Notes on Astrochemistry: From Astronomy to Astrobiology by Andrew M. Shaw, Chichester, UK: John Wiley & Sons, 2005
as compiled by William H. Waller (Tufts University) Copyright, W. H. Waller, December 2006
(Includes corrections and commentary) {additions are in brackets}
CHAPTER 1: THE MOLECULAR UNIVERSE
Page 1, last line: Only the galaxies are moving away from one another – not the stars inside the galaxies.
Page 2, Table 1.1, 7th row: Time = 3-7 x 105 years -- not seconds Comments should begin with “Electrons recombine to form neutral atoms of the light elements. The Universe is now …” deleting “Light element atoms form, and” The light elements formed during the first ~3 minutes or 200 seconds.
Page 2, paragraph 2, last line: Remove this last sentence.
Page 3, Table 1.2 This refers to the cosmic abundances by particle. To obtain abundances by mass, multiply by the atomic weight. For example the Helium abundance by mass would be 0.085 x 4 = 0.34 = m(He)/m(H). To get the actual fraction of the total cosmic abundance m(He)/m(tot) ~ m(He)/(m(H) + m(He)) which is easier to determine by taking the reciprocal (m(H) + m(He) )/ m(He) = 1/0.34 + 1 = 3.94, and then taking the reciprocal again 0.25 for the fractional helium abundance by mass.
Page 3, paragraph 3, 1st sentence The mass of the Milky Way is 1011 to 1012 solar masses.
Line 8 “Rapid rotation around the axis of the {inner nucleus} requires … Milky Way.” {Similarly rapid rotation is observed in the outer disk, prompting the call for “dark” gravitating matter to bind these motions.}
Page 6 There is a lot of biochemistry that is quickly introduced, including the likes of … Phospholipid and amphiphilic molecules, micelle concentrations, and peptide bonds … help! Brief explanations and pointers to later chapters would help. The U in UGU and UGA refers to the structure of RNA.
Page 9, line 1 Is the author suggesting that we have evolved from extremophilic microbes? Where is this going? There should be pointers to Chapter 9!
Equation 1.1 I prefer to start with the total number of stars in the Milky Way rather than the rate of star formation which has varied over cosmic time. For my alternative take on the Drake Equation, see http://cosmos.phy.tufts.edu/cosmicfrontier. Go to the Technical Notes, and click on the last note.
If you prefer to use the galactic star formation rate, it is more like 1-3 stars/year nowadays.
Page 10, Section 1.5, paragraph 1, last line The author refers to the recent discovery of habitable planets and life, but I am unaware of any beyond the solar system.
Page 11, paragraph 1, last sentence The author refers to the impact that caused the Chicxulub crater also should have produced global heating. It could have also produced global dimming by dust in the atmosphere and corresponding global cooling.
CHAPTER 2: STARLIGHT, GALAXIES, AND CLUSTERS
Page 15, paragraph 2, next to last line “… molecules present in the (stellar atmospheres) can be seen.”
Page 16, end of paragraph 1 Planck’s constant is h = 6.626 x 10-34 Joule seconds
Stefan-Boltzmann Law is subsidiary to Planck’s Law, in that it involves an integration of Planck’s Law over all wavelengths or frequencies.
Page 17, Example 2.3, last sentence This is an interesting result, as {it is close to} an absorption maximum in the spectrum …
Page 18, Planck’s Law, Equation 2.5 I think this is in units of Watts per wavelength interval per steradian.
Planck’s constant should be h = 6.626 x 10-34 J s
Page 19, Figure 2.2 There is no labeling of the vertical axis!! It certainly cannot be I(wavelength) in units of Watts/m2/nm. Perhaps it is I(frequency) with units of Watts/m2/Hz or frequency * I(frequency) in units of Watts/m2. This is left as an exercise for the reader, to confirm whether in fact the chlorophyll absorption peak at 420 nm actually coincides with the “energy flux” peak from the Sun.
Page 20, Section 2.2, line 3 {… revealed an explosion of energy} … not a ball of energy.
Line 6 “… photon-matter scattering {stopped}. Radiation from the “surface of last scattering” has permeated the Universe – redshifting as the Universe has expanded and cooled. “ The end of the sentence with “photon-matter scattering” should be removed.
Last line “Local Group is falling towards the Virgo {Supercluster} of galaxies.”
Page 21, paragraph 2, line 6 “{very early} Universe was a {homogenous} place with little in the way of luminous structure …”
Page 23, Table 2.1 The second column refers to the apparent magnitude (m) The third column refers to the Absolute magnitude (M) Where m – M = 5 log (d/10 pc)
Page 24, Figure 2.4 The vertical axis is better labeled as the (B – V) color in magnitudes, where (B – V) = m(B) – m(V). See magnitudes section in Technical Notes in http://cosmos.phy.tufts.edu/cosmicfrontier.
Page 25, line 3 Limiting angular measurements are around 0.01 arcsecond, not 0.01 degree. One arcsecond = 1/3600 degree.
Example 2.5 The parallax angle p = 1 / d(pc) = 1 / (4.34 ly/ 3.26 pc/ly) = 0.751 arcsec Ignore the next line!
Page 26, last paragraph, lines 14-15 “Sideral” should be spelled “Sidereal”
Page 28, paragraph 2, last line 2000 years have passed since Astrology was first setup. Precession of the Earth’s axis, and hence of the equinoxes has caused the Sun in November to no longer coincide with the constellation Scorpius. It’s one constellation off, which can be checked by using an Ephemeris and plotting the Sun’s position on the celestial sphere.
Page 31, paragraph 1 NGC 598 is Messier 33 or M33
The last line in this paragraph can be appended by … {but become increasingly necessary as the number of found objects has grown into the thousands.}
Paragraph 2, line 1 “… clearly not stars {or star clusters} and even …”
Page 33, Table 2.2 and paragraph 1 Diameter of the central bulge is more like 3300 ly The scale height of the thin disc at the Sun’s position is more like 330 ly, yielding a total thickness of no more than 1000 ly. A thicker disk of older stars is thought to be present, with a scale height of about 1000 ly for a total thickness of no more than 3300 ly. Perhaps that is what the author was supposing.
Page 34, last paragraph The Local Group occupies about 3 Mly, not 3 Gly, in space
Page 35, Figure 2.14 The two lines near the Milky Way refer to the Large Magellanic Cloud (LMC) and Small Magellanic Cloud (SMC). NGC 8822 should be NGC 6822 Sextane A and B should be Sextans A and B See Figure 8.1 on page 138 of W. H. Waller and P. W. Hodge’s Galaxies and the Cosmic Frontier (Harvard University Press).
Page 36, line 1 “The overall study of the Universe is {known as} cosmology. It addresses …”
Last line “…dimension over time. {In addition to dark matter, dark energy has been invoked to explain the observed acceleration of the Universe’s expansion. This unseen energy may amount to 75% of the total mass-energy of the Universe. If so, ordinary matter is but a small fraction of what the cosmos actually contains. These newfound} descriptions of the Universe…”
Page 38, Galaxies “The three broad classifications … of {vast stellar systems} that also cluster together to form {groups such as} the Local Group … Magellanic Clouds, {larger clusters, and superclusters}.”
Cosmology, last line “…mechanics and gravity {in the context of cosmic evolution.}”
Stellar magnitude “… radiation flux {ratios} and magnitude {differences}”
Page 39. Problem 2.2 “The brightest star in the northern hemisphere is {Sirius} in Canis Major, one of Orion’s dogs. The luminosity of {Sirius} is (35) LSun”
“(e) … planet around {Sirius} …”
CHAPTER 3: ATOMIC AND MOLECULAR ASTRONOMY
Page 41 Nice theme – “Atoms and molecules, wherever they are, can report on their local conditions and be used as probes.”
Page 42 A whole lot of quantum mechanics is summed up in this sentence -- “Interrogating the wavefunction with the Hamiltonian operator produces a series of allowed energy levels called eigenvalues, and the wavefunctions appear as eigenfunctions each described by a unique set of quantum numbers.” More elucidation would be helpful. Good luck!
Page 43, equation 3.1 Astronomers typically use the extinction A(mag) = -2.5 log (I/I_o) So I/I_o = 10-0.4A = 10-0.4kd, where k is the wavelength-dependent extinction coefficient in units of magnitudes per cm (or kpc), and d is the length of the column through which the light is propagating. The extinction coefficient k is a product of the extinction cross- section (in cm2) for a particular particle times the number density of particles (in cm-3). More information can be found at http://cosmos.phy.tufts.edu/cosmicfrontier, under Technical Note 15. There, k is in units of magnitudes per column density of particles and is multiplied by the column density, N, which is in units of particles per cm2. Shaw likes to keep the length of the column explicit so that it can be solved for.
Page 43, par 3, line 2 Shouldn’t the transmission be T = I/I_o, so that it is less than unity?
Page 43, Example 3.1 The denominator should be 0.0032
Page 45 Equation 3.3 refers to an absorption transition rate. Equation 3.4 refers to an emission transition rate.
Page 46, Equation 3.7
What is εο?
Page 47, par 1, last line … “in space anything goes!” Actually, forbidden transitions in space occur only in regions of relatively low density, where de-exciting collisions are rare. Forbidden emission is seen in photo-ionized nebulae (ie. HII regions) but not in the denser atmospheres of stars.
Page 47, Equation 3.8 Since ΔE = h Δν, then the spread in frequency Δν = ΔE/h. Equation 3.8 states that ΔEΔτ > h/2π, so ΔE > h/2πΔτ, and thus Δν > (h/2πΔτh) = 1/(2π Δτ). Therefore, knowing the transition lifetime (Δτ) yields the minimum spread in frequency (Δν) – the so-called natural linewidth.
Page 49, Equation 3.12 This can be approximated by setting the kinetic energy (½ m v2) equal to the thermal energy (kt/2) and using Equation 3.11.
Page 49, last par, line 1 Jupiter does not rotate at the same {angular} speed at all latitudes, {as occurs} on Earth.
Page 49, last par, last line The red colour of the red spot may be a temperature effect associated with a different height of the cloud layer, or it may be a chemical effect, or both.
Page 51, Equation 3.14 The degeneracy factor (g) refers to the fact that electrons in different quantum states of spin and orbital angular momentum can share the same energy level.
Page 52, Section 3.3, line 2 “…complicated optics in the form of {telescopes and detecting instruments such as cameras that are fed light through filters or spectrometers}. {Nowadays,} telescopes are not restricted … but {are designed to detect} radiation …”
Page 53, atmospheric window 4. “Radio wave (2mm – 10m)” I’m guessing here
Page 54, par 1, line 7 {Light wavefronts from a distant point source interact with an aperture of finite size (ie. a lens or mirror) by diffracting around it. This results in a blurred image of the point source. The larger the aperture, the less the blurring. Two point sources that are close together can become blurred beyond resolution. The resolving power is given by …}
Page 56 1. Advanced Camera … 2. Near Infrared Camera and Multi-Object Spectrograph 3. Space Telescope Imaging Spectrograph
Page 57 Top spectrum has wavelength increasing to the right. Bottom series of 4 spectra has wavelength increasing to the left.
Page 59, par 1, last 2 lines {…the Balmer series in the spectrum of a star is indicative of the population of the energy levels, which in turn is a direct consequence of the stellar surface temperature.}
Page 59, par 2, first line “One of the {characteristics} of atomic energy levels.”
Page 59, par 2, line 9 {etween n2 = (n1 +1) = 3 in the Balmer series this is red at 656 nm.}
Page 60, par 2, line 5 What does the “fingerprint region” refer to?
Page 61, last line For identical masses, the reduced mass is = ½. More disparate masses yield higher values that approach unity.
Page 62, Example 3.4 The reduced mass µ = (1 x 127)/(1 + 127) = 0.99219 x …
Page 63, Figure 3.6 The vertical axis has energy E increasing upward. The horizontal axis has frequency ν(GHz) increasing toward the right.
Page 63, par 1 The R-branch transitions involve absorption of energy, while the P-branch transitions are in emission.
Page 63, par 2 CO refers to the usual isotopes of Carbon and Oxygen 12C16O.
Page 63, par 2, last line. {40 K. Typical temperatures of molecular clouds in interstellar space are more like 5-10 K. The resulting CO spectra reach greatest intensity with the P(1) = 1 0 transition.}
Page 65, Equation 3.25 To get this, one had to assume equal bond lengths, r, for both 12CO and 13CO in the prior line of equalities.
Page 69, last line {Although H2 does not have any rotational transitions, it vibrates and so can be observed in the infrared. It also has electronic transitions which are evident in the UV. Conditions for exciting these sorts of transitions are fairly energetic and hence rather unusual in typically cold molecular cloud settings.}
Page 70, Equation 3.27 See also Equation 3.14
Page 72, Figure 3.14 Comparing to Figure 3.3 on page 53, the big absorption at 7 um is caused by H2O, and the big absorption at 15 um is caused by CO2.
Page 75, Figure 3.16 The upper vibrational state should be v’ = 1.
Page 76, par 2 The complexity of molecular spectra is nicely summarized in the sentence … “Each electronic level has a manifold of vibrational energy levels, which in turn has a manifold of rotational levels.”
Page 80, last par, line 10 “Species called polycylic {aromatic} hydrocarbons (PAHs) and dust, …”
Page 81, line 11 “There is {some} correlation between the location of H atoms and CO molecules within the {large-scale} distribution of matter in the Milky Way {with the exception of the galactic center.}”
Page 83, Problem 3.3 The distance to the Andromeda galaxy is {2.5 Mly}. (a.) The Andromeda galaxy is actually heading our way as is evident from its observed blueshifted emission! Therefore, Hubble’s Law between redshifts and distances is irrelevant as M31 is not participating in the so-called Hubble flow. Best to use another more distant galaxy that is actually expanding away from us!
Page 83, Problem 3.4 The Einstein A coefficient for the electronic transition – of what? The wavelength of the transition is at 153.67 nm in the UV, whatever it is.
CHAPTER 4: STELLAR CHEMISTRY
Par 1, line 6 “… they are younger stars {whose placental clouds had been chemically enriched by prior supernova activity.}”
The heavy elements in the spectra of stars in open clusters does not imply that the stars directly formed from supernova remnants, just that prior supernovae had injected heavy elements into the interstellar matter from which they formed … an important distinction.
Page 86, Figure 4.1 “Infrating” should be “Infalling” in the figure. “Astronomony” should be Astronomy” in the caption.
Page 86, par 1, line 4 “promoting” should be “exciting”
Page 87, par 1, line 5 “… important information on the {chemical} environment.”
Page 88, par 1, last sentence “This suggests {evolutionary processes that involved the formation of heavy elements and ultimately molecules, now made manifest in the spectra of stars.}”
It is not true that cool stars are more evolved chemically, as the current wording suggests.
Page 89, line 1 “… and stars found {in} this region …”
Page 89, par 3, line 3 “Astrochemically, the cooler giants and supergiants {show in their spectra} many more atomic and molecular species …”
Again, the author’s words suggest that cooler stars are more chemically enriched. That is not true. Their cool atmospheres, however, are amenable to hosting observable spectroscopic features that belong to a greater variety of elements and molecules.
Page 91, Figure 4.5, caption The comparison between infrared and visible views is not shown. The dust lane is seen as a horizontal dark band.
Page 91, par 1, line 1 The mass defect corresponds to 0.007 of the original combining masses … a fun number to remember.
Page 93, par 3, line 8 “The Sun will then become a red giant. {During the red giant phase}” … insert par 2 on page 94.
New par “The {Sun’s} core becomes …”
Page 95, par 1, line 5 “The outflow of mass from all {intermediate-mass stars (0.6 < M/MSun < 8.0) results} …”
Lower mass stars may not produce the degenerate states of matter that characterize white dwarfs.
Page 95, par 2, line 2 “This occurs for {stellar cores} greater than 1.4 solar masses.”
Page 95, last line “an event is called a {supernova}.”
A nova is caused when a red giant star dumps its atmosphere onto a white dwarf companion and causes runaway nuclear fusion on the surface of the white dwarf. This is a much less energetic event than a supernova.
Page 96, line 1 {The most recent naked-eye supernova explosion was observed in 1987. The HST captured an amazing sequence of images (including Figure 4.9).}
Page 96, par 1, line 4 “Kinetic energy of 1044 J and the {radiant} energy released in the visible {spectral} region {during} the year …”
Page 97, Table 4.3 The usual demarcations of mass are at 0.6 < M/MSun < 8 planetary nebula to white dwarf 8.0 < M/MSun < 30 supernova to neutron star 30 < M/MSun < 120 supernova to black hole
Page 97, par 2,, line 5 “Cycle of star evolution. {However, this estimate only pertains to Sun-like stars.}”
Page 97, par 2, line 7 “…entered the supernova phase quickly. {Massive star formation continues to the present day, and so has provided many cycles of chemical enrichment over the history of the Galaxy.}”
Delete last four lines.
Page 107, Equation 4.12 2 Left hand side should be ½ m ve =
Page 108, par 2, line 2 {Direct detection of black holes is elusive, but there is increasing indirect evidence for stellar black holes in several closely interacting binary stars systems, and for supermassive black holes in the centers of many galaxies.}
Page 108, par 3, line 2 “…supernova {terminates the life} cycle of {a massive star}, as shown in …
Page 108, last par, next to last sentence “The supernova also produces a shock wave in space, not just {from its high-speed ejecta}, but perhaps ripples in space-time itself.”
Page 109, Figure 4.15 “The cycle of star formation {for massive stars (M > 8 MSun)}.” Delete “Best resolution available.”
Page 109, par 1, line 1 “The interstellar medium is thus a chemically diverse medium (whose inventory of elements heavier than carbon is almost entirely the result of supernova explosions.)”
Page 110 “Supernova synthesis” should be “Supernova nucleosynthesis”
“Stellar evolution involves … The birth of a protostar and its life as a pre-main-sequence star, its {life on} the main sequence and death, starting with a red giant, leading to a planetary nebula, and ending in white and black dwarfs, {or to neutron stars or black holes for the massive stars.}”
“Cycle of {massive} star formation involves … The evolution of a {massive}star from …”
Page 111, Problem 4.6, line 3 …ω is the orbital frequency in units of cycles/second.
CHAPTER 5: THE INTERSTELLAR MEDIUM
Page 113, last par, line 2 Ca+ is not a molecule. Perhaps the author intended another species?
Page 113, last par, line 7 The R(0) transition of CO at 115 GHz suggests that it is observed in absorption (see p. 63). However, most observations of molecular clouds at this frequency detect CO in emission.
Page 114, par 1, line 5 “… star formation begins to occur. {CO maps also trace nebular pileups due to}supernovae or stellar winds:”
Page 114, par 2, line 3 Replace “and is” with “which are”
Page 114, par 5, line 3 “… turbulence. {Some of this difference is because the 12CO line emission saturates a lower densities, thus precluding reliable mapping above these densities.}”
Page 114, par 6, line 1 The distance to TMC-1 is 140 pc = 456 ly, not 45 ly.
Page 115, Figure 5.1 The name is Ronald Maddelena.
Page 116, Figure 5.4 Left circle portrays “icy dust” not “icy disk”
Page 117, line 2 “…emission of a photon. {The resulting radiation is called thermal Bremsstrahlung (or “braking”) emission. This continuum emission is most evident at radio wavelengths of a few cm and frequencies of a few GHz according to ν = c/λ, with a spectral intensity that varies as ν−0.1.}”
Page 118, next to last par, lines 1-3 Clouds do not evolve in time from dark clouds to giant molecular clouds unless gathered by some agent such as a spiral density wave or supernova shock wave. The important point here is that larger clouds give rise to the rare hot massive stars whose UV radiation will alter the cloud chemistry.
Page 119 The top figure features molecules with no oxygen, while the bottom figure features molecules that contain oxygen.
Page 121, bullet 3, line 1 “far-UV” not “for-UV”
Page 123, last par, line 4 “stoichiometry” not “stoichometetry”
Page 124, Equation 5.6 This simple differential equation states that the reaction depends on how much of the reactant is available. It leads to exponentially declining concentrations over time. Dividing both sides by [A] gives d[A]/A = -k dt, which when integrated yields ln [A] – ln [A]0 = -k (t – t0). Solving for [A] gives [A]/[A]0 = exp(-k(t – t0)) Similar linear dependences and exponentially declining amounts of “reactant” are found in measurements of star formation rates, where the rate depends on the amount of star- forming gas that is available.
Page 125, Equation 5.11 This is based on the simpler collisional rate formulation (assuming one molecule type). z = n σ v, where n is the number density (cm-3), σ is the collisional cross section (cm2), and v is the velocity (cm/s). The resulting product z has units of collisions/second. The velocity has been replaced by the temperature according to ½ m v2 = 3/2 k T, so v = [3 k T/m]1/2, and z = n σ [3 k T/m]2. Adding a second molecule type introduces another number density, requires use of the reduced mass, and leads to a rate Z that is in units of collisions/second/cm3.
Page 127, Equation 5.17 This comes from Equation 5.7 on page 124 and then using parts II and III in Equation 5.8.
Page 129, Figure 5.8 The energy difference between the initial state and final state is noted as ΔG. This could take the form of radiation or kinetic energy transferred to another particle … from “reactants to products,” as Shaw notes and promises more insights in Chapter 8.
This figure and the text help explain why gas phase chemical reactions are much rarer than those with catalyzing intermediaries, such as the surfaces of grains.
Page 130, par 1 For those of us who are chemical neophytes, here is a definition of “radical” radical, in chemistry, group of atoms that are joined together in some particular spatial structure and that take part in most chemical reactions as a single unit. Important inorganic radicals include ammonium, NH4; carbonate, CO3 ; chlorate, ClO3, and perchlorate, ClO4 ; cyanide, CN; hydroxide, OH; nitrate, NO3; phosphate, PO4; silicate, SiO3 (meta) or SiO4 (ortho); and sulfate, SO4. The use of these radicals simplifies the naming and description of inorganic compounds, since such usage does not consider the electronic charge on the group. (When ions are dealt with, electronic charge must be considered.) In organic chemistry, the term radical is sometimes used synonymously with group; e.g., the group CH3 is sometimes called the methyl radical instead of the methyl group. This use is limited chiefly to alkyl groups and aryl groups; it is usually not applied to functional groups, such as carbonyl. Because the term radical easily could be taken to mean a free radical, the term group is preferred by some. The Columbia Electronic Encyclopedia, 6th ed. Copyright © 2006, Columbia University Press. All rights reserved.
Page 133, Figure 5.11 There seem to be 2 H atoms missing on the right hand side of the carbon insertion reaction(?)
Page 135, Table 5.3 The ionization wavelength for hydrogen is 91.16nm not 90.73nm. Are the other wavelengths off?
Page 137, Figure 5.12 I think the author meant to say “Polycyclic aromatic hydrocarbon species:”
Page 137, Equation 5.29 The right hand side of the first line seems to be missing 2 H atoms(?)
Page 138, par 2, line 6 The term “aliphatic” is defined as follows … • An aliphatic compound is one that is not aromatic; i.e. it lacks a particular arrangement of atoms in its molecular structure. Aliphatic is especially used in reference to open-chain (non-cyclic) hydrocarbons. The term can also apply to open-chain hydrocarbon sub-units of larger organic molecules, for example "aliphatic group" or "aliphatic substituent".
More information is available at http://www.ilpi.com/msds/ref/aliphatic.html.
Page 139, line 13 “…on the surface of dust grains. {Regardless of the specific mechanism, the PAH synthesis in the ISM is well established. Therefore, the PAH molecules found in meteorites need not come from biogenic processes such as the formation of oil in planets.}”
Page 143, par 4 This is the important summary, beginning with … “Surface chemistry increases the molecular diversity in the ISM, further enhanced by the presence of UV or far-UV radiation.” …and ending with “The dust surface is a fertile ground for organic synthesis.”
Page 146, bullet 4 The dynamical timescale of the molecular cloud refers to its freefall collapse time which is solely dependent on the cloud’s density ρ according to t ~ [1/Gρ]1/2. For a large cloud of number density n ~ 102 cm-3, the corresponding timescale is about 6 Myr as noted.
Page 146, par 2, line 1 “If we take the total observed mass {of molecular gas in the Milky Way} as 2 x 109 MSun”
Page 146, par 2, end “…efficiency of star formation{, but implies that molecular clouds can persist for upwards of 100 Myrs. In other words, something is keeping these clouds from collapsing on their dynamical timescales.}”
Page 149, Equation 5.31 Again, are we missing an H-atom on the right-hand side(?)
Page 151, par 3, line 2 As shown in Figure 5.24, the glycine feature is observed in “emission” not “absorption.”
Page 152, Figure 5.23 Glycine is NH2CH2COOH Based on this formula, there should be C atoms at the various junctions of the stick figures.
Page 154, Figure 5.24, last sentence None of this is shown in the spectral plots.
CHAPTER 6: METEORITE AND COMET CHEMISTRY
Here the author hits his stride. This chapter and the next read very well and are chock full of valuable information.
Page 157, par 2, line 3 “Meteorites land on the Earth and {so} provide a unique chance to study the early solar system {through} intense laboratory examinations. Comets come close to the Sun, becoming very bright, and {so} spectroscopy {can yield detailed information on} their chemical composition.”
Page 157, par 2, line 9 “…long tails, (where they conducted) direct measurements and observations from within the tail. {In July 2006 the Deep Impact mission crashed a massive projectile into Comet Tempel 1, enabling detailed telescopic studies of the resulting ejecta plume.}”
Page 158, 2nd bullet defining Meteoroid Place before first bullet defining Meteorite
Page 161, par. 4 2. “Stony: principally silicate or {carbonaceous} rocky meteorites.” I’m guessing the author’s intention here.
Page 161, par 6, line 4 “… The Willamette meteorite in the {American Museum of Natural History}”
Page 165, par 1, last line “Analysis of carbon in {some} meteorites may be the first look at ancient life on other planets.”
Page 166, Equation 6.1 17 14 7N should be 7N
Here we have yet another instance of some activity (radioactive decay) depending on the amount of stuff available for that activity (the radionuclide). We encountered this before in simple chemical reactions (see page 124 and my notes citing star formation as another instance of an activity that declines exponentially with time).
Page 167, Figure 6.4 The complex sequence of radioactive decays from 238U to 206Pb is truly mind blowing!
Page 168, Equation 6.5 The decay constant λ looks the same as k in Equation 6.4.
Page 168, par 4, line 1 (after Eq. 6.6) “This {is} the reverse of the …”
Page 168, par 4, last sentence “When a tree is used for wood in an object such as a museum {artifact} then the 12CO/14C ratio changes {as the 14C decays} and the age of the …”
Page 172, first line “Acid and base extractions from this material ---“ Are these amino acids?
Page 173, Figure 6.8, line 2 “Green-fluorescing micrhystridid acanthomorph acritarchs …” Requires definition but is not discussed in the text
Page 174, Figure 6.9 Given the mass spectra of these meteorites, does this suggest that most interstellar PAHs have more than 100 carbons? Or does further processing in the host bodies erase all interstellar characteristics?
Page 175 The evidence for ALH84001 being of Martian origin is impressive and amazing!
Page 176, last full sentence “Poly{cyclic} aromatic hydrocarbons…”
Page 177, Figure 6.13 The mass spectral features at an atomic weight of ~600 could indicate the presence of PAHS consisting of C60+, based on reference to Figure 6.9. Otherwise, it is difficult to compare these spectra as the comet spectrum does not reach the heavier atomic weights shown in Figure 6.9.
Page 179, line 10 “Almost one ton of material arrives on Earth from Mars each year…” How do we know this?!
Page 180, par 2, line 9 “… remnant of the formation of the solar system. {The Oort cloud is surmised from the high velocities of some comets that enter the inner solar system. The high velocities imply a large semi-major axis, according to Kepler’s 2nd law and Newton’s Law of Gravitation. The comets in the Oort cloud probably formed in or near the orbits of Jupiter and Saturn (where the pre-planetary disk would still be sufficiently dense), but were then knocked out by these planets to the greater distance of 30,000 – 50,000 AU that characterizes the Oort cloud.}”
Page 180, par 3, line 8 “field lines of the Sun {which in turn are driven by the solar wind (Figure 6.66). The dust tail is driven by solar pressure on the dust grains. This slower ejection is seen to be directed away from the Sun’s motion.}”
Page 181, line 2 “dominate the tail, with the {blue} colour deriving from ions in the plasma {mostly Cyanogen (CN)}”
Page 186, last sentence The cometary origin of the Earth’s oceans and atmosphere remains controversial.
Page 191, problem 6.4 Perhaps the author meant to consider comets of diameter 103 and 105 m rather than km, as a comet 105 km in diameter would be the approximate size of Jupiter!
CHAPTER 7: PLANETARY CHEMISTRY
Page 194, par 2, after last sentence {In addition to the dominating gravity of giant planets, the solar wind also plays a role in stripping volatile gases from the inner solar system.}
Page 196, Example 7.1 Most planetary radii are determined by measuring their angular sizes and determining their distances, whereby D = 2R = (theta (arcsec) / 206265 radians/arcsec) x d. The distance d for the inner planets can be derived from solar transit data, or more recently, radar ranging.
Page 197, par 2, line 1 “The Earth and the other terrestrial planets formed by the process of accretion {onto} planetesimals {and aggregation among planetesimals}, which heat internally from the acquired gravitational energy and also from the decay of radioactive elements.”
Page 199, par 2, last sentence {The impact-driven escape of water and atmosphere from Earth then requires a replenishment of these essential components – either through cometary impacts or through more outgassing from the Earth’s interior.}
Page 200, par 2, line 6 What does “put paid” mean?
Page 205 Figure 7.7 shows that the location and the width of the habitable zone both depend on the host star’s luminosity. Example 2 derives the relation for location, with the distance depending on the square-root of the luminosity. The width also depends on the square- root of the luminosity, as will be shown in class.
Page 206, par 1 The author uses the slim habitable zone around the Sun plus several other favorable factors to suggest that the Earth was rather lucky. This is known as the “Rare Earth” hypothesis and is covered extensively in the book by that name.
Page 210, par 1 The author revisits the H/D isotope ratios of comets finding them higher than in the Earth’s oceans. This suggests a mix of primordial {outgassed} and delivered water.
Page 210, Table 7.3 This table of atmospheric composition of the inner planets is confusing. There are no entries under O2. The mix of % and ppm units is also confusing.
Page 211, line 1 Deriving the mass of a planet from its size and atmospheric surface pressure seems bizarre to me, given all the dynamical ways to derive the mass {timing falling objects, measuring periods of orbiting satellites, etc.}.
Page 211, Eq. 7.12 Here, the scale height is zo = H = kT/mg
Page 212, par 2, last sentence I’m surprised that water plays a significant role in the Venusian atmosphere, but Table 7.3 suggests otherwise.
CHAPTER 8: PREBIOTIC CHEMISTRY
Page 226 The unique qualities of water as a solvent are important. That its frozen form is less dense than its liquid form allows it to freeze over from the top down, thereby enabling insulated liquid zones as may exist beneath Europa’s icy crust.
Page 227-228 Chemical potential is introduced as a characteristic “that drives the formation of equilibria.” It is something inherent to the chemical species and its thermal state. It also relates to the change in Gibbs free energy from species to species in a reaction.
Page 229 When the Gibbs free energy goes through a minimum, its rate of change is minimal, and the reaction reaches equilibrium. Does that mean the chemical potential of the reactants are equal and opposite (see equation 8.7)?
Page 230 Enthalpy is not defined.
Page 232 The changes in Gibbs free energies for CH3OH and CO are listed as -134.27 and -155.41 respectively. Appendix C lists them as -161.96 and -137.17 respectively. What gives?
Pages 236-240 Prebiotic chemistry seems to hit a roadblock at the lower temperatures of early Earth and present-day Titan.
Page 237 The collision of Earth with a Mars size body is thought to have erased all water and associated bio-chemistry from the surface of Earth. However, outgassing from the Earth’s interior could have replenished the emergent biosphere.
Page 240 However, Urey-Miller type synthesis of amino acids seem to favor exogenous delivery of organics rather than an endogenous environment rich in outgassed carbon dioxide.
Page 241, Figure 8.4 The pyrimidines are on top … the bases in the nucleic acids cytosine and thiamine (thymine?). The purines are below … the bases in the nucleic acids adenine and guanine.
Page 242 The formose reaction creates sugars from formaldehyde (H2CO). The sugar ribose is then introduced but not described in the text. Webster’s New Collegiate Dictionary defines ribose as “a pentose (C5H10O6).” In the book’s glossary, ribose is the “sugar that attaches to the DNA bases to form part of the DNA backbone helical structure.” The author puzzles over its origins, as the formose reaction yields very little ribose.
In further pages, ribonucleic acid (RNA), ribozymes, and ribosomes are introduced but not explicitly related to ribose, alas. Webster’s New Collegiate Dictionary defines ribosome as “one of the RNA-rich cytoplasmic granules that are the sites of protein synthesis.” The author in the glossary defines “ribozyme” as an “RNA self-catalyzed replication structure.”
Page 243 Out of seemingly nowhere, the need for phosphorus arises in the synthesis of “oligonucleotides” such as RNA and DNA. The author seems as baffled by this special need as much as I am. We end up with both a “ribose and phosphate problem.”
Page 246-248 The chirality of terrestrial biochemistry is pretty awesome … “the choice in Nature for one handedness or another.” The author discusses possible origins, including highly polarized radiative environments imparting an “enantiometeric excess” in the pre-solar nebula. He also briefly notes that molecule growth on enantiomeric crystal faces may contribute to chirality. Feldspar crystals can provide these sorts of enantiomeric faces.
In this chapter and the next, “polymers” and “monomers” are frequently invoked. These terms along with “peptides” could use definitions for us novices in organic chemistry. According to Webster’s New Collegiate Dictionary, “Polymer” refers to a molecule made up of repeating sequences of smaller molecules. “Monomer” refers to a molecule that can be polymerized into a polymer. “Peptide” refers to any of various amides that are derived from two or more amino acids by combination of the amino group of one acid with the carboxyl group of another and are usually obtained by partial hydrolysis of proteins. Peptide bonds involve carbon and nitrogen.
Page 249-250 Chemosynthesis on the surfaces of clay minerals is enthusiastically promoted … up to the possibility of clay sources catalyzing the production of an “inorganic gene.” This sounds a lot like the story of the “Golem!”
Page 251-251 The sulfur and iron-rich nature of chemosynthesis on the ocean floor is also new to this book. The Fischer-Tropsch process is introduced but not described. Its result is to fix carbon into long aliphatic chains. Nowhere do I see phosphorus playing a role here?!
Page 253-254 Yet the author goes on to promote “the RNA World” as being the first self-replicating system, with possible origins in geothermal vents. RNA needs phosphorus, right? So, it looks like we still have lots to puzzle over … the lack of ribose and phosphorus from readily accessible sources, and the roles of iron and sulfur which are abundant in the deep sea smokers.
CHAPTER 9: PRIMITIVE LIFE FORMS
Pages 259-262 The figures go far in visualizing the basic chemical and structural steps that are necessary to form encapsulating cells. A good summary appears on p. 261, “Polymers and a localized optimized environment segregated from the rest of the world form the basis for protocell formation.”
Pages 265-270 The conditions for transporting materials between the cell and the outside environment depend on the relative concentrations (chemical gradient) and the availability of expendable energy (including electrochemical energy).
Page 273 The Bacteria branch of the Tree of Life is characterized by “no cell membranes…” What does this mean, if the bacterium has a cell wall and a plasma membrane as shown in Figure 9.7? Is the bacterial cell impermeable?
Page 273-274 The author finally explains why we probably evolved from thermophilic extremophiles. It is because “all species closest to the root of the tree are hyperthermophilic in nature (they live in hot springs)…” This determination is made by examining the amount of “junk” RNA in a species whose differences can be “used to mark the points of divergence from a common genetic ancestor.” The author further reasons that hot environments are more conducive to active chemistry.
Later, the author considers cold-tolerant bacteria as candidates for life on Mars. Here, the chemical activity is much lower, but the ability to persist or lay dormant at temperatures well below freezing becomes an advantage.
Page 277, line 6 The recent discovery of prokaryote bacteria deep within the Earth is of great import – both for estimating of the total amount of life on/in Earth and for the diagnosing the prospects of life in the interiors of other planets and moons.
Page 279, Figure 9.12 The x-axis should be labeled something like “Diversity (Number of Species)”
The y-axis should read “Ground-level oxygen {and} ozone column concentration{s}” “(abundance {as} fraction of {atmospheric pressure} level)”
Page 283, Universal tree of life, line 1 of definition “… length of intron DNA … “ The word “intron” needs definition or modification.
CHAPTER 10: TITAN
Page 288, par 1, line 1 “The Huygens probe has made a safe 2 h descent through Titan’s atmosphere …” The expression “2 h” needs definition or modification.
The author later waxes eloquently suggesting that “… it may be possible to listen to the waves breaking on a snowy methane shore of a hydrocarbon ocean.” Perhaps data from the Huygens lander has been able to address this wonderful prospect(?) This sort of information would make the book’s website worth browsing.
Page 290, Figure 10.3 The corresponding wavelengths along the x-axis are (200 cm-1 = 50.0 microns), (500 cm-1 = 20.0 microns), (1000 cm-1 = 100.0 microns). These should be noted along the top of the plot.
Page 291, par 2, line 4 “Ganemede” should be spelled “Ganymede.”
Page 292, par 3, 4th from last line “… formose {(creating sugars)} and Strecker syntheses {(leading to amino acids)} may occur.”
Page 293, line 1 The author suggests that the surface ocean on Titan had an initial temperature as high as 300 K. Why?
Page 296, par 3, line 9 “…heating of this region of the atmosphere due to the absorption {by} CH4 and radiation trapping by the aerosol particles.”
The vertical temperature profile of Titan’s atmosphere is certainly intriguing – implying lots of radiation trapping in the upper atmosphere.
Page 298, Figure 10.7 The corresponding wavelengths along the x-axis are (200 cm-1 = 50 microns), (1000 cm-1 = 10 microns).
Page 299, line 7 The term “methylene” refers to CH2.
Page 300, next to last sentence “It is clear that a complex hydrocarbon polymer chemistry must exist in the atmosphere of Titan involving polyyne species, polynitrile species and mixtures of the two, and additional routes to poly{cyclic aromatic} hydrocarbon formation.”
Page 301, line 1 “characteristic cracking profiles as seen in …” The phrase “cracking profiles” is not mentioned in pertinent section 6.5 and so needs defining.
The author goes on to suggest that information-bearing molecules are likely on Titan but that the formation of micelles and cells may be more problematic given the surface chemistry. An update from the Huygens probe would be very helpful here.
Page 302, last 4 lines The term “clathrates” needs a definition. They involve a chemical compound (e.g. ammonia-water-ice) that traps another (e.g. methane).
Page 303, Figure 10.13 The term “Hyphae” needs a definition … something along the lines of “long branching tubular filaments.”
Page 303, last line “…being maintained under the {subsurface} pressure – a lipothermal vent.”
Page 304, last line “…encapsulation {and metabolism} being possible, if a little slow.”
Page 305, Liposphere “{The part of Titan’s atmosphere where hydrocarbon-based materials circulate.} … analogous to the hydrosphere {which hosts water cycles} on Earth.”
Astrobiology of Titan “A diversity of {hydrocarbon-rich} environments for life …”
Insert following {Phase change} {Chemistry of the same substances in the gaseous and liquid states can be intractably different.}
GLOSSARY:
Page 308 Birth lines “The track{s} of stars as they evolve from {protostars to pre-main-sequence stars and} onto the main sequence of the Hertzsprung-Russell diagram.”
Black body {An object that absorbs all impinging radiation (light) and emits the same total power over a spectrum whose characteristics depend exclusively on the object’s temperature.}
Black hole {A mass so concentrated that its gravitational attraction will prevent photons of light from escaping beyond its Schwarzschild radius.}
Carbon insertion reaction This reaction does not appear to be well-known among geochemists. Is it something newly realized or is it uncommon?
Carbon-nitrogen-oxygen cycle “CNO fusion cycle in stars greater than 1 M(solar) that produces odd-mass nuclei 13C, 15O, and 15N {as part of catalyzing the fusion of 1H to 4He.}”
Cepheid variable “{Evolved supergiant star} that {has} a periodic variation in {its} luminosity {over days} with a direct relation between the {star’s} luminosity and {its} period {of variability}.”
Page 309 Collision number Shouldn’t it be “Collision rate”?
Cosmic microwave background radiation “Fossil radiation surviving {from} the Big Bang …”
Cycle of star formation “The collapse of a giant molecular cloud forms {stars}; nuclear synthesis within the star{s} produces more elements; {the more massive stars age quickly} and ultimately die in supernova event{s}; {heavy} elements are thrown into the interstellar medium {thereby enriching the next generation of molecular clouds and subsequent stars. Less massive stars contribute less to the enrichment cycle (via late-stage winds) and over longer timescales.}”
Diffuse interstellar bands (DIBs) Add -- {They are often attributed to the absorbing effects of polycyclic aromatic hydrocarbons (PAHs)}.
Doppler shift The apparent change in wavelength of {radiation} associated …
Flux The number or amount of substance passing a point or through an area {per unit time}: the {rate} of photons leaving a star {per unit area (surface flux) – or the photon rate/area that is received at a distance from the star (observed flux).}
Galaxy {A self-gravitating system of stars, gas, dust, and dark matter} located close …
Giant molecular cloud (GMC) Replace with -- {An interstellar cloud of gas and dust with a larger molecular mass of 104 – 106 M(sun) and mean number densities of 102 cm-3. GMCs contain smaller star- forming cores with densities of ~106 cm-3.}
Halley … The orbital period is 75 {years}, …
Helium flash A rapid burst of {He-fusing} reactions in the {core of a red giant star in the} hydrogen- shell burning phase of stellar evolution.
Interstellar medium (ISM) … rising to 106 molecules cm-3 in {the cores of} molecular clouds.
Iron catastrophe … density of iron causes {it} to sink to the core of the planet and{, by spinning,} generate a magnetic field.
Local group The collection of {~40} galaxies, including the Milky Way and Andromeda, that form(s) part of the Virgo {supercluster of galaxies.}
Luminosity The photon flux from the photosphere of a star {or other radiant source, integrated over its surface area. The total radiative power of a radiant source.}
Luminous arc … a gravitational{ly} lensed image of galaxies behind. Can be {many thousands} of light-years in length.
Main-sequence star … Herzprung-Russell diagram {-- characterized by fusing H to He in their cores.}
Microwave spectroscopy ... microwave region of the spectrum {(e.g. the 21 cm hyperfine transition of neutral atomic hydrogen)}.
Neutrino deficit {The rate of subatomic neutrino particles} predicted to be released by the nuclear reactions {in} the Sun {that} should be detected on Earth. The {rate} of neutrinos observed on Earth is {about 3 times} less than {is} predicted by the models of solar nuclear fusion.
Nova A temporary flash in the brightness of a {closely-interacting binary star system that is associated with sudden thermonuclear activity on the surface of a white dwarf star in the binary system.} Compare this with a supernova, which results {from} the destruction of a massive star.
Osmosis The movement of water {or other solvent} against a {solute} concentration gradient through a semi-permeable membrane.
Planck’s Law {The law of radiation characterizing black bodies, based on the quantization of light into photons, where} the relation between energy of a photon and its frequency is E = h ν.
Polycyclic aromatic hydrocarbons (PAHs) … building up from benzene {(C6H6).}
Proton-proton cycle The nuclear reaction sequence combining four hydrogen atoms to form one helium nucleus {plus 2 gamma rays and 2 neutrinos. The gamma rays convey the energy from the thermonuclear reaction.}
Purines One of the two types of {organic} bases in the nucleic acids {RNA and DNA – includes} adenine and guanine.
Pyrimidines One of two types of {organic} bases in the nucleic acids {RNA and DNA – includes} cytosine{, thiamine, and uracil.}
Red giant … resulting in an increase of the star{‘s} radius{, a drop in its surface temperature, and an overall increase (or constancy) in its luminosity.}
Red shift The shift of a transition wavelength to longer, redder wavelength{. For distant galaxies, this effect is associated} with the relative separating distance between the {galaxy} and an observer.
Reddening The preferential removal of short-wavelength, blue radiation from a star {(via absorption and/or scattering)} leaving it looking redder. {The red appearance of the Sun as it sets is a notable example.}
RNA World Hypothesis The recognition that RNA can {both} self-replicate {and govern metabolism} leads to the idea …
SETI Search for Extra Terrestrial Intelligence – a survey of the {electromagnetic sky} looking for signs of communication from other intelligent life.
Snow line The distance from the Sun at which ice and snow can form on the surface of a meteorite or comet{, moon, or planet}.
Solar nebula The {molecular cloud core} from which the Sun formed.
Spectral mapping Using a known transition in an {ion, atom, or molecule (such as the 155 GHz transition in CO)} to map the column density or concentration of the {species} within {an interstellar cloud or complex of such clouds.}
Stefan-Boltzmann Law The relation between temperature and {surface flux} of a star.
Stellar magnitude The astronomical definition of {observed radiant flux} divided {initially} into {the} six classes or magnitudes associated with the visibility of stars {– where 1st magnitude is brightest and 6th magnitude is faintest. This magnitude system now extends to much fainter stellar fluxes and correspondingly greater magnitudes. Absolute magnitudes refer to the apparent (observed) magnitudes of radiant sources when placed at a common distance of 10 parsecs. As such, an absolute magnitude is a measure of a source’s absolute luminosity.}
Stratosphere The layered region of the Earth’s atmosphere {between 18 km and 50 km.}
Strecker synthesis The prebiotic synthesis of amino acids{, involving simple molecules containing H, C, N, and/or O.}
Supernova The explosion of a star resulting {from} the destruction of a star {-- either through the implosion of a massive star’s dormant nucleus or through the annihilation of a white dwarf star upon exceeding the Chandresekhar limiting mass of 1.4 M(sun).}
Terraforming Adding chemicals to the atmosphere of a planet such as Mars {(and other modifications)} to initiate a …
T-Tauri stars Stars early in their evolution that throw off a dust jacket in the form of {bi-}polar jets and begin to shine.
Universal tree of life The categorization of {the} species on Earth {based on their} genetic material {as it relates to} a common genetic ancestor. {The greater the distance from its ancestor, the more recent the species.}
APPENDIX B: ASTRONOMICAL DATA
The rightmost column should be labeled “Apparent Magnitude” to distinguish it from the star’s Absolute Magnitude.
APPENDIX C: THERMODYNAMIC PROPERTIES OF SELECTED COMPOUNDS
For easier reference, the name for EACH compound should be listed next to the chemical formula.