Wednesday, March 5, 2014

Aging and the Human Lifespan


I noted earlier in this volume that one of the universally understood cycles among humans is the great arc of a lifetime, the transition (if a person survives to live out his or her “natural” life) from infant to toddler to pre-teen child to adolescent to young adult to middle aged adult to person in “early old age” to genuinely elderly person. Virtually all humans have seen people from each of these stages of life, and almost everyone older than a small child understands that they themselves are in this cycle. So both witnessing and experiencing the phenomenon of aging is fundamental to the human experience. Why do people age, what biological mechanisms drive this process? Why do we only live as long as we do? Why is our time in this world limited? These are the questions we will now plunge into, in order to complete our examination of the human as a physical being. For the fundamental fact of life is this: there will be a day when the world will be here—but we will not.

Aging

Many hypotheses about aging have been offered over the years, but a great deal of interest now seems to be focused either on how errors accumulate during the process of cell reproduction, or how cells degenerate over time. Cell reproduction is the product of mitosis, to which I have referred before.  Mitosis was the original means by which cells on Earth reproduced. It involves a parent cell making copies of its DNA, dividing, and giving rise to a daughter cell. Mitosis is separated into distinct phases, and the last part of the final phase is known as cytokinesis, in which the cell division process is completed.1 Those cells that reproduce do so at greatly varying rates.

When a cell has run its time, when it can no longer divide, it is destroyed in a process called apoptosis. Apoptosis is a sort of programmed cell death. At any given moment many cells in a human body are dying in a biologically “planned” manner. At any given moment many cells are being created. (You literally are not the person you were last year.) Cells, of course, can die from other causes, such as external injury that results in tissue necrosis.  Some cells do not reproduce at all. The permanent sets of cells we have don’t, such as neurons (although there is recent evidence that the cells in those brain structures associated with memory may in fact do so), and muscle cells. Other non-reproducing cells include the red blood cells, which, as we saw, last about 120 days.

When a human is young and growing, cell production is (generally) vigorous. In a young adult, cell production and cell repair processes (generally) work well. But as the aging process accelerates, cell death or cell deterioration begins to outweigh the ability of cells to repair and renew themselves. Those cells that are reproduced are reproduced with more and more flaws. Cell lines can accumulate mutations during the reproductive process, and even the control genes in charge of repairing mistakes can themselves mutate. Some scientists theorize that the accumulation of such errors and mutations is one of the principal causes of aging.

In fact, there are only so many divisions of which a particular kind of cell is capable. When a cell can no longer divide, it has reached an insurmountable barrier. Fetal cells are an example of this phenomenon. As one researcher has put it:

Due to the work of [Leonard] Hayflick … the finite lifetime of diploid cells in culture has become commonly known as the Hayflick limit. After a period of active multiplication, generally less than one year (approx. 50 cell divisions), primary human fetal cells in culture demonstrate an increased generation time, gradual cessation of mitotic activity, accumulation of cellular debris and, ultimately, total degeneration.2

It appears that different kinds of cells have different Hayflick limits, but many sources put the average number at around 50-52, with others citing a range of 50-70. Why do cells lose the ability to reproduce? At the ends of chromosomes are structures called telomeres. Telomeres are non-coding sections of DNA. They consist of a repeated series of bases, TTAGGG/CCCTAA. This same sequence of bases has been discovered in dozens of different vertebrates, including mammals, birds, reptiles, amphibians, and fish. In fact, this sequence of bases may be more than 400 million years old,3 and it is believed to be a universal vertebrate trait. Telomeres act as boundaries for chromosomes, in a sense. They help keep chromosomes from interfering with the functions of other chromosomes, and they protect the ends of chromosomes from degrading. Some observers compare telomeres to the plastic pieces at the ends of shoelaces; they keep chromosomes from “fraying”. In human cells, telomere lengths vary from 500 and 15,000 pairs of telomere repeats, depending on the kind of cell.4 Each reproduction of a cell shortens the length of the telomeres because some of the bases of which they are composed are lost. When telomeres become too short, the cell containing them can no longer reproduce. An enzyme called telomerase, which helps protect the ends of chromosomes, can keep the deterioration of the bases that comprise the telomeres at bay, particularly in the stem cells from which many kinds of other cells are constructed.  However, if telomerase mutates, it gives certain cells a way around the Hayflick limit, allowing  them to undergo unlimited reproduction. This growth is known as cancer.5

It would be far too sweeping a statement to say that telomere shortening alone is the chief cause of aging. Other factors bear consideration as well. Prominent among them are:

--Glycation, the ability of sugars in the body to link with proteins, lipids, and nucleotides to form advanced glycation end products (AGEs). It is these substances that are so dangerous to diabetics. They are implicated in every pathology to which diabetes sufferers are vulnerable, including, among others, damage to the retinas (retinopathy), damage to the kidneys, and atherosclerosis. Three medical doctors specializing in diabetes point out that tobacco consumption is a major source of AGEs. But the worst culprit?:

Food processing, heating in particular, has a significant accelerating effect in the generation of glyco- and lipoxidation products. Heat helps create tasteful flavors that humans have learned to enjoy. In recent decades, food manufacturers have been using this knowledge to boost the flavor of natural foods by incorporating synthetic AGEs into foods. Consequently, the AGEs content of the Western diet has increased vastly in the past 50 years, as has the quantity of food consumed.6

Moreover, there is evidence that glycation may not just be a threat to diabetics. It may have a generalized aging effect, and it may be implicated in the onset of neurodegenerative disorders such as Alzheimer’s Disease and Parkinsonism, although this conclusion may not yet be definitive.7 Glycation also appears to play a part in…

--Oxidative stress. The mitochondria in animal cells use oxygen and nutrients to manufacture ATP (adenosine triphosphate), the chemical that powers a cell’s metabolic processes. In the normal course of this function, they generate reactive oxygen species (ROS). ROS is a term used to describe varieties of oxygen atoms or oxygen atoms linked to hydrogen atoms, varieties called  free radicals. Free radicals have an unpaired electron, and they “seek” electrons to take from other atoms or molecules. The result of this is damage throughout the body’s systems, as free radicals destabilize and harm cells of all kinds. The mitochondria and the body’s cells do have their defenses against these free radicals (in mitochondria they are called detoxifying systems), but sometimes the defenses cannot be brought to bear fast enough to stop all of the radicals. A team of scientists studying this whole phenomenon has noted a dilemma here:

The mitochondrial ROS emission may be greatly exacerbated by ROS-inflicted damage that results in further activation of mitochondrial ROS generating sites (“vicious cycle”). For example, mitochondrial enzyme aconitase can be damaged and inactivated by ROS in a way that leads to elevated hydroxyl radical production, thereby adding an autocatalytic, positive feedback loop to the oxidative stress cascade…Therefore, preventing mitochondrial ROS emission rather than scavenging emitted ROS may perhaps be the most efficient strategy to minimize the contribution of mitochondria to oxidative stress.8

In other words, the more ROS damages a mitochondrion, the more ROS the mitochondrion will generate, allowing more damage to be inflicted, and so on—a vicious cycle indeed. It may be impossible to stop the leakage of stray oxygen atoms from our mitochondria. In effect, we may age in part simply because our metabolic system operates in the way it does. In a sense, we are burning ourselves out with the very oxygen we need to survive.

-- Senescent Cells

As we have noted, there are cells that are never replaced. A human may have them over the entire course of a lifetime. Cells, of course, can be damaged by free radicals. They can also suffer DNA damage caused by radiation and other external mutagenic factors. The structures of neurons, which include the axons, dendrites, and their substructures, may undergo deterioration, and the brain as a whole diminishes in size as humans age. Permanent cells are not immortal. They can function for decades, but they are still subject to degeneration. Increasing numbers of senescent cells may simply cause the areas of the body of which they are a part to decline in function, a decline that accelerates with age.

In truth, we do not yet know all the causes of human aging. There are promising areas of research being pursued, and there are even people talking about extending the human lifespan to centuries, which seems unlikely at the time of this writing. But however successful such efforts are, it is my view that life will always be finite. It certainly is in the modern world.

Life Expectancy

The extreme limits of human age appear to be in the 120 year range, + or – a couple of years, an age attained by only a handful of humans in the recorded history of our species.

Life spans of or in excess of 110 are an extreme rarity in human populations. Of course, it is only within the last 150 years or so that reliable mortality statistics have been gathered by the governments of the advanced nations, so we cannot judge previous eras with complete certainty. But given our understanding of aging, however incomplete, it does appear as if 115-120 years of life is indeed the maximum a human can attain.

The calculation of life expectancy is distorted somewhat by infant mortality statistics. We must assume, for example, that early sapiens lost a terrible number of children under the age of one to disease. Since many, if not all early sapiens groups engaged in frequent migratory behavior, this would have exposed young children to many harsh conditions and disease vectors.  The average age would have been dragged down by the numbers of children who died. So when we hear of early sapiens having a life span of 30 (by some estimates), we need to remember that for those people who got out of childhood alive, the odds were much better. Still, given the many difficulties our ancestors must have faced, it seems unlikely that there were many centenarians among them.

Women, as a rule, live longer than men. At the time of this writing, there are 67 nations or territories in which the female life expectancy exceeds 80 years of age. By contrast, there are only 4 in which the male life expectancy reaches 80 or more. In terms of life expectancy by nation, the major European states, plus Japan, Australia, Israel, New Zealand, Canada, and a number of small Asian and European entities dominate the top 30 places; African states form almost all of the bottom 20.9

There is definitely a genetic component in lifespan. Obviously, socioeconomic status, access to medical care, adequate nutrition, and other environmental factors play a major role in life expectancy. Yet, after all those variables are weighed, there still appear to be individuals who are genetically-well positioned to outlive most of their peers, and this genetic advantage does seem to run through certain family lines. A major study done on sets of twins in Scandinavia, comprising more than 20,000 individuals, found that genetic factors affecting lifespan didn’t seem to be very significant prior to age 60, but after that age their influence grew more important. The researchers conducting this study concluded,

Based on a large population-based and almost exhaustive sample of twins [with] more than 90 years of follow up, we find evidence of familial clustering of longevity. The present study is the first to demonstrate that at population level genetic variants for survival may exist with a pattern compatible with a significant and constant to increasing influence of genetic factors with age.10

Some of the most significant research on the genetic component of human lifespans is found in the Leiden Longevity Study. Three generations of long-lived siblings were compared in this study of Dutch families. The comparison also included the spouses of the siblings, the off-spring of the siblings, the spouses of their offspring, and a number of cousins of the siblings. The results demonstrated convincingly that genetic inheritance plays a major role in life expectancy. It is noteworthy that the long-lived individuals studied and examined, living in exactly the same environmental conditions as their spouses, exhibited longer lifespans at a rate beyond simple statistical probability. Further, siblings displayed a similarity of longevity to each other that can only be attributed to genetic familial clustering, and not environmental factors.11

Does Death Have a Biological Function?

Living beings display a tremendous range of lifespans. For example, it appears that at the colony level, if not at the individual level, many species of bacteria are virtually immortal, and examples of bacteria that apparently live for millions of years have been discovered. Sequoia trees are known to reach the age of 5,000. Conversely, many insects are very short-lived, living just a few days, or a few months at best, and many flowering plants are annuals. Humans find themselves in somewhat of a middle position (although not exactly so) in this astonishing range. Given such a wide breadth of lifespans in nature, we ask, why does death come to some beings so much more quickly than to others? Is there an evolutionary basis for death? More philosophically, perhaps, we ask, why do we die at all, what purpose does this serve? If the goal of life (at the biological level) is reproductive success, then why do humans age, lose the ability to reproduce, and get taken out of the game permanently? Countless humans have yearned for immortality throughout the ages. Why has natural selection not bestowed it on us, or at least given us the kind of vast lifespan granted to so many beings? No definitive answers to these questions can be given, but I have some of my own thoughts and conjectures about them.

First, natural selection operates solely on the basis of whatever works. It is a process, not a conscious entity possessing volition and moral agency. As I have noted, many of the solutions that natural selection has “devised” to meet the challenges of life are clumsy and suboptimal. Moreover, we need to remember something else about life on this planet: more than 99.9% of all species have gone extinct. They went extinct largely because environmental conditions changed, rendering their genetically-produced adaptations to previous conditions either useless or downright harmful. Humans are the product of this biological ferment. We are a product of the Law of Whatever Works. We are not evolved to be immortal because mortality “works” for beings like us. The fact that we die does not set up an insurmountable barrier to reproductive success. We can both reproduce and die, and just as long as the reproduction precedes the death, that system works. Moreover, there is an unconscious trade-off life seems to have made. In exchange for their multicellularity and ability to move independently through the air, landscape or seascape, animals have been given limits. Bacteria, being simple, can be immortal. Living animals, being complex and mobile, cannot be. That just seems to be the way things are.

One could argue that the repair processes of a human’s body could be made so efficient that the human could live indefinitely, but such a vast “upgrade” of our repair capabilities would require a fundamental reconfiguration of our entire physical being. It would be the ultimate in unnatural selection. It is possible, perhaps, but humans, like all other animals, are constructed out of basic, simple materials, as I have pointed out several times. The very stuff out of which we are made is impermanent, and subject to all the changes that every physical substance anywhere is subject to. Even a structure as seemingly permanent as a huge dam will begin to crumble within 100,000 years, and a dam is chemically far less complex and active than a living being. Reconstituting a human to be immortal would involve inconceivably huge efforts. We’re not built to last because we didn't need to be.

I do not want my words to be misinterpreted as misanthropy, but I have to be completely honest about my views here. The existence of the human race on this planet is not in itself a required condition for the survival of either the planet or the life on it. In fact, as far as the latter point goes, far from being essential for life, humans are the only beings on the planet with the capacity to abolish it. It will sound incredibly harsh, but from a biological standpoint, it did not “matter” whether humans came to exist or not. They were a by-product of the planet Earth’s physical, chemical, and biological processes, a particularly unique example of an emergent phenomenon, perhaps, but nothing more. Humans, naturally, see themselves as extraordinary, and in the context of this world they are, of course. But they are not necessary. Life would go on without them, and the planet Earth would still be destroyed by the Sun whether any human-descended animal were there to see it or not. Even the Sun that destroys the Earth will die—and so will we. There is no why to death. There is only the fact of it. We are, in that sense, no different than anything else that exists.

“Earth to earth, ashes to ashes, dust to dust.” So the phrase from a prayer book goes. We are of this planet. When the bodies we are finally and irrevocably break down, the atoms and molecules out of which we were composed will again join the mass of those from which the Earth itself is made. Our chemical elements will find their way into new forms and arrangements, perhaps even other living beings. Most people take consolation from the belief that a metaphysical existence will follow this one. The truth or falsity of that proposition cannot be demonstrated, and must necessarily be a matter of individual faith. But one thing is sure: our physical lives are fleeting and impermanent. We are, as I have said, probably the only animal that knows that death will come to everyone. One of the foundations of human cultural and social life has been our response to this knowledge. Human history is the story of physical beings, fallible, vulnerable—and mortal.


From such stuff as this has the human world been made.



Appendix: Sources of Information About the Age of the Universe, Methods for Dating the Past, and the Geological Eras of the Earth

A.  The Age of the Universe
Information about the Wilkinson Microwave Anisotropy Probe, which ascertained the age of the Universe to within 1%, is here:
http://map.gsfc.nasa.gov/
A more specific explanation of WMAP’s techniques is here:
http://map.gsfc.nasa.gov/universe/uni_age.html

B.  Methods for Dating the Past
Dr. Dennis O'Neil, from the Behavioral Sciences Department, Palomar College, San Marcos, California, has assembled an excellent collection of dating techniques located here:
http://anthro.palomar.edu/time/time_4.htm
http://anthro.palomar.edu/time/time_5.htm
Dr. O’Neil also links to a host of sites giving more detailed information on each method:
http://anthro.palomar.edu/time/links.htm

The Website Darwiniana also contains an excellent list of methods:
http://darwiniana.org/datingmethods.htm 

C.   The Geological Eras of the Earth
The International Commission on Stratigraphy has set the standard for the world with this chart of the Earth’s geological eras:
http://www.stratigraphy.org/column.php?id=Chart/Time%20Scale


Chapter Notes and Sources for Volume One

First Things

How It Looks to Us: The Human Frame of Reference: The concept of absolute perspective is discussed in Roger Scruton’s Modern Philosophy.

A Species Lost in Both Space and Time: I found Timothy Ferris’s Coming of Age in the Milky Way to be deeply impressive, and Atoms of Silence by Hubert Reeves provided additional evidence, although since its publication in the 1980s a great deal more has been discovered. The popular book Solar System in the Time-Life Planet Earth series got me to thinking about these issues and provided data on stars in our galaxy as they compare to our Sun. NASA’s wonderful web resources filled out the picture of these stars in greater detail, as well as providing data about galaxies “near” our own.

The Search: The Existential Dilemma of the Human Being: I have used quotes from The Brothers Karamazov by Fyodor Dostoyevsky and The Myth of Sisyphus by Albert Camus.

Hidden Realities

Self-Organization and Emergence:

1.   Deutsch, David, The Fabric of Reality, pp. 20-21
2.   F. Heylighen,  "Self-Organization, Emergence and the Architecture of Complexity", in:
      Proceedings of the 1st European Conference on System Science, (AFCET, Paris), p. 23-32., 1989
3.   Pagels, Heinz, The  Dreams of Reason,  pp. 65-66
4.   Jan Ambjørn, Jerzy Jurkiewicz, and Renate Loll, “The Self-Organizing Quantum Universe”, in Scientific American, July 2008
5.   Kauffman, Stuart, At Home in the Universe: The Search for the Laws of Self-Organization and Complexity, pp. 79-110
6.   Kauffman, pp. 74-79
7.   Kaufmann, pp. 77-83
8.   Waldrop, M. Mitchell, Complexity: The Emerging Science at the Edge of Order and Chaos, pp. 304-306
9.   Arshinov, Vladimir, and Fuchs, Christian, editors. Causality, Emergence, Self-Organization, pp. 5-8
10. Tom De Wolf, , and Tom Holvoet, “Emergence Versus Self-Organisation: Different  Concepts but Promising When Combined”,  Department of Computer Science, Kuleuven, Celestijnenlaan Leuven, Belgium, 2005
11. Hazen, Robert, Genesis: The Scientific Quest for Life's Origins, pp. 17-22
12. Laughlin, Robert B., A Different Universe: Reinventing Physics from the Bottom Down, pp. 173-221

The Rules of the Game: The Original Rulebook:

1.  Plumley, J. M., “The Cosmology of Ancient Egypt” in The World of Physics, Volume I: The Aristotelian Cosmos and the Newtonian System,  edited by Jefferson Hane Weaver, pp. 188-200
2.  Lindberg, David C., The Beginnings of Western Science: The European Scientific Tradition in Philosophical, Religious, and Institutional Context, 600 B.C. to A.D. 1450, pp. 13-20
3.  Needham, Joseph, Science & Civilisation in China. Volumes III and IV (Part 1), passim; Li, Dun J., The Ageless Chinese, pp. 94-96
4.  Basham A. L., The Wonder That Was India, pp. 488-503
5.  African megaliths are discussed in the June 2004 edition of Antiquity, linked here: 
http://findarticles.com/p/articles/mi_hb3284/is_300_78/ai_n29103192/?tag=content;col1 
6.  The decline in Arab science is discussed in the AAAS’s journal Science, dated 3 June 2005, in an article by Wasim Maziak, located here: 
http://www.sciencemag.org/cgi/reprint/308/5727/1416.pdf 
7.  The reference to Pawnee star observations is from a journal article: Fletcher, Alice C.  “Star Cult Among the Pawnee-A Preliminary Report” in American Anthropologist October-December, 1902 Vol.4(4):730-736. It is found here: 
 http://www.publicanthropology.org/Archive/Aa1902.htm
8.  The brief discussion of Aboriginal Australian astronomy is drawn primarily (but not exclusively) from the article, “The Astronomy of Aboriginal Australia” by Ray P. Norris and Duane W. Hamacher, published by the International Astronomical Union in 2009.
9.   Lindberg, pp. 25-32
10. Gottlieb, Anthony, The Dream of Reason: A History of Philosophy from the Greeks to the Renaissance, pp. 21-40
11. Lloyd, G. E. R., Greek Science After Aristotle, pp. 40-58
12. Lucretius, On the Nature of the Universe,  p. 79
13. Lindberg, pp. 98-105
14. Stanford Encyclopedia of Philosophy, http://plato.stanford.edu/entries/abelard/#The
15. The excerpt from the 1729 edition of Newton’s Principia Mathematica is here: 
http://gravitee.tripod.com/axioms.htm 
16. Atkins, P.W., The Second Law, p. 190
17. The section on thermodynamics benefited from information found on Hyperphysics and NASA’s web site, and P. W. Atkins’s study The Second Law. Information also came from John Gribbins’ The Scientists and  W.C. Dampier’s A History of Science.
18.  Oxtoby, David W., Gillis, H. Pat, and Campion, Alan, Principles of Modern Chemistry, pp. 10-12
19.  A useful and complete discussion of Faraday’s Law of Induction may be found here:
http://ocw.mit.edu/courses/physics/8-02sc-physics-ii-electricity-and-magnetism-fall-2010/faradays-law/MIT8_02SC_notes21.pdf
20.  A concise summary of Faraday’s two Laws of Electrolysis may be found here:
http://chemistry.proteincrystallography.org/article92.html
21.  A concise examination of James Clerk Maxwell’s equations, and a brief biography of Maxwell may be found here: http://scienceworld.wolfram.com/physics/MaxwellEquations.html. A more technical examination of Maxwell’s Equations may be found here:
http://hyperphysics.phy-astr.gsu.edu/hbase/electric/maxeq.html#c2


The Rules of the Game: The New Rulebook:

1.   Feynman, Richard,  Six Easy Pieces, page 23
2.   Greene, Brian,  The Fabric of the Cosmos, pp. 223-225
3.   Close, Frank,  Lucifer’s Legacy: The Meaning of Asymmetry, p. 7
4.   Halpern, Paul, The Great Beyond: Higher Dimensions, Parallel Universes, and the Extraordinary Search for a Theory of Everything, p. 4 
5.   Einstein, Albert,  Relativity: The Special and General Theory, pp. 18-21
6.   Einstein, pp. 22-28
7.   Einstein, pp. 29-30
8.   Einstein, pp. 31-35
9.   Einstein, pp. 36-38
10. Einstein, pp. 45-49
11. Einstein, pp. 56-58
12. Einstein, pp. 59-62
13. Einstein, pp. 63-65
14. Einstein, pp. 75
15. Einstein, pp. 79-82
16. Einstein, pp. 94-97
17. Einstein, pp. 98-100
18. Einstein, pp. 101-105
19. Einstein, pp. 109-115
20. Greene, pp. 47-50
21. Kirshner, Robert, Extravagant Universe: Exploding Stars, Dark Energy, and the Accelerating Cosmos p. 254
22. Hooper, Dan,  Dark Cosmos: In Search of Our Universe’s Missing Mass and Energy p. 62
23. Hooper, p. 129
24. Hooper, p. 78
25. Gates, Evalyn,  Einstein’s Telescope: the Hunt for Dark Matter and Dark Energy in the Universe, 159-167
26. Hooper, pp. 86-99
27. http://www.scholarpedia.org/article/Dark_energy
28. Kirshner, p. 258
29. http://hubblesite.org/newscenter/archive/releases/2009/08/full/
30. Information on the MOND hypothesis, admittedly slim in total,  has been gleaned from articles published by the Royal Astronomy Society's National Astronomy Meeting in 2008 and Scientific American, also in 2008. [Revise citation]
31.  Hooper, pp. 168-69
32.  Gates, pp. 208-212
33.  Smolin, Lee,  The Life of the Cosmos, pp. 44-46
34.  Hawking, pp. 67-68
35.  Clark, Ronald W., Einstein: The Life and Times, p. 421
36.  Gribbin, pp. 91-102
37.  Gell-Mann, Murray, The Quark and the Jaguar: Adventures in the Simple and the Complex,  p. 138
38.  Herbert,  Nick, Quantum Reality: Beyond the New Physics, pp. 240-245
39.  Gribbin, John, Schrödinger’s Kittens and the Search for Reality, p. 230
40.  Polkinghorne, J. C., The Quantum World, p. 18
41.  Gell-Mann, pp. 132-33
42.  Gell-Mann, p. 139
43.  Bruce, Colin, Schrödinger’s Rabbits: The Many Worlds of Quantum, p. 126
44.  Rees, Martin, Just Six Numbers: The Deep Forces That Shape the Universe, p. 106
45.  Rees, pp. 1-4
46.  Discover magazine, September 2009. It is here:
http://discovermagazine.com/2009/sep/06-discover-interview-roger-penrose-says-physics-is-wrong-string-theory-quantum-mechanics/article_view?b_start:int=0&-C=
47.  Omnes, Roland, Quantum Philosophy: Understanding and Interpreting Modern Science, pp. 212-213

In my quest to teach myself the elementary basics of the subjects I discussed, I found the following online sources useful: Hyperphysics, Wolfram Research, NASA, and a wide variety of university-based sites.

Information on dark matter and dark energy was drawn from Dan Hooper’s Dark Cosmos: In Search of Our Universe’s Missing Mass and Energy, Evalyn Gates’ Einstein’s Telescope: the Hunt for Dark Matter and Dark Energy in the Universe, and Robert P. Kirshner’s Extravagant Universe: Exploding Stars, Dark Energy, and the Accelerating Cosmos.

Dark energy is well discussed in an article written by U. C. Berkeley scientist Eric Linder in Scholarpedia (which is NOT an open wiki reference like Wikipedia, but rather a peer-reviewed scientific publication). A website devoted to the Chandra X-Ray Observatory, in association with NASA, defends the dark matter and dark energy hypotheses vigorously.

The history of the development of quantum mechanics is drawn from John Gribbin’s, The Scientists: A History of Science Told Through the Lives of Its Greatest Inventors, pp. 508-528, supplemented by Ronald W. Clark’s  Einstein: The Life and Times and the article “One Hundred Years of Quantum Physics” by  Daniel Kleppner and Roman Jackiw which appeared in the journal Science in 2000. Sources used in the discussion of quantum principles themselves included Nick Herbert’s Quantum Reality: Beyond the New Physics, Murray-Gell-Mann’s The Quark and the Jaguar: Adventures in the Simple and the Complex, Roland Omnes’s Quantum Philosophy: Understanding and Interpreting Modern Science, J. C. Polkinghorne’s The Quantum World, Gribbin’s Schrödinger’s Kittens and the Search for RealitySchrödinger’s Rabbits: The Many Worlds of Quantum by Colin Bruce, and A Brief History of Time: From the Big Bang to Black Holes by Stephen Hawking. The Stanford Encyclopedia of Philosophy also has an excellent array of articles on many aspects of quantum mechanics, and although it is not customary to rely on references as sources, I feel I am on solid ground with the SEP.

Particle physicists discuss the hypothesized Higgs Boson in a 1999 Scientific American article located here:  http://www.scientificamerican.com/article.cfm?id=what-exactly-is-the-higgs

Is Mathematics the Real Reality?

1.  Francis, John, Philosophy Of Mathematics, p. 50
2.  Monk, Ray, Bertrand Russell: the spirit of solitude, 1872-1921, Volume 1, p. 248
3.  Wigner, Eugene, Symmetries and Reflections: Scientific Essays, pp. 222-230
4.  http://www.exploringbinary.com/binary-code-on-the-pioneer-10-spacecraft/
5.  Russell, Bertrand, Logical and Philosophical Papers, Vol.4 1903-05, pp. 476-78
6.  Parson, Charles,  “Platonism and Mathematical Intuition in Kurt Gödel’s Thought” in The Bulletin of Symbolic Logic Volume 1, Number 1, March 1995
7.  Hersh, Reuben, What is Mathematics, Really?  p. 12
8.  Livio, Mario. Is God a Mathematician?, p. 237
9.  Livio, pp. 234-238
10. Livio, pp. 10-11
11. The Stanford Encyclopedia of Philosophy, article, “The Philosophy of Mathematics”
12. Hofstadter, Douglas, Gödel, Escher, Bach p. 99 
13. http://www.peterrussell.com/Reality/realityart.php
14. http://mathworld.wolfram.com/e.html
15. Davis, Philip J., and Reuben Hersh, Descartes’ Dream: The World According to Mathematics, p. 283

A statement by David Valdman, a PhD candidate in mathematics, was fascinating to me. I didn’t want to insert it into the chapter, as it was overly long for that purpose, but I didn’t have the heart to cut any of it, and so I will include it here:

However, the impurities in the physical representation of our world (from evolution), and our unreliable intuitive physical beliefs (from prejudice) are barriers to our understanding. In order to really grasp our reality, one needs to shed his potentially corrupt sensory data and any preconceived notions no matter how obvious seeming. All our experiences and observations are results of the interaction between our minds and bodies with an underlying reality, but if there were a way to bypass that interaction and reach the underlying reality directly only then would we grasp the essence of what is out there. We must literally study reality from the perspective of a rational inanimate object—a rock with reason—ignoring our internal reality and focusing only on the external. This requires a physics stripped of the physical. It requires mathematics.

External reality is the same whether you are blind or deaf, man or machine, alive or dead; only internal reality is concerned with such things because it relies on mechanisms of interpretation—it relies on senses. Difference is defined by assumption. Reality is experienced, and constantly created, internally within the mind. There are no pixels. Our image of the world is the product of chemical disturbances in our brains. A spatially extended reality need not even exist! So it is extremely fascinating: to wonder where the image of our reality appears, when we casually brush it off, assuming it to be “out there” when it is within us all along.

Our minds and bodies have grown to interpret reality in a certain, non-unique, way. It may be that there exists a most basic, most fundamental reality, of which scientific insights and natural experiences are translations. If such a reality existed, I would imagine it mathematical in nature. There would be no greater spiritual realization for me than to unify this beautiful world through the power of mathematics. Everything physical would disappear as mere fabrications of a deeper reality, independent of space and time. All we have come to know and experience would emerge as an epiphenomenon—a consequence—of pure math. But I could easily be getting ahead of myself. And the axioms on which reality is built may be physically inspired.

And about Kurt Gödel, as stated in the Stanford Encyclopedia of Philosophy:

Gödel held that there is a strong parallelism between plausible theories of mathematical objects and concepts on the one hand, and plausible theories of physical objects and properties on the other hand. Like physical objects and properties, mathematical objects and concepts are not constructed by humans. Like physical objects and properties, mathematical objects and concepts are not reducible to mental entities. Mathematical objects and concepts are as objective as physical objects and properties. Mathematical objects and concepts are, like physical objects and properties, postulated in order to obtain a satisfactory theory of our experience. Indeed, in a way that is analogous to our perceptual relation to physical objects and properties, through mathematical intuition we stand in a quasi-perceptual relation with mathematical objects and concepts. Our perception of physical objects and concepts is fallible and can be corrected. In the same way, mathematical intuition is not fool-proof …but it can be trained and improved. Unlike physical objects and properties, mathematical objects do not exist in space and time, and mathematical concepts are not instantiated in space or time.

Randomness, Probability, and Coincidence

1.  Mlodinow, Leonard, The Drunkard’s Walk: How Randomness Rules Our Lives, p. 23
2.  Mlodinow, pp. 33-34
3.  Mlodinow, p. 35
4.  Ash, Robert, Basic Probability Theory, passim
5.  Taleb, Nassim Nicholas, The Black Swan: The Impact of the Highly Improbable, passim
6.  Clarke, Arthur C., Profiles of the Future, pp. 12-21
7.  Grinstead,  Charles M. and Snell, J. Laurie,  Introduction to Probability, 2nd edition, pp. 305-312
8.  Paulos, John Allen, Innumeracy: Mathematical Illiteracy and Its Consequences, pp. 25-48
9.  “Synchronicity”, Skeptic’s Dictionary, located at: http://www.skepdic.com/jung.html
10. Paulos, pp. 33-34

Chains of Unintended Consequences 

1.  Rhodes, Richard, The Making of the Atomic Bomb, p. 13
2.  Messer, Ellen, “Potatoes (White)”, in The Cambridge World History of Food, edited by Kenneth R. Kiple and Kriemheld Coneè Ornelas, located here: 
http://www.cambridge.org/us/books/kiple/potatoes.htm

Synergy and Feedback Loops:

1.  Fuller, R. Buckminster, Synergetics: Explorations in the Geometry of Thinking, p. 3
2.  Fuller, p. 13
3.  Thomas, Gareth, Medicinal Chemistry: An Introduction, p. 184
4.  Corning, Peter, Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution, Pp. 40-41
5.  Corning, Peter, Nature's Magic: Synergy in Evolution and the Fate of Humankind, pp. 8-12 
6.  Xiao-Jun Tian, Xiao-Peng Zhang, Feng Liu, and Wei Wang, “Interlinking positive and negative feedback loops creates a tunable motif in gene regulatory networks” in Physical Review, E 80, 011926, 2009
7.  R. A. Bowen, “Control of Endocrine Activity” from Colorado State University, located here: http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/basics/control.html
8.  M. Moravec and J. Moravec, “Adrenergic neurons and short proprioceptive feedback loops involved in the integration of cardiac function in the rat”, in Cell and Tissue Research, 1989 November; 258(2):381-5
9.  Marta I. Garrido, James M. Kilner, Stefan J. Kiebel, and Karl J. Friston, “Evoked brain responses are generated by feedback loops”, in PNAS, 2007 December 26; 104(52): 20961–20966
10. Eric Davidson and Michael Levin, “Gene regulatory networks” in PNAS, 2005 April 5; 102(14): 4935
11. Tian, et al

Patterns, Shapes, and Cycles: 

An excellent gallery of naturally occurring patterns may be found here: 
http://photography.nationalgeographic.com/photography/article/patterns-nature-galleries.html

Another wonderful collection of natural patterns may be found here:
http://easyweb.easynet.co.uk/~iany/patterns/patterns.htm

In discussing the biogeochemical cycles, Physical Geography.net and Science Ray were very useful..

Solar and climatic cycles:
http://friendsofscience.org/assets/files/documents/Solar%20Cycle%20-%20Friis-Chr_Lassen-.pdf
http://www.sciencedaily.com/releases/2002/06/020607073439.htm

Ocean cycles:
http://www.physicalgeography.net/fundamentals/8b.html

1.  Boorstin, Daniel, The Discoverers: A History of Man’s Search to Know His World and Himself, pp. 4-12)
2.  NASA Goddard Space Flight Center, located here: http://www.nasa.gov/centers/goddard/home/index.html
3.  Ball, Philip, The Self-Made Tapestry: Pattern formation in nature,  pp. 9-10

The World as a Set of Interrelated Systems:

1.  Klir, George J.,  Facets of Systems Science, pp. 12-13
2.  Bertalanffy, Ludwig von, General System Theory, pp. 19, 34
3.  Bertalanffy, pp. 55-56, 83-86
4.  Peter Fryer and Jules Ruis, “What Are Fractal Systems?”, located here:  http://www.fractal.org/Fractal-systems.htm

The World as a Disequilibrium System:  The story of the Taiping uprising has been masterfully told in Jonathan Spence’s God’s Chinese Son: The Taiping Heavenly Kingdom of Hong Xiuquan. (Passim)

The Emergence of Human Consciousness: A Chronology

Beginning:

1.   Silk, Joseph,  Cosmic Enigmas pp. 13-14 
2.   Coles, Peter, and Lucchin, Francesco. Cosmology: The Origin and Evolution of Cosmic Structure, pp. 119-122;  
3.   Atkins, Peter, . Creation Revisited , p. 149;
4.   The statement by Paul Davies may be found here:
http://www.fortunecity.com/emachines/e11/86/big-bang.html
5    Genz, Henning, Nothingness: The Science of Empty Space, pp. 199-202
6.   Barrow, John D. The Book of Nothing: Vacuums, Voids, and the Latest Ideas About the Origins of the Universe, pp. 287-297;
7.   Genz, p. 262;
8.   Levin, Frank, Calibrating the Cosmos: How Cosmology Explains Our Big Bang Universe, p. 3
9.   Hawking’s 1988 statement may be found here:
http://www.ralentz.com/old/astro/hawking-1.html
10. Hawking’s 2007 statement may be found here:
http://berkeley.edu/news/media/releases/2007/03/16_hawking_text.shtml
11. New Scientist, 28 June 2008
12. Kaku, Michio, Parallel Worlds: A Journey Through Creation, Higher Dimensions, and the Future of the Cosmos p. 105; 
13. Tyson, Neil De Grasse, and Donald Goldsmith, Origins: Fourteen Billion Years of Cosmic Evolution, p. 39
14. PhysOrg, January 17, 2012,  “The perfect liquid -- now even more perfect” 
http://www.physorg.com/tags/quark+gluon+plasma/
15. Vilenkin, Alex, Many Worlds in One: The Search for Other Universes, p. 34
16. Ferris, Timothy, Coming of Age in the Milky Way, pp. 340-346
17. Levin, pp. 229-235;
18. Hawley, John F., Holcomb, Katherine A., Foundations of Modern Cosmology, p. 370 
19. Levin, p. 187 
20. Steinhardt, Paul J. and Turok, Neil, Endless Universe: Beyond the Big Bang—Rewriting Cosmic History, pp. 164-166; pp. 188-193

A useful discussion of Zero Point Energy may be found here:
http://www.calphysics.org/zpe.html

The First Stars:

1. Loeb, Abraham, How Did the First Stars and Galaxies Form? pp. 27-29
2. Loeb, p. 95
3. NASA, Hayflick Observatory, MIT;
4. E. Ripamonti, F. Iocco, A. Ferrara, R. Schneider, A. Bressan, P. Marigo, “First star formation with dark matter annihilation” , Cornell University, arXiv:1003.0676v2
5. Kaku, Michio,  Parallel Worlds: A Journey Through Creation, Higher Dimensions, and the Future of the Cosmos, pp. 65-66; Pagel, Bernard E. J., Nucleosynthesis and Chemical Evolution of Galaxies, pp. 132-133
6. Arnett, David, Supernovae and Nucleosynthesis: An Investigation of the History of Matter, From the Big Bang to the Present p. 182;
7. Arnett, 147 
8. Hyperphysics 
9. NASA
10. Turk, Abel, O’Shea
http://www.sciencemag.org/content/325/5940/601.full.pdf  
11. Alan Heavens (American Scientist 2005 93:36) 
12. http://www.space.com/9625-discovery-triple-number-stars-universe.html
13. Singh, Simon. Big Bang: The Origin of the Universe, pp. 385-397;  
14. Kaplan, S. A. The Physics of Stars, p. 134;
15. Asimov, Isaac. The Exploding Suns: The Secrets of the Supernovas, pp. 126-130
16. Burbidge, E. Margaret, Burbidge, G.R., Fowler, William A., and Hoyle, F.,  “Synthesis of the Elements in Stars” in Reviews of Modern Physics, Vol. 29, No. 4. October 1957. 548-558;
17. Umeda, Hideyuki and Keni’ichi Nomoto. “Nucleosynthesis of Zinc and Iron Peak Elements in Population III Type II Supernovae: Comparison With Abundances of Very Metal-Poor Halo Stars” in
The Astrophysical Journal, January 2002
18. Marschall, Laurence A. The Supernova Story, pp. 205-206;  
19. Asimov, p. 126 
20.Red giant stars and stellar winds”, Uppsala University, located here: http://www.teknat.uu.se/forskning/program.php?vetenskapsid=1&forskomr=14&id=126&lang=en
21. John F. Hawley and Katherine A. Holcomb, Foundations of Modern Cosmology, p. 326

I used information available online from The Haystack Observatory at MIT and NASA to educate myself about ionization and reionization in the early Universe.


The First Galaxies

1.   Adam Mann, “Oldest galaxy is lone ranger” in Nature News 26 January 2011 doi:10.1038/news.2011.47
2.   Benson, Andrew J. “Galaxy Formation Theory” in Physics Reports, Volume 495, Elsevier, October 1, 2010, p. 35.
3.   Loeb, pp. 62-63
4.   Benson, pp. 35-38 
5.   Benson, pp. 38-43 
6.   Benson, 46 
7.   Benson, 50-62  
8.   Benson, pp. 65-76 
9.   Larson, Richard, Galaxy Formation and Evolution, pp. 16-17 
10. Smith, Graham P. and James E. Taylor. “Connecting Substructure in Galaxy Cluster Cores At  z = 0.2 With Cluster  Assembly Histories” in The Astrophysical Journal, August  1, 2008.
11.  Larson, p. 4 
12. “Barred Spiral Galaxies Are Latecomers to the Universe”, Hubble Site, located at:
http://hubblesite.org/newscenter/archive/releases/survey/2008/29/full/  
13. “A Map of the Milky Way Galaxy”, Atlas of the Universe, located here: 
http://www.atlasoftheuniverse.com/milkyway.html 
14.  Kanipe, Jeff. Chasing Hubble’s Shadows: The Search for Galaxies at the Edge of Time. p. 140; University of Oregon 
15.  Bell, G. R.; Levine, S. E., “Mass of the Milky Way and Dwarf Spheroidal Stream Membership” (abstract only), located at: http://adsabs.harvard.edu/abs/1997AAS...19110806B  
16.  Benson, p. 76  
17.  Erik J. Tollerud, James S. Bullock, Louis E. Strigari, Beth Willman, Hundreds of Milky Way Satellites? Luminosity Bias in the Satellite Luminosity Function”, Cornell University, http://arxiv.org/abs/0806.4381 
18. “Ring of Stars around the Spiral Disk?” , http://www.solstation.com/x-objects/gal-ring.htm 
19.  NASA
20. “Milky Way Globular Clusters”, http://spider.seds.org/spider/MWGC/mwgc.html
21.  Forbes, Duncan A,  Bridges, Terry,   ‘Accreted versus in situ Milky Way globular clusters “      Swinburne Research Bank, located at: http://researchbank.swinburne.edu.au/vital/access/manager/Repository/swin:15955 
22. Don A. VandenBerg, Michael Bolte, Peter B. Stetson, “The Age of the Galactic Globular Cluster System” in Annual Review of Astronomy and Astrophysics, 1996, 34 :461-510
23. “New Hubble Pictures Suggest Milky Way Fell Together” in Science News, 5 May 2010
24.  “Multiple galaxy mergers continue in the Milky Way” in Sloan Digital Sky Survey,  located here: http://www.sdss.org/news/releases/20060508.mergers.html 
25.  “Twinkle, twinkle, another star: First cosmic census estimates there are 50 BILLION planets in Milky Way”, in Daily Mail, UK, 21 February 2011 http://www.dailymail.co.uk/sciencetech/article-1358838/Milky-Way-50-billion-planets-estimates-cosmic-census.html 
26.  “Superclusters”   in Universe Review, located here: http://universe-review.ca/F03-supercluster.htm#Virgo
27.  “New 3-D Map of Universe Is Best One Yet”, located here: http://www.space.com/11781-3d-map-universe-photo-revealed.html 
28.  Antonaldo Diaferio, “The Large-Scale Distribution of Galaxies”,  Max-Planck-Institut fur¨ Astrophysik, located at:  http://www.mariecurie.org/annals/volume1/diaferio.pdf    
29.  “Three Distant Quasars Found at Edge of the Universe”, Sloan Digital Sky Survey, located here: http://www.sdss.org/news/releases/20030109.quasar.html 
30.  NASA's Hubble Finds Most Distant Galaxy Candidate Ever Seen in Universe, NASA, located here: http://www.nasa.gov/mission_pages/hubble/science/farthest-galaxy.html
Vital information on the role of dark matter in the formation of the Milky Way was gleaned from the website called The Via Lactea Project. The project’s members run simulations of the effects of dark matter on our galaxy using some of the most powerful computers in the world.  It is located here:
http://www.ucolick.org/~diemand/vl/

Galaxy Formation and Evolution, Richard B. Larson, Yale Astronomy Department, New Haven Connecticut, 1992. Located here: http://www.astro.yale.edu/larson/papers/Tenerife91.pdf

The Sun:

1.   Fred C. Adams, “The Birth Environment of the Solar System” in The Annual Review of Astronomy and Astrophysics, 2010, p. 46.
2.   Adams, p. 54
3.   Adams, pp. 76-81
4.   Adams, p. 54
5.   Adams, p. 52
6.   N. Grevesse, M. Asplund, , A. J. Sauval, and P. Scott, “The chemical composition of the Sun” in Annual Review of Astronomy and Astrophysics, 2009
7.   Adams, pp. 53-54
8.   Adams, p. 74
9.   N. Dauphas et al, “Neutron-Rich Chromium Isotope Anomalies in Supernova Nanoparticles” in
      The Astrophysical Journal, Volume 720 Number 2, 2010
10. Rachel Courtland, “Titanium reveals explosive origins of the solar system” in New Scientist Space,
      16 April 2009
11.  C. M. O'D. Alexander, “Inherited material from the protosolar cloud: composition and origin” in Philosophical Transactions of the Royal Society, 2001, 359, 1973-1989
12.  Adams 71-72
13.  Lisa Grossman, “Age of Solar System Needs to Be Recalculated “ in Science News, via Wired, January 4, 2010
14.  Adams, p. 51
15.  Cambridge Encyclopedia of the Sun, pp. 10-11
16.  Adams, p. 50
17.  Adams, p. 51
18.  Adams, pp. 76-81
19.  Cambridge, 56
20.  Cambridge, p. 76
21.  Cambridge, pp. 57-61; Thermonuclear Fusion, located here: 
http://cde.nwc.edu/SCI2108/course_documents/the_sun/thermonuclear_fusion/thermonuclear_fusion.htm
22.  Zirker, Jack B., Journey from the Center of the Sun, pp. 40-43
23.  Zirker, pp. 61-71
24.  Zirker, pp. 57-59; p. 99
25.  Golub, Leon, and  Pasachoff, Jay M. Nearest Star: The Surprising Science of Our Sun, p. 56
26.  Mitalas, R.; Sills, K. R., “On the photon diffusion time scale for the sun”, Astrophysical Journal , December 1992, (abstract only), located at :http://adsabs.harvard.edu/abs/1992ApJ...401..759M
27.  http://www.astro.cornell.edu/share/sharvari/websiteV7/Etransport.htm
28.  Cambridge, p. 10
29.  Cambridge, pp. 102-105
30.  Golub and Pasachoff, pp. 98-100
31.  Zirker, pp. 3-4
32.  Golub and Pasachoff, p. 12
33.  NASA
34.  Zirker, p. 8
35.  Golub and Pasachoff, pp. 40-45
36.  NASA
37.  Cambridge, p. 10
38.  Martin Asplund, Nicolas Grevesse, A. Jacques Sauval, and Pat Scott, “The Chemical Composition of the Sun” in  Annual Review of Astronomy and Astrophysics Vol. 47: 481-522 (Volume publication date September 2009)
39.  Astronomical Institute Utrecht, formerly at: http://www.astro.uu.nl/~strous/AA/en/antwoorden/planeten.html#1_18
40.  Nine Planets: Mercury, located here: http://nineplanets.org/mercury.html
41.  The Solar Space Station: Venus, located here: http://www.solarspace.co.uk/Venus/venus.php


42.  Michael C. Malin, “An overview of the 1985–2006 Mars Orbiter Camera
science investigation” in Mars: The International Journal of Mars Science and Exploration, January 6, 2010
43.  NASA
44.  The Dwarf Planets, Caltech, located here: http://web.gps.caltech.edu/~mbrown/dwarfplanets/
45.  Adams, p. 52

Information on the Earth’s aphelion and perihelion can be found at http://science.nasa.gov/science-news/science-at-nasa/2000/ast30jun_1m/ .

The Earth Forms:

1.    Mathez, Edmond A., and Webster, James D., The Earth Machine: The Science of a Dynamic Planet, 5-7
2.    Chiang, E., and A. N. Youdin “Forming Planetesimals in Solar and Extrasolar  Nebulae” in  Annual Review          of Earth and Planetary Sciences, Volume 38, 2010, pp. 494-495
3.    Chiang , 498
4.    Chiang, 501
5.    Chiang, 504
6.    Chiang,  507
7.    Chiang, 516-518
8.    M. Lecar, M. Podolak, D. Sasselov, and E. Chiang, “On the Location of the Snow Line in a Protoplanetary Disk”, in Astrophysical Journal 1 April 2006
9.    University College London, located at: 
http://www.es.ucl.ac.uk/research/planetary/undergraduate/bugiolacchi/moonf.htm
10.  Bott, Martin H. P. The Interior of the Earth: its structure, constitution and evolution, pp. 21-22
11.  William F McDonough, “The Composition of the Earth”, Harvard University
12.  Bott, p. 73
13.  Mathez, and Webster, p. 8
14.  Anderson, Don. L. “The inner inner core of Earth”  from Proceedings of the National Academy of Sciences of the United States of America (PNAS), 29 October 2002
15.  Biju-Duval, Bernard, Sedimentary Geology: Sedimentary Basins, Depositional Environments, Petroleum Formation, pp. 17-18
16.  Anderson
17.  The Earth’s Crust, The United States Geological Service, located at: 
http://earthquake.usgs.gov/research/structure/crust/
18.  Vogel, Shawna,  Naked Earth: The New Geophysics, p. 96
19.  K. Zahnle, N. Arndt, C. Cockell, A. Halliday, E. Nisbet, F. Selsis, N.H. Sleep, “Emergence of a Habitable Planet” in Geology and Habitability of Terrestrial Planets, Edited by Kathryn E. Fishbaugh,
Philippe Lognonné, François Raulin, David J. Des Marais, and Oleg Korablev,  pp. 61-62
20.  David Graham, “Relict mantle from Earth’s birth”, Nature, 12 August 2010
21.  Zahnle, Kevin, Nick Arndt, Charles Cockell, Alex Halliday, Euan Nisbet , Franck Selsis, Norman H. Sleep. “Emergence of a Habitable Planetin Space Science Review, 25 July 200737-46
22.  Zahnle, et al, pp. 38-39
23.  Kent Condie, “When Did Plate Tectonics Begin on Planet Earth”, 2 October 2008, located here: 
http://www.scitopics.com/When_Did_Plate_Tectonics_Begin_on_Planet_Earth.html
24.  Linda T. Elkins-Tanton, “Formation of early water oceans on rocky planets” in Astrophysics and  Space Science,  (2011) 332: 359–364
25.  Hidenori Genda and Masahiro Ikoma, “Origin of the Ocean on the Earth: Early Evolution 
of Water D/H in a Hydrogen-rich Atmosphere” in Icarus (6 Sep 2007)
26.  Jun Korenaga, “Plate tectonics, flood basalts and the evolution of Earth’s oceans” in Terra Nova, 20, 419-439, 2008
27.  Henry H. Hsieh and David Jewitt, “A Population of Comets in the Main Asteroid Belt” in Science 28 April 2006: Vol. 312 no. 5773 pp. 561-563, DOI: 10.1126/science.1125150
28.  James F. Kasting and M. Tazewell Howard, “Atmospheric composition and climate on the early Earth”, Philosophical Transactions of the  Royal Society,  B Biological Sciences,  2006 October 29; 361(1474): 1733–1742
29.  Feng Tian, Owen B. Toon, Alexander A. Pavlov, H. De Sterck, “A Hydrogen-Rich Early Earth Atmosphere” in Science, 13 May 2005: Vol. 308 no. 5724 pp. 1014-1017  DOI: 10.1126/science.1106983
30.  Science News, December 10, 2009
31.  William F. Bottke, Richard J. Walker, James M. D. Day, David Nesvorny, Linda Elkins-Tanton,
“Stochastic Late Accretion to Earth, the Moon, and Mars” in Science 10 December 2010:
Vol. 330 no. 6010 pp. 1527-1530 DOI: 10.1126/science.1196874
32.  “Day” http://www.sizes.com/time/day.htm
33.  United States Naval Observatory, located at http://tycho.usno.navy.mil/leapsec.html
34.  “Year” http://www.sizes.com/time/year.htm
35.  NASA

The Earliest Life on Earth:

1.   Schopf, J. William. Cradle of Life: The Discovery of Earth’s Earliest Fossils, p. 107
2.   Schrödinger, Erwin, What is Life?, pp. 69-71
3.   Schrödinger, pp. 76-82
4.   The Principles of Life (Summary of Tibor Gánti’s work) located here:  http://home.planet.nl/~gkorthof/korthof66.htm
5.   Fry, Iris. The Emergence of Life on Earth: A Historical and Scientific Overview, pp. 66-71
6.   Fry, pp. 71-77
7.   Kimball’s Biology Pages
8.   Trefil, James Harold J. Morowitz, and Eric Smith. “The Origin of Life” in American Scientist, May-June 2009.
9.    Shapiro, Robert. Origins: a Skeptic’s Guide to the Creation of Life on Earth, pp. 224-247
10.  Introduction: More Than Panspermia, located at: http://www.panspermia.org/intro.htm
11.  Shapiro, pp. 98-106
12.  Fry, 104-105
13.  Fry, pp. 107-111
14.  Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth, pp. 76-80
15.  Trefil, et al.
16.  Trefil, et al.
17.  Cairns-Smith, A. G. Genetic takeover and the mineral origins of life, pp.  45-60
18.  Cairns-Smith, p.  70
19.  Cairns-Smith, p. 120
20.  Cairns-Smith, pp. 160; 257-258
21.  Cairns-Smith, pp.  264-273
22.  Cairns-Smith, pp. 357-365
23.  Lurquin, Paul F. The Origins of Life and the Universe, pp. 102-104 
24.  Wim Hordik, Jotun Hein, and Mike Steel, “Autocatalytic Sets and the Origin of Life”, from Entropy,  2010; Hordik, Kauffman, and Steel, “Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems” in International Journal of Molecular Sciences, 2011.
25.  Schopf, pp. 166-167
26.  S. J. Mojzsis, G. Arrhenius, K. D. McKeegan, T. M. Harrison, A. P. Nutman, and C. R. L. Friend,
“Evidence for life on Earth before 3,800 million years ago”, in Nature 384, 55 - 59 (07 November 1996); doi:10.1038/384055a0
27.  Knoll, pp. 64-71
28.  Schopf, pp. 75-99
29.  Brasier, et al,  “Questioning the Evidence for Earth’s Oldest Fossils” in Nature, March 2002.
30.  Schopf, et al, “Laser--Raman imagery of Earth's earliest fossils” in Nature, March 2002
31.  Marshall, et al, “Haematite pseudomicrofossils present in the 3.5-billion-year-old Apex Chert” in Nature Geoscience, February 2011.
32.  Schopf, p. 72
33.  Colin Barras, “Biology's 'dark matter' hints at fourth domain of life” in New Scientist, 18 March 2011
34.  “Dueling Scientists and the Tree of Life:  Analyzing the ID Response” in The BioLogos Forum,
March 14, 2011
35.  Theobald, Douglas. “A formal test of the theory of common ancestry” in Nature, 13 May 2010
36.  Theobald
37.  Theobald
38.  Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, and Manolo Gouy,Parallel adaptations to high temperatures in the Archaean eon”, in Nature 456, 942-945, Published online 26 November 2008
39.  Kyung Mo Kim and Gustavo Caetano-Anollés,  “The proteomic complexity and rise of the primordial ancestor of diversified life” in BMC Evolutionary Biology, 2011; 11: 140. Published online 2011 May 25
40.  Coyne, Why Evolution is True, p. 4
41.  Dawkins, The Blind Watchmaker, pp. 43-74
42.  Travis, Joseph, and David. N Reznick, “Adaptation” in Evolution: The First Four Billion Years, pp. 105-109
43.  Mark Ridley, Evolution, pp. 23-25
44.  Ridley, p. 25
45.  Ridley, pp. 27-30
46.  Coyne, p. 122
47.  Coyne, 122-124
48.  Kimura, Motoo, The Neutral Theory of Molecular Evolution, passim.
49.  Nosil, Patrik, and Schluter, Dolph, “The genes underlying the process of speciation” in Trends in Ecology and Evolution, 2011.
50.  Whale and Dolphin Evolution, American Museum of Natural History, located here: 
http://www.amnh.org/science/papers/spaulding_whales_2009.php
51.  Mayr, What Evolution Is, pp. 225-226
52.  Coyne, p. 13.
53. Some years ago, in the United States, the National Center for Science Education began a project, somewhat tongue-in-cheek, to deflate claims by creationists that there were many scientists who are creationists. Called Project Steve, it has shown that there are more pro-evolution scientists named Steve than there are creationists of all names put together in the scientific community. And only about 1% of all scientists are named Steve (or some variation of that name, like Stephen).
54. Wilkinson Microwave Anisotropy Probe, NASA, located here:  http://map.gsfc.nasa.gov/
55.  G. Brent Dalrymple, How Old is the Earth: A Response to “Scientific” Creationism, in Talk Origins Archive, located here: http://www.talkorigins.org/faqs/dalrymple/summary.html#h48 
56.  Francisco J. Ayala, “Molecular Evolution” in Evolution: The First Four Billion Years, p. 136.
57.  Donald R. Prothero, Evolution: What the Fossils Say and Why It Matters, pp. 249-268.
58.  Coyne, 35-37
             
The Reign of the One-Celled Life Forms:

1.  Koga, Williams, Perriman, Mann. “Peptide–nucleotide microdroplets as a step towards a membrane-free protocell model” in Nature Chemistry (2011) doi:10.1038/nchem.1110 2011 Published online 7 August 2011
2.  Margulis, Lynn, and Sagan, Dorion. Microcosmos: Four Billion Years of Microbial Evolution, pp. 54-55
3.   Armen Y. Mulkidjanian, Michael Y. Galperin, and Eugene V. Koonin, “Co-evolution of primordial membranes and membrane proteins”,  in Trends in Biochemical Science, 2009 April; 34(4): 206–215.
4.   Ion Channels: Structure and Function, http://www.whatislife.com/reader/channels/channels.html
5.   Pohorille A, Schweighofer K, Wilson MA, “The origin and early evolution of membrane channels” in
Astrobiology 2005 Feb;5(1):1-17.
6.   Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo and Patrick Forterre, “Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota” in Nature Reviews Microbiology 6, 245-252 (March 2008)
7.   Simonetta Gribaldo and Celine Brochier-Armanet, “The origin and evolution of Archaea: a state of the art” in Philosophical Transactions of the Royal Society, B Biological Sciences, 29 June 2006
8.   Simonetta Gribaldo, “The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?” in Nature Reviews Microbiology 8, 743-752 (October 2010)
9.   Kimball’s Biology Pages, Biology Pages, Archaea.
11. Berend Snel1Peer Bork,  and  Martijn A. Huynen,
“Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content” in Genome Research, 2002. Located at  http://genome.cshlp.org/content/12/1/17.long
12. Elizabeth A. Grice, et al, “Topographical and Temporal Diversity of the Human Skin Microbiome” in
Science 29 May 2009: Vol. 324 no. 5931 pp. 1190-1192
13. William B. Whitman*†, David C. Coleman‡, and William J. Wiebe, “Prokaryotes: The unseen majority” in PNAS, Vol. 95, pp. 6578–6583, June 1998
14. Jan Postberg, Hans J. Lipps, and Thomas Cremer, “Evolutionary Origin of the Cell Nucleus and Its Functional Architecture” in Biochemical Society Essays, 2010.
15.  Alberts, Bruce, Molecular Biology of the Cell, Volume 1, p. 481
16.  Alberts, p. 409
17.  Alberts, p. 482
18.  Buick, Roger. “Ancient Acritarchs” in Nature, February 2010

For the evolution of photosynthesis,  I relied heavily on recent research published in journals. These include:

Mulkidjanian , Armen Y.  and Eugene V. Koonin , Kira S. Makarova ,Sergey L. MekhedovAlexander Sorokin , Yuri I. Wolf , Alexis DufresneFrédéric PartenskyHenry Burd , Denis Kaznadzey, Robert Haselkorn and Michael Y. Galperin , “The cyanobacterial genome core and the origin of          photosynthesis” in Proceedings of the National Academy of Sciences of the United States of America, 21 August 2006.
               
A major source I used to teach myself the basics of photosynthesis  was “The Photosynthetic Process”, found here:
http://www.life.illinois.edu/govindjee/paper/gov.html#10

This is actually the first 51 pages of the book Concepts in Photobiology: Photosynthesis and Photomorphogenesis, Edited by GS Singhal, G Renger, SK Sopory, K-D Irrgang and Govindjee, Narosa Publishers/New Delhi; and Kluwer Academic/Dordrecht,

Dr. Carl Bauer has researched the evolution of photosynthesis extensively. His web pages at Indiana University on the subject can be found here:
http://www.bio.indiana.edu/~bauerlab/origin.html

19.  Bauer
20.  Singhal, et al
21.  Mulkidjanian, et. al
22.  Des Marais, David J.  “When Did Photosynthesis Emerge on Earth?” in Science, 8 September 2000
23.  Des Marais
24.  Luisa I Falcón, Susana Magallón, and Amanda Castillo, “Dating the cyanobacterial ancestor of the chloroplast  in The ISME Journal (2010) 4, 777–783; doi:10.1038/ismej.2010.2; published online 4 March 2010
25.  Fossil Museum, Tree of Life
26.  Margulis, pp. 128-131
27.  Margulis, p. 19
28.  Verma, Ashok,  Invertebrates: protozoa to echinodermata, p. 9
29.  The Proterozoic biosphere: a multidisciplinary study by J. William Schopf, p. 600
30.  Jörg Tittel, et al, Mixotrophs combine resource use to outcompete specialists: Implications for aquatic food webs, PNAS October 28, 2003
31.  Ranjan V. Mannige, Charles L. Brooks III,” Periodic Table of Virus Capsids: Implications for Natural Selection and Design”, in PLoS One 5(3): e9423. doi:10.1371/journal.pone.0009423, March 4, 2010
32.  Ed Rybicki, “Virus origins: from what did viruses evolve or how did they initially arise?” in ViroBiology, 28 September 2011
33.  Eugene V Koonin, Tatiana G Senkevich, and Valerian V Dolja, “The ancient Virus World and evolution of cells”  in Biology Direct, 19 September, 2006
36.  Michael Specter, Darwin’s Surprise, The New Yorker, December 3, 2007
37.  Specter
38.  Marilee A. Ramesh, Shehre-Banoo Malik, and John M. Logsdon, Jr. “A Phylogenomic Inventory of Meiotic Genes: Evidence for Sex in Giardia and an Early Eukaryotic Origin of Meiosis” in Current Biology, Vol. 15, 185–191, January 26, 2005
39.  Adam S. Wilkins, Robin Holliday, “ The Evolution of Meiosis From Mitosis” in Genetics, January 2009
40.  Peter A. Cawood, Alfred Kröner, and Sergei Pisarevsky, “Precambrian plate tectonics: Criteria and evidence” in GSA Today, July 2006.
41.  Kent C. Condie, Earth as an Evolving Planetary System. Boston: Elsevier Academic, 2005. p. 315.
42.  Zimmer, Carl, “Ancient Continent Opens Window on the Early Earth” in Science, 12-17-1999.
43.  Condie, p. 321
44.  Condie, pp. 316-319
45.  Robock, Alan, “Volcanic Eruptions and Climate” in Reviews of Geophysics, May 2000.
46.  DeConto, Robert M., “Plate Tectonics and Climate Change” in Encyclopedia of Paleoclimatology and Ancient Environments.
47.  Fortey, Life: A Natural History of the First Four Billion Years of Life on Earth,  p. 286
48.  Nicholas L. Swanson-Hysell, et al, “Cryogenian Glaciation and the Onset of Carbon-Isotope Decoupling” in Science 30 April 2010: Vol. 328 no. 5978 pp. 608-611
49.  “New evidence puts 'Snowball Earth' theory out in the cold” in PhysOrg, March 23, 2007, located at: http://www.physorg.com/news93869405.html
50.  Alberts B, Bray D, Lewis J, et al., “From Single Cells to Multicellular Organisms” in Molecular Biology of the Cell. 3rd edition, at NCBI Resources
51.  Bray, et al
52.  Simon E. Prochnik , et al, “Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri”  in Science 9 July 2010: Vol. 329 no. 5988 pp. 223-226
53.  Alberts B, Johnson A, Lewis J, et al, “Cell Junctions, Cell Adhesion, and the Extracellular Matrix” in
Molecular Biology of the Cell 4th edition, NCBI Resources
54.  Seth Tyler, “Epithelium—The Primary Building Block for Metazoan Complexity” in Integrative and Comparative Biology Volume 43, Issue 1, Pp. 55-63.
55.  Margulis, p. 17
56.  Mukund Sharma and Yogmaya Shukl, “Mesoproterozoic coiled megascopic fossil Grypania spiralis from the Rohtas Formation, Semri Group, Bihar, India” in Current Science, Vol. 96, 25 June 2009.

Life in the Oceans: The Animals Evolve and Begin to Spread:

1.  Niu, D.K, and  Chen, J. K. “Evolutionary advantages of cell specialization: save and protect DNA” in Journal of Theoretical Biology, 7 July 1997.
2. Willensdorfer, Martin. “Organism Size Promotes the Evolution of Specialized Cells in Multicellular Digital Organisms” in Journal of Evolutionary Biology, January 2008.
3. Michod, Richard E., “Evolution of individuality during the transition from unicellular to multicellular life” in Proceedings of the National Academy of Sciences of the United States of America, 9 May 2007.
4.  Michod.
5. Akashi, Hiroshi. “Gene Expression and Molecular Evolution” in  Current Opinion in Genetics and Development, 2001.
6.  “DNA structure and gene expression”, NCBI Books, http://www.ncbi.nlm.nih.gov/books/NBK7585/
7.  Strahl, Brian D.  & C. David Alli, “The language of covalent histone modifications” in Nature, Volume 403, January 2000.
8.  Bürglin, T.R, “The Homeobox Page”, http://www.biosci.ki.se/groups/tbu/homeo.html
9.  Garcia-Fernàndez, Jordi, “The Genesis and Evolution of Homeobox Gene Clusters” in  Nature Reviews: Genetics, Volume 6, December 2005
10.  Rose, Steven, The Conscious Brain,  pp. 140-141 
11.  Allman, John Morgan, Evolving Brains, pp. 3-5
12.  Ghysen, Alain, “The origin and evolution of the nervous system” in International Journal of Developmental Biology, 47, pp. 555-562, 2003.
13. “Possible discovery of earliest animal life pushes back fossil record” in e! Science News, 17 August 2010
14.  http://esciencenews.com/articles/2009/02/04/fossil.steroids.record.advent.earliest.known.animals
15.  Schierwater, Bernd Michael Eitel, Wolfgang Jakob, Hans-Jürgen Osigus, Heike Hadrys, Stephen L. Dellaporta, Sergios-Orestis Kolokotronis, Rob DeSalle, “Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern ‘Urmetazoon’ Hypothesis” in PLoS Biology, January 2009
16.  International Stratigraphic Chart, http://www.stratigraphy.org/column.php?id=Chart/Time%20Scale
17.  Carroll, Robert L., Patterns and Processes of Vertebrate Evolution, p. 343
18.  “An introduction to the Ediacaran fauna”,  http://ediacaran.blogspot.com/2008/11/introduction-to-ediacaran-fauna.html
19.  International Stratigraphic Chart
20. Prothero, pp. 161-165
21. Gould, Wonderful Life, p. 60
22. Zhao Fang Chen, Zhu Mao Yan, and Hu Shi Xue, “Community Structure and Composition of the Cambrian Chengjiang Biota” in Science China, December 2010
23.  Zhao, et al
24.  Briggs, et al, pp. 1-9
25.  Briggs, passim
26. Garrison, Essentials of Oceanography, 5th Edition, p. 133
27. Benjamin C. Gill, Timothy W. Lyons, Seth A. Young, Lee R. Kump, Andrew H. Knoll  Matthew R. Saltzman “Geochemical evidence for widespread euxinia in the Later Cambrian ocean” in Nature, Volume 469, 5 January 2011
28. Gould, p. 323
29.  Jaime E. Blair and S. Blair Hedges, “Molecular Phylogeny and Divergence Times of Deuterostome Animals” in Molecular Biology and Evolution, 27 July 2005
30.  Graur Dan, and William Martin, “Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision” in Trends in Genetics, February 2004
31.  “Sponge Reveals Animal Origins” in Astrobiology Magazine,  August 7, 2010 
http://www.astrobio.net/pressrelease/3578/sponge-reveals-animal-origins
32.  Henry Gee, Major Events in Early Vertebrate Evolution, pp. 1-12
33. “Introduction to the Chordata”,  http://www.ucmp.berkeley.edu/chordata/chordata.html
34.  Gee, Major Events, pp. 1-12
35.  http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/V/Vertebrates.html
36.  Holland, Linda Z and Nicholas Holland, Major Events, pp. 15-27
37.  Gee, Major Events, pp. 1-12
38.  Jianzhi Zhang, “ Evolution by gene duplication: an update” in Trends in Ecology and Evolution, June 2003
39. Paramvir Dehal, Jeffrey L. Boore, “Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate” in PLoS Biology, October 2005
40.  Bürglin
41.  Holland and Holland, Major Events, pp. 33-37
42.  Colbert, Edwin H, and Morales, Michael,  Evolution of the Vertebrates: A History of the Backboned Animals Through Time, Fourth Edition, pp. 5-6; Calloni, Giordano W., Nicole M. Le Douarin, and Elisabeth Dupin, “High frequency of cephalic neural crest cells shows coexistence of neurogenic, melanogenic, and osteogenic differentiation capacities” in PNAS, 2 June 2009
43.  Sweet, Walter C., and Donoghue, Philip C. J., “Conodonts: Past, Present, Future” in Journal of Paleontology, Volume 75, Number 6, 2001
44.  Donoghue, Philip C. J., and Aldridge, Richard J., “Origin of a Mineralized Skeleton” in Major Events
45.  Colbert and Morales, pp. 30-31
46.  Koob, T. J., and Long, J. H., “The Vertebrate Body Axis: Evolution and Mechanical Function” in Integrative and Comparative Biology, Vol. 40, 2000
47.  Carroll, pp. 174-176.
48.  Noriko Funayama, Yae Sato, Ken Matsumoto, Toshihiko Ogura, and Yoshiko Takahashi, “Coelom formation: binary decision of the lateral plate mesoderm is controlled by the ectoderm” in Development, 1999.
49.  Schmidt-Rhaesa, Andreas, The evolution of organ systems, p. 167
50.  Lee, Michael S. Y., James B. JagoDiego C. García-BellidoGregory D. Edgecombe, James G. Gehling, John R. Paterson, “Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia” in Nature, 29 June 2011
51.  John A. Long, Kate Trinajstic, Zerina Johanson, “Devonian arthrodire embryos and the origin of
internal fertilization in vertebrates” in Nature, Volume 457, 26 February 2009
52.  Levi-Setti, Riccardo, Trilobites, Second Edition, passim
53.  The Paleomap Project, http://www.scotese.com/precambr.htm
54.  Cocks, L. R. M., and T. H. Torsvi, “European geography in a global context from the Vendian to the
end of the Palaeozoic”, in Gee, D. G. & Stephenson, R. A. (editors) in European Lithosphere Dynamics, 2006
55.  The Paleomap Project, http://www.scotese.com/climate.htm

The Plant Kingdom Begins to Colonize the Land:

1.  C. V. Rubinstein, P. Gerrienne, G. S. de la Puente, R. A. Astini, P. Steemans, “Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)”,  in New Phytologist, 20 August 2010
2.  Mycorrhizal Associations: The Web Resource http://mycorrhizas.info/index.html
3.  Humphreys, Claire P., Peter J. Franks, Mark Rees, Martin I. BidartondoJonathan R. Leake, and David J. Beerling , “Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants” in Nature Communications, November 2010
4.  Bidartondo, Martin I., David J. Read, James M. Trappe, Vincent Merckx, Roberto Ligrone and Jeffrey
G. Duckett, “The dawn of symbiosis between plants and fungi” in Biology Letters, 9 March 2011
5.  Taylor, Thomas N., Edith L. Taylor, Michael Krings, Paleobotany: The Biology and Evolution of Fossil Plants, “The Move to the Land”*
6.  Paleobotany, “The Move to the Land”
7.  Paleobotany, “The Move to the Land”
8.  LiToL: Assembling the Liverwort Tree of Life located at:
10. Map of Life - "Secondary xylem (wood) in vascular plants" http://www.mapoflife.org/topics/topic_453_Secondary-xylem-(wood)-in-vascular-plants/
11. Paleobotany, “Early Land Plants with Conducting Tissue”
12. Friedman, William E., and  Martha E. Cook, “The origin and early evolution of tracheids in
vascular plants: integration of palaeobotanical and neobotanical data” in Philosophical Transactions of the Royal Society, pp. 857-868, 2000; Pallardy, Stephen G., and Theodore Thomas Kozlowski, Physiology of Woody Plants, pp. 62-63.
13.  Paleobotany, “Early Land Plants with Conducting Tissue”
14.  Paleobotany, “Early Land Plants with Conducting Tissue”
15.  Kenrick, Paul and Paul Davis, Fossil Plants, pp. 23-25
16.  Kenrick and Davis, pp. 28-29
17.  Kenrick and Davis, pp. 32-35
18.  Beerling, David J.,  “Leaf Evolution: Gases, Genes and Geochemistry” in Annals of Botany, September 2005
19.  Beerling
20. “The First Forests” from Devonian Times, http://www.devoniantimes.org/opportunity/forests.html; Paleobotany, “Progymnosperms”.
21.  Devonian Times
22.  Paleobotany, “Origin and Evolution of The Seed Habit”.
23.  Devonian Times, “Early Seed Plants (lyginopterids)”
24.  The Gymnosperm Database, http://www.conifers.org/zz/gymnosperms.php
25.  Paleobotany, “Origin and Evolution of The Seed Habit”
26.  Yin-Long Qiu, Jungho Lee, Fabiana Bernasconi-Quadroni, Douglas E. Soltis, Pamela S. Soltis, Michael Zanis, Elizabeth A. Zimmer, Zhiduan Chen, Vincent Savolainen & Mark W. Chase “The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes” from Nature, 25 November 1999
27.  McGhee, George R., The Late Devonian Mass Extinction: the Frasnian/Famennian Crisis, pp. 132-156
28.  Algeo, Thomas J., and  Stephen E. Scheckler,  “Terrestrial-marine teleconnections in the Devonian: links between the evolution of land plants, weathering processes, and marine anoxic events” in Philosophical Transactions of the Royal Society, 1998
29.  Devonian Times, “Late Devonian Mass Extinctions”
30.  Paleomap Project, http://www.scotese.com/earth.htm
31.  Joachimski, M.M. S. Breisig, W. Buggisch, J.A. Talent, R. Mawson, M. Gereke, J.R. Morrow, J. Day, K. Weddige, “Devonian climate and reef evolution: Insights from oxygen isotopes in apatite” in Earth and Planetary Science Letters, Volume 284, 15 July 2009

*The book Paleobotany is a Kindle edition that is unfortunately not paginated, nor is there an index which indicates pages of the original text in which specific information is located. I can only provide chapter locations in the notes.

The Animal Kingdom Begins to Colonize the Land:

1.  Devonian Times
2.  Schneider, Igor, Ivy AneasAndrew R. GehrkeRandall D. Dahn, Marcelo A. Nobrega, and Neil H. Shubin,  “Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature” in PNAS, June 21, 2011
3.  Clack, J. A., “The otoccipital region: origin, ontogeny and the fish-tetrapod transition” from Major Events in Early Vertebrate Evolution, pp. 392-396
4.  Dr. Per Ahlberg, 2007, "Eusthenopteron foordi" (On-line), Digital Morphology. at http://digimorph.org/specimens/Eusthenopteron_foordi/.
5.  Boisvert, Catherine A., Elga Mark-Kurik  and Per E. Ahlberg, “The pectoral fin of Panderichthys and the origin of digits” in Nature, 21 September 2008
6.  Boisvert,  Catherine A. “The humerus of Panderichthys in three dimensions and its significance in the context of the fish–tetrapod transition” in  Acta Zoologica by the Royal Swedish Academy of Sciences, 2009
7.  Devonian Times
8.  Clack, Major Events, pp. 392-401
9.  Clack, Jennifer A. 2006. Acanthostega. Acanthostega gunnari.
Version 13 June 2006. http://tolweb.org/Acanthostega_gunnari/15016/2006.06.13 in 
The Tree of Life Web Project, http://tolweb.org/
10. Shubin, Neil, Your Inner Fish: A Journey Into the 3.5 Billion-Year History of the Human Body, pp. 22-27
11. Shubin, pp. 37-43
12. Niedzwiedzki, Grzegorz, Piotr Szrek, Katarzyna Narkiewicz, Marek Narkiewicz, and Per E. Ahlberg, “Tetrapod trackways from the early Middle Devonian period of Poland” in Nature, 7 January 2010
13. Niedzwiedzki, et al.
14. Feder, Martin E., and Warren W. Burggren, Environmental physiology of the amphibians, p. 3
15. Armbruster, Jonathan W., “Modifications of the Digestive Tract for Holding Air in Loricariid and Scoloplacid Catfishes” in Copeia, 1998, No. 3 , published by the American Society of Ichthyologists and Herpetologists
16. Daniels, Christopher B. and Sandra Orgeig, “Pulmonary Surfactant: The Key to the Evolution of Air Breathing” in News in Physiological Sciences, Vol. 18, No. 4, 151-157, August 2003
http://physiologyonline.physiology.org/content/18/4/151.full
17. Torday, John S. and Rehan, V. K., “Cell–cell signaling drives the evolution of complex traits: introduction—lung evo-devo” in Integrative and Comparative Biology , Volume 49, Issue 2, 11 May 2011, located at 
http://icb.oxfordjournals.org/content/49/2/142.full
18.  Daniels and Orgeig
19.  Torday and Rehan
20.  Carroll, Origin and Radiation
21.  Gould, The Book of Life, pp. 84-85
22.  Geological Society of America, 2007, located at
http://gsa.confex.com/gsa/2007AM/finalprogram/abstract_127074.htm
23.  Carnegie Museum of Natural History, 2010, located at
http://www.carnegiemnh.org/press/10-jan-mar/031510fedexia.htm
24.  Grimaldi, David A., and Michael S. Engel, Evolution of the Insects, pp.
25.  Dudley, Robert, “Atmospheric Oxygen, Giant Paleozoic Insects, and the Evolution of Aerial Locomotor Performance” in The Journal of Experimental Biology, 1998
26.  Paleomap
27.  Bette L. Otto-Bliesner in Tectonic boundary conditions for climate reconstructions , edited by Thomas J. Crowley and Kevin Burke, pp. 100-104

The text Interrelationships of Fishes, by Melanie L.J. Stiassny, Lynne R. Parenti, and G. David Johnson, was a useful general reference for sections of this chapter. Fins into limbs: evolution, development, and transformation, edited by Brian Keith Hall was also briefly consulted.

The Johns Hopkins School of Medicine’s Interactive Respiratory Physiology page was also very useful.

The Reptiles and the Synapsids Evolve:

1.   Packard, Mary J., and  Roger S. Seymour, “Evolution of the Amniote Egg” in Amniote Origins: Completing the Transition to Land, edited by Stuart S. Sumida and Karen L. M. Martin, pp. 265-286
2.   Packard, Gary C. and Mary J. Packard, “Evolution of the Cleidoic Egg Among Reptilian Antecedents of Birds” in Integrative and Comparative Biology, Vol. 20, Issue 2, pp. 351-362, 1980
3.   Fastovsky, David E.  and David B. Weishampel, The Evolution and Extinction of Dinosaurs, pp. 77-78
4.   Kimball’s Biology Pages, located  at 
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/V/Vertebrates.html#Reptiles
5.   Benton, Michael, Vertebrate Palaeontology, p. 107; Benton and David. A. T. Harper, Introduction to Paleobiology and the Fossil Record, p. 448.
6.   Prothero, pp. 235-237; p. 271
7.   Kemp, T.S., The Origin and Evolution of Mammals, pp. 1-3
8.   Kemp, pp. 19-26
9.   Rose, Kenneth D., The Beginning of the Age of Mammals, p. 44
10. Angielczyk, Kenneth D., "Dicynodontia," in AccessScience, McGraw-Hill Companies, 2011, http://www.accessscience.com
11.  Prothero, pp. 236-237
12.  Erwin, Douglas H., The Great Paleozoic Crisis: Life and Death in the Permian, pp. 225-228
13.  Erwin 228-254
14.  Erwin 256-257
15.  http://science.nasa.gov/science-news/science-at-nasa/2002/28jan_extinction/
16.  Berner, Robert A., “Examination of hypotheses for the Permo–Triassic boundary extinction by carbon cycle modeling” in PNAS, 2 April 2002.
17.  Erwin, p. 39
19.  Paleomap Project
20.  http://geomaps.wr.usgs.gov/parks/province/appalach.html
21.  Rogers, John J. W., and M. Santosh, Continents and Supercontinents, pp. 114-126
22.  Rogers and Santosh, pp. 127-130
23.  Rogers and Santosh, pp. 184-185
24.  Rothschild, Lynn J., and Adrian Lister, Evolution on planet earth: the impact of the physical environment, pp. 239-240
25.  Carroll, Robert L., Patterns and Processes of Vertebrate Evolution,  p. 351

The Paleobiology Database was very useful as a reference for this chapter. It is located here: http://paleodb.org/cgi-bin/bridge.pl

The Mammals:

1.   Rose, The Beginning of the Age of Mammals p. 41
2.   Rose, pp. 41-42
3.   Rose, p. 44
4.   Cowen, Richard, History of Life, pp. 133-134
5.   Cowen, pp. 134-136
6.   Cowen, p. 214
7.   Chinsamy-Turan, Anusuya, Forerunners of Mammals: Radiation - Histology – Biology, pp. 223-225
8.   Chinsamy-Turan, pp. 228-229
9.   Lucas, Spencer G., Chinese Fossil Vertebrates, pp. 133-135
10. Vaughan, Terry A., James M. Ryan, and Nicholas J. Czaplewski, Mammalogy, Fifth Edition, p. 53
11. Ross Damiani, Sean Modesto, Adam Yates, and Johann Neveling,  “Earliest evidence of cynodont burrowing” in Proceedings of the Royal Society, 19 June 2003
12. Rose, pp. 50-51
13. Kielan-Jaworowska, Zofia, Richard Cifelli, and Zhe-Xi Luo, Mammals from the age of dinosaurs: origins, evolution, and structure, pp. 174-176
14. Lucas, Spencer G, Chinese Fossil Vertebrates, p. 152
15. Kielan-Jaworowska, et al, p. 175
16. Lucas, p. 152
17. Zhe-Xi LuoAlfred W. Crompton and Ai-Lin Sun, “A New Mammaliaform from the Early Jurassic and Evolution of Mammalian Characteristics”, in Science, 25 May 2001
18. Kielan-Jaworowska, et al, p. 19
19. Kielan-Jaworowska, et al, pp. 19-64
20. Kielan-Jaworowska, et al, pp. 19-64
21. Vincent J. Lynch, Robert D Leclerc, Gemma May and Günter P Wagner, “Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals” in Nature Genetics, 25 September 2011; “Invasion of Genomic Parasites Triggered Modern Mammalian Pregnancy, Study Finds” in Science Daily, 25 September 2011; Schubert, Charlotte, “Transposable Element May Have Jump-Started Pregnancy” in Biology of Reproduction, October 5, 2011
22. Kirstin Knox and Julie C. Baker, “Genomic evolution of the placenta using co-option and duplication
and divergence” in Genome Research, 13 March 2008
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 A Life in the Trees: the Primates Evolve:

1.  Conroy, Glenn C., Primate Evolution, pp. 4-7
2.  E. L Simons, “Convergence and Frontation in Fayum Anthropoid Orbits” in Primate Craniofacial Function and Biology, Chris Vinyard, Matthew J. Ravosa, and Christine Wall, editors, pp. 418-421
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5.  Robert W. Sussman, “Primate origins and the evolution of angiosperms” in American Journal of Primatology, Vol. 23, 1991. Article first published online 2 May 2005; Conroy, pp. 41-43
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12.  J. I. Bloch, M. T. Silcox, D. M Boyer, and E. J.  Sargis,  “New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primates”  in Proceedings of the National Academy of Sciences, 104(4):1159-1164, 2007.
13.  Christophe Soligo, Oliver Will , Simon Tavaré, Charles R. Marshall, and Robert D. Martin, “New Light on the Dates of Primate Origins and Divergence”, paper presented at the University of Southern California. Located at http://www.cmb.usc.edu/people/stavare/STpapers-pdf/SWTMM03.pdf
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17.  Michael Heads,  “Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics”, in  Zoologica Scripta, Volume 39, Issue 2, pages 107–127, March 2010
18.  Mary T. Silcox, Eric J. Sargis, Jonathan I. Bloch, and Doug M. Boyer, “Primate Origins and Supraordinal Relationships: Morphological Evidence” in Handbook of Paleoanthropology, Vol. I: Principles, Methods, and Approaches,  edited by Wilfried Henke and Ian Tattersall, pp. 830-832
19.  Mary T. Silcox, “The Biogeographic Origins of Primates and Euprimates: East, West, North, or South of Eden?” in  Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay, edited by Eric J. Sargis, pp. 207-209
20.  Silcox, pp. 199-209, 212, 214
21.  Cartmill, Matt, and Smith, Fred H., The Human Lineage, pp. 113-115
22.  Primate Info Net
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24.  Fridman, Eman P., and Nadler, Ronald D., Medical Primatology: History, Biological Foundations and Applications, pp. 70-71
25.  Beard, Chris, The Hunt for the Dawn Monkey, pp. 38-39
26.  Ian Tattersall, “Origin of the Malagasy Strepsirhine Primates” in Lemurs: Ecology and Adaptation, by Michelle L. Sauther,  pp. 3-14
27.  Fleagle, pp. 356-370
28.  Blythe A. Williams,  Richard F. Kay, and E. Christopher Kirk, “New perspectives on anthropoid origins” in PNAS, 10 March 2010; Fridman and Nadler, pp. 77-78, 81
29.  Fridman and Nadler, pp. 77-78, 81; Williams, et al; Ross, Callum, and Kay, Richard F., Anthropoid Origins: New Visions, p. 370
30.  Dixson, Alan F., Primate Sexuality: Comparative Studies of the Prosimians, Monkeys, Apes, and Human Beings, pp. 265-266, 316; A. H. Harcourt, and J. Gardiner, “Sexual Selection and Genital Anatomy of Male Primates” in Proceedings of the Royal Society, Biological Sciences, January 1994; Fridman and Nadler, p. 81
31.  Coolidge, Frederick L. and Wynn, Thomas , The Rise of Homo Sapiens: The Evolution of Modern Thinking, pp. 74-77
32.  Beard, Chris, The Hunt for the Dawn Monkey: Unearthing the Origins of Monkeys, Apes, and Humans, pp. 197-199, 215-245
33.  Paleobiology Database
34. Laurent Marivaux, Pierre-Olivier Antoine, Syed Rafiqul Hassan Baqri, Mouloud Benammi , Yaowalak Chaimanee, Jean-Yves Crochet, Dario de Franceschi, Nayyer Iqbal, Jean-Jacques Jaeger, Grégoire Métais, Ghazala Roohi, and Jean-Loup Welcomme, “Anthropoid primates from the Oligocene of Pakistan (Bugti Hills): Data on early anthropoid evolution and biogeography” in PNAS, June 14, 2005
35.  Sunil Bajpai, Richard F. Kay, Blythe A. Williams, Debasis P. Das, Vivesh V. Kapur, and B. N. Tiwari, “The oldest Asian record of Anthropoidea” in PNAS, August 12, 2008
36. K. Christopher Beard, Laurent Marivaux, Yaowalak Chaimanee, Jean-Jacques Jaeger, Bernard Marandat, Paul Tafforeau, Aung Naing Soe, Soe Thura Tun, and Aung Aung Kyaw, “A new primate from the Eocene Pondaung Formation of Myanmar and the monophyly of Burmese amphipithecids” in Proceedings of the Royal Society Biological Sciences, 22 September 2009, vol. 276 no. 1671, pp. 3285-3294
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40. Erik R. Seiffert, Elwyn L. Simons, William C. Clyde, James B. Rossie, Yousry Attia, Thomas M. Bown, Prithijit Chatrath, and Mark E. Mathison, “Basal Anthropoids from Egypt and the Antiquity of Africa's Higher Primate Radiation” in Science 14 October 2005: Vol. 310 no. 5746 pp. 300-304
41.  Rodolphe Tabuce1, Laurent Marivaux, Renaud Lebrun, Mohammed Adaci, Mustapha Bensalah, Pierre-Henri Fabre, Emmanuel Fara, Helder Gomes Rodrigues, Lionel Hautier, Jean-Jacques Jaeger, Vincent Lazzari, Fateh Mebrouk, Stéphane Peigné, Jean Sudre1, Paul Tafforeau, Xavier Valentin, and Mahammed Mahboubi, “Anthropoid versus strepsirhine status of the African Eocene primates Algeripithecus and Azibius: craniodental evidence” in Proceedings of the Royal Society, Biological Sciences,  9 September 2009
42. Blythe A. Williams, Richard F. Kay, and E. Christopher Kirk, “New perspectives on anthropoid origins” in PNAS, January 19, 2010
43.  David Tab Rasmussen, “Early catarrhines of the African Eocene and Oligocene” in The Primate Fossil Record, edited by Walter C. Hartwig, pp. 203-206
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45.  Iyad S. Zalmout, William J. Sanders, Laura M. MacLatchy, Gregg F. Gunnell, Yahya A. Al-Mufarreh, Mohammad A. Ali, Abdul-Azziz H. Nasser,              Abdu M. Al-Masari, Salih A. Al-Sobhi, Ayman O. Nadhra, Adel H. Matari, Jeffrey A. Wilson, and Philip D. Gingerich, “New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys” in Nature, Volume 466, 15 July 2010; Laursen, Lucas, “Fossil skull fingered as ape–monkey ancestor” in Nature News, 14 July 2010.
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48. George D. Koufos, “Potential Hominoid Ancestors for Hominidae” in Handbook of Paleoanthropology, Volume 1, edited by Winfried Henke and Ian Tattersall,  p. 1348
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51.  Terry Harrison,  “Late Oligocene to middle Miocene catarrhines from Afro-Arabia” in The Primate Fossil Record, ed. Hartwig, pp. 333-334
52.  David R Begun, “Fossil Record of Miocene Hominoids” in Handbook of Paleoanthropology, pp. 955-960
53.  Cela-Conde, Camilo J., and Ayala, Francisco José, Human Evolution: Trails from the Past, pp. 68-70
54.  Cela-Conde and Ayala, pp. 63-68
55.  David R. Begun, “Knuckle-Walking and the Origin of Human Bipedalism” in From Biped to Strider: The Emergence of Modern Human Walking, Running and Resource Transport, edited by D. Jeffrey Meldrum and Charles E. Hilton, pp. 9-10
56. Tracy L. Kivell, and Daniel Schmitt, “Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor” in PNAS, August 25, 2009
57.  Hall, Brian K., and  Hallgrímsson, Benedikt,  Strickberger's Evolution, Fourth Edition, p. 502
58.  Hart, Donna, and Sussman, Robert W., Man the Hunted: Primates, Predators, and Human Evolution, pp. 12-13
59.  W. E. H. Harcourt-Smith and L. C. Aiello, “Fossils, feet and the evolution of human bipedal
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60.  Klenerman, Leslie, and  Wood, Bernard A., The Human Foot: a Companion to Clinical Studies, pp. 45-48
61.  Strickberger,  Monroe W., Evolution, pp. 474-475
62.  Gen Suwa, Reiko T. Kono, Shigehiro Katoh, Berhane Asfaw, and Yonas Beyene, “A new species of great ape from the late Miocene epoch in Ethiopia” in Nature, 23 August 2007
63.  Yutaka Kunimatsu , Masato Nakatsukasa, Yoshihiro Sawada, Tetsuya Sakai, Masayuki Hyodo, Hironobu Hyodo, Tetsumaru Itaya, Hideo Nakaya, Haruo Saegusa, Arnaud Mazurier , Mototaka Saneyoshi, Hiroshi Tsujikawa, Ayumi Yamamoto, and Emma Mbua, “A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans” in PNAS, November 16, 2007
64.  M. Pickford, and H. Ishida, “Interpretation of Samburupithecus, an Upper Miocene hominoid from Kenya” in Comptes Rendus de l’Académie des Sciences, 1998
65.  Sudhir Kumar, Alan Filipski, Vinod Swarna, Alan Walker, and S. Blair Hedges, “Placing confidence limits on the molecular age of the human–chimpanzee divergence” in PNAS, December 27, 2005
66.  Asger Hobolth, Ole F. Christensen, Thomas Mailund, and  Mikkel H. Schierup, “Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model” in PLoS Genetics, February 2007
67.  Nick Patterson, Daniel J. Richter, Sante Gnerre, Eric S. Lander, and David Reich, “Genetic evidence for complex speciation of humans and chimpanzees” in Nature, 29 June 2006
68.  Masato Yamamichi, Jun Gojobori, and Hideki Innan, “An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees” in Molecular Biology and Evolution, September 8, 2011
69.  The Chimpanzee Sequencing and Analysis Consortium, “Initial sequence of the chimpanzee genome and comparison with the human genome” in Nature, 1 September 2005
70.  Paleomap Project
71.  Wolfram M. Kürschner, Zlatko Kvaček, and David L. Dilcher, “The impact of Miocene atmospheric carbon dioxide fluctuations on climate and the evolution of terrestrial ecosystems” in PNAS, 15 January 2008; R. F. Sage, “Environmental and Evolutionary Preconditions for the Origin and Diversification of the C4 Photosynthetic Syndrome” in Plant Biology, May 2001
72.  Michel Brunet, Franck Guy, David Pilbeam, Hassane Taisso Mackaye, Andossa Likius, Djimdoumalbaye Ahounta, Alain Beauvilain, Cécile Blondel, Hervé Bocherens, Jean-Renaud Boisserie, Louis De Bonis, Yves Coppens, Jean Dejax, Christiane Denys, Philippe Duringer, Véra Eisenmann, Gongdibé Fanone, Pierre Fronty, Denis Geraads, Thomas Lehmann, Fabrice Lihoreau, Antoine Louchart, Adoum Mahamat, Gildas Merceron, Guy Mouchelin, Olga Otero, Pablo Pelaez Campomanes, Marcia Ponce De Leon, Jean-Claude Rage, Michel Sapanet, Mathieu Schuster, Jean Sudre, Pascal Tassy, Xavier Valentin, Patrick Vignaud, Laurent Viriot, Antoine Zazzo, and Christoph Zollikofer, “A new hominid from the Upper Miocene of Chad, Central Africa” in Nature, 11 July 2002
73.  Brigitte Senut, Martin Pickford, Dominique Gommery, Pierre Mein, Kiptalam Cheboi, and Yves Coppens,  “First hominid from the Miocene (Lukeino Formation, Kenya)” in C. R. Acad. Sci. Paris, Sciences de la Terre et des planètes / Earth and Planetary Sciences 332, 2001
74.  Yohannes Haile-Selassie, Gen Suwa, and Tim White, “Hominidae” in Ardipithecus kadabba: Late Miocene Evidence from the Middle Awash, Ethiopia, edited by Yohannes Haile-Selassie and Giday WoldeGabriel, pp. 159-216
75.  Tim D. White, Berhane Asfaw, Yonas Beyene, Yohannes Haile-Selassie, C. Owen Lovejoy, Gen Suwa, and Giday WoldeGabriel, “Ardipithecus ramidus and the Paleobiology of Early Hominids” in Science, 2 October 2009
76.  White, et al
77.  White, et al
78.  Reader, John, Missing Links: In Search of Human Origins, pp. 187-196
79.  Fleagle, p. 511
80.  Cela-Conde and Ayala, p. 53
81.  Camilo J. Cela-Conde and Francisco J. Ayala, “Genera of the human lineage” in PNAS, June 24, 2003 vol. 100 no. 13 7684-7689
82.  Henry M. McHenry, “Human Evolution” in Evolution: The First Four Billion Years edited by Michael Ruse, Joseph Travis, pp. 270-71; Henry M. McHenry and Katherine Coffing,  “Australopithecus to Homo: Transformations in Body and Mind” in Annual Review of Anthropology, 2000; “2-million-year-old A. sediba cranium shows evidence of brain evolution, IU anthropologist finds” from Indiana University, September 12, 2011
83.  Tattersall, Ian, Becoming Human: Evolution and Human Uniqueness, pp. 112-113
84.  Yohannes Haile-Selassie, “Phylogeny of early Australopithecus: new fossil evidence from the Woranso-Mille (central Afar, Ethiopia)” in Philosophical Transactions of the Royal Society, Biological Sciences, October 2010
85.  Johanson, Donald, and Edey, Maitland, Lucy: the Beginnings of Humankind, passim.
86.  Kimbel, William H., Rak, Yoel, and Johanson,  Donald C., The Skull of Australopithecus afarensis,  pp. 11-15; Johanson  and Edgar, Blake, From Lucy to Language, p. 128
87.  Yoel Rak, Avishag Ginzburg, and Eli Geffen, “Gorilla-like anatomy on Australopithecus afarensis mandibles suggests Au. afarensis link to robust australopiths” in PNAS, April 17, 2007
88.  Carol V. Ward, William H. Kimbel, and Donald C. Johanson, “Complete Fourth Metatarsal and Arches in the Foot of Australopithecus afarensis” in Science, 11 February 2011
89. William H. Kimbel, and Lucas K. Delezene,., “’Lucy’ Redux: a Review of Research on Australopithecus afarensis” in Yearbook of Physical Anthropology, 2009.
90.  Kimbel and Delezene.
91.  Henry Gee, “A 3.5-million-year-old skull is a baffling mosaic of primitive and advanced features” in Nature News, 22 March 2001.
92.  Michael Balter, “What Ever Happened to Kenyanthropus platyops?” in Origins: a History of Beginnings, October 29, 2009, a blog attached to the journal Science
93. Australian National Museum, http://australianmuseum.net.au/Australopithecus-bahrelghazali
94.  Cartmill, Matt, Smith, Fred H., The Human Lineage, p. 133; eFossils, University of Texas at Austin, http://www.efossils.org/species/australopithecus-africanus
95.  Cartmill and Smith, pp. 133-136
96.  Cartmill and Smith, pp. 198-199, 158
97.  Phillip V. Tobias, “”Robust” Australopithecine and Homo Similarities” in Evolutionary History of the "Robust" Australopithecines, edited by Frederick Grine, pp. 301-302
98.  Berhane Asfaw, Tim White, Owen Lovejoy, Bruce Latimer, Scott Simpson, and Gen Suwa, “Australopithecus garhi: A New Species of Early Hominid from Ethiopia” in Science,  23 April 1999
99.  Lee R. Berger, Darryl J. de Ruiter, Steven E. Churchill, Peter Schmid,  Kristian J. Carlson, Paul H. G. M. Dirks, and Job M. Kibii, “Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa” in Science, 9 April 2010
100. Berger, et al
101. Tracy L. Kivell, Job M. Kibii, Steven E. Churchill, Peter Schmid, and Lee R. Berger, “Australopithecus sediba Hand Demonstrates Mosaic Evolution of Locomotor and Manipulative Abilities” in Science, 9 September 2011
102. http://www.wits.ac.za/academic/research/ihe/sediba/13730/frequently_asked_questions.html
103. Catherine Brahic, and Rowan Hooper, “Skeleton of ancient human relative may yield skin” in New Scientist, 16 November 2011
104. Ishida, Hidemi, Human Origins and Environmental Backgrounds, p. 252
105. Sarmiento, Esteban E., Sawyer, Gary J., Milner, Richard, Deak, Viktor, and Tattersall, Ian, The Last Human: a Guide to Twenty-Two Species of Extinct Humans, pp. 108-112
106. Sarmineto, et al, pp. 133-134, and 136
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Evolution of the Genus Homo:

1.  L. S. B. Leakey, P. V. Tobias, and J. R. Napier, “A New Species of the Genus Homo from Olduvai Gorge” in Nature, April 4, 1964
2.  Leakey, Richard, The Origin of Humankind, pp. x-xv
3.  Bernard Wood and Mark Collard, “The Meaning of Homo” in Ludus Vitalis, Vol. IX, Number 15, 2001
4.  Lewin, Roger, Human Evolution: an Illustrated Introduction, p. 149
5.  Cladograms of various kinds tracing the phylogeny of the hominids  may be found at the following locations:

Access Science:
http://accessscience.com/abstract.aspx id=270300&referURL=http%3a%2f%2faccessscience.com%2fcontent.aspx%3fid%3d270300  [Subscription  may be required]

The Smithsonian National Museum of Natural History:
http://humanorigins.si.edu/evidence/human-evolution-timeline-interactive

Darwiniana and Evolution:
http://darwiniana.org/trees.htm

An unusual site that nonetheless displays about two dozen different cladograms:
http://www.the-goldenrule.name/Marriage_Hera-Juno_FIG_Homo-erectus/Marriage_Hera-Juno_FIG_Homo-erectus_--_MORE.htm

6.  B Wang and J Brand-Miller, “The role and potential of sialic acid in human nutrition” in European Journal of Clinical Nutrition (2003) 57, 1351–1369
7.  Hsun-Hua Chou, Toshiyuki Hayakawa, Sandra Diaz, Matthias Krings, Etty Indriati,  Meave Leakey, Svante Paabo, Yoko Satta, Naoyuki Takahata, and Ajit Varki, “Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution” in PNAS, August 21, 2002
8.  The Cambridge Encyclopedia of Human Evolution, edited by Steve Jones, Robert Martin, and David Pilbeam, pp. 242-243; Encyclopedia of Human Evolution and Prehistory, Second Edition, edited by Eric Delson, Ian Tattersall, John A. Van Couvering, and Alison S. Brooks, p. 329-330
9.  Grine, Frederick E., John G. Fleagle, Richard E. Leakey, The First Humans: Origin and Early Evolution of the Genus Homo, pp. 34-36
10. From a compilation by Steven Heslip of Michigan State University, located at: 
https://www.msu.edu/~heslipst/contents/ANP440/habilis.htm
11. Lieberman, Daniel, The Evolution of the Human Head, p. 480
12.  S. C. Anton, “Framing the Question: Diet and Evolution in Early Homo” in Primate Craniofacial Function and Biology, edited by Chris Vinyard , Matthew J. Ravosa, and Christine Wall, pp. 455-456
13.  Joseph M. A. Miller, Gene H. Albrecht, and Bruce R. Gelvin, “Craniometric variation in early Homo compared to modern gorillas: a population-thinking approach” in Shaping Primate Evolution: Form, Function, and Behavior, edited by Fred Anapol, Rebecca Z. German, and Nina G. Jablonski, pp. 66-93
14. “Homo habilis” from the Institute on Human Origins, located at: http://www.becominghuman.org/node/homo-habilis-essay
15.  Smithsonian, eFossils
16.  Reader, John, Missing Links: In Search of Human Origins, pp. 329-332
17.  Archaeology Info.com, a website maintained by two researchers who have worked at Lake Turkana in Kenya, located here:  http://archaeologyinfo.com/homo-rudolfensis/
18.  Heslip, located at https://www.msu.edu/~heslipst/contents/ANP440/rudolfensis.htm
19.  Sawyer and Deak, The Last Human, pp. 127-128, 119
20. Sileshi Sema, “The World’s Oldest Stone Artefacts from Gona, Ethiopia: Their Implications for Understanding Stone Technology and Patterns of Human Evolution Between 2·6–1·5 Million Years Ago” in Journal of Archaeological Science, (2000) 27, 1197–1214
21. Melissa A. Panger, Alison S. Brooks, Brian G. Richmond, and Bernard Wood,  “Older Than the Oldowan? Rethinking the Emergence of Hominin Tool Use” from Evolutionary Anthropology, 11:235–245 (2002)
22.  Handbook of Paleoanthropology, p. 1656
23.  http://archaeologyinfo.com/knm-er-3733/
24. Ronda R. Graves, Amy C. Lupo, Robert C. McCarthy, Daniel J. Wescott, Deborah L. Cunningham, “Just how strapping was KNM-WT 15000?” in Journal of Human Evolution, 2010, 06.007
25. Robin Dennell, “’Out of  Africa I’: Current Problems and Future Prospects” in Out of Africa I: The First Hominin Colonization of Eurasia, edited by John G. Fleagle, pp. 247-249
26.  Dennell, p. 250
27.  Willoughby, Pamela R., The Evolution of Modern Humans in Africa: a Comprehensive Guide, pp. 165-167
28.  Willoughby, pp. 172-173
29.  eFossils, http://www.efossils.org/page/specimens/Homo%20ergaster
30.  Gilbert, W. Henry, and Berhane Asfaw, Homo erectus: Pleistocene Evidence from the Middle Awash, Ethiopia, pp. 355-356
31. Prins, Harald E. L., William A. Haviland and Bunny McBride, Evolution and Prehistory: The Human Challenge, pp. 182-183
32. Matthew R. Bennett, John W.K. Harris, Brian G. Richmond, David R. Braun, Emma Mbua, Purity Kiura, Daniel Olago, Mzalendo Kibunjia, Christine Omuombo, Anna K. Behrensmeyer, David Huddart, and Silvia Gonzalez, “Early Hominin Foot Morphology Based on 1.5-Million-Year-Old Footprints from Ileret, Kenya”, in Science 27 February 2009: Vol. 323 no. 5918 pp. 1197-1201
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The Diaspora of Modern Consciousness: Homo Sapiens Spreads Throughout the World:

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Humans as Physical Beings 

Humans in the Context of Life:

1.  The Timetree of Life, S. Blair Hedges and Sudhir Kumar, editors, p. 51
2.   “Hominoid Taxonomies”, Science Week, 1 August 2001, referenced here: http://cogweb.ucla.edu/ep/Hominoids.html

General information on methods used to date the emergence of clades may be found here:
Michael J. Benton and Philip C. J. Donoghue, “Paleontological Evidence to Date the Tree of Life” in
Molecular  Biology and  Evolution (2007) 24 (1): 26-53. doi: 10.1093/molbev/msl150

The Human Animal: A General Survey of Its Composition, Structure, Function, Capacities, and Limitations

1.   Robert A. Freitas Jr., Nanomedicine, Chapter 3,  “Human Body Chemical Composition” located here: 
http://www.foresight.org/Nanomedicine/Ch03_1.html
2.   http://www.bio.miami.edu/~cmallery/150/life/elements.htm
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16.  Frisancho, A. Roberto, Human Adaptation and Accommodation,  pp. 177-182
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18.  White and Folkens, pp. 31-33
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20.  Gray’s Anatomy, pp. 34-37
21.  Gray’s Anatomy, pp. 124-131
22.  Gray’s Anatomy, pp. 134-215, plus online edition, located here: http://www.bartleby.com/107/17.html
23.  “Joints and Movements”, located here: http://www.physioweb.org/skeletal/joint.html
24.   Duggan, Christopher, John B. Watkins, and W. Allan Walker, Nutrition in Pediatrics: Basic Science, Clinical Applications, p. 31
25.  Scott, Ann Senisi and Elizabeth Fong, Body Structures and Functions, pp. 117-118
26.  “Biomechanics of Muscular Movement”, located here: http://www.alteregofitnessgroup.com/digital-media-samples/personal-trainer-e-book.pdf
27.  Scott and Fong, 119-121
28.  The Digestive System, edited by Kara Rogers, pp. 19-36
29.  Rogers, The Digestive System, 36-40
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34.  Tortora and Grabowski, pp. 891-895
35.  Kimball’s Biology, “Sexual Reproduction in Humans”, located here: 
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36.  Robert C. Dean and Tom F. Lue, “Physiology of Penile Erection and Pathophysiology of Erectile Dysfunction” in NIHPA Author Manuscripts, January 25, 2006
37.  Bering, Jesse, Why Is the Penis Shaped Like That?: And Other Reflections on Being Human, pp. 17-27
38.  Summers, Paul R., “Vaginal Anatomy”, American Society for Colposcopy and Cervical Pathology, located here: http://www.asccp.org/practicemanagement/vagina/vaginalanatomy/tabid/7488/default.aspx
39.  Jones, Richard Evan, and Kristin H. López, Human Reproductive Biology, pp. 234-235
40.  Sloane, Ethel, Biology of Women, pp. 42-44
41.  Jones and López, pp. 235-236
42.  This account of follicle development and ovulation has been distilled from the first two chapters of Jones and  López’s brilliant work.
43.  Jones and López, pp. 236-238, 241-243
44.  The Visible Embryo, located here: http://www.visembryo.com/baby/1.html
45.  Ferin , Michel, Raphael Jewelewicz,  and Michelle P. Warren, The Menstrual Cycle: Physiology, Reproductive Disorders, and Infertility, pp. 3-7
46.  Greenberg, Jerrold S., Clint E. Bruess, Sarah C. Conklin, Exploring the Dimensions of Human Sexuality, Fourth Edition, p. 398
47.  Stewart, Donna E., Menopause: A Mental Health Practitioner's Guide, p. 17
48.  Jones and López, p. 234
49. “ Hormones, Receptors and Target Cells”, from Colorado State University, located here: 
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50.  Arendt, J., Melatonin and the Mammalian Pineal Gland, pp. 6-10
51.  Becker, Kenneth L., Principles and Practice of Endocrinology and Metabolism, pp. 84-86, 91-95;
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52.  University of Pittsburgh Department of Neurological Surgery, located here: 
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53.  Merck Manuals, located here: 
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54.  Sompayrac, Lauren M., How the Immune System Works, 4th Edition, pp. 1-3
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60.  Anthony McGrath, “Anatomy and Physiology of the Bowel and Urinary Systems”, located here:
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63.  Histology Guide, University of Leeds, located here: http://www.histology.leeds.ac.uk/skin/skin_layers.php
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Aging and the Human Lifespan

1.   For a fuller explanation of mitosis, see Clare O'Connor, “Cell Division: Stages of Mitosis”, in Nature Education, 2008 1(1)
2.   David Rasnick, “Auto-catalysed progression of aneuploidy explains the Hayflick limit of cultured cells, carcinogen-induced tumours in mice, and the age distribution of human cancer” in Biochemistry Journal, (2000) 348, 497-506
3.  Julianne Meyne, , Robert L. Ratliff,  and Robert  K. Moyzis, “Conservation of the human telomere sequence (TTAGGG)n among vertebrates” in PNAS, September 1, 1989 vol. 86 no. 18 7049-7053
4.   Geraldine Aubert and Peter M. Lansdorp, “Telomeres and Aging” in Physiological  Reviews, April 2008 vol. 88 no. 2 557-579
5.   Ewen Callaway, “Telomerase reverses ageing process” in Nature News, 28 November 2010
6.  Melpomeni Peppa, Jaime Uribarri, and Helen Vlassara, “Glucose, Advanced Glycation End Products, and Diabetes Complications: What Is New and What Works” in Clinical Diabetes October 2003 vol. 21 no. 4 186-187
7.   Alan R. Hipkiss, “Glycation, ageing and carnosine: Are carnivorous diets beneficial?” in Mechanisms of Ageing and Development, 13 June 2005, 126 1034–1039
8.   A. Yu. Andreyev, Yu. E. Kushnareva, and A. A. Starkov, “Mitochondrial Metabolism of Reactive Oxygen Species” in Biochemistry (Moscow), February 2005
9.   Life expectancy at birth > female by country", CIA World Factbooks 18 December 2003 to 28 March 2011. Retrieved from http://www.NationMaster.com/graph/hea_lif_exp_at_bir_fem-health-life-expectancy-birth-female; "Life expectancy at birth > male by country", CIA World Factbooks 18 December 2003 to 28 March 2011. Retrieved from http://www.NationMaster.com/graph/hea_lif_exp_at_bir_mal-health-life-expectancy-birth-male
10.  Jacob B. Hjelmborg, Ivan Iachine, Axel Skytthe, James W. Vaupel, Matt McGue, Markku Koskenvuo, Jaakko Kaprio, Nancy L. Pedersen, Kaare Christensen, “Genetic influence on human lifespan and longevity” in Human Genetics, (2006) 119: 312–321
11.  Manja Schoenmaker, Anton J M de Craen, Paul H E M de Meijer, Marian Beekman, Gerard J Blauw, P Eline Slagboom, and Rudi G J Westendorp, “Evidence of genetic enrichment for exceptional survival using a family approach: the Leiden Longevity Study” in European Journal of Human Genetics (2006) 14, 79–84. doi:10.1038/sj.ejhg.5201508; published online 26 October 2005











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