the form of mineralized bones, shells, etc., or as casts, impressions, and molds, and as frozen preserved organisms. They are useful for:

• Paleoecology: Reconstructing the paleoenvironment of a fossil assemblage (looking for the lost baseline!).
• Biostratigraphy: Using fossils for dating and correlating the rocks.
• Paleobiogeography: The distribution of fossils in the past, in different geological contexts (co-evolution of lithosphere and biosphere).

Evolution of life on Earth

Species concept: The species is the common unit used. It’s named by Linnaeus and the binomial nomenclature of taxa.

In biology, the most common definition of species is that of a group of populations that can reproduce sexually and that is reproductively isolated from other species, having with them only sterile hybrids.

• The species is a reproductive community.
• The species is a natural taxon.
• The species is defined by its own genetic pool (DNA).
• The species is made of individuals genetically and phenetically very similar but not identical (intraspecific variability) e.g. Homo sapiens is the same species but all of us have different characteristics and we look different not to the same species.

In paleontology, the reproductive concept of species cannot be applied, we cannot know if the species we found was reproductive itself. We have the fossilized rest, and they can be only described about morphology and dimension. In fact, paleontologists rely on a morphological species concept: similar individuals belong to the same species. The definition in paleontology: the species is a group of individuals sharing a unique combination of features, that separate them from other groups of individuals, belonging to different species. A paleontologic species is a morphospecies.

Intraspecific variability

How similar are individuals of the same species? Causes of intraspecific variability:

• Sexual dimorphism: Male different from female in dimension, etc. A lot of examples in fossil records, such as ammonoids, focus on the starting point of the spire of the ammonoids. In ostracods, the female has the marsupium containing the eggs and has a different profile from the male one.
• Ontogenetic changes: Along the individual growth and aging, e.g., male and female in children compared to adults, we see the differences. In ammonoids, the diameter of the shell changes during its life. In mollusks, it is the same as the ammonoids, we can see the apex (protoconch). Different kinds of feeding, when young is only protoconch, then becomes benthic. Difference in the ratio and square of the opening. In Brachiopods, the brachidium changes a lot during life.
• Di(poli)morphism of phase: Foraminifers are important, e.g. Nummulites compose the rock predominantly. Two phases one the opposite the other, megalocephalic and microspheric generation.
• Phenotypic variation: Adaptation to physical factors, e.g., coral can adapt their morphology, responding to environmental pressures. Same species but different morphology. There is a hierarchy to follow to define a species fossil.
• Genetic variation: Adaptation to the environment + isolation + selection. Each individual has its unique genetic and morphologic features. Each species (the group of interfecund populations) has a certain degree of genetic and phenotypic variability.

Intrapopulation polymorphism = minor differences in the genome do not reduce interfecundity but support morphological variability. No diagnostic character changes to define 2 different species. The character does not have to be data missing, e.g., the ornamentation of the shell, the presence of the ribs changes in time. The character changes but is continuous.

Statistical methods in paleontology

To define and delimit a morpho-species we need statistics:

• An adequate number of comparable specimens (30-40).
• Only the measurable characters can be considered.
• Only well-preserved specimens can be considered.

Across a population, the character has range variation, and it is impossible to study all the individuals, so we study a part of the population (sample) and generalize the results = statistical inference. The sample must be larger if the variance is large, and we want high confidence. Practically, 30 observations are the minimum for descriptive statistics.

The basic is to measure one character, this can change across the sample. The variability of a measurable morphological feature of a species may be represented with a distribution curve. For example, the number of the ribs, we built a histogram by the variation of the number of the ribs. A histogram is used for continuous distributions (any value within the interval). Weight and height are examples of continuous data distributions. For non-continuous character, we use the bar graph, used for discontinuous distributions (e.g., the occurrence of a species in the coeval outcrops A-D of different sites). Unlike the histogram, the bars are drawn separately from one another.

Once we have our database, we can have different indices: a measure of central tendency is a value that represents a typical or central element of a data set. Most important indices: mode, mean, median. We can express this data using a graphic solution to indicate our statistics (cumulative curve). The dispersion of the values in a series of measures on the sample is indicated by the standard deviation. It describes the distribution of the data: variability of a measure. The variability of a statistical value (a percentage, a mean) calculated on the sample is indicated by the standard error. It describes the uncertainty of the estimate: variability of a statistical value.

The level of confidence in a confidence interval is the % probability that the calculated statistical value will contain the parameter if we repeat the observations. The level of confidence is denoted in %. The narrower the width of the confidence interval, the lower is the error of the estimate it contains.

Why do we do statistics? The same genus can have different characters in the species. Some characters are typical of a species, and statistics help us to recognize a species. Our statistics is simple: univariate (one character) and bivariate (2 characters).

Independent variables: The color of the eye of a man and the height of his boss at work—no point in associating independent variables. Covariant variables: E.g., age and height of children. One changes the other. They are correlated. They may be represented by a regression line. The result can be a straight line or a curve. Curves can become straight lines by logarithmic transformation. We can get the regression line, the best line represents all the sample plotted.

Binomial nomenclature

Hierarchical system of classification, Linnaeus (1758). The species is the only natural taxon. The species is identified by the name of the genus followed by the specific epithet. Binomials are normally in italics or underlined in texts. To be precise, always indicate the author of the species (who described it first).

Homotypic synonyms: A species has two names (only one is valid), based on the same holotype (what is characteristic to define a species = physical representation of what a species is). This is set in a museum to keep stability in nomenclature. Several authors describe the same species with different names in ancestral times because they were far away from each other.

Heterotypic synonyms: A species has two names (only one is valid), each one based on its holotype. Homonym: Two different species have the same name. Sometimes a species has not only a holotype but also paratypes and others. The author selects one specimen that best represents the characteristics of the new species = holotype. All specimens are considered syntypes in old age, now we have holotype + paratype.

The Locus typicus describes the locality where the fossils are found. Describe the derivation nomini: why you chose this name instead of others.

Imagine we are the authors revising the name of one species. No holotype describes it, so we have to select the holotype, this is no more called holotype but lectotype from the collection. The other specimen is a paralectotype. Imagine no original materials are left, but description of locus typicus exists, so we go there and get new material to enforce the name, this is the topotype. We may have no indication of location, we can provide a neotype, just relying on the original description.

In zoology, each desinence of super specific taxa describes subfamily, family, superfamily, order, and class. The epithet is concordant with the genus in Latin (male, female, neutral). It can derive from:

• Morphology: Trigonia costata
• Locality: Epitonium algerianum
• Dedicated to a person: Astarte montagui

Biomineralization

The process by which organisms convert ions in solution into solid minerals. Cell systems are proteins in salt solution, enclosed within lipid membranes. We can have 2 transport: diffusion through the lipid bilayer and facilitated diffusion without energy. Salt concentration and composition are different inside and outside cells. Osmotic steady state by active ionic transport across membranes:

• Mg²⁺ accumulates in cells, Ca²⁺ expelled (mostly).
• PO₄⁼ and CO₃⁼ are cell buffers.

How can form crystal? Precipitation of a crystal from a solution occurs when free energy of the precipitate is lower than that of the solution. At the end, due to low energy, small clusters are formed and dissolved until we reach the critical size of nucleation. It is important to preserve the organism, and some molecules can concentrate in some parts, giving an idea of the condition.

Common minerals

Carbonate, phosphate, and silica are common minerals in extant organisms; they are available, moderately soluble, and nontoxic. CaCO₃ has 2 different polymorphs:

• Aragonite
• Calcite

Major (common) processes:

• Membrane transport of ions (formation of supersaturated solutions).
• Proteins and polysaccharides as a matrix for crystal formation.
• Enclosing of a space to enhance reactions (compartmentalization).
• Inside the compartment, new crystal(s) reach a particular size becoming a skeleton unit, with species-specific morphology (i.e., coccoliths).
• Silica is amorphous (no regularly repeated geometric units).
• Microbial systems: the internal environment of the cells is modified to induce mineral deposition.
• Metazoans: more complex processes of biomineralization, under biological control.

The active transport protein uses energy (ATP); if it loses phosphate, we lose energy in ADP. Calcium is toxic to the organism, producing calcium phosphate.

Organic matrix

Any organized organic surface that acts as a mediator of mineralization:

• Different composition depending on taxonomy.
• Anions group on the matrix, and make Ca⁺⁺ concentrate: supersaturation leads to nucleation.
• Matrix proteins can favor or inhibit one polymorph or one crystal face (shape and orientation!).
• Insoluble matrix may be covered by soluble matrix.

Phanerozoic and the importance of biomineralization

In the first billion years, there was no calcification, so no mineralized hard parts. At the beginning of the Phanerozoic, biomineralization appeared, essential for organism preservation.

Soda Ocean Hypothesis (SOH): The Precambrian Ocean was alkaline. Total alkalinity (TA) is the measure of water's ability to neutralize acids. Provides stability against pH fluctuations. Evidence of SOH: elemental mass balances, thermodynamic and kinetic arguments, analogy to modern soda lakes: pH > 10.5, alkalinities > 150 meq/l, widespread Precambrian stromatolites, and cherts peptide bonds are more stable in alkaline than in acidic environments.

The Precambrian ocean had total alkalinity > Ca+Mg and a high supersaturation of carbonate minerals (saturation index=SI about 1). The soda ocean was lost by subduction of seawater and replaced by a NaCl-dominated ocean toward the end of the Precambrian. Over time, the volatile acids dropped pH to about 8, and a NaCl ocean was formed. Meanwhile, the O₂ level rose by photosynthesis, and CO₂ decreased, favoring carbonate minerals production.

Aware of the change from a soda ocean to a halite ocean. 2 Ga marks the first appearance of cyanobacteria, increasing O₂ and much later the colonization of the planet.

Phosphate is crucial for metabolism and energy-trapping reactions (ADP-ATP). Presently 0.5-20 mM within cells. Seawater and body fluids have Ca 10 mM. Ca-phosphate would form in cells: not soluble! To avoid Ca poisoning within cells, extrusion of Ca from cell membranes evolved (Ca-binding proteins; membrane Ca-pump). Hard parts (jaws, teeth, and skeletal protections) evolved under the pressure of increasing competition by evolving organisms.

Important calcified organisms

One of the most important calcified organisms are coccolithophorids, with each single element. Foraminifers are composed of layers of calcite. Proton pumping to inside to upside the cell. During calcification of a new calcitic layer (CL) on a primary organic sheet (POS), the protective envelope (PE) separates the growing calcite surface from the surrounding seawater. The reduced pH in the foraminifer shifts the inorganic carbon speciation, thereby increasing pCO₂ directly outside the PE. The large gradient in pCO₂ across the PE results in diffusion of CO₂ into the site of calcification (SOC). Once inside, the CO₂ reacts to form CO₃^-- due to the high pH, sustaining CaCO₃ precipitation by reacting with the Ca⁺⁺. The incorporation of Mg follows temperature, so in warmer parts of the planet, forams incorporate a major quantity of Mg, making it an important proxy.

Corals produce aragonites. It's important to know what happened inside. Two epithelia separated by mesoglea, a glycoprotein secretion, it’s always flexible. The organic matrix of the skeleton is released by the calicoblastic epithelial cells into the subepithelial space where crystals form and grow within the mat.