Life Ascending

Life Ascending: The Ten Great Inventions of Evolution by Nick Lane, W. W. Norton & Company, 2010. 

Alkaline Hydrothermal Vents

The prime example is the Atlantis massif in the mid-Atlantic, also called the Lost City. The tectonic plates are spreading apart to expose fresh mantle. Seawater invades mantle, which then emits hydrogen, methane, and ammonia. Alkaline hydrothermal vents generate acetyl thioesters. Carbon dioxide plus acetyl thioester produces pyruvate. Phosphate plus acetyl thioester produces acetyl phosphate. Acetyl phosphate is an energy source similar to adenosine triphosphate (ATP). Acetyl phosphate drives the Krebs cycle backwards, forming organic molecules from CO2 and hydrogen, using as catalysts the iron-nickel-sulphur compounds on the inner walls of the tiny holes inside the rocks. Membranes form between tiny holes in porous rocks, with a different pH on either side of the membrane. This creates a pH gradient (also called a proton gradient). Proton gradients can be used to drive chemical reactions that build new molecules and that store chemical energy. An ancient kind of bacteria called Archae are found in alkaline vents. Archae are methanogens that eat carbon dioxide and hydrogen, producing methane as a waste product. Methane is a raw material for synthesizing other molecules found in cells

The RNA World

RNA came earlier in history, before DNA and proteins occurred. RNA molecules can catalyse chemical reactions (as do proteins). RNA can carry heredity information (as does DNA). RNA is less chemically stable than DNA, causing it to accumulate too many mutations, so its heredity function was eventually replaced by DNA. The RNA function of catalyzing chemical reactions was eventually replaced by protein molecules called enzymes. We no longer live in the RNA world. We live in the DNA world. But vestiges of the RNA world remain: messenger RNA and ribosomal RNA, for example

Photosynthesis

A photosystem is a large complex of molecules that use the energy of an absorbed photon of light to perform chemical reactions. There are two kinds photosystems: one converts light energy into chemical energy, the other produces carbohydrates. They evolved in separate strains of bacteria. These two strains of bacteria sometimes lived symbiotically. Eventually, they combined to produce cyanobacteria, that had both kinds of photosystems. Cyanobacteria can split two water molecules (H2O) into molecular oxygen (O2) and 4 hydrogen atoms. The hydrogen atoms produced from splitting water are added to carbon dioxide to make carbohydrates. 

Eukaryotes

Eukaryotes arose through a merger between bacteria and archae. Archae are a separate kingdom from bacteria. The evolutionary split between archae and bacteria occurred very early in the evolution of life. Archae were discovered by a scientist who made a genetic tree of the evolution of ribosomal RNA. Like eukaryotes, Archae have histones, proteins that DNA wraps around to assume a more compact shape. After the merger, the archae became the main part of the cell, and the bacteria became mitochondria, which are located outside the nucleus.

Mitochondria

Gradually, most of the genes in the mitochondria have migrated into the nucleus. Mitochondria retained only those genes important for energy production. Eukaryotic cells have multiple mitochondria, which makes them much better at producing energy than are bacteria and archae.

Chloroplasts

Some cyanobacteria became chloroplasts in plant eukaryotic cells. With more energy,  the eukaryotic cell was able to become much larger than the prokaryotes (bacteria and archae). In turn, this larger size allowed eukaryotes to evolve phagocytosis, the swallowing of bacteria. In messenger RNA splicing, catalytic RNA introns splice themselves out of messenger RNA, leaving only the exons, the part of the gene that is expressed (translated into protein). The “ex” in exon is for “expressed”. The nuclear membrane evolved to give messenger RNA enough time to splice out its introns before the ribosomal translation of its exons.  

Muscles

Muscles movement is caused by filaments of polymers of actin protein sliding over polymers of myosin protein. The actin in muscle cells evolved from the actin that forms the cytoskeletons of individual cells. These cellular cytoskeletons enable internal transport and pseudopodia. The divergence between smooth and skeletal muscle is very ancient, predating even the origin of bilateral symmetry. Another pair of proteins, tubulin and kinesin, form a different kind of mechanical part, the spindle apparatus that separates the chromosomes during cell division. Microtubules are made out of the tubulin protein. 

The Eye

The light-sensitive protein rhodopsin first occurred in chloroplasts. The retina is made up of cells that contain rhodopsin. The retina evolved first, the lens later. Blind shrimp near oceanic black smokers have naked retinas on their backs, that is, retinas without lenses. The nautilus, which is a cephalopod mollusk, has a pinhole, not a lens. The trilobite had the first image-forming lens, and it was made of calcite. A currently living species, the brittlestar, also has a calcite lens. The human lens is made of a protein called crystallin. Light-sensors with lenses have greater resolution than naked retinas. There is a trade-off between resolution and sensitivity

The Heart

Heat is a side-effect of the high energy requirements of mammals and birds. This is why mammals and birds are warm blooded. The 4-chambered heart probably preceded being warm-blooded. Turtles and Tortoises (cold-blooded, 3-chambered hearts). Lizards and Snakes (cold-blooded, 3-chambered hearts). Crocodiles and Alligators (cold-blooded,  4-chambered hearts). Archosaurs evolved into Crocodiles and Birds. Therapsids evolved into Mammals (4-chambered hearts, warm-blooded).