The body and thermodynamics — bioenergetics

Thermodynamics and metabolism – an overview of bioenergetics

The human body (like other living organisms) is a complex, multi-level symbiosis of parts. The most basic constituent of any organism is the atom, because atoms make up chemical molecules. In biology, molecules can be of an astonishing and enormous complexity. Molecules join to make cells, which in turn make up tissue, such as skin, bone or muscle tissue. Tissues comprise organs, like the heart or liver, which are grouped into systems, such as the nervous or digestive systems. The systems in turn make up the organism. All those different levels of organization add up to a very complicated and highly organized system.

Levels of organization of the body, from Openstax College

Organisms are maintained in working order by a group of processes called metabolism, the set of all the chemical reactions which take place in the body in order to ensure life, including the maintenance of homeostasis. Homeostasis is the environment necessary to ensure proper functioning. It includes temperature, blood pressure and glucose level. At the same time it maintains the ordered state of the body, this energy is fighting against entropy increase in the body. In doing so, it is increasing the entropy of the universe. Food entering the body is highly organized, so in a state of low entropy, whereas waste products are in a state of much higher entropy. Also, much energy is dissipated as heat, as in any machine.

Metabolism is a two-faced affair, composed of two groups of processes:

Catabolism is the breaking down of large molecules into smaller ones, a good example being the breaking down of food molecules to obtain energy. In general, a larger number of molecules tends to be more disordered and so catabolic reactions tend to increase entropy.
Anabolism is the opposite of catabolism, so it is the combining of smaller molecules to produce larger ones, such as the formation of proteins from amino acids. Anabolic reactions tend to decrease entropy locally.

Reactions inside the body may occur spontaneously or not. Biochemists use the concept of free energy, or Gibbs free energy, the change of which is defined by

ΔG = energy_prod – energy_reac,

i.e., the energy of the products minus the energy of the reactants. But input (reactant) and output (product) energies are related by

energy_reac → energy_prod + ΔE,

where ΔE is the energy released. So

ΔE = energy_reac – energy_prod = -ΔG

Since nature (physics) likes systems to go towards states of lower energy, the reaction will take place spontaneously if the emitted energy ΔE is positive and therefore ΔG is negative.¹.It seems to me the sign is backward. Such reactions are said to be exergonic. So we have two possible cases:

The energy of the products is less than the energy of the reactants (ΔG < 0), so the reaction is exergonic and takes place spontaneously, or
the energy of the reactants is greater than the energy of the reactants (ΔG > 0), so the reaction is endergonic and does not occur spontaneously.

Such organization is quite unlikely and is therefore in a state of very low entropy. The struggle against increasing entropy (disorganization, like decay) requires the addition of significant amounts of energy. How does this take place?

Global bioenergetics

Movement is a form of energy (kinetic) and everything which moves (steam engines, electric motors or animal muscles) requires input of the energy it expends – and more, since some is lost as heat. Animals get their energy from the nutrients they ingest – food. Plants are autotrophs, meaning that they make their own nourishment, converting energy from the sun into mostly carbohydrates, which we can then eat. Humans are heterotrophs, “hetero” meaning “other”. We must get our nourishment from others, meaning plants and other animals.

Global bioenergetic cycle, from Openstax College

On a global scale, energy transformations are cyclic. Sunlight strikes plants and, in doing so, provides energy to power photosynthesis which produces carbohydrates from CO₂ and water. Some of these are eaten directly by us and some indirectly, as we eat the animals which have consumed the plants (or other animals which have…). Our digestive system and cells convert what we eat and breathe into usable energy. Our waste products include CO₂ and water, which are then reused by plants. The details go way beyond this overly simple illustration, but the idea is the same – a cycle of substances through plants, then animals, then back to plants, and so on. But the initial solar energy is eventually re-radiated into space as heat and is lost. New solar energy must continually be pumped in to keep the cycle running, in accordance with the Second Law of thermodynamics.

Calculation shows that the Earth obeys the Second Law of Thermodynamics.²Carroll (2010), 192-3. Energy from the Sun is at high temperature and therefore has relatively low entropy, whereas the energy radiated back into space from the Earth is at a lower-temperature and so has higher entropy, which guarantees that the entropy of the whole system increases. (Mathematically, entropy is heat emitted divided by the temperature.)

Energy flow in the human body

Two main energy input paths exist in the human body, respiration and diestion –air and food.

Oxygen is distributed by the circulatory system. When we breathe, air enters through the nose, then passes through the pharynx, the larynx, the trachea and the bronchi and into the lungs. There, it passes into the alveoli where oxygen is transferred to the blood which has been pumped into the lungs from the right ventricle of the heart through the pulmonary artery. After oxygenation in the alveoli, the blood is pumped through the pulmonary vein³The pulmonary veins are the only veins to convey oxygenated blood, so it is convenient to think of veins as conveying blood toward the heart. into the left atrium of the heart, then out from the left ventricle through the rest of the body’s arterial system finally passing from tiny capillaries into the cells. De-oxygenated blood is pumped back through the veins into the right atrium of the heart and then the process starts over.

Pulmonary circuit, by Openstax College via Wikimedia Commons

The blood circulates all kinds of things, not just oxygen. For instance, it carries products of digestion such as glucose to the cells and removes waste products.

The second energy-input pathway, digestion, takes place as food enters the body through the mouth, where it is partially broken down (hydrolyzed) by enzymes and chewing. It then passes through the pharynx and esophagus to the stomach and intestines, where it is digested by various processes using different enzymes depending on composition (carbohydrates, lipids or proteins). The result is principally glucose, which enters the blood from which it may be used immediately or stored for later use.

When the cell needs energy, a series of processes called cellular respiration takes place, mostly in the mitochondria. Glucose from digestion is combined with oxygen from the lungs to liberate energy. This is the fun part! What happens is this.

C₆H₁₂O₆ + 6O₂ → 6H₂O + 6CO₂ + energy

which in plain English reads

glucose + oxygen→ water + carbon dioxide + energy

This is where the two input paths come together. Glucose from digestion is combined with oxygen from the lung to make water, carbon dioxide and much energy. It is glucose catabolism, or breakdown. The liberated energy supports metabolism.

Next chapter, energy input through digestion.

Notes[+]

Notes
↑1	.It seems to me the sign is backward.
↑2	Carroll (2010), 192-3.
↑3	The pulmonary veins are the only veins to convey oxygenated blood, so it is convenient to think of veins as conveying blood toward the heart.

Plant life cycles and taxonomy

Plant life cycles – alternation of generations

Cell growth and reproduction employ three processes:

mitosis: diploid cell → two diploid cells, or haploid cell → two haploid cells
meiosis: diploid cell → two haploid cells (gametes or spores)
fertilization: two haploid cells (gametes) → one diploid cell (zygote)

Mitosis can duplicate cells for growth or for reproduction, depending on the organism; meiosis only serves reproduction, and fertilization is its inverse.

Cells of different organisms may spend different relative amounts of time in haploid and diploid states. Humans cells spend most of their time in the diploid state, going haploid only for the short period required for sexual reproduction. This is not true for plants. Biologists use the following terms to classify organisms by the relative duration spent in stages of their life cycle.

haplontic – The organism’s life cycle is comprised of a dominant haploid stage.
diplontic – The diploid stage is dominant (in humans, for example).
haplodiplontic – The two stages alternate more or less equally (the case for most plants).

The alternating stages of haplodiplontic organisms is called the alternation of generations. The following figure illustrates the heterosporous case.

Alternation of generations (heterosporous)Author's own work.

Alternation of generations (heterosporous)¹Author’s work, based on Openstax BIology, itself modification of work by Peter Coxhead.

We use the notation 1n for haploid and 2n for diploid, meaning one or two times the number, n, of chromosomes in the organism.. The steps in alternation of generations are the following.

Fertilization of two haploid gametes produces a diploid zygote, which duplicates and grows by mitosis to form the sporophyte, the diploid multicellular form of the organism.
The sporophyte carries sporangia (spore-containing sacs), in which diploid sporocytes produce haploid spores by meiosis. The spores may be homosporous (containing male and female spores) or heterosporous (different spores for male and female).
The spores grow by mitosis to form the haploid multicellular form of the organism, the gametophyte. In the case of heterosporous organisms, separate male and female gametophytes are formed.
Inside the appropriate gametophyte, antheridia produce sperm and archegonia produce eggs, haploid gametes which join through fertilization to form the diploid zygote, bringing us back⁴“…by a commodius vicus of recirculation…” to the beginning of the cycle. Generically, antheridia and archegonia are called gametangia.

In plants, multicellular individuals exist in both the diploid and haploid states, as in the above figure. In the life cycle of a diplontic individual such as a human, there are neither a gametophyte stage nor spores. An individual produces gametes by meiosis, which are quickly fertilized (or lost) to become a diploid zygote from which a new individual will grow.

Life cycle of diplontic individual.Author's own work.

Life cycle of diplontic individual.⁵Author’s own work.

Plants vary in several significant ways.

Different plants have different dominant states: A moss’s dominant stage is the gametophyte; a fern’s, the sporophyte. All seed plants (angiosperms) are sporophyte-dominant.
Plants may be homosporous or heterosporous. Homosporous plants produce both male and female gametangia from the same gametophyte. Heterosporous plants may have the male and female spores occuring on the same flower or plant (monoecious), on different flowers or cones (pine) or even on different plants (dioecious, like gingkos). Seed plants are heterosporous and the seed grows from the female spore; the pollen, from the male.
Plants may be vascular, containing cells which conduct water and solutes throughout the plant, or non-vascular.
Plants may or may not flower.

In haplodiplontic plants, alternation of generations refers to the reproductive cycle. The whole plant does not exist as a sporocyte and then disappear to reappear as a gametophyte, or vice versa. The less dominant phase exists on the dominant stage. A tree appears as a tree, which is its sporophyte stage. The gametophyte stage takes place on the various parts of the flowers or in the cones.

Trees and bushes are vascular plants. Their dominant phase is the sporophyte. Heterosporous plants produce male microspores, so called because of their small size, which then form pollen grains. The much larger female megaspores form ovules. After fertilization by pollen, ovules become seeds, but this takes time, maybe two years.

The differences between spores and seeds (both haploid) are summarized in the following table.

	spore	seed
size	microscopic	large
cell	unicellular	multicellular
type plant	non-flowering	flowering
dissemination	gravity,wind	animals

Land plants are commonly divided into four major divisions, as shown in the following figure.

Major divisions of plants, from Openstax College.

The group of non-vascular plants, commonly called bryophtyes, includes moss, whose dominant stage is the haploid gametophyte. The sporophyte stage grows on the gametophyte plant. Moss is heterosporous and so produces male and female spores.

Moss with sporophytes, by James919 via Wikipedia.

A fern is a seedless vascular plant and its dominant state is the diploid sporophyte. The tiny dark-colored objects under the fronds are spore-containing vessels called sori.⁶Singular, sorus. Ferns are homosporous and their gametophytes are independent of the sporophytes.

Gymnosperms are non-flowering seed plants, like conifers or the gingko.⁷Also called at least in French, l’arbre des quarante écus. The tree is the diploid sporophyte phase. Conifers are heterosporous: The male gametophytes lives in the smaller, pollen cones lower on the tree; the female gametophyte is in the form of the harder, upper ovulate cones. Wind carries the pollen from the male cones to the female ones.

Angiosperms, flower-bearing vascular plants, are also heterosporous and their dominant phase is also the diploid sporophyte. The male and female gametophytes are found in the flowers, in the anther and the ovary, as in the following figure.

Angiosperm life cycle, by Mariana Ruiz Villareal, via Wikimedia Commons

Angiosperms are fertilized through the rather complex process of double fertilization.

In the anther, on the stamen, male microsporocytes divide by meiosis to produce haploid microspores, which grow by mitosis to produce pollen grains, each of which contains two cells: one with two sperm and one which will grow a pollen tube.

In the ovule, female megasporocytes develop similarly through division by meiosis and growth by mitosis to form the female gametophyte, the megagametophyte, or embryo sac. Typically, the embryo sac contains seven cells, one of which contains two nuclei and so is diploid. Of the other six haploid cells, one is the egg.

When the pollen grain enters in contact with the embryo sac, it germinates, sending forth a pollen tube which extends into the embryo sac and allows passage of the two sperm cells. One fertilizes the egg. The other fertilizes the double-nucleus cell, forming a triploid nucleus, which later develops into food for the zygote and Is called the endosperm. On the wheat plant, the endosperm is the part we grind to make bread.

The group of non-vascular plants, or bryophytes, is the oldest. Spores attributed to bryophytes date from the Ordovician, c. 490 Mya.1 Vascular plants appeared later, in the Silurian, c. 440 Mya. By the Late Devonian period (385 Mya) vascular plants had developed leaves and root systems. During the Carboniferous period (359-299 Mya), they grew to immense heights, and when they died, they were the basis for the fossil fuels we are burning today. Ferns became enormous during the Carboniferous. Gymnosperms probably appeared during the Carboniferous and were dominant in the Mesozoic Era (251-65.5 Mya). Angiosperms had become dominant by the middle of the Cretaceous period (145.5-65.5 Mya) and are still the most abundant of the plant groups.

Taxonomy – classification of species

Biologists classify all life in a hierarchical system of classifications, or taxa. These classification schema have varied over time. Current stages of the classification for animals are shown in the figure.

Biological taxonomic classification system, by Pengo [Public domain], via Wikimedia Commons

From the original two suggested kingdoms of 1735, we are now up to six in the latest suggested version. This document will stick with the three – Bacteria, Archaea and Eucarya – we have been using so far. The system is most simply explained by some examples. Plant taxonomy is very different, using different terms for Domain, Phylum and Class, so we will skip them.

Domain	Animalia
Kingdom	Eukarya
Phylum	Chordata
Class	Mammalia				Actinopterygii
Order	Primates	Carnivora			Salmoniformes
Family	Hominidae	Felidae		Canidae	Salmonidae
Genus	Homo	Felis	Felinae	Canis	Salmo
Species	H. sapiens	F. catus (domestic cat)	A. jubatus (cheetah)	C. lupus (common dog)	S. salar (Atlantic salmon)
Sub-species	H. sapiens sapiens (you know who)

Next, anatomy and physiology and bioenergetics.

Notes[+]

Notes
↑1	Author’s work, based on Openstax BIology, itself modification of work by Peter Coxhead.
↑2	For humans, n = 23, of course
↑3	Note that this discussion concerns land plants only.
↑4	“…by a commodius vicus of recirculation…”
↑5	Author’s own work.
↑6	Singular, sorus.
↑7	Also called at least in French, l’arbre des quarante écus.
↑8	There are various mnemonics for remembering the order. My favorite is “King Phillip came over for good spaghetti”. Other versions vary in the word “spaghetti”…

Cell division and reproduction

In order for cells to increase in number, either for growth or replacement of old cells, they go through the process of cell division – the cell cycle. Although the cycle is generally considered to consist of three major phases, there is a fourth phase to cell life. Cell cycles in various parts of the human body may last anywhere from 10 hours (bone marrow cells) to a lifetime (neurons).

G₀ is the “fourth” state, where the cell is not waiting to divide but is just doing its cellular thing. It may stay in this state indefinitely or eventually enter into the first phase of the cell cycle.

The cell cycle.. PPMAT = Prophase, Prometaphase, Metaphase, Anaphase and Telophase. Thick black lines are checkpoints. Author’s own work.

The interphase

The first major phase of the cell cycle is the so-called interphase, in which the cell fulfills its normal activities while preparing for cell division. The interphase is itself divided into three steps.

During G₁, or the first gap, the cell procures and stores proteins and energy for the task ahead. Near the end of G₁, a checkpoint controls the cell’s readiness for the next phase.
During the S (synthesis) phase, DNA replication takes place. Chromatin is condensed and each chromosome is duplicated into two copies, sister chromatids, which are attached at a point called the centromere. DNA replication takes place in much the same way as RNA transcription except that both strands are duplicated, entirely. The cell’s centrosome, the organizing center for microtubules, is also duplicated.
The G₂ (gap 2) phase is another moment for storing energy and making proteins. Also, the cytoskeleton is dismantled and some organelles are replicated. Near the end of the phase, another checkpoint is performed.

Mitosis

The mitosis phase does all the rest of the replication and localization of organelles, leaving only the actual division of the cell in two. It too is understood to take place in a number of steps.¹Some sources omit the prometaphase. There is also disagreement as to what goes into each step. For instance, Katz and Openstax say the nuclear envelope breaks down in the prophase; Bear et al., in the prometaphase.

Stages of mitosis, after Ali Zifan via Wikimedia Commons

During the first phase, prophase, the two centrosomes move towards opposite sides of the cell and microtubules form between them an array of links called the mitotic spindle. The chromosomes condense more and the nuclear envelope and the nucleoli break down.
The main event of the prometaphase is the connection of the sister chromatids to the microtubules of the spindle by protein complexes called kinetochores .
During the metaphase, the still condensing chromosomes are lined up in the equatorial plane of the cell, the metaphase plate.
The actual split of chromosomes takes place in the anaphase² Why is it not called the cataphase?, with sister chromatids pulled towards opposite poles of the cell by the kinetochores, which crawl along the spindle tubules much as myosin crawls along actin during muscle contraction.³See the section on muscles later in this document.
During the telophase, chromosomes decondense and the mitotic spindle breaks down in preparation for making new cytoskeletons. Portions of the endoplasmic reticulum are used to form new nuclear envelopes around the two separate chromosomes.

Cytokinesis

The actual division of the cell into two takes place differently in plant and animal cells, since plant cells are surrounded by a stiff outer cell wall.

In animal cells, a ring of actin filaments contracts around the center of the cell and pinches it in two. The contraction of the ring is probably due to actin and myosin acting as in muscles.

In plant cells, the Golgi apparatus has stored up enzymes, proteins and glucose molecules during the interphase. During the telophase, these components move along microtubules to the metaphase plate. There, they grow and fuse and eventually form a new cell wall.

Checkpoints

At several points in the cell cycle, there are checkpoints at which the readiness of the cell to enter the next part of the cycle is controlled. The fresh copies are compared to the original strands and any divergent segments replaced. If the DNA is not intact, the whole process may be restarted or canceled altogether. The cell may actually be instructed to commit apoptosis, cell suicide.

If ever, due to a mutation or bad gene copy, for instance, a checkpoint does not function properly, defective DNA could be passed on to daughter cells. This may lead to the unchecked replication of such cells and genes – cancer.

Reproduction — meiosis

Most animals and plants are diploid, meaning they have two sets of chromosomes, one copy from each parent. A cell containing only one copy of its chromosomes is called haploid. Cell growth and doubling take place through the cell cycle and mitosis, but reproduction of the organism depends on another cycle, meiosis.

Eukaryotes participate in both mitosis and meiosis:

Mitosis grows new cells identical to the original. A diploid (or 2n) cell duplicate itself into two diploid (2n) cells.

diploid cell → (mitosis) → two diploid cells

Meiosis, for reproduction, creates two haploid cells from one diplod cell.

diploid cell → (meiosis) → two haploid cells

Then two haploid cells, one from each parent, join to make a child diploid cell.

Meiosis is preceded by an interphase, composed of G₁, S and G₂ phases, which travels essentially the same path as in mitosis. Eukaryotic meiosis takes place in two cyclical parts:

Meiosis I splits the cell’s DNA into two diploid pairs.
Meiosis II splits the pairs into haploid sister chromatids.

The splitting is illustrated in the second figue below. How it all works on the chromosomal level is sketched in the next figure,

At the top of the figure (a) are shown two homologous chromosomes, meaning that they have the same chromosome number (between 1 and 23, in humans) and so correspond to the same genes. For clarity, they are labeled 1 and 2. Suppose that one (colored blue) comes from the father and the other (pink), from the mother.

During the S part of interphase, duplicates of all chromosomes are made, called, as in mitosis. sister chromatids. The two blue chromosomes (1 and 3) are sisters and so are the two pink ones (2 and 4). All four are homologous. Sister chromatids are bound together at the centromere and will remain so bound until meiosis II.

During prophase I (prophase of meiosis I), the two pairs, which are now visible under a microscope, are closely and precisely aligned, a pairing called synapsis (c). Being homologous, a gene on a pink chromosome is aligned with the corresponding gene on a blue one. The proximity of the two allows crossing over, or recombination, to take place (d), the reciprocal exchange of genetically equivalent sequences of DNA between two non-sister chromosomes, in this case numbers 1 and 2. Genes are exchanged between the chromosomes of the father and those of the mother. Since this is random, it is the first source of randomness in the resulting chromosome. The synapsis then loosens (e), but the pairs remain linked at the chiasmata (singular = chiasma), the loci where crossing over has taken place. The four chromosomes are said to constitute a tetrad. In general, a sister chromatid is no longer composed of genes from only one parent, but a mix of maternal and paternal genes.

Chromosome mixing in meiosis in animals⁴Author’s own work.

It can happen that a piece of one chromosome may break loose and join on to another. Such translocations have been observed in persons suffering from a specific kind of leukemia.

At the end of prophase I, homologous, non-sister chromatids are held together at chiasmata; sister chromatids, at centromeres.

During prometaphase I and metaphase I, microtubules of the spindle from the centrosomes, which are now on opposite side of the cell, attach via kinetochores to the centromeres of the chromosomes, i.e., to sister pairs. These connections are also random. Any pair of the 23 chromosomes may be pulled to one side and the other pair to the other side. This introduces a second source of randomness in the final product. In the case of human beings with 23 chromosomes, there are 2²³ – over eight million – possibilities.

Next, during anaphase I, the spindle fibers pull the chromosomes to either side, with sisters breaking apart at the chiasmata, but remaining together, since the kinetochores are attached to the centromeres.

In the cytokinesis phase, the two cells separate. In our case, chromosomes numbers 1 and 3 remain together, as well as 2 and 4. Each cell contains two chromosomes, but they are sisters, so the cell is considered to be haploid.

In summary, at the end of meiosis I, parental genes have been exchanged on chromosomes by crossing over, and the distribution of parental gens is mixed by their random distribution to the two resultant cells, rather like cards which are shuffled and then dealt into two decks.

During meiosis II, a kinetochore is formed on each sister chromatid. Phases similar to those of meiosis I take place until, in anaphase II, the chromatid pairs of each cell are pulled apart and nuclear envelopes form around each. Cytokinesis finishes the separation, leaving only one chromosome in each cell, which is therefore haploid. Each one contains a random mix of maternal and paternal genes and forms a unique gamete (egg or sperm cell) of the species.

One more time: Mitosis assures growth and cell replacement and serves reproduction in some simple organisms. Sexual reproduction, as in animals, requires meiosis. The process is shown in the following figure.

Stages of meioosis, after Ali Zifan via Wikimedia Commons

Now let’s go see how meiosis and mitosis work in plant life cycles and take a look at the science of taxonomy.

Notes[+]

Notes
↑1	Some sources omit the prometaphase. There is also disagreement as to what goes into each step. For instance, Katz and Openstax say the nuclear envelope breaks down in the prophase; Bear et al., in the prometaphase.
↑2	Why is it not called the cataphase?
↑3	See the section on muscles later in this document.
↑4	Author’s own work.

DNA expression and regulation– protein synthesis

DNA, RNA and ribosomes, in that order, are essential components in the synthesis of proteins. DNA contains the information necessary not only for reproduction, but also for daily cell growth and maintenance. Messenger RNA carries the information to the ribosomes. With the help of yet another kind of RNA, the ribosomes assemble the proteins. All this depends on gene regulation.

The use of DNA to initiate protein synthesis is called DNA expression.

This sequence of events is summed up in the so-called central dogma of molecular biology, often paraphrased as “DNA makes RNA and RNA makes protein.” More precisely, DNA is transcribed inside the nucleus to make mRNA, which is expelled from the nucleus to the cytoplasm, where it is translated to protein by ribosomes.

DNA –> transcription (nucleus)→ mRNA→ translation (ribosome)→ protein.

The recipe is expressed in “bytes” of three nucleobases; one three-base byte is referred to as a code-word. When transcribed to its complementary form in mRNA, it is called a codon. Since each base can have one of four values (C, G, A or T, in DNA), the codon can take on 64 values.

RNA transcription

The enzyme which does the work of “reading” a gene on the DNA and building a corresponding gene of RNA is called RNA polymerase¹In fact, there are several forms of RNA polymerase, but that complexity is well beyond the scope of this document.. There are at least four types of RNA and transcription makes them all. For protein synthesis, the RNA constructed is called mRNA, or messenger RNA. The DNA recipe begins with a sequence called the promoter. RNA polymerase contains a complementary sequence which binds to the promoter and launches transcription. As will soon be seen, transcription is started only if it is allowed by gene regulation. RNA polymerase unwinds a part of the DNA chain and reads code-words, starting with the promoter. As it reads the DNA, it constructs a complementary chain, called pre-mRNA, from nucleotides. It is complementary in the sense that if the DNA contains a C (or A or G or T) then the pre-mRNA contains a G (or U or C or A – remembering that RNA replaces T by U).

The raw materials RNA polymerase uses to construct RNA are nucleoside triphosphates (NTPs). An NTP molecule has two of its phosphate groups which contain a significant amount of energy from ATP. This energy is used to bond the nucleotides together to form RNA.

The RNA polymerase moves along the DNA, unwinding sections as it goes, reads the code words and assembles the appropriate pre-mRNA codons from NTPs. The separated DNA strands recombine in its wake. Eventually, it reaches a transcription-terminator sequence in the DNA and ends transcription. It now has gone through three steps, known as initiation, elongation (of the produced pre-mRNA) and termination. The pre-mRNA then is released into the nucleoplasm.

Splicing mRNA, from Openstax College

Before leaving the nucleus, the pre-mRNA must be cleaned up. This is needed because DNA contains non-coding, or junk, sequences. The codons which should be kept are called exons (like “expressed”) and those which should be deleted are called introns (like “interrupted”).²I would have preferred for exon to mean “exclude” and intron to mean “include”, but some contrary biologist decided otherwise. He could at least have taken a vote! Small particles called “snurps” (for snRNPs, or small nuclear ribonucleoproteins), made up of RNA and proteins, bind together to form spliceosomes, which remove introns and splice the exons back together again, resulting in a cleaned-up form of mRNA.³Are you wondering how the snurps can recognize the introns an exons? So am I. All I can say is that it is quite complicated and has something to do with methylation of the DNA strands. It is currently not completely understood why there are introns at all, but there are indications that they may be of importance.

The mRNA is then moved out of the nucleus for the next step.

Protein synthesis – translation

After the mRNA leaves the nucleus, it is used to provide the input data for the synthesis of proteins. This takes place on ribosomes.

There are two sorts of ribosomes in eukaryotic cells, depending on their location.

Free ribosomes float in the cytoplasm and make proteins which will function there.
Membrane-bound ribosomes are attached to the rough endoplasmic reticulum; they are what makes it look “rough”. Proteins produced there will either form parts of membranes or be released from the cell.

In most cells, most proteins are released into the cytoplasm.

Ribosomes are made of ribosomal RNA, or rRNA (one more kind of RNA), and proteins. They are constructed within the nucleolus as two subunits, which are released through the nuclear pores into the cytoplasm.

In addition to the mRNA and the ribosome subunits, a method Is needed for supplying the appropriate amino acids to be linked by peptide bonds to make up the protein or enzyme being constructed. Enter still one more kind of RNA, transfer RNA, or tRNA.

Transfer RNA, tRNA, from National Human Genome Research Institute

A molecule of tRNA is a molecule of RNA folded into a double strand with loops which give it a precise 3-dimensional shape. The loop on one end has an anticodon, the function of which is to match its complement codon on mRNA. The other end has a binding site (adenylic acid) for a specific amino acid. So the tRNA is the “dictionary” which converts codons into amino acids⁴This of course poses the question, where do the tRNA molecules come from? Good question.. A tRNA molecule is “charged” with an amino acid molecule by a tRNA-activating enzyme which uses energy from ATP to covalently bond the appropriate amino acid from molecules in the cytoplasm. Such tRNA molecules, carrying an amino acid, are called aminoacyl tRNA.

The ribosome itself contains three assembly areas or spaces called, in order of occupation, the A-site, the P-site and the E-site. Initially, the ribosome subunits are floating independently in the cytoplasm or attached to the RER. The initiation of translation begins when the small subunit binds at its P-site to the START codon of the mRNA strand. Then the corresponding tRNA (methionine) binds to the START codon and the large ribosome subunit is attached, completing assembly of the ribosome. Now the first tRNA is in the P-site and next mRNA codon in the A-site. The methinone constitutes the beginning of the peptide chain which will become the protein. Then a cycle takes place in which the ribosome reads in the mRNA strand, like computers of my youth read in paper tape, each new codon arriving in A.

Gene translation in the ribosome, from Openstax College

The process then pursues the elongation stage of translation. The aminoacyl tRNA for the codon in the A-site is carried in, so the first two amino acids are now in the P and A sites. The ribosome then catalyzes the formation of a peptide bond between these two amino acids. The ribosome then moves the mRNA so the P-site amino acid enters the E-site, the A-site one enters the P-site, and a new one enters the A-site. It continues like that until a STOP codon enters the A-site and brings about termination of translation and release of the completed peptide chain.

All these steps of transcription and translation require energy, so protein synthesis is one of the most energetically costly of cell processes. Much of this energy is used to make enzymes essential to the functioning of the cell. Most enzymes are proteins.
Once part of a strand of mRNA has left one ribosome, it can enter another. One strand may actually be in 3 to 10 ribosomes at once, in a different step of translation in each one. Such clusters of ribosomes translating the same mRNA strand are called polyribosomes.

Regulation of gene expression

Every cell in an organism has the same complete genome in its nucleus and so has access to all the same protein “recipes”. But, for example, heart cells should not produce proteins used only by the liver and no cell should produce proteins in quantities beyond what it can use. Cells change over time too: Think of the adaptation to pregnancy or disease.

Cells are specialized and so express different genes: Differential gene expression leads to cell differentiation. Controlling which proteins to express and when is called regulation. Note that this is one more instance of communication in the body, telling genetic machinery what to express when.

Regulation of prokaryotic cells

Regulation in prokaryotic cells is relatively simple, as there is no nucleus. so transcription and translation take place almost in the same place and at the same time. Regulation in prokaryotic cells, though, almost always concerns transcription.

An example from a prokaryotic cell will show how this works – and introduce some new terminology.

The bacterium E. Coli normally uses glucose for energy. But if glucose is absent and lactose is present, it can use the lactose. Bacteria arrange groups of genes to be controlled together into a structure called an operon. The set of proteins necessary for the use of lactose are part of the lac operon. The operon begins with a promoter, which indicates the beginning of the operon and is the site where RNA polymerase binds to begin the transcription. In between the promoter and the set of genes, of which there may be any number, is a sequence called the operator, which is where DNA-binding genes bind to regulate transcription⁵Look out for the terminology: Sean B. Carroll refers to the operator as a genetic switch, a term we will meet with in the disussion of regulation in eukaryotes.

When no lactose is present, a protein called the lac repressor is bound to the operator and the state of the lac operon is “off”. (Figure.) This is because the repressor blocks access to the rest of the operon.

The gene for the lac repressor is a constitutive gene: It is always expressed because it is the recipe for an essential protein. On the other hand, a regulated gene, is expressed selectively.

Regulation of the lac operon, from Openstax College

In addition to the binding site for the operator, the lac repressor has a second, allosteric, binding site. When lactose is present, an isomer of lactose binds to the allosteric site of the repressor, which causes it to change its form and unbind from the operator. The lac operon is now in the “on” state. This form of regulation is called induction: Lactose is said to be the inducer of the lac operon and acts through the allosteric site of the lac repressor. Transcription now occurs, but slowly. Because some glucose still may be present, it is not certain that the proteins mapped by the lactose-digesting genes are needed. This depends on how much glucose is lacking.

The second part of this process depends on the presence of glucose and is regulated by a second DNA-binding protein, CAP (catabolite activator protein). CAP is also an allosteric protein with one DNA-binding site and one allosteric site which binds to cyclic AMP (cAMP). CAP is only active when it is bound to cAMP. You guessed it, cAMP levels are high when glucose levels are low.⁶If we go one step back, we see that glucose binds to an allosteric site on the enzyme adenylate cyclase, which makes cAMP from ATP, and disables it. So lack of glucose stimulates production of cAMP, which binds to CAP, which binds to the promoter to enhance synthesis. In that case, cAMP-CAP binds to the promoter and enhances transcription of the genes. So lactose can be considered the “on-off” switch for transcription of genes for lactose-digestion and cAMP-CAP, the “volume control”.

Regulation of eukaryotic cells

In eukaryotic cells, transcription occurs inside the nucleus and translation outside, so mRNA is shuttled across the nuclear membrane in between the two processes. Regulation in eukaryotic cells therefore may take place inside or outside the nucleus or at any step in the expression pathway, including control of access to the gene in the DNA, control of transcription, pre-mRNA processing, mRNA lifetime and translation, and modification of the final proteins. Even the activity levels of enzymes which facilitate expression can be controlled.

Pre-transcription regulation

Inside the nucleus, histones, around which chromatin is wound to make nucleosomes, can wind or unwind to change spacing of the nucleosomes and thereby allow or deny access to genes. This process is a form of epigenetic regulation.⁷Look out, epigenetic regulation is used for somewhat different notions, too, and they are not all necessarily so. Since histones are positively charged and DNA, negatively, modifying the charge by adding chemical “tags” to either modifies the configuration of the DNA.

Transcription regulation

The most frequent regulation of expression in eukaryotes is during transcription. Control of transcription by the prokaryotic lac operon is a relatively simple process: In order to begin transcription of a gene, RNA polymerase must bind with the gene’s promoter but cannot do so if a lac repressor is bound to the operator region which follows the promoter on the gene.

Eukaryotic gene transcription is regulated similarly, but with more of everything. Instead of a repressor which binds to an operon, eukaryotes have a slew of transcription factors which bind to multiple regulatory sequences. Regulatory sequences, sometimes referred to as switches, may be almost anywhere on the DNA strand, even far from the gene. The existence of multiple switches for each gene allows the gene to be present In different types of cells, but activated selectively in each by different switches.

There are two types of transcription factors.

general transcription factors affect any gene in all cells and are part of the transcription-initiation complex;
regulatory transcription factors affect genes specific to the type of cell.

The two types of transcription factors work together with three types of regulatory sequences (transcription-factor binding sites).

promoter proximal elements are, of course, near the promoter and turn transcription on;
enhancers are far from the regulated genes or in more than one place and also turn the transcription on;
silencers are also far away from the regulated genes but turn transcription off.

Activator transcription factors are those which bind to enhancers to promote expression, repressor transcription factors, to silencers to decrease expression.

The promoter in eukaryotic cells is more complex too, The basal promoter begins with the TATA box, recognized by its beginning which contains the seven-nucleotide sequence TATAAAA, followed by a set of transcription-factor binding sites.

The whole set of transcription factors is summed combinatorially to determine whether or how much the gene will be expressed. Selective promotion or inhibition at combinations of these sites can therefore bring about tissue-specific gene expression. Each tissue type may have its own specific enhancer or silencer sequence for the same gene. For instance, the neuron-restrictive silencing element (NRSE) is a repressor which prevents genes from being expressed in any cells which are not neurons. In addition, environmental changes may bring about different gene expression according to current, perhaps temporary needs.

Coactivator proteins bind with general and regulatory transcription factors to form the transcription-initiation complex. RNA polymerase only binds to the transcription-factor complex.

Transcription factors in eukaryotic cells⁸Author’s own work

The above figure shows the case of an enhancer bound by activator transcription factors. The enhancer, on the left, originally is quite far from the promoter, until DNA bending causes it to change its shape, allowing the enhancer to come in contact with the promoter and the rest of the transcription-initiation complex.

Since transcription factors are proteins, they too are coded by genes and these genes are regulated in turn by other transcription factors. Eventually, it is the original cell (such as a fertilized egg) plus the environment which start the chain going. Of course, only genes which are present can be influenced; it’s nature and nurture.

Transcription factors and signaling elements coded by some of these genes make up the genetic toolkit, as we will see in a moment.

Splicing regulation

In between transcription and translation, proteins may interfere with spliceosomes to modify splicing of pre-mRNA. Different intron selections can allow different mRNAs to be produced from the same pre-mRNA, a phenomenon known as alternative splicing.

Pre-translation and translation regulation

RNA does not hang around forever, nor should it. Eventually, it is degraded and is no longer functional. So controlling its lifetime is another way of regulating its activity.

Yet another type of RNA, very short-stranded microRNA or miRNA, can bind with complementary mRNA before it is translated and signal that it should be destroyed by the cell. For this purpose, miRNA also associates with RISC (RNA-induced silencing complex).

Other proteins, RNA-binding proteins (RBPs), can bind with the 5′ cap or the 3′ tail of the mRNA and either increase or decrease its stability.

Phosphorylation or attachment of other chemicals to the mRNA protein initiator complex also inhibit translation.

Similar bindings may take place on the protein after translation and modify its stability, lifetime or function.

The development genetic toolkit – what evo devo tells us

Development, meaning embyronic development, is the process in which a genotype, a set of genes, becomes a phenotype, a particular living organism. Mutation works on genes, but natural selection works on phenotypes, the results of development. So evolution and development work hand in gene, so to speak, and the branch of biology which studies them together is called “evo-devo“.

The homeobox is a genetic sequence of DNA about 180 bases long. It is a sequence of DNA, of genetic material. It codes for about 60 amino-acid residues and these proteins are the homeobox domain, or the homeodomain. The reason the homeobox is really special is that it is “conserved” across most species of eukaryotes, meaning they all have similar homeobox sequences. Some such sequences are the same in frogs and mice by up to 59 of 60 base pairs. It is thought that there are about two dozen types of homeodomains, therefore of homeoboxes. The ubiquity of the sequence is fairly astounding in itself. It means that the sequence could not have evolved independently all those many times – think of the number of species concerned. So the homeobox must date back to be on the order of 500 millions years old.

But there’s more. The homeobox is not a gene by itself, but exists within many different, much larger genes – indeed, hundreds of times larger. Since they all contain the homeobox, they are called homeobox genes.

Many animals have a disposition of body parts along an axis, such as the antennae, wings and legs along the body axis of a fruit fly, or the existence or not of ribs along the vertebrae of a vertebrate animal. It turns out that the choice of body part at each segment along the axis is regulated by a transcription factor coded by a single gene – the Hox gene. Hox genes are an example of homeobox genes; they contain the homeobox sequence. These Hox “master” genes control the developmental differentiation of, for instance, a fruit fly’s serially homologous body parts;¹⁰The front legs of a cat and our arms are considered homologous body parts. Structures along a body axis, similar but different, are called serially homologous with respect to each other. in simpler terms, its body pattern. They are “master” genes because they determine whether a given part will form or not, leaving the details to genes farther down the chain. But such “detail” genes will not function at all without the “master” gene, which therefore regulates quite a large number of genes. Hox genes are sufficiently similar that introduction of mouse Hox genes into a fly can cause the growth of the indicated organ — in fly format. They also control the very different serial structure of snakes.

Homeotic genes occur in clusters. One more amazing fact is that the genes of a cluster are in the same order as that of the body segments they control. It is sufficient to replace the gene in a given cluster, say at the antenna position on a fruit fly, with another, say a leg gene, and a leg develops at the antenna position on the fly. Since the transcription factors coded by such genes can change the cells they regulate into something else, they are called homeotic¹¹Homeosis is the transformation of one organ into another. transcription factors and their genes are homeotic genes. The protein domain they express is therefore a homeotic domain, Hox, for short.

Other homeobox families also exist, as we will see a few in a moment. Hox genes are just one family of them.

It is remarkable that quite similar homeodomains have been found in almost all animals. Such conservation of homeobox genes across species shows that embryonic development of most animals, fungi and plants is controlled at some level by approximately the same genes. They must have been around since animals diverged from each other over 500 Mya. The original Hox gene was duplicated and then each copy took on slightly different functions. Subsequent duplications and modifications have led to the diversity of animals today. Comparison of the genes can contribute to building at least a partial tree of life.

Because the homeobox genes code for transcription factors, each of which is used in so many organisms in similar ways, the proteins coded by homeobox genes are constituents of what some biologists call the genetic toolkit. It’s like using a common screwdriver to drive screws in different contexts. Just as one screwdriver serves in many contexts, so does each type of homeobox gene. A homeobox gene is therefore in some way a “master” gene. The toolkit is common to almost all animals, with only little variation from one to another. It contains genes not only for transcription factors, but also for various molecules which are signaling elements. They play important roles in embryonic development, or embryogenesis.

In other animals also, the genes exist in clusters, with the gene order in the cluster corresponding to that of the organism’s parts. Different Hox genes, being similar but slightly different, bind to different regulatory sequences on DNA and therefore regulate different genes. One homeobox protein may regulate many genes and a number of homeobox proteins may work together to refine selection. Because of this possibility of multiple binding, a small change in activation of toolkit genes can bring about a large change in the phenotype. So the genetic toolkit may explain development more simply than if all genes had to be specific to each different part, location and development time of an organism.

Toolkit genes themselves have multiple switches. Switches are the means by which a relatively limited set of toolkit genes may be used differently in different regions, or even different animals, or at different times in embryonic development – which furnishes material for evolution.

The existence of different layers of transcription factors also explains how a small genetic change (in a transcription factor) can bring about a relatively important change in the phenotype of the organism.

A specific bodily environment (liver, heart, blood, …) contains some set of organic molecules specific to that environment. These molecules or a sub-set thereof will serve as transcription factors to activate a particular sub-set of the toolkit. In other words, the environment chooses which tools to use.1 The proteins expressed by toolkit genes will activate or suppress expression of body-part proteins at that place and time.

Environmental molecules ==> toolkit proteins ==> body parts

Each arrow indicates that the object to the left switches on expression of the object to the right.

Some terminology helps to understand the evo-devo literature.

Transcription factors are proteins and so are not on the DNA string, therefore not on the same molecule as the DNA which is regulated. They therefore are called trans-acting regulatory elements (TRE).¹²In Latin, “cis” means “this side of” and “trans” means “the other side of”. Think of cis-Alpine (this side of the Alps) and trans-Alpine.
Switches are on the same string of DNA as the regulated gene and are called cis-acting regulatory elements (CRE).

So one can say that TREs bind to CREs to regulate gene expression. Got that?

The following table lists just a few of the homeobox families and the organism components they regulate. As is clear, they regulate quite different structures.

Protein name	Penotype regulated
Hox	body regions (e.g., head, thorax or abdomen)
Pax-6	eyes
Distal-less (Dll)	limbs
Sonic	organogenesis (tissue patterns)
Ulrabithorax (Ubx)	represses insect wing formation

In all animals, there exist similar gene sequences corresponding to protein domains which are transcription factors for that animal’s version of some phenotype. A Pax-6 gene from a mouse makes an eye form in a fruit fly – a fruit-fly eye, not a mouse eye.

Cell differentiation

Stem cells are those which may split and form any kind of cell.¹³Usually to make an identical stem cell and another cell, which may or may not be a stem cell. But once a specific type of cell is made, it can only do certain things. This is because it no longer has access to the entire recipe book (genome), but only those recipes which it needs. The cell is then said to be differentiated and the process for making it is differential gene expression. Such gene regulation or differentiation depends on the cell’s environment. We have seen an example where the presence of lactose induces the expression of the lac operon.

Gene regulation can fill a book. And cell differentiation can fill another.

Continue with cell division and the cell cycle.

Notes[+]

Notes
↑1	In fact, there are several forms of RNA polymerase, but that complexity is well beyond the scope of this document.
↑2	I would have preferred for exon to mean “exclude” and intron to mean “include”, but some contrary biologist decided otherwise. He could at least have taken a vote!
↑3	Are you wondering how the snurps can recognize the introns an exons? So am I. All I can say is that it is quite complicated and has something to do with methylation of the DNA strands. It is currently not completely understood why there are introns at all, but there are indications that they may be of importance.
↑4	This of course poses the question, where do the tRNA molecules come from? Good question.
↑5	Look out for the terminology: Sean B. Carroll refers to the operator as a genetic switch, a term we will meet with in the disussion of regulation in eukaryotes.
↑6	If we go one step back, we see that glucose binds to an allosteric site on the enzyme adenylate cyclase, which makes cAMP from ATP, and disables it. So lack of glucose stimulates production of cAMP, which binds to CAP, which binds to the promoter to enhance synthesis.
↑7	Look out, epigenetic regulation is used for somewhat different notions, too, and they are not all necessarily so.
↑8	Author’s own work
↑9	The bobby-pin curl is an idealization; DNA shapes are far more complex than that.
↑10	The front legs of a cat and our arms are considered homologous body parts. Structures along a body axis, similar but different, are called serially homologous with respect to each other.
↑11	Homeosis is the transformation of one organ into another.
↑12	In Latin, “cis” means “this side of” and “trans” means “the other side of”. Think of cis-Alpine (this side of the Alps) and trans-Alpine.
↑13	Usually to make an identical stem cell and another cell, which may or may not be a stem cell.

Cell structure

Dogs and cats, butterflies and crayfish, lizards and birds, poison ivy and rosebushes and strawberry plants are all organisms. Organisms are composed of organ systems (digestive, circulatory or immune systems, to mention three examples). These systems are in turn composed of organs, which are composed of tissues which are composed of cells. The cell is where the action is!

The definition of life usually includes the requirement that whatever lives is capable of viable reproduction, which makes it subject to evolution. All life is composed of cells and they reproduce.

There are two kinds of cells, which have already been mentioned in the geology (!) chapter:

Eukaryotic contain structures called organelles, many of which are not found in prokaryotic cells. One such organelle is the nucleus, which houses the DNA.
Prokaryotic cells are usually smaller. They do not contain nuclei, so their DNA is floating around in the cytoplasm. They do contain ribosomes to carry out protein synthesis.

Cells come in a huge variety of shapes and functions. They are the basis of all living beings. Whether they are nerve cells, muscle cells, skin cells, bone cells or any other kind of cells; whether they come from humans or cats or grasshoppers or oak trees or bacteria, they all are based on common features like a membrane filled with cytoplasm, DNA or RNA along with ribosomes for reproduction, and the fabrication by cellular respiration of ATP for energy. This fact seems to represent a certain indication of the common origin of all life.

Plasma membrane

As we saw in the discussion of water, lipid bilayers, in this case, phospholipid bilayers, can form membranes. All cells are surrounded and protected by such membranes, also called plasma membranes. The membrane contains various proteins which serve to pass substances across the membrane, to identify it or to fulfill other functions. (More on that shortly.) This view of the cell membrane, as a mosaic of elements, is called the fluid mosaic model.

Everything inside the cell except the nucleus is the cytoplasm, including the cytosol, the jelly-like fluid in which other structures float, the organelles, including the nucleus, the mitochondria, and other structures.

Structure of cell membrane, by “LadyofHats” via Wikimedia Commons

The membrane is capable of forming pockets called vesicles. They can form on the inside of the cell membrane and surround material, then close and reopen on the outside in order to eject the material stored in them. In the other direction, they may form around external material and carry it into the cell.

The cell nucleus

The nucleus holds the DNA, normally wrapped with other proteins into strings of chromatin. Chromosomes are only constituted when needed to facilitate reproduction. The nucleus is surrounded by its own double membrane. The nucleolus within the nucleus serves to synthesize ribosomes, which in turn are sites for synthesis of proteins. The greater the number of proteins produced by a cell, the larger its nucleolus.

Typical animal (a) cell, from Openstax College

Mitochondria

Mitochondria are where the final products of digestion, mainly glucose, are converted into ATP, the body’s “energy currency”, which transports energy to whatever metabolic process may need it. A mitochondrion has both an external and an internal membrane. ATP is produced by processes taking place along the inner membrane. The interior of the mitochondrion is called the matrix. Cellular respiration (energy production) will be discussed in detail in the chapter on anatomy and physiology.

According to symbiogenesis, or endosymbiotic theory, mitochondria originally were prokaryotic bacteria which moved into other cells and formed a symbiotic relation with them. Similarly, choroplasts are prokaryotic bacteria which have moved into plant cells. Mitochondria still have their own DNA, independent of that in the cell nucleus, although they have abandoned or given up much of their original DNA.

The current model of eukaryotic evolution starts with an anaerobic eukaryote which absorbed an aerobic bacterium which later became a mitochondrion. Subsequently, some of these now aerobic eukaryotes absorbed photosynthetic bacteria, probably cyanobacteria, which became chloroplasts. The latter eukaryotes formed plants, whereas those which did not absorb the photosynthetic bacterium became animals.

Mitonchondrion structure, by "Kelvinsong" via Ma href="https://commons.wikimedia.org/wiki/File:Mitochondrion_structure.svg"

Mitonchondrion structure, by “Kelvinsong” via Wikimedia Commons

Ribosomes

Ribosomes are where proteins are built following instructions contained in DNA; the instructions are transmitted to the ribosome in the form of messenger RNA, mRNA, about which more later. Ribosomes consist of two subunits, large and small, both of which are constructed in the nucleolus from ribosomal RNA (~75%) and proteins.

Endomembrane system

The endomembrane system has been referred to as the “post office” of the cell, as its components produce, package and export certain cell products, such as proteins or lipids. It has several components.

Endoplasmic reticulum — This is actually an extension of the membrane of the nucleus outwards to form folds. The rough ER is studded with ribosomes, to make proteins. The smooth ER is not and produces lipids.
Golgi apparatus – This serves to dispatch the various products to their final destinations.
Lysosomes – These “garbage-collection” modules contain enzymes which can break down and digest molecules and even cells. In the process of phagocytosis, for example, macrophages, a type of white blood cell and part of the immune system, gobble up pathogens and then deliver them to lysosomes for destruction. They do not exist in plant cells.
Peroxisomes – These also contain enzymes for decomposing various molecules by transferring hydrogen to oxygen to produce hydrogen peroxide, H2O2. In the liver, they break down ethanol (alcohol from alcoholic beverages).

“Form follows function”, in biology. Cells which produce large amounts of proteins have voluminous endoplasmic reticulums and those which secrete much have large amounts of Golgi bodies. Those, like muscles, which need great amounts of energy contain many mitochondria.

Cytoskeleton

Proteins of the cytoskeleton support the cell and give it shape. They are of three varieties.

Microtubules are made of the protein tubulum and provide structure, like scaffolding, which allows the cell to resist compression. They also form something like a railroad track for RNA to flow along during protein synthesis, rather than letting it float loose in the cytoplasm.

Microtubules make up two important structures:

flagella, the tail-iike appendages existing in humans only on sperm, and which allow them to move about;
cilia, fine, hair-like structures which wave continuously and move such things as waste in the respiratory system or egg cells in fallopian tubes.

Microtubules form the centrioles, the principal part of centrosomes, which play an essential role in chromosome splitting during reproduction (explained later in this chapter).

Microfilaments are made of actin. They are thinner than microtubules and form chains responsible for muscle contraction with the cooperation of myosins. (See the section on muscles.)

Microtubules and microfilaments are like cables and work with motor proteins which pull themselves along the cable. A family of motor proteins, kinesins, attach to vesicles carrying, for instance, RNA and crawl along the microtubules similarly to the way myosin crawls along actin in muscle cells.

Since motor proteins move themselves along the support structure of the cell, they are probably evolved forms of the cytoskeleton of bacteria.¹This was only observed in the mid-1990s. Lane (2009), 167. Bacteria can be motile in their way too, since they change by adding on elements at one end and leaving them off at the other, effectively moving and generating force. The evolution of motility was an essential step in the spread of plants and – especially – animals some 250-or-more million years ago.

Intermediate filaments are made of keratin and serve, like microtubules, for maintaining cell shape, but, contrary to microtubules, they resist tension which tries to pull apart the cells.

In addition to the support they receive from the cytoskeleton, many animal cells have an extracellular matrix of connective tissue composed of long proteins like collagen which help support the cell and bind cells together. Plants have cell walls composed of a reinforcing layer of cellulose.

Plant cells

Plant cells differ from animal cells in that they have cell walls outside the cell membrane, and contain a central vacuole and chloroplasts.

Typical animal (a) and plant (b) cells, from Openstax College

Typical plant (b) cell, from Openstax College

The cell wall is a stiff outer layer which supports and protects the plant. The large central vacuole contains liquid which exerts pressure to maintain the plant’s standing position, just like air in a balloon makes the balloon stiff. The liquid also stores proteins.

The chloroplasts are where photosynthesis takes place. Like mitochondria, they contain their own simple form of DNA as well as ribosomes, because, like mitochondria, they originated as bacteria which moved into another cell, felt at home and stayed.

The structure of chloroplasts and their use of energy from sunlight to convert CO₂ and H₂O into sugar will be presented in the next chapter.

Viruses

Viruses are not cells because they do not contain all the good things described above. A virus consists of a protective protein coat called a capsid, which contains the viral DNA or RNA (but not both). It may also be surrounded by an envelope which closely resembles a cell membrane – because the virus has stolen it from a cell and adapted it to its own nefarious ends — a virus in cell’s clothing. Viruses have no ribosomes or other organelles to synthesize proteins, so they are dependent for reproduction on normal cells which they invade, substituting their own genetic material for that of the cell and then letting the cell do the job of protein synthesis – but using the virus’s recipe. Real Trojan horses!

Electrochemical considerations – the action potential

Cells are surrounded by a membrane composed of a phospholipid bilayer arranged in such a way that the membrane surfaces are hydrophilic and the interior hydrophobic. No charged ion, hydrophilic molecule or very large molecule can traverse the membrane. But the cell needs to receive nutriments, expel waste, receive hormonal messages, and so on, so the membrane must not be completely impermeable.

Membrane channels

In order to allow the necessary passage of chemicals, the cell membrane is studded with proteins which control the passage of such objects.

Ion channels are passageways through the cell wall which allow ions to pass naturally in a direction tending to equalize their electrochemical or concentration gradients inside and outside the cell. Such channels may be ion-specific (for instance, allowing only K⁺ ions to pass), charge-specific (allowing either negative or positive ions, but not both) or size-specific. Some ion channels are leakage channels, opening randomly.
Gated ion channels allow ions through the channel on occurrence of some event. This might be the arrival, for instance, of an electric potential (voltage-gated ion channel) or a specific chemical substance (ligand-gated channel). Voltage-gated channels are essential to the formation of action potentials.
Ion pumps, especially the sodium-potassium (Na-K) pump and the calcium pump, run all the time in most animal cells, using energy from ATP to pump ions across the membrane against their concentration or electrostatic gradient.

The concentration of chemical substances inside and outside the cell generally are not the same and this is crucial to their functioning.

Membrane potentials

It all starts with a pump, the sodium-potassium (Na-K) or ATPase pump. This object is powered by ATP to flip back and forth between two states. In one state, it pumps Na⁺ ions out of the cell; in the other, it pumps K⁺ ions into the cell. Soon, a concentration gradient is established for each ion, tending to pull the Na⁺ back into the cell and to push the K⁺ out.

The pump does more than that, because for every two K⁺ ion it pulls into the cell, it pushes three Na⁺ out. The result is the establishment an electrostatic potential across the cell membrane. Because the extra positive charges outside attract any negative charges inside, they tend to be concentrated close to the membrane surfaces, so the membrane forms an electrical capacitance.

Sodium-pottasium pump, from Wikimedia Commons

So the result of the pump is triple:

a Na⁺ concentration gradient tending to pull Na⁺ back into the cell;
a K⁺ concentration gradient tending to push K⁺ out;
an electric potential across the membrane due to the greater number of positive ions outside the cell.

Note that there are also lots of large anions, such as phosphate or negatively charged proteins, inside the cell. Ion channels for K+ tend to leak K+. The K+ tends to follow its concentration gradient out of the cell, but this leaves behind a more negative interior, which attracts it back toward the interior. Eventually, an equilibrium state is reached where the outward pressure due to the concentration gradient balances the inward pressure due to the electrostatic gradient. Measurements show that the interior has a potential of -92 mv (relative to the exterior). The cell is said to be polarized. In this state, opening an ion channel would allow positive ions to flow into the cell, depolarizing it.

If we start over and do the same thing, but open a Na⁺ channel, Na⁺ rushes into the cell, bringing up the cell’s potential until equilibrium is reached between the concentration and electrostatic forces, this time at a potential of +62 mV. So each ion has an equilibrium potential which is a function of the concentration difference across the cell membrane. The membrane potential of the cell as a whole depends on the concentration differences of all the ions inside and outside the cell. A very small change in ionic concentration can bring about a much greater change in membrane potential.

Since both K⁺ and Na⁺ leakage channels exist, but the Na⁺ channels leak much more slowly than the K⁺, the result is to increase somewhat the Na⁺ concentration within the cell and hence raise the potential a little to around -70 mv.²Some authors say -65 mv.

Enter the third type of channel, the gated ion channel. This may be of various types depending on the ion allowed to pass and on the circumstances which gate it, i.e., which initiate the passage. The latter property may be of different types:

mechanically-gated, subject to pressure, for instance, on the surface of the skin or on auditory cilla in the ear;
temperature-gated;
voltage-gated, i.e., to charged ions;
ligand-gated, i.e., sensitive to certain molecules (taste, smell, neurons);
photosensitive (retina).

The action potential

Consider a nerve or muscle cell at rest, with a membrane potential of around -70 mV, so the cell is polarized. Suppose something happens which causes the membrane potential to increase (i.e., to become less negative). This could be due to entry of ions through a ligand-gated channel (as in neurons) or a mechanically-gated channel (as in a somatosensory channel) or simply due to K⁺ leakage (as in a pacemaker cell of the heart). If the increase is small, nothing happens. But if it becomes sufficient to bring the potential up to the threshold value of -55 mV, then a voltage-gated Na⁺ channel opens, allowing Na⁺ to come rushing into the cell, quickly raising the potential to a positive value and depolarizing the cell. When the potential reaches 30 mV, the voltage-gated Na⁺ channels close but voltage-gated K⁺ channels open and K⁺ starts rushing out of the cell, bringing the potential back down (positive charges are leaving the cell) and repolarizing it.

Action potential, from Wikimedia Commons

In muscles, release of the neurotransmitter acetylcholine (ACh) by motor nerves opens ligand-gated channels which allow the cell to depolarize to the threshold for voltage-gated sodium channels, which in turn cause an action potential which eventually opens another channel which allows Ca⁺⁺ into the cell. The Ca⁺⁺ binds to troponin in the muscle fiber and unlocks it, so that myosin heads can “walk” along the thin filament and contract the muscle.

The heart is special in that it initiates its own action potentials in a repeated, periodic way. The cycle is initiated not by a ligand-gated channel, but mostly by leakage channels which allow some Na⁺ to enter the heart, gradually raising the membrane potential from about -60 mV to -40 mV. This is the threshold value for a gated channel to open, allowing depolarization of the cell. However, because of the leakage, only slow Na⁺–Ca⁺⁺ channels are opened, which explains the relatively slow rise of the potential. After about 100-150 milliseconds, the Na⁺–Ca⁺⁺ channels close and K⁺ channels open. As K⁺ rushes out of the cell, the potential redescends to a bit under its initial resting value. Then the K⁺ channels also close and the cycle starts over. So the heart beats all by itself due to the membrane potential of the cardiac muscle cells, the slow leakage of Na+ and the voltage-gated Na⁺–Ca⁺⁺ and K⁺ channels.

Continue reading about DNA expression and protein synthesis.

Notes[+]

Notes
↑1	This was only observed in the mid-1990s. Lane (2009), 167.
↑2	Some authors say -65 mv.

Some basic biochemistry

Understanding physiology and neuroscience requires knowing a certain amount of biochemistry. Most of the building blocks of our bodies are macromolecules composed of proteins (long chains of amino acids), polysaccharides (carbohydrates), lipids (fats) and nucleic acids (which make up DNA and RNA).

Amino acids and proteins

Amino acids are the basic building blocks for proteins. In a way, they are quite simple, all being variations on the same basic formula.

Common formula for amino acids, by “GyassineMrabetTalk” via Wikimedia Commons

Each amino acid consists of a central carbon atom, an amino group (NH₃⁺), a carboxyl group (COO^–) and a variable group, designated by the letter “R”, for residue. In the figure, the third H in NH₃ has been transferred to one O on the COO^– to make COOH and balance out the total charge.

The complete set of amino acids comprises only 21 acids and is shown in the following figure. It is often stated that there are only 20 amino acids, in which case selenocystein, which occurs rarely, has been omitted.

The amino acids, by Dan Cojocari via Wikimedia Commons

Amino acids are the basic building blocks of proteins. A protein is a polypeptide, that is a polymer (a chain of linked subunits) formed by condensation (ejection of water molecules) so as to link the amino acids by peptide bonds. Schematically, it looks like the example in the following figure, which shows the OH^– on the left combining with an H⁺ on the right to make a water molecule and leave the two amino acids connected by a peptide bond. Actually, the process is not that direct, but goes through several enzyme-assisted steps in order to achieve the peptide bond. (We’ll get back to enzymes shortly.)

Peptide formation by condensation of two amino acids, by “GyassineMrabet” via Wikimedia Commons

The bonding properties of proteins depend largely on their shape. The shape of the protein depends first on the sequence of amino acids, which constitutes the protein’s primary structure. The polypeptide chain may then coil up into a secondary structure called the alpha helix. The R groups may interact among themselves, bringing about a change in the 3-dimensional shape, or conformation, the tertiary structure. Different polypeptide chains then may bind to form a quaternary structure. In this way, proteins can take on very intricate shapes.

Four hierarchical structures of hemoglobin, by OpenStax College via Wikimedia Commons

Symmetry does not seem to be well respected in biology. A helical protein with a right-handed twist can not generally be substituted for one with a left-handed twist: It just will not work the same way. This differing of the two versions is called chirality.

3D structure of myoglobin protein. Alpha helices are turquoise. By AzaToth via Wikimedia Commons

Proteins may be enormously long polypeptide chains.

Enzymes

Enzymes, which are usually proteins¹RNA can also function as an enzyme and it is not a protein., serve as organic catalysts, meaning that they help to bring about reactions that otherwise would not happen or would happen far too slowly. They only bring about reactions which are energetically possible but which nevertheless need a “push” to get started. Enzymes provide the push by lowering the activation energy of the reaction. Complete equations for different reactions would include the enzymes on both sides, but they are usually omitted. Every physiological process in the body depends on enzymes. Enzymes themselves only work under rather strict conditions of temperature and acidity. If the pH or temperature is not just right, the enzymes will not work, the reactions will not take place and the organism will suffer. The names of enzymes generally end in -ase, for example, lactase.

An enzyme can do its work because of its shape. It folds itself so as to form a pocket called the active site. A molecule which fits into the active site is called a substrate. The enzyme can then usher the substrate through the reaction. This “lock and key” model of enzyme-subtrate interaction is refined further in the induced-fit model, wherein dynamic modifications in the enzyme’s structure enable It to exactly fit the substrate, like a glove stretching to fit a hand.

The body can regulate the rate of such reactions by regulating the efficiency of the enzymes which catalyze it. One way to do this is to have a molecule similar in shape to the substrate and use it to block the active site. Or a molecule can bind to what is called an allosteric site on the enzyme, meaning a site which is not the active site. Binding to such a site changes the shape of the molecule and thereby renders it ineffective for binding with its usual substrate. If the enzyme catalyzes a reaction too much, so that there is an excedent of end products, the end products themselves may attach to an allosteric site and block further reactions, resulting in a feedback mechanism which reduces the rate of the reaction.

Reactions catalyzed by enzymes generally take place in a number of small steps rather than all at once. This has a double advantage:

At each step, the enzyme can bring the reactants together, reducing the activation energy, the amount of energy needed for the reaction to begin.
The energy output from each small step will not be so much as to harm the cell.

The sum of all the small steps is referred to as a metabolic pathway.

Carbohydrates

Carbohydrates are molecules composed of carbon, hydrogen and oxygen, usually with the latter two elements in the same relative amounts as in water. So a generic “carb” could be represented by the formula

C_m(H₂O)_n

Carbohydrates are saccharides, or sugars, and referred to as monosaccharides or polysaccharides, depending on the length of the molecule.

The most important monosaccharides in the body are: two, ribose and deoxyribose, based on rings of five carbon atoms (pentoses) and three, glucose, fructose and galactose, based on rings of six carbon atoms (hexoses).²In fact, glucose, galactose and fructose all have the same formula, C6H12O6, but differ in their conformations. Similarly, ribose and deoxyribose share the same formula, C5H10O5, but different conformations.

The five common monosaccharides, from Openstax College

Saccharides formed from two monosaccharides are called disaccharides. Important ones for the human body are sucrose (table sugar), lactose (milk sugar) and maltose (malt sugar).

Polysaccharides may contain thousands of monosaccharides. Common ones are starches (polymers of glucose found in plant foods), glycogen (a polymer of glucose used for storage in the body) and cellulose (“fiber”, found in the cell walls of plants).

We will be considering the importance of carbohydrates in the body’s production of energy from food.

Lipids

Lipids are mostly hydrocarbons with very little oxygen and so forming only non-polar C-C or C-H bonds, making them hydrophobic. They consist of triglycerides, phospholipids, cholesterol and small quantities of other substances. Lipids are necessary for the formation of cell membranes and for other functions within cells.

Trigylcerides

The commonest form of lipid (“fat”) in the body is triglyceride, consisting of a glycerol nucleus covalently bonded to the ends of three fatty-acid chains, long hydrocarbon chains terminated at one end by a carboxyl group (COO-) and at the other by a methyl group (CH3). The C=O link to the glycerol is an ester linkage.

Triglyceride structure, with three fatty acids (orange background) attached to glycerol (pink), adapted from Openstax College

Fatty acids may be saturated or unsaturated, meaning saturated in bonds with hydrogen. A saturated fatty acid has only single bonds between carbon molecules, leaving two bonds free to connect with hydrogen. An unsaturated acid may have a double bond between carbons, meaning each one can only bond with one hydrogen. The double bonds between carbons may change the shape of the fatty acid.

Saturated and unsaturated fatty acids, from Openstax college

Saturated fatty acids pack tighter and so exist generally as semi-solid substances called fats. Unsaturated fatty acids pack more loosely (because of the kinks) and are the constituents of more liquid oils

It is currently thought³Or, at least, recently. It’s hard to keep up with what nutritionists tell us. that saturated fats lead to increased risk of heart disease, relative to unsaturated fats. The worst, though, is thought to be so-called trans fats.⁴The word trans comes from biochemistry and indicates functional groups on opposite sides of the carbon chain. In order to ensure longer shelf life, food producers sometimes convert unsaturated fats into saturated ones by hydrogenation, the addition of hydrogen atoms⁵The first such hydrogenated shortening was marketed under the brand name Crisco. It was partially hydrogenated cottonseed oil.. Trans fats are those which have only been partially hydrogenated⁶In more detail, a cis double bond is converted to a trans double bond, hence the trans.. On the other hand, there is evidence that omega-3 unsaturated fats are effective in reducing the risk of heart disease and perhaps beneficial in other ways. They are called omega-3 because the word “omega” is used in biochemistry to refer to the methyl end of the fatty acid chain and the double carbon bond is the third from that end.

Phospholipids

Phospholipids are similar to triglycerides, but the glycerol is attached to only two fatty acids, the third being replaced by a “head group” containing phosphate.

Phospholipid structure, from Openstax College, via Wikimedia Commons

The phosphate “head” is negatively charged and therefore hydrophilic but the fatty acid tails are hydrophobic, so the molecule is ampiphatic (as discussed in the chemistry chapter) and forms micelles or membranes in an aqueous environment. Of major importance for life, phospholipids are the principal component of cell membranes.

Nucleotides

Just as proteins are polymers formed from chains of amino acids, nucleic acids – DNA and RNA – are polymers made up of chains of linked nucleotides. A nucleotide is composed of a pentose (five-carbon) sugar molecule like deoxyribose (which gives the “D” in DNA) or ribose (in RNA), a nitrogenous base (or nucleobase) and one phosphate group.⁷Common usage employs the term nucleotide for those with more than one phosphate group. Different nucleotides contain different bases.

Nucleotides, from Openstax College

There are five possible nucleobases in two groups:

pyrimidines – cytosine, thymine and uracil, with a single-ring structure; and
purines – adenine and guanine, with two rings and therefore two nitrogen atoms.

Another, very special nucleotide is adenosine monophosphate, or AMP. When a second phosphate group is added to AMP, it makes ADP (adenosine diphosphate); addition of a third phosphate group makes adenosine triphosphate, or ATP, the “energy currency” or energy carrier in cells of all living organisms. Like all nucleotides, AMP consists of a nitrogenous base attached to a pentose sugar attached to a phosphate group; in this case, the nitrogenous base is adenine and the pentose sugar is ribose. It takes energy to add a Pi (phosphate) to make ADP or a Pi to ADP to make ATP. This energy is stored in the ATP molecule as chemical potential energy and can be recovered later to do useful biological work, such as to flex muscles (including heart muscles), make blood flow, power peristaltic movement of the intestines or permit action potentials in neurons. We will talk much more of this in the next chapter.

A nucleotide without the phosphate group is called a nucleoside, so ATP may also be referred to as a nucleoside triphosphate. Nucleoside triphosphates are the raw materials for building RNA molecules.

ATP and ADP, from Openstax College

Nucleic acids – DNA and RNA

The nucleic acids, DNA and RNA, are assembled from nucleotides. They differ in three ways:

DNA, deoxyribonucleic acid, contains deoxyribose as its sugar; RNA, ribonucleic acid, contains ribose.
The “allowed” nucleobases for DNA are cytosine (referred to in this context as C), guanine (G), adenine (A), and thymine (T); in RNA, T is replaced by uracil (U).
DNA molecules form a double strand; RNA, a single one.

The IUPAC (International Union of Pure and Applied Chemistry) has a rather hairy set of rules for numbering carbon atoms in organic compounds. In the case of the sugar in a nucleotide, the 1′ carbon (one-prime, prime to denote sugar) is the one attached to the nitrogenous base. The count moves around the ring away from the oxygen apex.

Nucleic acids are formed by dehydration (or condensation, removal of a water molecule) between a pentose sugar of one molecule (the 3′ carbon) with the phosphate (on the 5′ carbon of the pentose) of another. The result is called a phosphodiester bond. The chain is thus held together by a sugar-phosphate backbone, independently of attached nucleobases, which protrude out from the chain.

DNA chains form double strands due to hydrogen bonds between nucleobases on each chain, with C bonding only to G and A only to T. So a purine (A or G) is always bonded to a pyrimidine (C, T or U). The result forms a double helix, like a twisted ladder. Note from the preceding figure that there are three hydrogen bonds between guanine and cytosine, but only two between adenine and thymine.

DNA structure, from U.S. National Library of Medicine

The combination of two DNA strands into a double helix offers the advantage that the nucleobases are not sticking out into the cytoplasm where they may be more easily mutated. Rather, the bases of the two strands are “holding hands” (through hydrogen bonds) to protect each other from mutation. This increased security may explain why DNA, which stores genetic information, forms a double helix, but RNA does not.

Some detail: The nucleic acid strand is polar, i.e., the ends are not the same. One end has a phosphate group attached to the 5′ carbon of the sugar; this is called the 5′ end. The other end has a hydroxyl group (OH^–) attached to the 3′ carbon of the sugar, so this is called the 3′ end. When combining into a double helix, the ends are reversed, i.e., the 3′ end of one is opposite the 5′ end of the other.

Since the total length of all the DNA strands in a human nucleus would equal 2-3 m, it must be compacted in order to fit into the nucleus. The helical strand is wrapped around histone proteins to form nucleosomes. The string of nucleosomes is then twisted and re-twisted, like a piece of cord, until it forms a compact string called chromatin. The chromatin will be used to form chromosomes (only) when needed for reproduction.

DNA compaction, from Openstax College

Oxidation-reduction and electron carriers

The concept of oxidation and reduction is essential to biochemistry, so let’s beat on it a while. Actually, it also is important to other domains of chemistry. Oxidation and reduction occur together in oxidation-reduction, or redox, reactions.

An entity which loses electrons is said to be oxidized; if it gains electrons, it is reduced. Think of its charge, which becomes more negative as it gains an electron. Oxygen likes to gain electrons, so when it pinches one from another substance, that substance is oxidized. A simple example is Na and Cl going together:

Na + Cl → Na⁺ + Cl^–

The Na loses an electron and becomes positive; it is an electron donor and is oxidized. The Cl gains an electron, becoming negative, and is reduced.

A substance which is oxidized, i.e., gives up electrons, is an electron donor or reducing agent or reductant. One which is reduced, i.e., gains electrons, is an electron receptor or oxidizing agent or oxidant. Schematically, we can write

donor (reductant) <—> e- + electron receptor (oxidant)

where the reductant and oxidant together are said to constitute a conjugate redox pair.

The term oxidation is understood perhaps most clearly in a reaction like the rusting (oxidation) of copper:

2 Cu + O₂ → 2 CuO

One can see that:

At the same time as oxygen receives electrons from Cu and so is reduced,
copper, in releasing electrons to oxygen, adds on oxygen to become copper oxide (rust).

So we can see that adding oxygen is also oxidation and releasing it is reduction.

Again,

H₂ + F₂ → 2 HF

which is perhaps not easy to recognize as an oxidation of hydrogen. But consider the two half-reactions, the obvious oxidation part

H₂ → 2 H⁺ + 2 e^–

and the reduction part

F₂ + 2 e^– → 2 F^–

Put them together to get

H₂ + F₂ → 2 H⁺ + 2 F^– → 2 HF

But now, look at combustion (oxidation) of propane. It can be complete combustion

C₃H₈ + 5 O₂ → 3 CO₂ + 4 H₂O

or partial combusion

C₃H₈ + 2 O₂ → 3 C + 4 H₂O.

Carbon is obviously oxidized in complete combustion, since it adds oxygen. Partial combustion, even though it does not add oxygen, is still considered oxidation. So we can add:

Releasing hydrogen is also a sign of oxidation.

It’s inverse therefore must be reduction.

A less obvious example is oxidation of copper oxide:

2 Cu₂O + O₂ → 4CuO.

The thing to notice here is that the first oxide of copper is cuprous oxide, where copper has a valency state of +1. On the right, though, it has valency state of +2 and so this is cupric oxide. Copper has changed valency states and In so doing has given up an electron, which indicates oxidation.

Chemists also talk about oxidation-reduction in term of oxidation states, but those are complicated too, so we will ignore them. Finally oxidation-reduction criteria can bet represented in the following table.

redox process	electron	oxygen	hydrogen
oxidation	release	add	release
reduction	add	release	add

Getting back to biochemistry, more interesting examples, which are important in cellular respiration, are those of the coenzymes⁸A coenzyme is a non-protein compound that is necessary for the functioning of an enzyme. Enzymes are macromolecular catalysts, most of which are proteins. nicotinamide adenine dinucleotide and flavin adenine dinucleotide, better and more simply known as NAD and FAD. These two molecules are electron carriers and they pick up and leave off their electrons through redox reactions. If a reaction such as

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

is allowed to take place all at once, it releases a useless and dangerous amount of energy. So the reaction is broken up into intermediate steps with these cofactors as intermediate oxidizing and reducing substances. Their oxidized forms are NAD⁺ and FAD and they are reduced to NADH and FADH₂.

NAD is a dinucleotide, meaning it is composed of two nucleotides, which are joined by a phosphate group. One nucleotide has an adenine base, the other, nicotinamide.

NAD molecule by “NEUROtiker” via Wikimedia Commons

During cellular respiration (explained later), a molecule referred to as the substrate gives up two H atoms, and so is oxidized, bringing about the reduction of NAD⁺ in the following way, where R means “residue” and indicates a substrate:

RH₂ + NAD⁺ → NADH + H⁺ + R

Ignoring R on both sides

NAD⁺ + 2H → NADH + H⁺

or, in more detail,

NAD⁺ + 2H → NAD⁺ + H^– + H⁺ → NADH + H⁺

which shows that one of the H atoms is in the form of hydride, H^–, with two electrons.The NAD⁺ absorbs the hydride, equivalent to two electrons electrons and one proton, thereby gaining electrons and so being reduced to NADH. (Remember, NAD+ and NADH are abbreviations, not chemical forumulas.) In a later step, both the H atoms will be used for energy transfer and the NADH will give up two electrons and so be re-oxidized to NAD⁺. In this way, NAD transports electrons from one reaction to another.

NAD oxidation-reduction by Fvasconcelllos via Wikimedia Commons

The equivalent formula for the reduction of FAD goes in two steps:

FAD + e^– + H⁺ → FADH

FADH + e^– + H⁺ → FADH₂

to make

FAD + 2H → FAD + H^– + H⁺ → FADH₂

which shows that FAD is reduced to FADH₂ since it adds both electrons and hydrogen.

Now we are ready to look at cells, the basic units of life.

Notes[+]

Notes
↑1	RNA can also function as an enzyme and it is not a protein.
↑2	In fact, glucose, galactose and fructose all have the same formula, C6H12O6, but differ in their conformations. Similarly, ribose and deoxyribose share the same formula, C5H10O5, but different conformations.
↑3	Or, at least, recently. It’s hard to keep up with what nutritionists tell us.
↑4	The word trans comes from biochemistry and indicates functional groups on opposite sides of the carbon chain.
↑5	The first such hydrogenated shortening was marketed under the brand name Crisco. It was partially hydrogenated cottonseed oil.
↑6	In more detail, a cis double bond is converted to a trans double bond, hence the trans.
↑7	Common usage employs the term nucleotide for those with more than one phosphate group.
↑8	A coenzyme is a non-protein compound that is necessary for the functioning of an enzyme. Enzymes are macromolecular catalysts, most of which are proteins.

What biochemistry and cellular biology tell us

We have seen how the universe grew from a tiny point to become the enormous – probably infinite – place we see about us. We have focused on a small part of this huge entity and have seen how our solar system has formed and then our planet; how the Earth evolved to reach its current – but temporary – state of support of life; when life was born and how it evolved from bacteria to plants and marine creatures, then land creatures like dinosaurs, then mammals and primates and – currently – us.

So now what? Well, there’s us. But a complete study of that subject is well beyond the domain of this document, so let’s concentrate on a limited subset of it. As a former physicist and informaticien, and so naturally interested in energy and communications, I will emphasize those two threads in studying the human body. That, at least, is the goal. This route should lead to the ultimate and most subjective-seeming domain, cognitive science – the study of the brain.

We must start small, though, with cells, as all else follows from them. And in order to understand them, we need to know

Pre-modern and modern Homo, and tools

Pre-modern Homo

Homo habilis fossils have been found in East and South Africa and dated to 2.4-1.4 Mya. His brain was slightly larger (550-680 cm³) than those of his predecessors. It has been claimed that the cranium shows evidence for a developed Broca’s area1, suggesting that he may have used spoken language to communicate, although Broca’s area is hardly a sufficient condition for speech. His face and teeth were smaller than those of australopiths, so maybe he was more carnivorous, but his body was more ape-like. He may have used stone tools, but it is difficult to know if these were made by him or by other species in the same region. Whatever the case, the supposition that he had done so resulted in his being considered the first homo. Nevertheless some researchers find little to distinguish between H. habilis and australopithecus. It also is not clear that H. habilis was an ancestor of H. erectus, as the time periods of the two overlapped by a half million years.

Skull of Homo habilis, photographed by author at Olduvai Gorge Museum, Oct 2012.

A recently found jawbone dating from 2.75-2.8 Mya, pushes back the date of the oldest fossil of genus Homo.¹“Oldest human fossil found, redrawing family tree:, http://news.nationalgeographic.com/news/2015/03/150304-homo-habilis-evolution-fossil-jaw-ethiopia-olduvai-gorge/.

Homo rudolfensis lived in East Africa around 1.9-1.8 Mya. His brain was larger and his face longer than those of H. habilis, but his chewing teeth were larger, more like those of Paranthropus. Some paleontologists think he was an Australopithecus; some others, the same species as H. habilis. No good example of his skeletal structure has been discovered. A recent find of a cranium and jawbones.²New fossils confirm diverse species at the root of our lineage”. Smithsonian Human Origins Program,http://humanorigins.si.edu/research/whats-hot/australopithecus-sediba-%E2%80%93-new-analyses-and-surprises. http://humanorigins.si.edu/research/whats-hot/new-fossils-confirm-diverse-species-root-our-lineage supports the idea of H. rudolfensis as a Homo.

Homo ergaster (considered by many paleontologists to be early African H. erectus) lived 1.9-1.5 Mya in East Africa. He was the first hominin to have a body silhouette similar to that of modern humans and his proportions indicate that he lived on the ground. He was 1.7 m tall and capable of running and of walking long distances. His brain, at 850 cm³, was bigger than that of Paranthropus, but not yet that of a modern human, one more piece of evidence that larger brain size followed bipedalism on the evolutionary time scale, rather than preceding it. It is easy to imagine H. ergaster as the first “naked ape”. H. ergaster used primitive tools of the “Olduwan” culture.³Tools will be discussed in more detail in a later paragraph.

Homo erectus lived 1.9-0.14 Mya (or even later), making him the longest lived human species to date. Modern humans are far from having achieved such a long species lifetime. Like H. ergaster, H. erectus had a habitually upright posture and his or, in this case, her wide pelvis would have permitted birth of larger-brained babies.

H. ergaster/erectus (hereafter referred to simply as H. erectus) needed good nutrition in order to provide energy to that enlarging brain, so he may have mastered the use of fire and cooked his food, thus making food digestible even with his relatively smaller teeth. He was generally carnivorous, and the richer nutritive value of meat meant he could have a shorter digestive tract, which in turn made energy available faster. Hunting and butchering were enhanced by the use of double-sided stone cutting tools, which the archaeological record shows started around 1.76 Mya – the Acheulean technology. Note that 1.9 Mya, H. erectus coexisted with H. rudolfensis, H. habilis and P. boisei, and by .143 Mya, with H. sapiens.

H. erectus was the first species to expand beyond Africa, starting as early as 1.8 Mya. This was the first of many surges of expansion of hominins from Africa. Remains have been found in Asia (“Java man” in Indonesia, “Peking man” in China, Georgia), Africa and maybe Europe, although it is not impossible that some of these were different species. Migration will be discussed more later.

Several recent discoveries witness the work-in-progress character of paleoanthropology.

A skull discovered in 2001 from Dmanisi, Georgia, dated at 1.8-1.7 Mya possesses certain features of Homos habilis, erectus and rudolfensis, suggesting that they may not be distinct species.⁴“Complete skull from Dmanisi”. Smithsonian Human Origins Program, http://humanorigins.si.edu/research/whats-hot/complete-skull-dmanisi. This also is the oldest good fossil evidence for hominins outside Africa. Oldowan tools were found on the site.

Two more recent discoveries either clear up or confuse questions concerning H. erectus, depending on one’s point of view. One is the discovery in Buia (Eritrea) in 1998 of a nearly complete cranium, some pelvic bones and two incisors dated to 1.4-0.6 Mya. The long, ovoid brain case, wide cheekbones, massive brow ridges and medium-sized brain (~750-800 cm³, a preliminary result) make him look like H. erectus. However, the parietal bones of the cranium are claimed to represent a more modern trait. The discoverers see him as a link between H. erectus and H. sapiens and claim that the date of first H. sapiens morphology has been pushed back to around 1 Mya.

The second discovery comes from the Afar region of Ethiopia, where in 1997 a crushed skull was found in the Dakanihylo sedimentary layer, also dated to around 1 Mya. The reconstructed skull of this “Daka man” has a long, sloping forehead, massive brow ridges and brain case shaped rather like that of Buia man, giving him a resemblance to H. erectus specimens found at that time in far-away Asia. Since H. erectus first appeared around 1.8 Mya in Africa, the discoverers of Daka man claim this to be evidence that by 1 Mya, he had become one single world-wide species.

From 1.8 to 0.7 Mya, during the Pleistocene, glacial cycles increased in intensity. It was during this period that H. habilis and H. rudolfensis died out. The paranthropi soon followed suit, leaving only the genus Homo to spread to three continents.

Modern Homo

Homo heidelbergensis is considered by many paleontologists to be the first modern human. Fossils attributed to this species have been found in Germany, Greece, Ethiopia, Gambia, the U.K. and Spain, although he certainly originated in Africa. Some paleontologists think some specimens represent different species, such as H. antecessor (from Spain), H. cerpanensi (Italy) or H. rhodesiensis (Zambia). His large brain capacity of 1000-1300 cm³ confirms him as a Homo, although he had very large brow ridges and a flat face. He used fire and wooden spears, hunted large animals and built shelters of wood or rock. Some paleontologists think he was our ancestor, but wonder who was his. Many consider him to be a transition species between H. erectus and H. neanderthalensis. They lived between about 0.6 and 0.1 Mya.

Neanderthals

Homo neanderthalensis lived about 400-40 Mya over a large region extending from Western Europe into Asia, but concentrated mostly in Europe and the Near East. His body was shorter and more robust than that of modern humans, well adapted for cold, mountainous environments. His brain was even larger than ours, 1500-1750 cm³, but he weighed more, so his encephalization (ratio of brain mass to body mass) was similar. Neanderthals hunted large animals but also ate plants. They controlled fire, used sophisticated tools, lived in shelters and wore clothes they made themselves. Indeed, it is now thought that Neanderthals participated in about the same activities as H. sapiens. Discovery first of a Neanderthal hyoid bone (a throat bone necessary for enunciation) and then of his possessing the FOXP2 gene required for speech and language indicate that he may well have used language. Rock paintings found in Spain and dating from 43.5-52.5 Kya show that Neanderthals were artistic.

Much has been written about Homo neanderthalensis – entire books, including at least one novel sympathetic to him (William Golding, The Inheritors). Neanderthals are usually portrayed as ugly, ignorant, primitive and lacking in culture. They coexisted with H. sapiens for over 100,000 years and, in comparison with them, they were primitive and ignorant. But “ugly” is is in the eye of the beholder. And culture they had, though it is debated as to how much. There is evidence that they buried their dead and scratched designs into shells, an early example of art. It has recently been discovered that intercourse did take place between the species, as modern Europeans and their descendants have about 1-4% of their genes from Neanderthals. They therefore might be considered the same species as H. sapiens in spite of morphological differences. Which idea raises the question of what is a species.

Global temperature over 6 My, from NASA Goddard Institute for Space Studies

The Earth was now subject to Milankovich-cycle glacial periods which came all the way down into northern continental Europe. During interglacial periods, such as those 500 and 400 Kya, Neanderthals penetrated northwards. During those of 320 and 220 Kya, they made it as far north as England and Wales. Between 120 and 70 Kya, they advanced as far as Siberia. But as the Earth became cooler after 100 Kya, they were forced to move south again. Their last holdouts were in Croatia, Russia and Gibraltar, not later than 28 Kya.

Neanderthals evolved during their long stay on Earth, as did their contemporary African Homos. Morphological traits distinguishing Neanderthals from modern man are more and more accented, the farther west they are found. Genetic studies of Neanderthals from across Eurasia suggest three different groups according to where they lived — western Europe, the Mediterranean and the East. So as modern man moved west from the Middle East, he met populations showing more distinct, because more developed, Neanderthal morphology. Neanderthal extinction followed the same East-West gradient, those in the east disappearing before those farther west.

Evolution and variation within a species complicates distinguishing the species from others. So stating that such a fossil is such a species is rather like taking a snapshot of a moving object.

Theories abound as to what brought about the demise of the H. neanderthalensis species. The principle accused are the rapidly fluctuating climate, competition for resources and physiological differences from their fellow man, H. sapiens. Opinions on this question are often influenced by species identification or political correctness. The jury is still out.

Denisovans

Less well known is the recently found Denisovan species, discovered only in 2008. First, a young girl’s finger bone was found in the Denisova cave in Southern Siberia. Since then, a toe and some teeth have also been found. While this may not sound like much, the important thing is that scientists have been able to make analyses of both nuclear and mitochondrial DNA of the species. Denisovans were found to be genetically closer to Neanderthals than to H. sapiens, but distinct enough to deserve being considered a separate species. More recent genetic studies suggest that Denisovans and Neanderthals had a common origin about 1 Mya which may have been H. heidelbergensis. Denisovans and Neanderthals then diverged around 640 Kya, after leaving Africa.

Denisovan genes have been found in the Melanesian people of Papua, New Guinea. Apparently, the people who migrated there first shared genes with the Denisovans before moving on to New Guinea 45 Kya. Denisovans may also have given present-day Tibetans a gene which facilitates living at high altitudes. And they make up around 1% of the genes of modern Europeans.

Homo sapiens

Bipedalism, temperature and a larger brain

To simplify only a little, all the characteristics of modern humans are due to two main traits: bipedalism and bigger brains. That is the correct chronological order, as small-brained Australopiths were already bipedal to some extent and evenly completely bipedal H. ergaster had a brain of only about 850 cm³. In some ways, bipedalism provided conditions necessary for an enlarged brain.

Bipedalism led to a non-grasping foot, simplified ankle and knee joints, a narrow, vertical and bowl-shaped pelvis (to support innards), related modifications to the hip joint and femur (the thing old folks break so easily), and a vertical, S-shaped spine (which pains many of us). It also freed up the hand, which could then develop other skills, such as making tools. Upright walking is thought to have brought modifications in the spatial relations of throat components (pharynx, larynx) necessary for speech, but keeping us from breathing and swallowing simultaneously, once we are past puberty.

Most important, bipedalism led to temperature regulation in the body and to improved brain nourishment. Under the hot African sun, being upright meant that less light hit the body during the hottest time of day. So fur could disappear (except on top of the head). Improved temperature control came from sweat glands in the skin coupled with blood circulation, together constituting a natural heat pump capable of cooling or warming the body depending on external conditions. This allowed the maintenance of the strict temperature range needed by enzymes responsible for metabolic processes. Since a significant part of this takes place in the brain, bipedalism indirectly allowed a bigger brain. Also, upright walking requires less energy than moving about on all fours, leaving more energy for the brain. And since the upright posture allowed faster movement, men became better hunters and were able to obtain more meat protein, which provided more energy, from which – again – the brain gained. All these features reinforced each other.

In addition to an improved nervous system and cognitive ability, a larger brain contributed to changes in the face and skull structure. Food not only nourished the larger brain, it also played a roll in the evolution of the jaw and teeth needed for mastication. The chin, unique to H. sapiens, attaches muscles used for fine lip movements necessary for speech. The brain developed a basic language function, at least for a default form of grammar found the world over.

Bipedalism also is important because before man could move “out of Africa”, he had first to move out of the trees! Otherwise, he could never have crossed the very different landscapes which he encountered – forests, grasslands and sometimes even seas.

So changes in posture, internal organs, brain size and interaction with the environment followed one upon another in a continual evolution towards our present (temporary) state.

Where, when and how?

To answer the first two questions, where and when, the oldest fossils of H. sapiens are from Ethiopia and date from 200 Kya. Fossils, archeology (tools and art), genetics and language studies confirm (with some reservations) the “Out of Africa” model, which holds that hominoids all developed in Africa, mainly East Africa, and then expanded to the west of the world. The alternative model, the “multiregional” hypothesis, which posits that hominoids migrated long before and then developed into local variants on site, is generally considered erroneous. Still, it is true that a number of migrations did take place, such as the one by H. erectus around 2 Mya and the more recent ones around 60-45 Kya by modern humans. It seems that when modern humans, or archaic H. sapiens, wandered out to the rest of the world, they met and to some extent mixed genes with locally variant species evolved from the earlier migrants. This would explain the small percentages of Neanderthal and Denisovan genes in those of modern humans.

As usual in paleontology, there is dispute about which was the first modern human fossil to be found. Deserving or not, Cro-magnon man generally wins the prize, having been found in a cro (shelter) on the farm of Mr Magnon in south-central France in 1868.⁵Modern Homo bones known as the “Red Lady”, because they were smeared with ochre, had been discovered in Wales in 1822-23. These early H. sapiens were more robust than modern humans, but otherwise resembled them closely. Actually, some of them had bigger brains than we do.

Fossil remains of H. sapiens have been found in Romania from 35 Kya; southeast Asia, maybe 40 Kya; and in the New World in Alaska, c. 12 Kya, and the Clovis Culture in North America, 11 Kya. Evidence for the existence of pre-Clovis cultures in Pennsylvania dating from 14 and possibly up to 20 Kya is controversial.

By 40 Kya, Homo’s skill at tool-making had increased to the point where he began to make works of art – cave paintings and engravings, and carved bones.

Painting in the Grotte de Lascaux, by Prof saxx via Wikimedia Commons

More about tools – the Paleolithic

Establishing a chronology for tool fabrication and use is difficult for at least two reasons. First, the only tools which have remained over time are the hard ones – made of stone or fossilized bone. Tools made of softer materials such as wood or bone have not survived. Second, finding tools near a fossilized hominin remain does not necessarily prove that the tools were made or used by that particular hominin. Still, we must do our best with the facts available.

The Paleolithic, or Old Stone Age, is taken as extending from the first known appearance of stone tools about 3.3 Mya in Kenya⁶Before 2014, the oldest was 2.6 Mya in Ethiopia. and extending to the end of the last Ice Age about 10 Kya. It is divided into three periods.

The first is the Early Paleolithic (also called the Lower Paleolithic, because the corresponding geological layer is located below the others), which is divided into two overlapping periods according to prevalent technologies.
- The first period, the Oldowan (after Olduvai Gorge), extended from at least 2.6 Mya to about 1 Mya. During this time, hammerstones were used to knock sharp-edged chips off core rocks to make choppers. They were made and used by late australopithecines and maybe by paranthropus and H. ergaster/habilis. It was also during this time that the first expansions of Homo from Africa took place.
- The second period, from 1.7 Mya to about 250 Kya, was that of the Acheulean technology, which spread from Africa into the Middle East and on to India, south of the Movius Line. This technique made double-sided chips to use for such items as hand axes. Such technology required planning by the toolmaker and therefore augmented brain power. Hominins of the period were H. erectus and, later, H. heidelbergensis.

Oldowan chopper from Ethiopia, by Didier Descouens via Wikimedia Commons

Biface from Saint Acheul, France, from Wikimedia Commons

The Middle Paleolithic, about 250-30 Kya, introduced the technique of making fine flakes of stone which could be attached to sticks to make spears. Fire came into general use. Principal hominins were Neanderthals and earliest modern humans.
The Late Paleolithic, about 40-10 Kya, saw the use of bone, antlers and ivory to make still finer tools such as needles or harpoons. Hunting and fishing thus improved. Symbolic art, musical instruments and throwing devices dating from this period were made and used by anatomically modern humans. The oldest known musical instruments are bone flutes from 35 or more Mya, but most likely there had been previous instruments of less survivable material.

Paleolithic flute from about 43 Kya, by José-Manuel Benito Álvarez via WIkimedia Commons

As mentioned, examples of H. erectus have been dated in Asia up to around 2 Mya. The tools found with them were those of the Oldowan technique. Acheulean tools date back to to 1.76 Mya and have been found only south of a line running from present-day Denmark to the Gulf of Bengal, the so-called Movius Line, named after the paleontologist who first noted this distribution. The explanation for this geographical distribution is generally agreed to be that H. erectus first took his Oldowan tools with him when he migrated east before around 2 Mya. Later, the Acheulean developed in East Africa (even though it is named after a site in France where it was first discovered) and subsequent migrations carried it to most of the rest of Africa and the Near East (Georgia), from where it moved east into India and northwest into Europe around 600 Kya. Asiatic H. erectus eventually died off and were replaced by H. sapiens.

Similar considerations hold for the arrival of modern man in Europe. H. erectus seems to have arrived in southern Europe over 1 Mya; chipped stone tools have been found from 1.2 Mya. Although the Acheulean technology originated in Africa around 1.4 Mya, there are no examples of it in Europe from this time, This fact is explained if we accept that early hominins in Europe descended from those in Georgia 1.7 Mya, as this was a logical station between eastern Africa and Europe. Because of glacial periods which affected Europe over this period, there were most likely numerous attempts at settling during warm periods, many of which failed due to climate extremes: The settlement of Europe was not a one-time event. Only for the last 600 Kys has northern Europe (north of the Alps) been permanently settled and these settlers brought the Acheulean technology with them.

So for the cases of both Asia and Europe, absence of Acheulean tools for the earlier peoples leads to the recognition of different waves of migration across hundreds of thousands of years.

Summary of expansion of Homo sapiens

Evidence from paleontology, archeology and genetics all concur that modern man originated in Africa around 150 Kya. But even before that time, pre-modern Homo had begun what became the expansion of man from Africa to the rest of the world. The first step took place about 2 Mya when H. erectus, or whatever preceded him, spread out into Eurasia. His earliest known descendants lived in Georgia about 1.8 Mya. A second migration may have taken place about 200 Kya into China and India. Another around 130 Ky spread into the Middle East. Humans may have reached Australia 60 Kya.

But the big one, “ours”, so to speak, was the expansion around 60-50 Kya into the Middle East and thence into Europe and Asia. These Homo sapiens replaced the Neanderthals and H. erectus and, about 11 Kya, they made it to the Americas via Siberia. Man became the dominant species on Earth, for better and for worse.

Overall summary

After dinosaurs disappeared from the surface of the Earth about 65 Mya, the number and size of mammal species took off, eventually ranging in size from tiny mouse-like creatures up to elephants and whales. During a particularly warm period of the mid-Eocene, primates came into existence, at first small squirrel-like creatures. About 23 Mya, the primate line split into Old-World Monkeys (catarrhines) and hominoids and the latter split into hylobatids (gibbons and the like) and hominids. From hominids sprang pongines (orangutans) and hominines and the latter begat panins (chimps and bonobos) and hominins. The first hominins were the precursors of man, but not all of them were his ancestors. No direct line from the LCA⁷Last Common Ancestor of chimps and hominins can be distinguished; the tree of life is rather a bush, with the branches hidden and many twigs representing dead ends. However, there is clear evidence for over twenty species intermediate between the time of the LCA and modern Homo.

First, there were some fairly difficult-to-classify species found in East and Central Africa, dating from 7 to 4.5 Mya. Though the consensus seems to be that these represented steps in a generally man-like direction, they are all subject to controversy as to whether they are hominins or on another line. Some even may have lived before the LCA.

Then, from 4.5 to 2.5 Mya, there evolved a fairly heterogeneous group called australopithecines, one genus of which was australopithecus. Although they possessed varying degrees of bipedalism and stronger chewing teeth, their brains were still about the size of a chimp’s. Up to at least four of these species lived at the same time. A second group, which followed up to about 1 Mya was paranthropus, sometimes classed as a genus of australopithecines. These were more robust versions of australopithecus, with a chewing apparatus capable of masticating tough roots and nuts.

From around 2.5 Mya, true Homo, the same genus as modern humans, appeared on the scene. Members of these species tamed fire and invented cooking, made and used stone tools and hunted large animals. The first one to really look more or less like a modern human, Homo ergaster, had long legs, an upright body and could walk long distances and even run. Another (or maybe they were the same), Homo erectus, migrated out of East Africa as far as Asia around 2 Mya, taking along Oldowan tool technology. More migrational surges took place until finally, around 60,000 years ago, another, more modern species made their way into the Middle East and from there to Europe, Asia and, eventually, the Americas, this time with the Acheulean technology. Along the way, they mixed their genes with those of the local populations evolved from earlier H. erectus – Neanderthals and Denisovans and perhaps others. Nevertheless, most of our genes originated in Africa over ~60 Kya.

The best-known of the Homo which became extinct is Homo neanderthalensis. Neanderthals have been the victims of much bad press. Compared to the H. sapiens, with whom they shared the environment during their last 100,000 years or more, they were primitive. But they made and used tools and their own clothing, they probably buried their dead and they made decorations which may be considered an early form of art. And they left some of their genes in us.

The demise of the Neanderthals left, for the first time, only one species of hominin on Earth – H. sapiens sapiens. We are now up to the geological present.

Notes[+]

Notes
↑1	“Oldest human fossil found, redrawing family tree:, http://news.nationalgeographic.com/news/2015/03/150304-homo-habilis-evolution-fossil-jaw-ethiopia-olduvai-gorge/.
↑2	New fossils confirm diverse species at the root of our lineage”. Smithsonian Human Origins Program,http://humanorigins.si.edu/research/whats-hot/australopithecus-sediba-%E2%80%93-new-analyses-and-surprises. http://humanorigins.si.edu/research/whats-hot/new-fossils-confirm-diverse-species-root-our-lineage
↑3	Tools will be discussed in more detail in a later paragraph.
↑4	“Complete skull from Dmanisi”. Smithsonian Human Origins Program, http://humanorigins.si.edu/research/whats-hot/complete-skull-dmanisi.
↑5	Modern Homo bones known as the “Red Lady”, because they were smeared with ochre, had been discovered in Wales in 1822-23.
↑6	Before 2014, the oldest was 2.6 Mya in Ethiopia.
↑7	Last Common Ancestor

Hominins, geology and climate

“In short, paleontology is the study of what fossils tell us about the ecologies of the past, about evolution, and about our place, as humans, in the world.”¹University of California Museum of Paleontology, http://www.ucmp.berkeley.edu/paleo/paleowhat.html. Paleontology, the study of the evolution of ancient life, draws information not only from the discovery and study of old bones, but also from archeology, genetics, linguistics, climatology and other fields. Interpretations of existing data differ and can change with each new discover of fossils. Since new bones are discovered quite often, paleontology is constantly a Work in Progress.

That explains why this article may well be the one with the most occurrences of words like “maybe”, “perhaps” or “thought” (as in “thought to be…”), indicating uncertainty in the understanding of some findings. This situation casts no doubt on the overall results showing the evolution of our species, Homo.

The evolution of man and his family bush

It would be nice to be able to draw a family tree for mankind. There exists much evidence for numerous intermediate species between man and his last common ancestor (LCA) with chimpanzees. But it is currently impossible to distinguish a linear sequence of species on such a tree. To continue the metaphor, the tree really looks more like a bush, with twigs sticking out in all directions, masking the underlying branches. Nevertheless, it is convenient to group together some twigs whose similar characteristics indicate they may sprout from a common branch.

Before going further, some vocabulary is necessary. A primate is a mammal of the order Primates (logically enough), mostly arboreal, ranging in size from lemurs to gorillas, and including, among others, monkeys, chimpanzees, gibbons and man. Hominins are species on the main human twig of the bush of evolution, members of the family Hominidae.²Wikipedia lists six classifications for humans beneath the family Hominidae: subfamily Homininae, tribe Homini, subtribe Hominina, genus Homo, species, H. Sapiens, subspecies H. s. sapiens. Who can possibly remember and distinguish those three different endings for homini – ai,i and a? Members of the chimpanzee twig are called panins.

There are some points of which we are quite certain:

Man has evolved from some creature which was the common ancestor of both man and the chimpanzee, which genetic analysis shows to be the current species closest to us.
Among all the forms of primates which have preceded modern man, it is difficult to distinguish a unique, linear sequence of forms, each one evolved from the one before. Nevertheless, overall changes show clearly that evolution has taken place.
The genetic notion of “molecular clocks” indicates that hominin evolution has taken place for up to 7 million years, often during periods of extreme climate change (shown in a later figure) which some species survived better than others.³The so-called genetic clock calculates duration based on the number of genetic changes taken place multiplied by an approximate time per change.
Astounding as it may appear to us now, at most times in our evolutionary history, different forms of man existed at the same time. The best known example is that of Neanderthals and Cro-Magnons. They lived near each other in western Europe and even shared some genes, so it is clear that “social” interaction took place between the species. Imagine living near a group of animals of another species, another kind of animal, a sort of ape with which you could communicate (and even copulate). Would we try to enslave or annihilate them (or use them for experiments), as is our wont?
“It” (the evolution of primates from earlier forms into man) all started in Africa.

Characteristics of hominins

The following criteria are generally taken to show that a given fossil is more like a hominin than a panin. Hominins are all creatures attached to the human branch since the LCA; panins, to the chimp branch.

More perfected bipedalism, a greater ability to walk upright on the two hind legs. A number of factors are associated with this ability:
- a more vertical trunk, wider hips, straighter and lockable knees, lower limbs longer than upper, feet suited for walking rather than for climbing in trees;
- relatively forward placement of the foramen magnum, the hole where the spinal column enters the skull, due to the erect posture;
- greater height;
less prognacious (flatter) face;
greater cranial volume and brain size (larger for hominins), which is correlated with increased pelvic size necessary for such large-brained babies to be born;
skull, jaw and dental structure (related to diet):
- teeth in a parabolic row;
- smaller and less protruding canines, relatively larger incisors and larger chewing teeth (molars);
- more robust mandibles (lower jaws).

Two somewhat linked developments are bipedalism and increased brain size. Bipedalism seems to have prepared the way for bigger brains (as we shall see shortly).

Either such taxonomic⁴Taxonomy is the practice and science of classification. characteristics or genetic analysis may be used to classify different families and species of primates as shown in the figure. Results from the two methods are not necessarily the same.

Hominoid families with dates, diagram by author.

Another way to see this is in the following table. The difference between the table and the diagram in the placement of the Gorillini may indicate the method of analysis used (taxonomic or genetic)⁵There is disagreement about placing gorillas under hominoids or hominids. See www.hominides.com/html/dossiers/hominoide.php (in French).

Hominoidea super-family

Groups of hominins

Species may be grouped together according to some common characteristics. The next figure indicates the time period of most currently known fossil hominins. Different colors indicate different groups.

Timeline and grouping of principal fossil hominid species, diagram by author

In this figure, a significant number of hominin species are grouped in two different ways. One grouping⁶Based on Wood, 2005, is indicated by the background colors:

beige – possible and probable hominins
blue – archaic and transitional Homo
green – pre-modern Homo
pink – Homo group

The color of the vertical bars representing the time when the species lived represents the grouping of the Smithsonian Museum of Natural History:

brown – Ardipithecus group
green – Australopithecus group
magenta – Paranthropus group
blue – Homo grouping
pale green – not grouped by Smithsonian (considered controversial)

While general characteristics of different species among the Australopiths and others evolve across the ages, different parameters do not always evolve together. For instance, Au. anamensis has chimp-like canines but fairly evolved bipedalism, whereas Pa. aethiopicus has smaller canines but its foramen magnum is near the back. Nevertheless, from the bottom of the bush to the top, overall evolution does occur and near the top we find our modern species panins and hominins – in particular, us.

Many paleontologists think that H. erectus is a later and Asian version of H. ergaster; others think they are different. In either case, there were at least four species of hominins living around 2 Mya,

Before considering these groups in detail, it is necessary to consider the preceding rise of mammals and the role of climate in evolution.

Geology, climate and evolution

Global temperature is a function of many variables, but there are two main ones:

how much energy is received from the sun and
how much of it is trapped by the oceans and the atmosphere, rather than being reflected back out into space.

Considerations of energy received must take into account solar activity.

The energy falling onto the Earth’s surface depends on its orbit – the angle of its rotational axis relative to the plane of the orbit, the precession of the orbit⁷The elliptic orbit depends on two foci, one of which is at the sun. The other rotates slowly around the sun and the changing shape of the orbit, which modifies the distance of the Earth from the Sun. Taking all these into account leads to the calculation of so-called Milankovitch climate cycles. These agree largely with temperature-variation results from geology.

How much energy is retained by the Earth depends on the distribution of land and sea, the properties of the land’s surface (reflective or absorbing) and the composition of the atmosphere (the much-discussed greenhouse effect and the ozone barrier).

The period when primates developed, the beginning of the Eocene epoch (55 Mya), was the warmest moment in the Tertiary and the warmth spurred growth and evolution. Since the Eocene peak, global temperatures have been gradually decreasing, with short-term fluctuations superimposed on the general background. The next figure shows the general behavior that has been observed.

At the beginning of the Oligocene (33.9 Mya), a period of rapid cooling brought to an end the warmth of northern forests, with disastrous effects which almost wiped out our ancestral line.

65 million years of climate change, from Wikimedia Commons

As we have seen, these changes in temperature are to a great extent due to geology – the movement of tectonic plates. As plates have moved, oceans have opened (such as the separation between Antarctica and Australia or South America) or closed (Tethys Sea, Isthmus of Panama). This opening and closing of channels changed sea currents (e.g., the Gulf Stream) and led to formation of the antarctic and arctic ice caps⁸This paragraph is only a summary, ignoring chronology. Formation of the antarctic ice cap coincided with the drop in temperatures at the beginning of the Oligocene, c. 35 Mya, whereas the Isthmus of Panama was closed c. 4-3 Mya and the arctic ice cap formed around 2.5 Mya., which in turn brought about lowering of global sea levels. The ice caps themselves reflect solar energy back into space, causing further cooling. Coming together of continents has created mountain chains (Africa pushed up the Alps; India, the Himalayas) which have altered meteorological conditions, especially rain patterns (such as the Asian monsoon). During the latter part of the ice age, melting continental ice sheets have caused sea levels to rise. Geology and climate and, hence, evolution all go together.

The next figure shows the general lowering of temperatures over the last 5 My, as well as the cyclic character of temperatures. The relative increase over the last 10,000 years began at the end of the last great Ice Age, which started some 130 Kya and only ended about 10 Kya. We are currently in a warm, interglacial period. There is no reason to expect this warmth to continue very long (on a geological time scale).

Global temperature over 6 My, from NASA Goddard Institute for Space Studies

Now continue to the rise of mammals and early hominins.

Notes[+]

Notes
↑1	University of California Museum of Paleontology, http://www.ucmp.berkeley.edu/paleo/paleowhat.html.
↑2	Wikipedia lists six classifications for humans beneath the family Hominidae: subfamily Homininae, tribe Homini, subtribe Hominina, genus Homo, species, H. Sapiens, subspecies H. s. sapiens. Who can possibly remember and distinguish those three different endings for homini – ai,i and a?
↑3	The so-called genetic clock calculates duration based on the number of genetic changes taken place multiplied by an approximate time per change.
↑4	Taxonomy is the practice and science of classification.
↑5	There is disagreement about placing gorillas under hominoids or hominids. See www.hominides.com/html/dossiers/hominoide.php (in French)
↑6	Based on Wood, 2005,
↑7	The elliptic orbit depends on two foci, one of which is at the sun. The other rotates slowly around the sun
↑8	This paragraph is only a summary, ignoring chronology. Formation of the antarctic ice cap coincided with the drop in temperatures at the beginning of the Oligocene, c. 35 Mya, whereas the Isthmus of Panama was closed c. 4-3 Mya and the arctic ice cap formed around 2.5 Mya.

Archean, proterozoic and paleozoic — the rise of life

The Archean Eon – appearance of life

The period from about 3.8 to 2.5 Gya is referred to as the Archean Eon.¹The International Commission on Stratigraphy, apparently the expert in these matters, places the beginning of the Achean at 4..0 Gya, but I have no book which says other than 3.8.

Geology and atmosphere

Over the period of about 3.2-2.7 Gya, rocks on the surface came together to form the first cratons, which would become the central cores of continental plates. Sediments from the eon, which indicate that the rock cycle (volcanism-sedimentation-metamorphism) was in action, provide evidence for the existence of continents and oceans. The oldest existing continental rocks date from the Archean at about 4 Gya.²Spooner, 255. By the end of the Archean, plate tectonics was under way.

Solar energy received at the surface of the Earth was about 20 to 25 % lower than present, which could have made the planet too cold for life to be established³“Climate puzzle over origins of life on Earth”, http://www.manchester.ac.uk/discover/news/article/?id=10798., but the CO₂ retained heat beneath the atmospheric layer, causing a greenhouse effect which slowly raised atmospheric temperatures. Sunlight striking the water vapor caused photochemical dissociation, the breaking up of the water molecules and the bonding together of the resulting oxygen atoms to create ozone, or O₃. In time, the ozone came to protect the surface of the Earth from ultraviolet radiation from the sun. At the same time, it prevented further chemical dissociation, which therefore has not played an important role in the oxygenation of the atmosphere. Further increase of atmospheric oxygen had to wait for photosynthesis, as described below.

Life and atmosphere

Arguments over what was the earliest form of life (and who discovered it) probably are not over yet. Currently, the oldest fossils would be of bacteria from Australia, dating from 3.4 Gya.⁴Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia, Nature Geoscience https://www.nature.com/articles/ngeo1238. What makes them interesting is the fact that their metabolism was based on sulfur rather than oxygen, which was not yet common in the atmosphere.

For comparison, the oldest fossil evidence for cyanobacteria dates from 2.22 Gya⁵Ward and Kirschvink, 81; for eukaryotes, 1.78-1.68 Gya.⁶j. Brocks, cited by Ward and Kirschvink, 75.

Life may be defined as “… a self-sustaining chemical system capable of incorporating novelty and undergoing Darwinian evolution.”⁷Gerald Joyce, NASA, quoted by Hazen, 130. There are several hypotheses about its origin on Earth, especially

the “primordial soup” hypothesis,
the hydrothermal vent hypothesis
the volcanic pool hypothesis.

The “primordial soup” hypothesis considers life to have been brought about using energy from electricity (lightning) in a mixture of gases including water and methane. Such production of organic molecules has been demonstrated in the laboratory, but fails to convince many scientists because it depends greatly on the composition of the atmosphere at the time. In particular, it is now thought that CO2 was far more prevalent than methane. More recent experiments with different mixtures have produced similar organic compounds. The discovery of amino acids on meteorites adds weight to the hypothesis that varying atmospheric conditions could lead to production of organic molecules.⁸Prothero (2007), 147-52.

The hydrothermal vent hypothesis exists in two varieties. The first supposes that life came into being in “black smokers”, hydrothermal vents formed along undersea ridges such as the Mid-Atlantic Ridge. Sea water leaks down through fissures in the rock and is super-heated by magma. The super-heated water may attain a temperature of 400°C, but the immense pressure keeps it from boiling. When the mineral-laden water rises and hits the relatively colder sea water, dissolved minerals are liberated, emitting sulfur-bearing black molecules which look like, but are not, smoke and which pile up to produce “chimneys”. White smokers, which carry barium, calcium and silicon, also exist. It was thought that the reaction of hydrogen sulfide from the vent with water would provide the energy necessary for the formation of life. Although life does abound in these vents, it is not at all like ours. One finds, for instance, extremophile organisms which live in darkness and obtain their nourishment from hydrogen sulfide.

“Nature Tower”, an alkaline “chimney” in the Lost City group. From NOAA.

Whorls and pores in a thin section of a Lost City chimney, from NOAA.

The second hydrothermal-vent model proposes that life originated in alkaline hydrothermal vents. In places on the ocean floor, peridotite rock, which is normally found deep in the Earth’s mantle, has been pushed up to the surface by faulting. The rock contains olivine, which reacts with sea water to form the minerals serpentine and magnetite; the process is called serpentinization, The reactions are exothermic and increase the volume of the reactants. The heat is generated by chemistry and does not come from hot magma, as is the case with “black smokers”. The result is an alkaline solution (pH = 9-11) rich in calcium and H₂. The rocks produced have lower density and so expand and push up. They crack and more sea water moves in to react with remaining olivine. On contact with colder sea water, the calcium precipitates out, forming white structures like chimneys.⁹These results are for the Lost City Hydrothermal vents. Results differ some for other vents. Eventually, small cracks and “cells” form within the rock. Rising fluids are very alkaline (basic) and thereby precipitate out calcium carbonate and other alkaline substances when they hit the cold sea water. These then build up on the pile of rock already started and soon “reverse stalactites” are produced by the carbonate left behind by the thermally rising water. Iron in the olivine is oxidized, leading to production of reducing gases hydrogen, methane and hydrogen sulfide.¹⁰“The Lost City 2005 expedition”, NOAA, http://oceanexplorer.noaa.gov/explorations/05lostcity/background/serp/serpentinization.html. These gases in turn are a source of energy. So the rising “chimneys”, which may reach many meters in height, are associated with a source of energy, gases like those in the “primordial soup” and small cell-sized alveoli or compartments. Such an environment may well be suited to abiotic hydrocarbon production.¹¹https://www.researchgate.net/profile/Marvin_Lilley/publication/5613067_Abiogenic_hydrocarbon_production_at_lost_city_hydrothermal_field/links/0c960520e90a17f539000000.pdf The compartments contain and protect their contents as well as ensuring their concentration, making excellent conditions for the production of inorganic precursors to organic life. From these, prokaryotes and archea could have evolved independently around 3.8 Gya and eukaryotes later, around 2 Gya.

The volcanic pool hypothesis is more recent.¹²Van Kranendonk, Martin J., Deamer, David, and Djokic, Tara, “Life springs”, Scientific American, August 2017, 22. It posits the combination of simple molecular building blocks, perhaps from space, using thermal energy from volcanic pools, like those at Yellowstone or in Iceland. As external conditions change, they could evolve in a Darwinian manner as they survive through wet, dry and moist cycles in land-based hot springs. Such organisms have been called progenotes.¹³There is some disagreement as to whether progenote simply means LUCA (last universal common ancestor). Others, more specifically, call it ‘”a theoretical construct, an entity that, by definition, has a rudimentary, imprecise linkage between its genotype and phenotype (Woese, 1987)”—a creature still experiencing progressive Darwinian evolution, in other words.’ From https://www.ncbi.nlm.nih.gov/books/NBK232215/.

Be that as it may, the appearance of cell membranes meant that different environments and molecules could be separated from each other, a kind of biological differentiation. This led in turn to the the formation of simple cells, called prokaryotic cells.As we have already stated, the earliest clear occurrence of life is in the form of microscopic cells in Archean sediments in Australia, dating from about 3.4 Gya. Cyanobacteria existed by 2.22. Gya and are still alive all over the globe today. The “cyan” in their name refers to their blue-green color. They are the oldest currently-living beings. But they are extremely important for another reason.

Some of these bacteria mixed with sand to make microbial mats. As the sandy mixture became muddy, the cyanobacteria migrated upwards and the process repeated, resulting in lumpy layers of colonies called stromatolites. Stromatolites thrived over the period from about 3.5 Gya to 0.5 Gya, but are still found in a few places such as Shark Bay, Australia, or the Pacific Coast of Baja California. They survive only in especially salty water (twice the sea’s normal saltiness) or in places with especially strong currents, as both conditions limit predators such as snails which otherwise would devour them.

Stromatolites in limestone near Saratoga Springs, NY, by M. C. Ryget via Wikimedia Commons

In addition to that, phylogenetic studies show that eukaryotes form, usually, five supergroups, all of which evolved from a common eukaryotic ancestor. The members of each group have then evolved independently of the other groups. Only eukaryotes have evolved to form complex life and it all conserves properties of the common ancestor. Eukaryote cells are all very similar, all of them having, for example, common methods of cellular respiration, sex and DNA contained in nuclei.

Living stromatolites in Shark Bay, Australia, by Paul Harrison via Wikimedia Commons

Cyanobacteria have been called the “working-class heroes of the Precambrian Earth”¹⁴Knoll (2003), 42 and were fundamental to the development of life. The importance of these organisms cannot be stressed too much, as they were the first organisms to carry out photosynthesis, the use of energy from the sun to convert carbon dioxide into nutrients and free oxygen, which is returned to the atmosphere. Over hundreds of millions of years during the Archean and Proterozoic Eons, as cyanobacteria used photosynthesis to recover the energy necessary for their own metabolism, they brought about the gradual transformation of atmospheric CO₂ into the oxygen necessary for other forms of life¹⁵The capability of stromatolites to accomplish this task alone has been questioned and other mechanisms suggested., such as ourselves. At the same time, the greenhouse effect was reduced and, thereby, global temperatures. Much CO₂ was also dissolved in the seas, where it combined with calcium to form calcium carbonate, which in turn solidified to form limestone. Limestone, ocean water and corals are huge stores of carbon dioxide (carbon sequestration).

Interestingly, thousands of the minerals found on Earth today are due to oxidation by oxygen dissolved in water. So oxygen has not only allowed life to begin, but has also thoroughly changed our mineral environment. In other words, the biosphere and the geosphere have evolved together.

Photosynthesis took place in the top layer of stromatolites and each layer lived off the layer above. As such, they represented an early symbiosis or way of living together – an example of what we now call ecology. Notice that ecology (water, atmosphere) led to biology (stromatolites), which in turn influenced ecology (atmospheric oxygen).

The Proterozoic Eon — the dance of the continents

The Proterozoic Eon runs from 2.5 Gy to 542 Mya. It has been so named because of the appearance of more complex organisms during this period,

Geology and atmosphere

In spite of widespread glaciation early on. During this eon, plate tectonics came into its own, with cratons moving about on the surface of the Earth in what has been called a “stately dance”, i.e., a slow one. It was like some kind of round, with one continent dancing for a while with another, then separately, then with a third. At least five times, they all came together to form a single supercontinent. As they smashed into each other, they brought about the rise of mountains, a process geologists call orogeny. As they rifted and came apart, seas formed between them.

There is rather weak evidence for a perhaps small-continent-sized landmass dubbed Vaalbara 3.3 Gya. It is much more certain that there existed a continent-sized landmass called Ur about 3.1 Gya, made up of cratons from what now are South Africa, Australia, India and Madagascar. Ur lasted for about 300 Gy, undergoing various combinations with other continents, until the breakup of Pangea. Ur was not a supercontinent, but it’s about all there was.

It should be remembered that these reconstructions of ancient cratons or continents from geological and other data are to varying extents uncertain as to the details.

About 2.7 Gya, the first supercontinent came into being – Kenorland (also called Superia). Since the atmosphere was devoid of oxygen at the time, only acid rain fell, and this eroded and dissolved the land, leading to the deposit of sediments along the continent’s coasts. About 2.4 Gya, just as oxygen started accumulating in the atmosphere, Ur broke away and Kenorland began its fragmentation.

By 2 Gya, there were at least five separate cratons:

the Laurentian supercraton, the geological core of North America;
Ur, composing current India, western Australia and South Africa;
Baltica and Ukrainian cratons, making up eastern Europe;
cratons comprising most of what are now South America, China and Africa.

By about 1.8 Gya, all these cratons had collided and coalesced to form the supercontinent Columbia¹⁶Also called Nena, Nuna or Hudsonland.. Since it was situated on the equator, its interior was hot and dry. There were therefore no or few ice caps and ocean levels were relatively high.

Around 1.6 Gya, Ur split off from Columbia and a new sea formed between them. Since they were still at the equator, ice remained low and ocean levels high.

About 1.2 Gya, a new supercontinent now called Rodinia was forming, again near the equator, so its interior was again hot, dry and lifeless and no sediments were formed. Evidence for Rodinia comes from the so-called Grenville orogeny, rocks of which are found in the cratons of all current continents. Also, the absence of sedimentary rocks from this period suggests an absence of shallow seas, which would have been the case if there was only one supercontinent. Rodinia now was surrounded by a single superocean called Mirovia. About 850 to 800 Mya Rodinia broke apart and then, somewhere around 700 Mya, it may have reformed with the pieces in a different order to form another supercontinent, Pannotia, which only lasted about 60 million years before It broke up in term.

Reconstruction of the supercontinent Rodinia, by John Goodge [Public domain], via Wikimedia Commons

The next supercontinent, Pangea, formed only later, in the Phanerozoic Eon.

It was during the Proterozoic and beginning of the Phanerozoic Eons that the oxygen content of the Earth’s atmosphere began to increase significantly. Alternating layers of red, iron-containing minerals and silica minerals called banded iron formations (or BIFs) indicate fluctuations in the oxygen levels of oceans about 2.5-1.8 Gya, at least not before 1.8 Gya. Iron(II), or Fe²⁺, is soluble in water, but is oxidized by atmospheric oxygen to iron(III), or Fe³⁺, which precipitates. Since BIFs exist in sedimentary rocks, it is thought than fluctuating levels of oxygen in the sea water led to the alternating bands of minerals.

Later formations called red beds, which are sedimentary sandstone or shale, exist from 1,8 Gya. Their red color is due to the mineral hematite, Fe₂O₃, formed by the oxidation of iron, but this time on land. So by this time, the air must have contained enough oxygen to oxidize iron. Red beds are also common in rocks from the Phanerozoic Eon.

The Lal Qila, or Red Fort, in Delhi is built of red-bed sandstone. Photo by author's wife.

The Lal Qila, or Red Fort, in Delhi is built of red-bed sandstone. Photo by Siv O’Neall.

In summary:

From 2.5-1.8 Gya, fluctuating oxygen content in seawater formed BIFs.
Since 1.8 Gya, increasing atmospheric oxygen has oxidized Fe to hematite.

Atmospheric oxygen also allowed the formation of new types of minerals, so once more life influenced geology.

Life

Once the great oxidation event had taken place, life now went through a long, slow period often referred to as the boring billion. Nevertheless, it included the oxidation of the atmosphere and evolution of eukaryotes.

Evolution and the atmosphere

As shown by fossil evidence, stromatolites thrived in the Proterozoic and continued their conversion of atmospheric CO₂ into O₂. The first oxygen produced had been gobbled up by chemical reactions like the oxidation of iron. Several types of indirect evidence, based on the presence of certain molecules in rocks, indicate that around 2 Gya, the content of free oxygen in the atmosphere increased significantly. It is generally accepted that this increase began about 2.4 Gya in what is called the Great Oxidation Event. In spite of evidence for important fluctuations in oxygen levels over the millenia since then, the average oxygen content of the atmosphere has been increasing for the last two billion years. It is now at about 21%, a figure to be compared with less than 1% at the beginning of the Proterozoic.

Estimated evolution of atmospheric O2 percentage, by Heinrich D. Holland via Wikimedia Commons. The red and green lines are ranges of estimates.

With the atmosphere richer in oxygen, other forms of life evolved. More complex cells called eukaryotes appeared about 1.4 Gya. Such cells incorporate smaller components called organelles. Examples are the cell nucleus and the mitochondria¹⁷Singular, mitochondrion. essential to the generation of energy for the cell. It is now widely accepted that organelles within eukaryotes were bacteria which entered the original cell, be it prokaryote or some sort of proto-eukaryote, and stayed – a process referred to as endosymbiosis.

Prokaryotes reproduce by a process of mitosis, duplication and division, after which each “child” organism is essentially a clone of the “parent”. Eukaryotes also duplicate themselves by mitosis, but they reproduce by meiosis, a process in which a selection of genes from each parent is combined with a selection from the other.¹⁸The subject of reproduction through mitosis and meiosis will be discussed in more detail in the chapter on biochemistry and cellular biology. This method of reproduction leads more rapidly to greater diversity of genes and, so, to the formation of new species. Only eukaryotes form multicellular organisms, a necessity for more advanced forms of life.

Taking into account biochemistry and evolutionary history, biologists now usuall divide life into three domains: bacteria and archaea, (both prokaryotes), and eukarya, the last two being descended from the first in a yet-to-be-agreed-on order. Current eukarya include plants and animals – such as us. One proposed Tree of LIfe is shown below.

Tree of Life. Eukaryotes are colored red, archaea green and bacteria blue. From Wikimedia Commons

Such trees of life depend on comparisons of certain genes across species and the choice of genes has an influence on the resulting tree. So this is one among many. It is also argued that life forms not a tree, but a network, or mesh.

In addition to that, phylogenetic studies show that eukaryotes form, usually, five supergroups, all of which evolved from a common eukaryotic ancestor. The members of each group have then evolved independently of the other groups. Only eukaryotes have evolved to form complex life and they all conserve properties of the common ancestor. Eukaryote cells are all very similar, all of them having, for example, common methods of cellular respiration, sex and DNA contained in nuclei.

Climate instability and glaciations

The Earth’s climate now entered a period of great instability. The initial cause may have been imbalances in the geosphere and biosphere. The period of existence of a single continent, Rodinia (or Pannotia), surrounded by a single ocean under an atmosphere still low in oxygen was coming to an end around 750 Mya. New coasts brought more shallow coastal seas and bays which in turn allowed more algal blooms. These may have gobbled up CO₂ as did rock weathering, leading to a global cooling.

Whatever may have been the cause, Earth now embarked on an instable period of glaciations referred to as Snowball Earth, although “slushball” might be a better term. Evidence for glaciers between 740 and 580 Mya ago comes from all around the Earth. Life survived, probably in warm, underwater hydrothermal vents. Eventually, CO₂ pumped into the atmosphere and methane, CH₄, perhaps manufactured by methanogen bacteria, conspired with other feedback effects to bring about global warming and end the glaciations. Then it started all over again. Over 150 million years, at least three cycles of ice age followed by global warming occurred.

The Sturtian glaciation peaked about 720 Mya;
the Marinoan glaciation, about 650 Mya; and
the Gaskiers glaciation, about 580 Mya.

Characteristic rocks left behind by retreating glaciers attest to these cycles of cold and hot. Between the second and third cycles, oxygen levels reached levels near those of today and animal life took off.

Ediacaran fossils

Fossils usually only show the harder body parts of the fossilized organisms. But from the end of the Proterozoic, around 575-542 Mya¹⁹The Vendian Period of the Proterozoic Era ran between 600 and 542 Mya., fossils were discovered which also showed the softer body parts of strange and complex organisms. Named after the Ediacaran Valley in Australia where they were first discovered, they have since been found around the world in places such as Charnwood Forest, England, or Mistaken Point, Newfoundland.

Charnia, from Charnwood Forest, by Verisimilus via Wikemedia Commons

Charnia, from Charnwood Forest, by Verisimilus via Wikimedia Commons

Dickinsonia costata, by Verisimilus via Wikemedia Commons

Dickinsonia costata, by Verisimilus via Wikimedia Commons

The Ediacaran fossils are difficult to interpret. They seem to be generally flat, multi-sectioned organisms, often described as “quilted”, without any internal structure. Charnia, for instance, seems to be a flat, fractal construction without any central stalk. They do not resemble any modern organisms and are generally considered to represent an evolutionary dead end in spite of their being complex, multi-celled organisms. In any case, since they date from as much as 575 Mya, they do show that multi-cellular life existed before the Cambrian. After the Ediacarans had lived alone for up to 90 million years, they disappeared forever as small shelled organisms and trilobites took over.

The Phanerozoic Eon – rise of complex organisms

The Phanerozoic Eon is divided into three eras:

the Paleozoic (542-251 Mya),
the Mesozoic (251-65.5 Mya) and
the Cenozoic (65.5 Mya to today… about).

The Paleozoic Era

During the Paleozoic, the buildup of cratons and mountains continued; glaciers and shallow seas were formed. Life spread from the sea to occupy the land; and fishes, reptiles and primitive mammals evolved.

Geologists have found a huge increase in the number, variety and, especially, the complexity of fossils dating from around 542 Mya in western Canada and in China. This date has therefore been adopted as the beginning of the Paleozoic Era, which is considered to run from 542 to 250 Mya. It is itself broken down into six subdivisions called periods, named as follows:

Cambrian (542-500 Mya),
Ordovician (500-440 Mya),
Silurian (440-410 Mya),
Devonian (410-360 Mya),
Carboniferous (360-290 Mya) and
Permian (290-250 Mya).

Geology

Around the beginning of the Paleozoic, as tectonic plates continued moving, Rodinia broke up into Gondwana and Laurentia. About 300 Mya, the sea between them shrank and they collided to form the supercontinent, Pangea²⁰Also spelled Pangaea.. The superocean surrounding it is called Panthalassa. For once, a supercontinent was not located right at the equator; about ¾ of Pangea was in the southern hemisphere.

Life in the sea

The extraordinary increase in the number of multi-cellular animal phyla which took place at the beginning of the Paleozoic has been referred to as the Cambrian Explosion. It is seen today especially as an explosion of fossils. In fact, the word “explosion” is an exaggeration which has led at least one scientist to react and call it the Cambrian “slow fuse”.

For 2 billion years after the appearance of life on Earth before or around 3.5 Gya, only single-celled prokaryotes existed, cyanobacteria diligently working to increase the oxygen content of the atmosphere. Then the enigmatic fossils of the Ediacaran fauna show that multi-celled, invertebrate organisms came and, it seems, went between about 600 and 545 Mya.

The next logical step, the development of some sort of skeleton or carapace, came about in the early Cambrian, about 545-520 Mya, in the form of “small shelly fossils” (SSFs), or just “little shellies”. These tiny creatures had shells of calcium phosphate, presumably because atmospheric conditions did not yet favor the calcium carbonate shells of today. So for about 25 My, the so-called Cambrian Explosion was represented simply by small shelled creatures – not much of an explosion!

Somewhat later, extraordinary fossils including soft parts of the animals were deposited in two remarkable sites. The first one was Chengjiang, China, with fossils dating around 515 Mya. Among the Chengjiang finds is the oldest fish, which is also the oldest vertebrate, dating from about 500 Mya.²¹The last few paragraphs are based on Prothero (2007), 161-70.

Haikouella lanceolata, from the Chengjian fossils, by Didier Descouens via Wikimedia Commons

Probably the most famous of the Cambrian fossils are those of the Burgess Shale field of about 505 Mya (Middle Cambrian), now in Canada.²²Burgess shale fossils and their importance. http://www.burgess-shale.bc.ca/discover-burgess-shale/burgess-shale-fossils-and-their-importance Some of them were pretty strange and are still the subject of study and hypotheses.

Opabinia, a Burgess Sha Nobu Tamura via Wikimedia Commons

Opabinia, a Burgess Shale fossil, by Nobu Tamura via Wikimedia Commons

Hallucigenia, Burgess Shale fossil by Apokryltaros via Wikimedia Commons

Sponges, considered to be the most primitive animals alive today, had appeared in the late Vendian²³Or Ediacaran, about 650-450 Mya. (end of the Protozoic).

In the early Cambrian, radially symmetry echinoderms were the ancestors of today’s starfish and sea urchins. From about 530 Mya, other invertebrates like brachiopods and worms started to leave fossil traces. Brachiopods, which were shellfish with hard upper and lower valves (as opposed to the left and right valves of modern oysters and scallops, to mention the most edible of them), grew wild on the sea floors.

About 520 Mya, trilobites appeared and invertebrate, multi-celled life was off and running.

Although there do exist fossil tracks of mostly worm-like creatures from 555 Mya, the organisms represented by the Cambrian-period fossils were of a new kind. Cambrian organisms grew to be larger and more complex because of their support structure. During the early Paleozoic, continents were under shallow seas for periods of several million years at a time, so life was dominated by creatures of the seas, including reef builders. These organisms had no internal skeletons, meaning they were invertebrates, but they did have a hard exoskeleton or carapace. The support this gave was advantageous in several ways: It shielded them from the sun, allowed them to retain moisture, gave support for a muscle system and protected them to some extent from predators. Later, skeletons would provide a mineral store, since bones store minerals like calcium and phosphorus from the blood and are able to pass them back to body cells when they are needed. Many types of these creatures existed in the Paleozoic seas. From tiny creatures, larger ones evolved.

Trilobites, a type of arthropod²⁴An arthropod is “…an invertebrate animal having an exoskeleton (external skeleton), a segmented body, and paired jointed appendages.” Wikipedia, https://en.wikipedia.org/wiki/Arthropod., became a dominant form of marine life. They existed in thousands of different species on every continent for some 270 million years, so long that they have been referred to as the “mascots” of the Paleozoic. They ranged in size from several millimeters to over 50 centimeters. Some had eyes with many crystalline lenses, like fly eyes. Over time thousands of species of trilobites existed – in shallow seas on every continent. Near the end of the Cambrian, there were three trilobite mass extinctions due to climate change and other factors (continental movements, evolution of predators). But trilobites survived.

Small trilobite, 5cm (Ohio), photo by author.

Larger trilobite, ~40 cm (Lourinho, Portugal), photo by author

Larger trilobite, ~40 cm (Lourinha, Portugal), photo by author

At the end of the Ordovician and the beginning of the Silurian, two mass extinctions took place, separated by around 4 million years. They are referred to as the Ordovician-Silurian extinction events. Since most life was in the sea, it was this sea life which suffered, It is estimated that 60% of marine invertebrates were destroyed. The extinctions were probably largely caused by climate change due to movement of the continents.

Mass extinctions, from Openstax College

In the Silurian period, eurypterids (looking like scorpions or crayfish) developed which were capable of living in salt or fresh water, an important step in animal evolution. The ammonoids and nautiloids whose fossils we find so beautiful appeared toward the end of the Paleozoic.

The first fossil evidence of fishes show species which had spinal cords (making them chordates) but no internal skeletons or jaws. The latter evolved from gills only later. Fish became numerous in the Devonian Period, which is often referred to as the “Age of fishes”. Although many types later became extinct, some of their ancestors survive even today: cartilaginous fish, like sharks or rays; fish with bones, like today’s trout or bass; and lobe-finned fish, like today’s lungfish.

At the end of the Devonian, another series of extinctions referred to collectively as the Late Devonian mass extinction took place. Individual events may have been separated by over millions of years. Mostly marine life was affected and trilobites were almost finished off.

Life on land

Plants first developed in water. The date of their migration onto land is still debated but seems to have taken place at least by around 480 Mya and perhaps as early as 600 Mya, in the late Precambrian. Low mossy plants appeared on land during the Ordovician. The migration of plants to land was facilitated by the development of a cellulose-based support structure and the ability to transport water in their stems. The oldest known such vascular plant dates from the mid-Silurian, about 430 Mya, and represents an important advance, as such plants had internal tubes by which water and nutrients could mount from the soil to replace moisture that was eliminated from the plant’s upper parts.

With the advent of woody stems, plants developed to the point where the Carboniferous Period was one of dense areas of vegetation, tree-like plants and swamps. Carboniferous plants were all seedless and so had no flowers. This plant material decayed and was eventually transformed by heat and pressure into the fossil fuels we are busily burning up in a tiny fraction of the time it took to make them.

Such carbon sequestration lead to higher oxygen levels in the atmosphere. The oxygen content of the Carboniferous atmosphere was 50-100% greater than now (as seen in a preceding figure) and this had an effect on evolution. Giant insects evolved, including a dragonfly with a 65 cm wingspan. Later, when oxygen levels came back down, the giant insects disappeared.²⁵In my opinion, fortunately.

During the Silurian, tiny arthropods appeared on land. They did not have a digestive system capable of making them herbivores, but lived off decayed matter. During the Devonian, skeletal changes which permitted animals to support themselves on land facilitated the transition from fishes to tetrapods (four-limbed animals, including birds). The first land-based tetrapods were still aquatic or amphibious animals and probably lived mainly in ponds. But they were capable of breathing air, so they could move to another pond in times of drought. They also laid their eggs in water, which furnished nutrients for the young, which were essentially fish (like tadpoles).

So first plants moved onto the land. They were followed by small arthropods, which ate decayed matter from the plants. And then tetrapods followed and ate plants and arthropods. It is all about getting enough to eat.

A very important evolutionary step was the development of the amniotic egg. This protected the young inside a protective cover and provided the nutrients that young amphibians could only get from water. This development contributed greatly to the evolution of amniotes (the first of which resembled small lizards), which now could leave the water completely. These animals split into two groups, synapsids (early mammals) and sauropsids (early reptiles).²⁶There is some disagreement here. Some authors refer to the first amniotes as reptiles and later speak of “mammal-like” reptiles. or “stem mammals”. It seems easier to speak of amniotes which were the ancestors of both mammals and reptiles. The first reptiles date from the mid-Carboniferous, during which life on land and sea reached a new peak of development and diversity.

Tectonically, what today would be Europe and North America were then situated in tropical climates near the equator. Indeed, because no land mass was over either pole, polar ice caps were limited and the Earth’s temperature gradient was less pronounced. On land, huge tree-like plants grew in swamps and life reached all the continents. Insects and tetrapods swarmed through the undergrowth. But no bird sang and no flower lent color to the scene.

Near the end of the Carboniferous, as Gondwana (the southern continent comprising today’s South Africa, South America, Antarctica, Australia and India) approached the poles, as seen in a preceding figure, there was a period of glaciation which lasted into the Permian. Remaining glacial features on these continents provide evidence for plate tectonics, as some of these continents now occupy much warmer latitudes²⁷Benton, 90.

The Permian Period was dominated by the existence of the supercontinent Pangea. Around the equator, the Carboniferous swamps had given way to deserts and these arid conditions were well suited to the development of reptiles.

To the east, projecting into the continental land mass, was the Tethys Sea, which was swarming with life. This was also true of the Zechstein Sea in the north, the area of current northern Europe. Parts of the Zechstein evaporated, leaving behind minerals (evaporites) which helped furnish raw materials for the Industrial Revolution – plaster of Paris, gypsum and substances used for the production of acids and ammonia.

The distribution and variety of organisms today is a result of the existence and subsequent breakup of Pangea. During its existence, no waterways blocked migration routes, so animals, at least those who could support the aridity of the interior, were free to move about to new habitats. The later breakup of Pangea was an equal boon to evolution as organisms isolated from one another tend to evolve in different ways from similar beginnings. Simply put, “isolation begets diversity.”

The time of Pangea was one of much development in the forms of life. By its end, dinosaurs and early mammals had developed. Many insects existed, including cockroaches, which are still with us, alas.

The end-Permian extinction, among others

The Paleozoic Era ended with the greatest of all the mass extinctions, the end-Permian extinction (or Permian-Triassic extinction), sometimes referred to as the Great Dying. It is estimated that 96% of sea and 70% of land species disappeared²⁸McDougall (1998), 321.. The date of the extinction marks the end of the Paleozoic and the beginning of the Mesozoic Era, largely accepted as 251 Mya.

Studies of the Cretaceous Period have discovered several possible ways in which geology can influence life – especially negatively:²⁹Most of the following discussion is based on MacDougall 2011, 188-202.

Intense volcanic activity at various times and places has produced immense quantities of flowing lava called flood basalts, for which geologists have coined the acronym LIPs (large igneous provinces). LIPs were formed quickly on the geological timescale, in less than a million years, but may cover up to millions of square kilometers and be several km thick. They are thought to have formed over deep plumes of magma, much like the Hawaiian Islands, and so can form on land or under seas, independently of plate boundaries.
Black shales are darkly colored Cretaceous rocks rich in carbon which form when large amounts of plant and animal life die and descend to the sea floor. The shales only can form when the deep water contains no or almost no oxygen. The periods when such conditions hold are referred to as oceanic anoxic events, or OAEs. OAEs have been discovered worldwide, in all oceans and on land. They arise and disappear abruptly and have been shown to be associated with times of global environmental change. Their tendancy to occur at the same time as LIPs is circumstantial evidence associating the two phenomena.
Isotope ratios of osmium in sedimentary rocks depend on whether the sediment comes from continental rocks or sea-floor volcanic activity. The data show that during periods of black-shale production osmium in sediments comes almost all from underwater volcanoes and not from continental weathering. So LIPs and OAEs seem to occur at the same time as strong sea-floor volcanic activity.

Although these findings concern the Cretaceous period, they suggest strongly that LIPs have had significant effects on global climate, mainly originating in the emission of large quantities of carbon into the atmosphere, disrupting the carbon cycle.

Other suggested causes are the following.

So-called green sulfur bacteria live in the ocean by photosynthesis and by consumption of sulfur dioxide. Biomarkers for these bacteria therefore indicate the presence of sulfur dioxide. Their presence at the same time as OAEs suggests that some of the extinctions may have been due to this toxic gas.
A recent study³⁰“Ancient whodunit may be solved: The microbes did it!|” March 2014: MIT News, newsoffice.mit.edu/2014/ancient-whodunit-may-be-solved-microbes-did-it. indicates that the eruptions in the Siberian Traps increased the amount of nickel in the Earth’s crust and this was a nutrient for a microbe, a methane-producing archaea called Methanosarcina, which had undergone a genetic change at about that time. It is suggested (claimed, even) that the microbe emitted vast amounts of methane into the atmosphere and so changed the climate.

So much for the details. The important finding based on the importance of LIPs for global change is the discovery of three major LIPs which occurred at the same time as three major mass extinctions:

The Siberian flood basalts, or Siberian traps³¹“Traps” from the swedish word for staircase, “trappa”., occurred around 252 Mya – at the time of the end-Permian extinction.
The Central Atlantic Magnetic Province (CAMP) occurred about 200 Mya – at the time of the Triassic-Jurassic mass extinctiona.
The Deccan traps in India were formed about 65 Mya at the time of the K-T extinction.

So the end-Permian extinction was probably initiated by volcanic eruptions in Siberia which increased the amount of methane and CO2 in the atmosphere, disrupting the carbon cycle and bringing about a “runaway greenhouse phenomenon” ³²Benton, p. 118.. This in turn would have caused oceans to release dissolved oxygen. It could have caused acid rain which killed land plants vital to survival of animals. The CO2 would have been absorbed by the oceans and led to their acidification, wiping out many marine organisms.

What is clear is that it took around 20 million years for life to recover, far longer than after the other known mass extinctions. When life did attain its previous diversity, its forms had changed. The few remaining trilobites had been completely eliminated.

In spite of a wealth of possible explanations, there is yet to be a clear consensus as to which are correct.

Don’t stop now. Continue global history with the ages of reptiles and mammals.

Notes[+]

Notes
↑1	The International Commission on Stratigraphy, apparently the expert in these matters, places the beginning of the Achean at 4..0 Gya, but I have no book which says other than 3.8.
↑2	Spooner, 255.
↑3	“Climate puzzle over origins of life on Earth”, http://www.manchester.ac.uk/discover/news/article/?id=10798.
↑4	Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia, Nature Geoscience https://www.nature.com/articles/ngeo1238.
↑5	Ward and Kirschvink, 81
↑6	j. Brocks, cited by Ward and Kirschvink, 75.
↑7	Gerald Joyce, NASA, quoted by Hazen, 130.
↑8	Prothero (2007), 147-52.
↑9	These results are for the Lost City Hydrothermal vents. Results differ some for other vents.
↑10	“The Lost City 2005 expedition”, NOAA, http://oceanexplorer.noaa.gov/explorations/05lostcity/background/serp/serpentinization.html.
↑11	https://www.researchgate.net/profile/Marvin_Lilley/publication/5613067_Abiogenic_hydrocarbon_production_at_lost_city_hydrothermal_field/links/0c960520e90a17f539000000.pdf
↑12	Van Kranendonk, Martin J., Deamer, David, and Djokic, Tara, “Life springs”, Scientific American, August 2017, 22.
↑13	There is some disagreement as to whether progenote simply means LUCA (last universal common ancestor). Others, more specifically, call it ‘”a theoretical construct, an entity that, by definition, has a rudimentary, imprecise linkage between its genotype and phenotype (Woese, 1987)”—a creature still experiencing progressive Darwinian evolution, in other words.’ From https://www.ncbi.nlm.nih.gov/books/NBK232215/.
↑14	Knoll (2003), 42
↑15	The capability of stromatolites to accomplish this task alone has been questioned and other mechanisms suggested.
↑16	Also called Nena, Nuna or Hudsonland.
↑17	Singular, mitochondrion.
↑18	The subject of reproduction through mitosis and meiosis will be discussed in more detail in the chapter on biochemistry and cellular biology.
↑19	The Vendian Period of the Proterozoic Era ran between 600 and 542 Mya.
↑20	Also spelled Pangaea.
↑21	The last few paragraphs are based on Prothero (2007), 161-70.
↑22	Burgess shale fossils and their importance. http://www.burgess-shale.bc.ca/discover-burgess-shale/burgess-shale-fossils-and-their-importance
↑23	Or Ediacaran, about 650-450 Mya.
↑24	An arthropod is “…an invertebrate animal having an exoskeleton (external skeleton), a segmented body, and paired jointed appendages.” Wikipedia, https://en.wikipedia.org/wiki/Arthropod.
↑25	In my opinion, fortunately.
↑26	There is some disagreement here. Some authors refer to the first amniotes as reptiles and later speak of “mammal-like” reptiles. or “stem mammals”. It seems easier to speak of amniotes which were the ancestors of both mammals and reptiles.
↑27	Benton, 90
↑28	McDougall (1998), 321.
↑29	Most of the following discussion is based on MacDougall 2011, 188-202.
↑30	“Ancient whodunit may be solved: The microbes did it!\|” March 2014: MIT News, newsoffice.mit.edu/2014/ancient-whodunit-may-be-solved-microbes-did-it.
↑31	“Traps” from the swedish word for staircase, “trappa”.
↑32	Benton, p. 118.