Student Participation (Fall 2022)
Contents
Student Participation (Fall 2022)#
Students will work in pairs to produce summaries of each class meeting. These summaries should list the main topics discussed and emphasized ideas/examples during the respective lecture. Students are encouraged to be as detailed as possible without being overly verbose. The summaries should be submitted as a pull request before the next class meeting. See BlazeView announcement for some simplified instructions.
Aug 15#
Introductions
Dr. Quarles told us about his research and how it connects to Astrobiology through climate variations.
He studies how a planet’s orbit evolves with two stars, where the changes in the planet’s orbit can affect the climate through obliquity variations. Obliquity is a way of describing a planet’s spin axis, where it can precess (like a top) due to the perturbations from the companion star. This precession can be responsible for large changes in obliquity. Current models suggest that Mars may have undergone a climate catastrophe in part due to its obliquity variations, while the Earth’s climate has been regulated by the Moon.
Syllabus
The class syllabus provides us with a roadmap for the course. The course is structured for the students to learn through class participation/activities and homework. Student learning will be assessed through exams, a term paper, and an in-class presentation.
Course website
Class notes are provided on the course website, which includes web urls (for jargon) and video explanations of some topics.
Aug 17 (Avery, St. John, & Speldrick)#
1.1 A Brief History of the Planetary Sciences
The study of Astronomy existed long before there was even a name for it. Many ancient civilizations even knew of the existance of planets and wrote about them. These civilizations also used the planets and stars to help them navigate. As civilization advanced, new technological advances allowed us to see and learn more about space. They allowed us to see a different view of the Moon (Luna 3). They also allowed us to find planets outside our own solar system (Kepler and TESS), and helped put to rest some theories about Earth itself (Earth’s water didn’t come from comets).
All planets were visited by spacecraft during the cold war.
Planets derived from the Greek word πλανήτης(planetes, which is the term for wandering stars). Many ancient civilizations would use a written language to describe many events that would take place within the celestial world.
The rings of Saturn are not primodial. The planet had a possible collision with a previous moon that became what is now known as its famous rings.
Analysis of comet G7P revealed that Earth’s water did not come from foreign bodies, but was present at formation. This was done by comparing the Deuterium/Hydrogen ratio (D/H ratio). The D/H ratio of comets matches water on Mars, but differs considerably from water present on Earth, suggesting different origins.
Astronomers research exoplanets and their ability to formulate the possibility of there to be life on other planets. These requisistions happen to be based on their mass, how close they are to their star, their orbits, radii, and golden zones.
Onto biology, they study the aspect of how life can survive. For example would be the life that is able to survive in the depths of the ocean off of thermonuclear energy collection.
EM Spectroscopy allows us to study the atmosphere and geology of most celestial bodies
\(M_\oplus\) represents units of Earth mass; \(R_\oplus\) represents units of Earth radius
\(M_\odot\) represents units of Solar mass; \(R_\odot\) represents units of Solar radius
AU represents astronomical units, the length of the semimajor axis of a massless particle whose orbital period is 1 year around a Solar-mass star
1.2 Inventory of the Solar System
Solar System
The solar system is dominated by a single objection, which is our Sun. The sun is fat and uses its gravity to hold its 4.571 billion year old debris in its orbit.
The Sun contains almost all of our solar system’s mass. The Sun is a plasma ball powered by fusion. Compared to the Sun, the planets are debris.
Giant Planets
The two major giant planets (Saturn and Jupiter), mainly consist of gases (hydrogen and helium).
Jupiter is 318 Earth masses (\(9.54 \times 10^{-4}\) Solar masses) while Saturn is 1/3 of Jupiter’s mass.
The astrophysical ices are Water (\(\rm H_2O\)), Ammonia (\(\rm NH_3\)), and Methane (\(\rm CH_4\)).
Uranus is 14 Earth masses and Neptune is 17 Earth masses. Uranus and Neptune are mainly composed of water, ammonia, and methane ices.
Neptune and Uranus are ice giants. Brrr! Is it cold over there, am I right? Pretty sure it rains diamonds on Neptune or something.
Terrestrial Planets
They are made up of silicates and many chemicals.
Earth and Venus have the two largest with defined atmospheres.
Earth and Venus are the largest two and are similar in size. Mars is smaller than Earth. Mercury is very tiny compared to the others.
Earth, Mars, and Mercury have an internally generated magnetic field.
Mercury has the thinnest atmosphere, Venus has the thickest.
Mercury has an atmosphere by definition, although it is essentially just a thin layer of surface particles kicked up by solar winds.
Minor Planets and Comets
The Kuiper belt consists of a thick disk of small bodies beyond the orbit of Neptune. These bodies are composed of a mixture of ice and rock, where the two largest members are Eris and Pluto. A minor planet include asteroids, as well as distant minor planets.
Kuiper belt objects, like Pluto and Eris, are mixtures of rock and ice, and have eccentric orbits. They are so far away that we can only observe them at perihelion. The alignment of orbits in the outer solar system suggest that many of these objects are orbiting an unknown body beyond Neptune that may be as large as 5 Earth masses.
The Kuiper belt is a thick disk of small bodies, it is mainly composed of rock and ice. Eris and Pluto are the largest of the bodies in the Kuiper belt. The objects in the Kuiper belt can only be observed at their perihelion due to faintness.
Pluto and Neptune have a crossing orbit, but never collide.
Comets are ice-rich objects that shed mass when subjected to solar heating. Comets may have formed near the giant planet region initially, were transported and stored in the Oort Cloud, Kuiper Belt, or the scattered disk. Comets are ice-rich objects that shed mass when subjected to solar heat. Comets are ice rich objects that can originate from the Asteroid belt or the Kuiper belt.
Satellite and Rings Systems
Mercury and Venus are the only two planets in the solar system without natural satellites.
All gas giants have rings, Jupiters rings are faint and spread out. This is primarily due to Jupiters large and numerous moons. Saturn has the most pronounced rings.
All major satellites (except Triton) orbit in the direction of the host planet’s rotation (i.e. prograde).
Venus and Uranus are the only two planets that move in retrograde.
Each of the giant planets have rings!
Heliosphere
The planetary orbits that lie within the region of space containing the Sun’s magnetic fields and ionized gas. The solar wind consists of plasma.
This is the region the Sun’s solar winds act on.
The area it merges with the Interstellar medium is the heliopause. Voyager 1 and 2 have gone beyond this region.
The Interstellar medium is mostly composed of \(\rm H\) and \(\rm He\).
1.3 What is a Planet?
Planet: A celestial body that orbits the Sun, has a sufficient mass to assume a nearly round shapeshape through its self-gravity, and has cleared its orbital neighborhood of similar sized-bodies.
Dwarf Planet: A celestial body that orbits the Sun, has sufficient mass to assume a (nearly round) shape through its self-gravity, has not cleared its orbital neighborhood of similar sized-bodies, and is not a satellite. Dwarf planets are objects that fit the definition of a planet but have not clearied the orbital neighborhood.
Star: A self-sustaining (proton-proton chain) fusion is sufficient for thermal pressure to balance gravity.
Stellar remnant: no more fusion (dead star)
Brown dwarf: substantial deuterium (proton + neutron) fusion, where more than of the object’s original deuterium inventory is destroyed by fusion.
Planet: negligible fusion, with a precise mass limit depending on the initial composition. It can orbit one (or more) stars, a stellar remnant, or no stars at all.
Aug 22 (Bostic & Knox)#
Today, we learned about Planetary Properties, what makes a planet a planet, and how do we detect and find these things
1.4 Planetary Properties
Orbit: A planet’s orbit follows along an elliptical path. The distance of a planet from the Sun is a line segment that connects the planets with the Sun. The planet sweeps out an area at a constant rate (i.e., equal area in equal time). The planetary period is proportional to the its semimajor axis (\(P^2 \propto a^3\)). These are Kepler’s Laws. A planet’s orbit can be defined using 6 orbital elements (\(a\), \(e\), \(i\), \(\omega\), \(\Omega\), \(f\)). Two of the angles can be combined to make varpi (\(\varpi = \omega + \Omega\)), where the difference between the angles is used when in retrograde. The orbit can also be specified in Cartesian coordinates and velocities relative to the Sun at any given time (epoch). Inclination is measured relative to Earth’s orbital plane.
Mass: A planet’s mass is deduced by the gravitational force of nearby bodies, which can include the orbits of moons. Some planets (e.g., Neptune) have been deduced through gravitational perturbations. Some other methods of determining the planetary mass include: spacecraft tracking, spiral density waves (e.g., in Saturn’s rings), and nongravitational forces.
Size: A planet’s size includes its angular diameter, which requires an estimate of the distance of the planet using parallax. Other ways to determine a planet’s size are occultation (using the Moon), radar, photometric observations (e.g., exoplanets), and spacecraft (landers and orbiters). Planets are nearly round, but asteroids and comets come in different shapes.
Rotation: A planet’s rotation includes its rotation period (or spin frequency) and axial tilt (or obliquity) as a vector quantity. The rotation can occur in either a prograde or retrograde (i.e., backwards) direction depending on the whether the axial tilt is less than or greater than \(90^\circ\), respectively. The rotation of an object can be measured using surface markings, magnetic fields, doppler shifts, and photometric observations.
Shape: Most celestial bodies are nearly spherical in shape due to self-gravity and rotation. However, small bodies can be quite oddly shaped (e.g., Mars’ moon Phobos). Some ways that we can determine the shape of an object is through direct imaging, chord lengths, radar echoes, and lightcurves (e.g., asteroids).
Temperature: The equilibrium temperature can be determined using the incoming short wave radiation and outgoing longwave radiation through energy balance.
Magnetic Field: Magnetic fields are created by moving charges. These charges are typically within the interior of a planet and move due to convection.
Surface composition: Most of the major planets (and Titan) are surrounded by atmospheres. The surface composition is determined through direct imaging and reflectivity measurements.
Interior: The planetary interiors are not directly accessible, but information can be derived from variations in the gravitational field and the rotation.
1.5 Formation of the Solar System
Stars form from molecular cloud cores, which are the coldest and densest parts of the interstellar medium. As stars are forming, they can acquire a disk of material that acts to distribute angular momentum. Planets form within the protoplanetary disk from either planetary embryos (Moon-Mars mass) or cores (\({\sim}8\ M_\oplus\)). The terrestrial planets went through a much longer accretion process as compared to the gas giants.
Aug 24 (Dubose, Rios, & Freeman)#
2.1 Overview of Dynamics
Orbital Dynamics –> study of planetary bodies.
Gravitational interactions determine how a planet’s distance from the Sun varies over time and thus how much solar radiation the planet receives.
Rotation rates determine the length of the day.
Obliquity influences the temperature differences between the pole and equator, as well as seasonal variations.
Tidal heating (from tidal distortions) produces extensive volcanism on bodies such as Jupiter’s moon Io.
Development
The study of planetary motions goes back to old age through observational studies and kinematic modeling. It begins with Tycho Brache and Johannes Kepler.
Newton showed that the motion of two bodies, resulting from their mutual attraction is described by two conic sections: ellipses for bound orbits and parabolas and hyperbolas for unbound trajectories.
The first law of Kepler’s planetary motion: All planets move along elliptical paths with the Sun at one focus.
The second law of Kepler’s planetary motion: A line connecting any given planet and the Sun sweeps out an area [Equation] at a constant rate.
The third law of planetary motion: The square of a planet’s orbital period [Equation] about the Sun (in years) is equal to the cube of its semimajor axis [Equation] (In AU).
Newton’s first law of motion and gravity: A body remains at rest or in uniform motion unless a force is exerted upon it. It is also called the law of inertia and is a restatement of Galileo Galilei’s work from the 16th century
Newton’s second law of motion and gravity: When a body is acted upon by a force, the time rate of change of its momentum equals the force.
Newton’s third law of motion and gravity: If a body [Equation] that exerts a force on another body [Equation], there is a force of equal magnitude and opposite direction exerted by body [Equation] onto body [Equation].
Newton’s universal law of gravity: Everybody in the universe exerts an attractive force on every other body that is directly proportional to the product of their masses and the inverse square of the distance between them.
2.2 Connections Between Physics, Astrophysics, and Planetary Science
A planet is composed of 10^50 molecules, so large that is impossible to model planets on a molecule-by-molecule bases.
The radial structure of planets and stars is determined by a balance of the inward gravitational force and the resistance to collapse provided by a pressure gradient.
Sun is the dominant body in our solar system. Without the Sun, there would not be life in Earth’s surface.
The properties of a planetary system depend on the composition of individual bodies.
2.3 Thermodynamics
Analysis of difference systems of matter.
When the latent heat of transformation is absorbed, can be induced by melting, boiling, sublimation, or condensation.
2.3.1 Laws of Thermodynamics
Closed systems: mass transfer to and from the external environment are not permitted.
Open systems: allows mass and energy to freely flow between the system and its environment.
Closed systems are in equilibrium, where this is known as the zeroth law of thermodynamics.
The thermodynamic state of a system refers to the system’s physical properties (density, pressure, and temperature.)
2.3.2 Barometric Law and Hydrostatic Equilibrium
The large-scale structure of a planetary body or star is governed by a balance between gravity and pressure= hydrostatic equilibrium.
An equation of state (EOS) describes the relationship between two or more state variables (e.g., pressure, density, and temperature of a substance).
If the body is highly compressible the body may be centrally condensed.
The Earth is differentiated (i.e., not homogeneous), and the increase in density towards the center compensates for our overestimate in gravity.
Aug 29 (Avery, St. John, & Speldrick)#
2.4 Stellar Properties and Lifetimes
Planets and stars are intimately related through stellar gravitational interactions and energy transfers.
2.4.1 Virial Theorem
Virial Theorem provides a pwerful tool for the analysis of many different types of astrophysical problems that include kenetic energy and gravitational potential energy.
\(E_G\) is potential gravitational energy and \(E_K\) is kinetic energy.
\(m\) is a particle of mass at rest an infinite disatance from a massive body of mass \(M\) and \(r\) is a distance from \(M\).
2.4.2 Luminosity
Stars are huge balls of gas and radiate energy from their surface and produce energy by thermonuclear energy in their cores.
Structure of Stars is determined by hydrostatic equilibrium (balance between gravity and pressure)
Quasi-equilibrium state maintained due to the cooling of the star’s interior causing it to contract and heat up which causes addtional heating and increases the internal pressure.
During a star’s main sequence phase Hydrogen fuses into Helium to maintain the pressure balance.
High mass stars or more luminous than low mass stars because greater pressure and temperature are required to balance their larger amounts of gravity.
Luminosity \(L\) is roughly proporional to a star’s mass \(M\) \begin{split}L_\star \approx \begin{cases} 0.23M_\star^{2.3}, \qquad &(M_\star < 0.43M_\odot) \[5pt] M_\star^4, \qquad &(0.43 \leq M_\star \leq 2 M_\odot) \[5pt] 1.4M_\star^{3.5}. \qquad &(M_\star > 2M_\odot) \end{cases}\end{split}
Low mass stars are more common than high mass stars because they age slower.
High mass stars can be seen from much farther away.
Pauli exclusion principle: particles can not occupy the same quantum state simultaneously.
Stars that have a lot of electron degeneracy can not attain necessary temperatures for fusion to produce elements more massive than carbon or oxygen. They evolve into white dwarfs.
In very massive stars fusion builds until iron is created. At this point no more energy can be liberated, and the star can not maintain its equilibrium. Its core collapses releases massive amounts of gravitaional energy. This produes a supernova explosion.
2.4.3 Stellar Size
Nuclear reations keep the core temperature of low mass stars at around 3 x 106 K.
Fusion rate is roughly T10.
Thermal energy and gravitaion energy are in balance at equilibrium.
More massive stars are larger than low mass stars, and can radiate more energy due to hotter temperatures.
Hydrostatic structure of low density stars is determined through balance of gravity and thermal pressure.
High density hydrostatic structure is determined by electron degeneracy pressure. - Bodies supported primarily by degeneracy pressure are called compact objects.
R decreases with increased mass. The most massive cool brown dwarfs are expected to have slightly smaller radii than their lower mass brethren.
2.5 Size and Densities of Massive Planets
The electromagnetic repulsion of electrons plays a role in the internal pressure of a planet, influencing the radius of the planet as: $\(R \propto M^{\frac{1}{3}}\)$
The Coulomb pressure and quantum degeneracy pressure result in Juptier-like radii for giant planets and low mass stars
Polytrope equations can describe fluid bodies, with \(K\) being the polytrope constant and \(n\) being the polytrope index, example being: $\(P=K\rho^\frac{n+1}{n}\)$
Considering \(n=1\), and \(P=K\rho^2\), then radius \(r\) can be expressed as: $\(R=(\frac{6K}{G})^{1/4}\)$
Density can be expressed as: $\(\rho = \rho_c (\frac{\text{sin}C_Kr}{C_Kr})\)$
Where
The maximum radius for cold self-gravitating spheres is 82600 km for a pure hydrogen planet, given by:
2.6 Nucleosynthesis
The strong nuclear force overcomes the Coulomb repulsion of protons, and is responsible for holding together nuclei. The mass of a nucleus is less than the mass of the individual particles, where the missing mass contributes to the stability of the particle in the form of binding energy, given by: $\(\Delta E=\Delta Mc^2\)$
Higher binding energy ultimately means a more stable nucleus, and this energy can be released on fusing or splitting the nucleus.
Formation of nuclei is called nucleosynthesis. Nuclei were created at the beginning of the universe, and are created in stellar environments. They can also be created from high energy nuclei from supernovae, called spallation, and from radioactive decay.
2.6.1 Primordial Nucleosynthesis
After the Big Bang, the universe primarily consisted of protons and neutrons. As the universe spread out, it lacked the energy density necessary to form heavier nuclei, and formed mostly hydrogen and helium, with trace amounts of lithium, beryllium and boron.
2.6.2 Stellar Nucleosynthesis
Larger nuclei require the temperature and pressure of a stellar core to form. As young stars radiate their heat away, they contract and increase the pressure and density of their core until thermonuclear fusion occurs. Equilibrium is maintained through fusion by expanding if too much heat is generated, and by contracting if not enough heat is generated
Aug 31 (Bostic & Knox)#
Sept 7 (Dubose, Rios, & Freeman)#
3.2 Radiation
3.2.1 Photons and Energy levels in an atom When we talk about radiation it is when photons transport energy. The radiation efficiency depends critically on the (photon) emission and absorption properties of the atmospheric gas.
\(E=h\nu\)
\(E=pc\)
Planck’s constant \(h\), the speed of light \(c\), and the frequency of light \(\nu\).
Emission and absorption of photons by atoms or molecules occur by a change in the energy state.
Electrons are in orbits, where the angular momentum is quantized, or depending on the principal quantum number, which is formed by Plank’s constant.
The radius of the lowest energy state (n=1) for the hydrogen atom is called the Bohr radius
The transitions between a given state (1,2,3) and higher levels in an hydrogen atom are named after the scientist that discovered the series within an emission spectrum.
These information tells us about the hydrogen we have in the atmosphere, in our case, Earth, we do not have hydrogen in the atmosphere.
Fact: Jupiter is mostly hydrogen.
The Lyman series corresponds to transitions from n=1, while the Balmer and Paschen series correspond to transitions from n=2 and n=3, respectively.
3.2.2 Spectroscopy
We can have a source in this a blackbody which we distinguish three different types of spectrum representing Kirchoff’s laws of radiation.
The interior of the star is the source, and the atmosphere is the clouds.
Continuous spectrum: no gaps
Light composing a continuous spectrum passes through a cool, low-density gas, the result will be an absorption spectrum
A low-density gas excited to emit light will do so at specific wavelengths and this produces an emission spectrum
Sunlight itself displays a large number of absorption lines (Fraunhofer absorption spectrum) absorb part of the sunlight coming from the deeper, hotter layers.
Example: Uranus and Neptune are greenish-blue because methane gas (within their atmospheres) absorbs in the red part of the visible spectrum, so the sunlight reflected back into space is primarily bluish.
Lines formed in a planet’s stratosphere are visible as emission profiles. The cause of this difference is due to the optical depth τν, which is defined as the integral of the mass extinction coefficient αν along the line of sight s.
Large objects, decrease in the intensity of light can be measured that changes with distance from the center of the object to the limb (i.e., edge) called limb darkening. The inverse effect (i.e., a gradual brightening) is called limb brightening.
The frequency of the object’s emission and absorption lines is Doppler shifted Δν depending on the velocity vr of the object along the line of sight.
A positive Doppler shift occurs if the object moves towards the observer (blue shifted) and negative if the object moves away from the observer (red shifted).
In an atmosphere, the motion of atoms and molecules occur in all directions, which broadens the line profile more than the natural line profile. This is called Doppler broadening.
Pressure broadened profiles tend to be broader than Doppler broadened profiles.
3.2.3 Radiative Energy Transport
The equations of radiative energy transport govern the temperature-pressure profile when the absorption and re-emission of photons dominates.
3.2.4 Radiative Equilibrium
Energy transport in a planet’s stratosphere is usually dominated by radiation. If the total flux is independent of height, the atmosphere is in radiative equilibrium
3.3 Greenhouse Effect
Greenhouse effect: A planet’s surface temperature can be substantially raised above its equilibrium temperature, if the planet has an optically thick atmosphere at infrared wavelengths.
Net effect: the atmospheric (and surface) temperature increases until an equilibrium is reached between the input from solar energy and the planetary flux escaping into space
The calculation for a temperature profile of an actual planetary atmosphere must include the energy absorbed from incident light and the emitted thermal flux.
Almost 25% of the Sun’s radiation that intercepts the top of Earth’s atmosphere is absorbed by the atmosphere.
50% of the Sun’s radiation is absorbed at the surface.
Almost 33% of the Sun’s radiation is reflected back to space without being absorbed.
3.3.1 Quantitative Results
The greenhouse effect is particularly strong on Venus, where the surface temperature reaches 733K.
Anti-greenhouse effect: cooling produced by small haze particles in the stratosphere that block short-wavelength sunlight, but are transparent to long-wavelength thermal radiation
Solid-state greenhouse effect: Icy material allows sunlight to penetrate several centimeters (or more) below the surface but is mostly opaque to re-radiated thermal IR emission. The subsurface region can become significantly warmer than the equilibrium temperature would indicate.
3.3.2 Thermal Profile Derived
Diffusion equation: an expression for a time-dependent flow through space.
The general equation of radiative transport can be integrated over a sphere by using the relations between the specific radiative flux and mean intensity
3.3.3 Greenhouse Effect Derived
Two-stream approximation: single layer atmosphere that is transparent to sunlight, opaque to longer wavelengths, emits according to LTE, does not scatter, and is gray.
3.4 Thermal Structure
Volcanoes and geyser activity may modify the atmosphere
Chemical reactions in an atmosphere alter its composition, which leads to changes in its opacity and affects thermal structure.
Clouds form in the troposphere. The temperature decreases with altitude
In the stratosphere, above the troposphere, the temperature increases with altitude
At higher altitudes, the mesosphere is characterized by temperature decreasing with altitude.
The outermost part of the atmosphere is the exosphere.
3.4.1 Sources and Transport of Energy
Solar radiation heats planetary atmospheres through absorption of photons
Re-radiation of sunlight by a planet’s surface or atmospheric molecules, dust particles, or cloud droplets occurs primarily at IR wavelengths
3.4.2 Energy Transport
There are three distinct mechanisms to transport energy: conduction, convection, and radiation
Conduction is important in the very upper part of the thermosphere, in the exosphere, and very near the surface (if one exists). It equalizes the temperature distribution
Convection is important in the troposphere. The formation of clouds reduces the temperature gradient through the heat of condensation.
Radiation is important when the absorption and re-emission of photons (i.e., radiation) is the most efficient.
Which process is most efficient depends on the temperature gradient
3.4.2 Observed thermal profiles
Effective temperatures of Jupiter, Saturn and Neptune is larger than the equilibrium temperature.
At optical and IR wavelengths, the radiative part of an optically thick atmosphere is probed.
3.4.2.1 Earth
The average temperature just above Earth’s surface is 288K.
It is above the equilibrium value (33K above due to greenhouse effect)
In Earth’s thermosphere, the temperature increases with altitude
3.4.2.2 Venus
Venus has a very strong greenhouse effect (in the current epoch) primarily due to its massive CO2 atmosphere.
The night time and the day time is very hot.
3.4.2.3 Mars
The low temperature can be explained by the efficiency of CO2 as a cooling agent.
Mars and Venus lack a stratosphere.
3.4.2.4 Titan
At the surface the temperature and pressure were measured at 93.65 K and 1.467 bar
3.4.2.5 Gas Planets
Jupiter, Saturn, and Neptune emit roughly twice as much energy as they receive from the Sun.
It is not known why Uranus’ internal heat sources is so different from the other three giant planets.
Sept 12 Class canceled#
Sept 14 (Avery, St. John & Speldrick)#
Sept 19 Exam I#
Sept 26 (Rios & Bostic)#
4.3.1 Natural Kinds
Definitions do not supply good answers to question about the identity of natural kinds, or categories carved out by nature. It is important to astrobiology because it seems likely that life is a natural kind term and represents an objective fact about the natural world.
“What is water?” by defining the natural kind term ‘water.’ The term ‘water’ could be defined by reference to its sensible properties
The identification of water with \(H_2O\) explains why liquids can resemble water and not be water because their molecular composition is more than \(H_2O\) alone.
The claim that water is H2O began as a testable empirical conjecture, and it is now considered so well confirmed that most scientists characterize it as a fact.
4.1.4 What is Life?
If life is a natural kind, then attempts to define life are fundamentally misguided.
We could define ‘life’ to mean whatever cyanobacteria, hyperthermophilic archaeobacteria, amoeba, mushrooms, palm trees, sea turtles, elephants, humans, and everything else that is alive (on Earth or elsewhere) has in common.
We want theories that settle our dilemmas in classification by explaining puzzle cases:
Why things that are alive sometimes lack features that we associate with life?
Why things that are non-living sometimes have features that we associate with life?
No scientific theory can be conclusive, but someday we may have a well-confirmed, adequately general theory of life that will allow us to formulate a theoretical identity statement (e.g., “water is \(H_2O\)”) providing a scientifically satisfying answer to the question “What is life?”
4.1.4.1 Dreams of a General Theory of life
To formulate a convincing theoretical identity statement for life, we need a general theory of living systems.
Darwinian evolution then explains how this common biochemical framework yielded such an amazing diversity of life.
Many definitions of life cite sensible properties of terrestrial life, such as metabolism, reproduction, complex hierarchical structure, and self-regulation. But defining life in terms of sensible properties is analogous to defining water as being wet, transparent, tasteless, etc. Reference to sensible properties for water is unable to exclude things that are not water and to include everything that is water
4.1.4.2 How to search for Extraterresrial Life
Treat the features that we currently use as tentative criteria for life.
The purpose of using tentative criteria is not to definitively settle the issue of whether something is alive, but rather to focus attention on possible candidates (i.e., physical systems whose status as living or non-living is genuinely unclear).
The basic idea behind our strategy for searching for extraterrestrial life is to employ empirically well-founded (albeit provisional) criteria that increase the probability of recognizing extraterrestrial life while minimizing the chances of being misled by inadequate definitions.
The important point is to include the potential boundaries of our current concept of life. It is only in this way that we can move beyond our geocentric ideas and recognize genuinely weird extraterrestrial life, should we be fortunate enough to encounter it.
4.5.1 Requirements and Limits for Life in the Context of Exoplanets 4.1.5.1 Limits to Life
to determine the requirements for life
to determine the extreme environments in which adapted organisms (i.e., extremophiles) can survive.
The requirements for life on Earth broadly include four items: (1) energy, (2) carbon, (3) liquid water, and (4) various other elements. Methane-producing microbes use the reaction of \(CO_2\) with \(H_2\) to produce \(CH_4\).
Carbon has the dominant role as the backbone molecule for Earth life and is widespread in the Solar System. However, carbon may not be that useful as an indicator because the Earth is significantly depleted in carbon compared with the outer Solar System.
Life on Earth uses a vast array of the elements available at the surface. However this does not prove that these elements are absolute requirements for carbon-based life in general. The elements \(N\), \(S\), and \(P\) are probably the leading candidates for the status of required elements.
4.1.5.2 Strategy for Exoplanets
The most important parameter for Earth-like life is the presence of liquid water, which directly depends on pressure and temperature. Temperature is key because of its influence on liquid water and it can be directly estimated from orbital and climate models of exoplanetary systems.
Temperature, Cold limit: Many organisms can grow and reproduce at temperatures well below the freezing point of pure water because their intracellular material contains salts and other solutes that lower the freezing point of the solution.
Temperature, Hot limit: As water is heated (and maintained as a liquid under pressure), the dielectric constant and the polarity of the liquid decreases sharply.
Water, Dry limit: On worlds where the temperature is within the appropriate range (for Earth-like life), life may be limited by the availability of water (i.e., low water activity), where we only have to look at Mars for an example.
Energy: Energy for life can come from chemical redox couples generated by geothermal processes or light from the central star. Geothermal flux can arise from (i) the planet cooling off from its gravitational heat of formation, (ii) decay of long-lived radioactive elements, or (iii) tidal heating for a close-orbiting world or moon.
UV and Radiation: Complex lifeforms (e.g., humans) are sensitive to radiation but the does that can be tolerated by many microorganisms is astonishingly high.
Sept 28 (Dubose & Speldrick)#
4.2 Evolution: a Defining Feature of Life
4.2.1. From Lamarck to Darwin to the Central Dogma
The basic notion of evolution is that inherited changes in populations of organisms result in expressed differences over time.
The important underlying fact of evolution is that all organism share a common ancestor.
We see this in the universal nature of the genetic code and in the unity of biochemistry:
All organisms share the same biochemical tools to translate the universal information code from genes to proteins,
All proteins are composed of the same twenty essential amino acids,
All organisms derive energy from metabolic, catalytic, and biosynthetic processes from the same high energy organic compounds (e.g., adenosine triphosphate (ATP)).
Darwin’s On the Origin of Species describes his theory of evolution using evidence that included an ancient Earth, which geologists at the time (in 1859) believed to be in the millions of years.
The key to his evolutionary theory was that inherited characteristics of organisms can change through time and that these changes occurred gradually and without discontinuities.
Jean-Baptiste Lamarck recognized (in 1809) a similar principle of evolution and offered an explanation generally referred to as inheritance of acquired characters. His theory however was wrong while Darwin’s was correct.
Darwin’s theory about evolution was correct while Lamarck’s was wrong. One of Darwin’s major contributions was his explanation of how and why organisms change over time and how they acquire characteristics useful for living in different environments. (Natural Selection)
Natural selection is based on the idea of the struggle for existence (i.e., survival of the fittest) in populations where there are more individuals of each species than can survive.
Mendelian genetics established that phenotypes are transmitted from one generation to another following statistical principles and that these phenotypes reside in simple heritable “characters.”
The nature of these heritable characters were unknown to Mendel but their location was confined to chromosomes by 1910 and then to DNA as the genetic material by Hershey & Chase (1952).
This immediately led to the discovery by Watson & Crick (1953) of the double-helix structure of DNA.
The steps leading from DNA to a specific protein are referred to as the central dogma:
A DNA gene is transcribed to make messenger RNA (mRNA)
Followed by translation of mRNA into a protein
The exceptions to the central dogma are those genes that specify not proteins, but instead the various classes of RNA that are involved in both transcription and translation (e.g., ribosomal RNA (rRna) and transfer RNA (tRNA)).
4.2.2 Evolution at the Molecular Level
The discovery by Watson and Crick opened the doors to studies of evolution at the molecular level and helped develop classification schemes that allow for the evolutionary comparisons of groups of extant organisms.
Most functional RNA molecules have secondary structure that are associated with their function.
Mutations that change the secondary structure of RNA molecules will frequently render them inactive.
A central concept in evolutionary theory is that a gene coding for a characteristic is subject to mutation (i.e., change) in a random fashion, which in some cases can lead to variability in that characteristic in the next generation.
Mutations come about due to mistakes made during DNA replication, or through external factors such as ionizing radiation or toxic chemicals.
Most mutations have little or no effect on the protein product of the gene or the function of the RNA.
Those that involve deletions or insertions can result in structural changes in the transcribed protein or render structures inactive int the ribosomal RNA.
The most lethal mutations are those that damage the genes involved in DNA replication, transcription of DNA into mRNA, or translation of mRNA into a protein.
Changing environmental conditions can negatively affect growth and survival (e.g., inducing stresses), which can result in the death of an organism depending on the degree and kind of stress.
All extant organisms have a set of conserved genes for repairing mutations or proteins affected by environmental stresses.
Stress genes greatly reduce the number of deleterious mutations, while they are not 100% effective.
The same genes can also targe other specific genes for an increased mutation rate under stress conditions, which are called stress-directed adaptive mutations.
In evolution, adaptation means more than simply being well suited to the environment, where it also involves (in any generation) the selection of one particular genetic change (over many other possibilities) that results in maximum reproductive success.
Two kinds of evolutionary change are recognized:
Microevolution results in changes at the species level and accounts for the short term variability observed in populations.
Macroevolution involves the more substantial changes that over long time result in the development of a new hierarchy, or higher taxa (e.g., genera, families, orders, etc.).
It affects the genotypes of individuals within populations and also involves microevolution.
It is also invoked as the mechanism that results in the gradual formation of novel complex structures that involve multiple genes.
One group of genes called HOX genes accounts for the incredibly high diversity found in animal body plans.
The three principal anatomical plans for wings exemplified in birds, bats, and pterosaurs were also though to be products of convergent evolution.
The bird wing developed from the entire arm.
The bat wing developed from a hand.
The pterosaur wing from a single finger.
The new combination of evolution with developmental biology is called Evo-Devo and is revolutionizing our understanding of macroevolution and embryology.
Evo-Devo studies indicate that this sudden emergence of highly diverse animal forms was due to the evolution of key regulatory HOX genes in the common ancestor to all Cambrian animals.
Computer algorithms have been developed that are inspired by Darwinian evolution and are aptly named genetic algorithms due to how they can modify populations of data over generations.
These algorithms mimic the process of natural selection by employing a fitness function, which evaluates data within the domain and modifies it based on a set of rules.
Oct 3 (Knox & Freeman)#
4.3 Planetary Requirements for Life
4.3.1 Biochemical cycles
CO and Silicate weathering comes out and the weathering enters the ocean and release CO2 into the air. The idea is to move carbon around to substain life. The ocean make carbonic acid.
Nitrogen is a limiting nutrient for life on Earth, despite its abundance in the atmosphere.
N2+2CO2 2NO+2CO is the reaction for Nitrogen fixation.
Nitrogen fixation enters the soil and plants take out nitrogen from the atmosphere and put it into the soilso that the plants can grow and the roots can be healthy.
Anoxic-environment without molecular oxygen
Anaerobic-organisms can survive without molecular oxygen
4.3.2 Gravitational and Magnetic fields
Too much or too little gravity can shpae how life works
Magnetic fields help by blocking out charged particles from the Sun’s radiation
4.3.3 Can moonless planets host life?
Magnetic fields have a minor effect on life
The magnetic field plays a protective role by stopping charged particles from eroding the atmosphere or reaching the surface.
4.3.4 Giant planets for life
Unlikely to have life on the planet because of high pressure on any surfaces.
Giant planets may harbor habitable moons, where moons of giant planets seems to have a similiar potential for habitability as do terrestial planets of the same mass and distance from their star.
Tidal interactions between large moons and giant planets are likely to be much more substantial than between stars and planets within the respective habitable zones due to the close proximity of moons to their host planets.
The length of the day on such a moon would be slowed to approximately the moon’s orbital period about its planet.
4.4 How life affects Planets
Forests, for example, cover large fractions of continental crust. It changes the albedo, soil composition, and local climate.
Microorganisms also change the soil composition through metabolism.
The second most abundant gas is oxygen.
Oxygenic photosynthesis bacteria produce O2 as a waste product, while methanogenic organisms release CH4.
Fossils fuels were produced from partially decayed planets and many now extinct organisms.
Oct 5 (Avery & St. John)#
Oct 12 (Bostic & Speldrick)#
5.1.3.3 Organized at the Molecular Level: Proteins, Nucleic Acids, and Lipids
Proteins
form gateways in membranes
act as highways for electrons
functions as bioweapons and poisons
forms scaffolding for cells
Amino Acids are what proteins are composed of.
folds to hold more data
folds can determine the function of a protein
Nucleic Acids
store hereditary information and reproduce themselves
transported to ribosome by transfer RNA
Bacterial cells contain over 20,000 ribosomes.
RNA and DNA bases
adenine
cytosine
guanine
uracil (RNA)/ thymine (DNA)
Lipids
form boundary separating cells and holds them in
Amphiphiles: hydrophilic and hydrophobic parts
open and close mechanisms allow access to cells
5.1.4 Central Ideas About the Origin of Life
5.1.4.1 Thermodynamics and Probability
Second law: spontaneous processes in a closed system are characterized by the conversion of order to disorder
Living systems create disorder globally even though they are orderly locally.
Living systems “pay” for their existence by creating more disorder elsewhere in the system.
“No such thing as a free lunch.”
if you create order locally, disorder is created by existing
Spontaneous Generation
originally thought to be origin of life, found to be improbable
5.1.4.2 Separate Problems: Origin of Life vs. Origin of Organics
original distinction of life and non-life was organic and inorganic
organic contained carbon
Wöhler found a substance that would be considered organic even though it wasn’t living because it contained carbon.
We now know that mixtures of simple organic chemicals are produced in many locations off this planet:
carbonaceous chondrites
interstellar dust clouds
cometary tails
the atmosphere of Titan
One such object landed on Earth, The Murchison meteorite.
more than 70 amino acids were found on it, but only 8 of the ones needed for Earth life.
5.1.4.3. Possibilities for Reduced Organics
Primitive atmosphere of Earth was Hydrogen rich
Adding a lot of energy to this expected to give rise to “prebiotic soup”
Current assumption suggests primary atmosphere of Hydrogen was lost and replaced due to outgassing.
Some organics can be supplied by comets and meteorites, but only a small amount.
Central problem for the origin of life remains.
5.1.5. Replicator-first Theories
The double helix convinced many in the field that nucleic acids were at the center of life.
5.1.5.1. Advantages of the Replicator Theory
To explain the origin of life, one only had to account for the origin of the first replicator.
Spiegelman and his group used a virus called \(\rm Q\beta\) to find the first replicator.
\(\rm Q\beta\) uses RNA rather than DNA as its genetic material.
With the appropriate enzyme and four necessary building blocks, RNA can be replicated in a test tube.
Synthesized RNA can act as a template for producing more RNA.
They created over 70 RNA generations.
5.1.5.2. A Problem with a Solution
Problem: naked replicators could carry information, but were unable to carry out tasks that are performed by proteins today
Nucleic acids and proteins seem necessary for the conduct of life, but hard to account for these substances on early Earth
Solution: RNA could carry out some functions done by proteins
RNA World is the term used to describe where RNA did all the key functions of life before proteins took over
5.1.5.3. Just a Problem
Problem: RNA is too complicated to form spontaneously. Nucleotides were presumed to be available on Earth, but evidence hasn’t supported this.
Ribose formation: Ribose is the sugar backbone of RNA. Plausible source on early Earth is believed to be a reaction with formaldehyde. Ribose has a short time until it decomposes.
Adenine formation: Adenine can be made only if the concentration of HCN remains around 0.1 Molarity (M).
Combination of adenine and ribose to form adenosine: If ribose and adenine formed separately, then complex reactions could bring them together in order to react. The product wasn’t the one used in RNA.
5.1.6. Pre-RNA World
Two candidate structures were synthesized to prepare analogs of RNA and DNA: p-RNA and TNA
p-RNA (pyranosyl-RNA): retained the sugar ribose, but replaces the five-membered ring in RNA with a six-member (pyranosyl) ring which is preferred by free ribose in a solution
TNA (threose nucleic acid): contains only 4 carbons, and is possibly more accessible to abiotic synthesis than ribose. A TNA strand will cross-pair with both DNA & RNA.
PNA (peptidyl nucleic acid): a third example of RNA precursors. PNA contains 2 alternating units with no chiral center. It can form double helices with itself and be cross-paired with DNA and RNA.
5.1.7. Metabolism-first Theories
Metabolism First theories believe that small molecules the processes of catalysis, reproduction, and information storage using a cycle of chemical reactions, and the theories provide alternatives for how the small molecules carried out the life processes.
Information is stored in the mixture: a set of molecules would carry their own hereditary information. This type of informational system is called a “compositional genome”
Reproduction is carried out by splitting the compartment: A primitive replicator-free cell could reproduce by acquiring a duplicate of its contents from the environment, if a list isn’t present.
Energy-driven catalytic cycles perform the essential processes of the cell: Possible important functions are the synthesis of improved catalysts and membrane components that permit improved interaction with the energy supply.
The Lipid World: Scenario includes a self-assembling lipid micelle that would catalyze necessary reactions by itself
The Iron-Sulfur World: The evolving system is separated from the environment by being stuck to the surface of a positively charged mineral like pyrite. The formation of pyrites provide a source
Oct 17 (Rios & Knox)#
5.2. The Earliest Records of Life on Earth
5.2.1 Problems with the record
Ancient rocks are rare: Almost all potential information about the first half of Earth’s history is contained in geological materials. Such rocks have been mostly hidden or destroyed by geological processes (e.g., erosion, burial, or subduction).
Metamorphism and/or deformation damages the information content of rocks: Radioactive heating was greater on the Archean Earth (2.5-4 Gyr ago), and tectonic activity may have been more intense, with post-depositional modification of rocks correspondingly more likely. Temperatures above \(300^∘C\) are significantly destructive to most chemical biosignatures. Therefore rare, ancient rocks are even more rare to contain contain astrobiologically important information.
Surviving rocks are located in unfortunate places: Some rocks are situated where prolonged weathering under subtropical climates has transformed most surface rocks into varieties of soil. Others have endured glaciation over the past million years which has covered them with till, shattered them by frost action, swamped them with lakes, or encouraged the overgrowth lichens and mosses.
Not all rock were formed in settings likely to yield evidence of life: Sedimentary rock are the only ones from which paleobiological data can be readily obtained. For the early Earth, these are commonly shales, cherts, banded iron formations, and carbonate rocks. The primordial geological record mainly consists of granites, basalts, and other highly metamorphosed and deformed materials.
Very few well-preserved remnants of the early Earth have not yet been studied systematically: The geological features of the rocks and their environments must be understood before paleobiological and paleo-environmental interpretation can be deduced. Determining whether or not a specimen is of biological origin (i.e., biogenicity) is contentious for many putatively primordial fossils because early organisms are expected to be morphologically simple, chemically unsophisticated, and environmentally benign.
5.2.2. Types of Evidence
5.2.2.1. Microfossils
Microfossils are the preserved remains of microbial organisms, which are exclusively organic-walled prokaryotes on the early Earth. These micron-sized lifeforms are only evident in the second half of Earth’s geological record. The oldest suspected microfossils were found in the Nuvvuagittuq Supracrustal Belt in Québec and appear in rocks dated to 4.28-3.75 Ga (Papineau et al. (2022)). Discoveries made in ancient rocks typically carry a great deal of controversy, where the sample for Canada is no exception.
Microbial fossils are generally only preserved where lithification (entombment in rock) was almost instantaneous upon death, the host sediment is extremely fine in grain size, and the mineralizing material is hostile to microbial activity. The two main rock types that satisfy these requirements are chert and shale.
Cherts readily precipitated in evaporative carbonate environments during the Proterozoic and Archean before silica-shelled organisms had evolved and thereby lowered dissolved silica concentrations in the oceans to levels far below saturation.
Shales are widespread in Archean terrains, but are generally recrystallized or sheared along bedding planes to the great detriment of fine-scale fossil preservation.
Biogenicity (whether a presumed microfossil is actually biogenic): arises as a problem because of the extreme morphological simplicity of prokaryotic organisms and their likely remains. The best way of discriminating fossilized simple lifeforms from non-life is to find evidence of past biological behavior that is not explicable in terms of physical or chemical processes (e.g., varying orientations with respect to environmental gradients or indications of reproduction).
Syngenicity(whether a presumed microfossil has an ancient origin): arises as a problem becaus of the long and complex geological history even of the best preserved Archean rock. This provides many potential opportunities for younger biological contaminants to infiltrate.
The only convincing Archean microfossils (found in South Africa) are assemblages of ellipsoids. (0.2−2.5 μm in diameter), spheroids (1.5−20μm in diameter), tubular filaments (0.5−3μmin diameter), and interwoven mats of tubular filaments (10−30μm in diameter). They are composed of replacive iron oxides (kerogen) that has similar isotopic values to younger biogenic carbon.
5.2.2.2. Stromatolites
Stromatolites are laminated sedimentary structures accreted as a result of microbial growth, movement, or metabolism. Their shapes vary, but they often show a predominance of convex-upward flexures forming domes or columns, although some conical forms show the converse. The constructing microbes accrete sediment by three distinct processes.
Trapping occurs when erect microbial filaments baffle passing water currents, causing entrained sediment to be deposited, just as a carpet traps dirt.
Binding happens when passively deposited sediment is caught up in and overgrown by a microbial mat, either by lodging in irregularities in the mat or getting stuck in the extracellular mucilage secreted by the microbes.
Precipitation results from microbial photosynthesis removing \(CO_2\) from the surrounding water, causing calcium carbonate to be deposited as the equilibrium of the following reaction is forced towards the right side because of product depletion
5.2.2.3. Carbon Isotopes
In isotopic chemofossils, particularly the carbon isotope ratios of sedimentary rocks. Autotrophic metabolisms that use \(CO_2\) for manufacturing cellular carbon compounds preferentially incorporate the light stable isotope of carbon \(12_C\) over the heavy \(13_C\) into their synthesized organic matter.
On Modern Earth, organic carbon has a carbon isotopic value (called \(δ^13C_org\)) that averages around -22‰ (i.e., depleted in \(13_C\) by 22 parts per thousand relative to an arbitrary standard), where carbonate has a δ13Ccarb of about 0‰ and the entire Earth is near -6‰.
When extrapolating back to more ancient rocks, one must consider a few complicating factors.
Older rocks tend to be metamorphosed, which contain a low ΔC that is indistinguishable from non-biologic fractionation. \(13C_org\) can shift to heavier values at lower metamorphic grades becaus of loss of light hydrocarbons. Isotopically light hydrocarbons can migrate into ancient sedimentary rock and become solidified (i.e., contamination). Metasomatism (i.e., chemical alteration of the rock) and metamorphism can introduce secondary carbonate or graphite into ancient rocks by precipitation from or reaction with migrating fluids rich in dissolved carbonic species.
5.2.2.4. Sulfur Isotopes
Some microbial metabolic processes also fractionate the stable isotopes of sulfur, \(32_S\) and \(34_S\).
The fractionation is preserved in the geologic record when the metabolic product hydrogen sulfide reacts with dissolved ferrous ion during early diagenesis to form sedimentary pyrite.
However, evidence ot the isotopic composition of seawater sulfate is only rarely preserved in rocks, principally in evaporitic sulfate minerals (e.g., gypsum and anhydrite), or in trace quantities of carbonate minerals.
5.2.2.5. Nitrogen Isotopes
Nitrogen is an essential nutrient for all living things, as it is a key constituent of the amino acids of proteins and the bases of nucleic acids. It has two stable isotopes: \(14_N\) and \(15_N\) , and predominantly resides in a single reservoir, the atmosphere, as \(N_2\) gas.
5.2.2.6. Molecular Biomarkers
In mature sedimentary rocks, the functional groups are removed and multiple bonds are broken, but their carbon skeleton is intact and clearly indicates their parent biomolecule. At high temperatures, the abundance and range of hydrocarbon molecules decreases markedly because long chains break down into methane. But it is now clear that hydrocarbon biomarkers can also be used to inform us about life’s early diversity.
Oct 19 (Dubose & St. John)#
Oct 24 (Avery & Freeman)#
Oct 26 (Bostic & St. John)#
6.1: Evolution of Metabolism and Early Microbial Communities
The metabolism process is the hallmark of all living organisms.
Catabolic: reactions that generate energy for the organism
Anabolic: reactions used for synthesis of cell material
Metabolism ranges: the use of various inorganic chemicals, several forms of photosynthesis, metabolism of hundreds of organic compounds
6.1.1. The Setting: Conditions on Early Earth
The evolution of metabolic processes were influenced by physical and chemical conditions on early Earth.
Physical conditions were influenced by an instability in the environment (ex. Impact of an asteroid)
Chemical conditions were influenced by a relative absence of nutrients that are present today (ex. ph balance being too high or too low)
First metabolisms were carried out anaerobically due to the lack of free oxygen
6.1.2. Evidence for the Nature of Early Metabolisms
The evidence comes from three main sources: biomarkers, phylogenetic evidence, and the geochemical records.
Biomarkers: Hopanoids are found in the cell membranes of the bacterial group cyanobacteria. The presence of hopanoids have been used to date evolution back to 2.5 Ga and supports the view that the first oxygenic photosynthetic organisms were cyanobacteria.
Geochemical records: Used in establishing evidence for certain types of metabolic processes. Primary production (when CO2 is taken up and the carbon is incorporated into organic matter) is indicated to be an early metabolic event on Earth due to evidence from geochemical records.
Phylogenetic evidence: used to determine which bacterial groups were involved in early metabolism.
Two important issues: the discernible details regarding the major groups of microorganisms are inadequate, so which organisms that were the earliest is still questions, and horizontal gene transfer
6.1.3. Contemporary Metabolisms
The essential metabolic features of modern day organisms are studied in order to understand how metabolism evolved.
6.1.3.1. Anabolism
Anabolism: one of the major parts of metabolism; responsible for the building of new cell material for growth and reproduction
Heterotrophs: synthesize cell material from organic molecules that are present in the environment
Autotrophs: make organic molecules from carbon dioxide in a process called carbon dioxide fixation; primary producers that provide the entire biosphere with organic material
6.1.3.2. Catabolism
Catabolism: destructive metabolism
Catabolic Pathways: generate energy needed for anabolism
Lithotrophs: “eat” hydrogen, sulfur, ammonia, and other foods
Phototrophs: harvest the energy of light
6.1.3.3. Oxidation, reduction, and electron flow
Catabolism follows the principles of oxidation and reduction.
Respiration: oxidation corresponds to “eating” as reduction corresponds to “breathing”; energy is generated when the organism oxidizes the electron donor, while reducing the electron receptor
6.1.3.4. Respiration, photosynthesis, and fermentation
Respiration, photosynthesis, and fermentation are the three forms of catabolism.
Respiration: most straightforward because separate substances are used as the electron donor and acceptor
Photosynethsis: take advantage of the the chlorophyll, which functions as an electron acceptor and an effective electron donor
Fermentation: an electron-donating substrate is oxidized and the electron acceptor is an internal metabolic immediate
6.1.3.5. ATP and the proton-motive force
Adenosine triphosphate (ATP): energy currency of biology; contains phosphoanhydride bonds that yield energy upon hydrolysis (breakdown through combination of water)
ATP generation is simplest in fermentation due to ATP being generated directly by reactions that are a part of a metabolic intermediate
In respiration and photosynthesis, ATP is generated in a two stage process: the flow of electrons through a membrane-bound electron transport chain crates a potential between the interior and exterior of the cell, protons then move across the potential because of the electromotive force and gradient in pH (the movement is called the proton-motive force), energy supplied by the proton-motive force is then used to make ATP
The process is called electron transport phosphorylation or oxidative phosphorylation.
6.1.3.6. Energy yields of catabolism
All catabolic mechanisms lead to the generation of ATP.
Gibbs free energy: quantity used by chemists to evaluate the energy yield of a reaction
A large negative G indicates high yield of energy, but a positive G signifies energy consumption
The G depends on the relative electrical potential of the electron donors and acceptors.
Oxygenic photosynthesis: reverse of aerobic respiration
Lactic acid fermentation: (ATP = 2) has a low ATP yield and G = -196kJ
Oct 31 (Rios & Avery)#
6.1.4. Early Metabolic Mechanisms
Metabolism today is complex and diverse. One of our tenets is that life, and metabolism, began simpler and more uniform.
Oparin originally hypothesized that the first metabolisms were not photosynthetic, where organisms obtained organic carbon from their surroundings rather than synthesizing it photosynthetically from carbon dioxide (i.e., heterotrophic).
A simple type of catabolism is the Stickland reaction that occurs in certain bacteria and involves the fermentation of amino acid pairs. In this reaction, only two amino acids are needed and very few enzymes are required for catabolism and generation of ATP.
The hypothesis that heterotrophic metabolism arose first ignores the importance of primary production (i.e., the production of organic material either by chemosynthesis or photosynthesis). Heterotrophic organisms require preformed organic material.
6.1.5.Evolution of Methanogenesis and Acetogensis
6.1.5.1. Today and on the early Earth
Methanogens and acetogens partly share analogous metabolic pathways, although not phylogenetically related. Methanogens and acetogens are both anaerobes that specialize in metabolism using one-carbon intermediates. Hydrogen is a common electron donor and carbon dioxide a common electron acceptor.
Analogs of the early Earth may exist today:
Microbial communities in the Earth’s subsurface are apparently dominated by methanogens that obtain hydrogen from reduced minerals in rock.
Deep basalt aquifers, hot springs, and submarine hydrothermal vents are examples of sites where microbial ecosystems may be supported by hydrogen of geological origin. 6.1.5.2. Metabolic simplicity and the acetyl CoA pathway
It is reasonable to assume that the earliest organisms were also the simplest. Frequent bombardment of the early Earth might have limited the time available for complexity ot evolve. From this standpoint, methanogenesis and acetogenesis are appealing as the earliest metabolisms.
reduction of carbon dioxide to a methyl (\(CH_3\)) group 6.1.5.3. A prebiotic precursor for acetyl COA pathway
Further support for the ancient nature of the acetyl \(CoA\) pathway comes from evidence that the crucial reaction could have occurred prebiotically. Günther Wächtershäuser proposed the theory that metabolism evolved from prebiotic chemistry
The enzyme that catalyzes the reaction in present-day organisms also contains a nickel-iron-sulfur center. A core step in the metabolism of methanogens and acetogens may have derived from a prebiotic chemical reaction.
6.1.5.4. Hydrogen oxidation and the proton-motive force
Another significant feature of the methanogenic and acetogenic metabolism is the use of \(H_2\) as the catabolic electron donor. The electron transport chain of many organism is a complex multi-component assembly that moves proteins from inside to the outside of cells as electrons flow from one electron carrier to another.
The use of hydrogen offers the possibility of a simpler mechanism of a simpler mechanism in which a proton-motive force is generated without the transport of protons. The products of hydrogen oxidation are simply protons and electrons.
This simple mechanism requiring only an extracellular hydrogen-oxidizing enzyme (hydrogenase) and a membrane-bound electron carrier (e.g., iron-sulfur protein) has not yet actually been demonstrated in the methanogens or acetogens.
6.1.6. Evolution of Photosynthesis
The evolution of photosynthesis greatly enhanced the capability of the planet to carry out primary production. organisms have evolved to make efficient use of light energy, which has always been available and abundant on the surface fo the planet.
Photosynthesis has been found in Bacteria and Eukarya. A remarkable variety of photosynthetic bacterial groups exists. Within the Bacteria, five of the major phyla contain photosynthetic members: Protobacteria, Fimicutes, Chorobi, Choroflexi, and Cyanobacteria.
The availability of suitable substrates is not a constraint because they were all available, as was light. The main constraint has to do with complexity. To generate a proton-motive force photosynthetically requires the addition of chlorophyll, as well as a relatively complex electron transport chain involving the transport of protons across the membrane.
The time of cyanobacterial emergence has been dated to 2.1−2.5 Ga on the basis of protein sequences, which is consistent with the geochemical estimate for the era of oxygenation of Earth’s atmosphere and oceans (i.e., from the banded iron formations).
The innovation of oxygenic photosynthesis began a remarkable evolutionary progression, culminating in the development of complex animal and planet species. The development of an oxygen-rich atmosphere prepared the biosphere for the emergence of higher life forms. Only by burning reduced carbon with oxygen (via an electron transport chain) could sufficient energy be released to fuel large multicellular organisms.
6.1.7. Aerobic Metabolism
Aerobic metabolism is the culmination of metabolic evolution on Earth. This was made possible due to the superior energy yield from using oxygen as an electron acceptor. The microbial world expanded along with multicellular organisms.
The innovations in the electron transport chain that came with photosynthesis allowed aerobes to take advantage of this new source of energy. Indeed, many of the same components of the electron transport chain that evolved for photosynthesis are used in aerobic respiration.
6.1.8. Earth’s Earliest Communities
For most of Earth’s history it was the planet of the microbes. The land would be mostly barren of visible life. Only in shallow freshwater and intertidal marine basins would there be visible accumulation of life, in the form of microbial mat communities. Microbial mats are macroscopically visible microbial ecosystems in which microbes build communities that in may ways are analogous to rain forests.
The most impressive mat communities occur in extreme environments (compared to conditions for multicellular life), since significant biomass accumulation can only occur in the absence of grazing.
The fossil record suggests that mats were once widely distributed on early Earth. The decline of extensive microbial mat systems in the rock record is generally attributed tot he emergence of multicellular grazers and water planets that ultimate forced them to a much more limited habitat range. The most conspicuous and often enigmatic vestiges of the early microbial biosphere and microbial mats are stromatolites.
Today there is increasing recognition that microorganisms are extremely promiscuous. Horizontal gene transfer is not restricted to closely related organisms. Exchange within and between domains is now well documented and increasingly recognized to be a major force in shaping metabolic innovation. We speculate that the high density and close associations among microorganisms in microbial mat provided a superb environment for genetic exchange between populations.
Nov 2 (Knox & Speldrick)#
6.2.1 Extremophiles and the Limits of Life
Extreme conditions that can limit growth or kill most organisms can be the “Garden of Eden” conditions for other organisms.
Extremes that kill most organisms:
high and low temperature
high and low \(pH\)
high salt concentration
toxic metals
toxic organic chemical compounds
high levels of radiation
There are organisms in all three domains of life that can survive these extremes.
There are very few natural environments on Earth were life is not present.
Life is the rule rather than the exception
Intracellular biosynthesis, metabolism, and macromolecular structures in extremophiles are adapted to function under extremes in pressure and temperature.
Organisms capable of growing in extremes of \(pH\) , salinity, irradiation, and in the presence of high levels of toxic metals are adapted to either
maintain intracellular conditions that are typical for non-extremophiles, or
compensate for the extreme condition
Some exeptions:
Acidophiles
Halophilic Archaea
There are some combinations of extremes That prevent cells from growing.
no organisms have been able to survive high salt concentrations at the upper and lower limits of temperature and \(pH\).
Some combinations of extreme conditions have a synergistic effect on the growth or survival of cells.
6.2.2 Water, Desiccation, and Life in Non-aqueous Solvents
The absence of available water and extremes of temperature are the only single variables known to prevent growth and survival of organisms.
There are some combinations of physical and chemical conditions for which no known organisms have been found to grow.
environments that have both high salt and
low temperatures ( sea-ice inclusions) or,
high temperatures (brine pools beneath the Red and Mediterranean Seas)
Earth Life can be described as a web of aqueous chemical reactions.
Desiccation (removal of water) causes DNA to break, lipids to undergo permanent changes and proteins to crystallize, denature, and undergo condensation reactions.
Organisms that grow or survive in dry environments or in solutions with low water activity match their internal water activity with that of their surroundings.
An issue regarding water and astrobiology is the degree with which water is required for carbon-based life. This also brings up the issue of if an organic solvent could replace water as the primary solvent.
These issues are important in assessing whether or not carbon-based life could
exist in liquid methane or ethane pools on Titan
survive the harsh physical conditions that would be encountered during transport from one planet to another
survive long periods in completely desiccated state and still retain the ability to grow if water is eventually introduced.
The degree of antimicrobial action of a solvent depends on its hydrophobicity. The more hydrophobic a solvent, the more readily it can accumulate in cellular membranes.
There are some bacteria that can tolerate relatively high concentrations.
Two mechanisms have been identified for solvent tolerance:
membranes that limit the diffusion of solvents into the cell
specialized mechanisms that remove any solvents that have diffused into the cell
Another key issue is whether the carbon-based biochemistry can occur in non-aqueous solvents. It appears that carbon-based life is unlikely to able to adapt to a pure solvent environment unless
it has mechanisms to form water from solvents
it can produce all the necessary water de novo (anew) from biochemical reactions
6.2.3. Temperature Extremes
Temperature is a fundamental thermodynamic parameter that affects all biochemical reactions, in particular setting limits on life because temperature and pressure determine whether water is in the liquid phase.
Microorganisms have been cultured with growth observed at temperatures as high as 121 ∘C or as low as −15 ∘C.
Freezing temperatures can kill cells if internal ice crystals are formed.
Microorganisms that grow best at temperatures above 80∘C are called hyperthermophiles.
The maximum growth temperature of cultured hyperthermophiles varies from 80−121∘C
the minimum growth temperature varies from ∼40−80 ∘C, depending on the organism.
Hyperthermophiles have protein and lipid structures that are adapted to high temperatures.
Protein structures are stabilized at high temperature through amino acid substitutions and most importantly through use of disulfide bonds for structural stabilization.
Heat stable, ether-linked lipids are universal in hyperthermophilic Archaea and in some bacteria.
Fundamental changes in protein and lipid structure compensate for the increased mobility and fluidity at high temperatures.
All hyperthermophiles studied have a reverse gyrase that positively supercoils DNA, which along with cationic proteins increases the thermal stability of the DNA.
Nov 7 (Dubose & Freeman)#
Nov 9 Exam II#
Nov 14 (St. John & Rios)#
7. Hadean Earth & Archean Climate
7.1. Hadean Earth
The period from the formation of the Earth (∼4.56Ga) up to the age of the oldest rocks (∼3.8−4 Ga) is referred to as the Hadean eon.
The term Hadean refers to the classical Greek domain of Hades, which our modern sensibilities would call hell.
This time encompasses the assemblage of Earth from the smaller planetesimals, dramatic internal rearrangement such as core formation, the creation of the ocean and earliest atmosphere, and the origin of Earth’s Moon.
7.1.1.Internal Structure of Earth
The center of the Earth lies over 6000km from the surface.
Earthquakes provide the key to inferring the structure of Earth, which is deduced from a network of seismometers.
A seismometer was part of the scientific instrument panel of the Mars Insight Mission, which detected a magnitude 5 quake.
An earthquake is an oscillatory movement of the ground, generated by the sudden slippage of rock along a fault in Earth’s crust.
Seismometers measure the amplitude of the waves and the time of arrival at various stations from a given earthquake. From this information, the velocity of the seismic waves can be determined, where shifts in velocity correspond to waves encountering different media through reflection and refraction.
The core is an alloy of nickel and iron (with less than 10% Ni), where the nickel is required to lower the melting point of iron so that the outer core can exist as a liquid.
Changes in the seismic velocity are seen in the upper 700km of the Earth’s mantle, which indicate transitions from lithosphere (stiff upper layer) and the asthenosphere (soft, plastic layer).
At 400 km, there is a sharp change in velocity due to the mineral olivine is forced by pressure to assume a more compact form.
At 700km, pressure forces some of the silicon, magnesium, iron, and aluminum into simpler oxide forms (\(SiO_2\), \(MgO\), \(FeO\), and \(AlO_2\)). The bulk of the magnesium and iron from mineral structures called magnesium silicate and iron silicate (perovskite), where silicate is \(SiO_3\).
7.1.2.Accretion: the building up of planets
As material is added to the forming planets by collisions, where little chucks of rock combine to make bigger rocks, the kinetic energy of impact is converted to heat.
The potential energy of dust and small rocks is larger than the potential energy of material gravitationally bound to the growing planet.The potential energy of dust and small rocks is larger than the potential energy of material gravitationally bound to the growing planet.
The potential energy is proportional to the density and radius of the growing planet, which defines the gravitational well into which the material falls. In the early Solar System, Earth and Venus were heated the most, where the other terrestrial bodies (Mars, Mercury, and the Moon) were heated less.
Two complications are: (1) the average size of the impacting planetesimals at the end of accretion and (2) the assembly time, where longer times allow more heat from the impacts to leak out at the planetary surface and creates lower temperatures overall.