The Origin of Life
Mike Russell and Bill Martin proposed that the origin of life emerged from alkaline vents. Formed by hydroxide minerals that derive from superheated hydrated rocks, these vents contained labyrinths of porous compartments. Acetyl thioesters form as the result of carbon dioxide reacting with hydrogen, the energy for the reacting being provided by the reactive free radical fragments of carbon and sulphur. Acetyl thioesters react with carbon dioxide to from pyruvate, the entry point into the Krebs cycle. Krebs cycle in reverse can build organic molecules by consuming energy, and this energy is provided by acetyl phosphates, a simpler form of ATP that are formed by acetyl thioesters reacting with phosphates. The porous compartments make it possible for the organic molecules to concentrate and form polymers like RNA. Indeed, nucleotides condense spontaneously into long chains under high concentrations, but break down under low concentrations.
The above process allowed life to form in those vents, but what allowed life to form outside the vents was chemiosmosis. Lacking the free radicals in the vents, cells used the natural proton gradient between the acidic ocean and alkaline fluids to generate ATP.
Without oxygen, there would be no life on Earth. Oceans are maintained only because oxygen captures rising hydrogen to come down to Earth as rain, and the ozone layer formed from oxygen in the atmosphere ablates the searing intensity of ultraviolet rays. Oxygen also makes development of large organisms to form, since oxygen respiration releases much more energy than other forms of respiration, allowing longer food chains to form, and since oxygen is a component of collagen and lignin, which are substances that provide strength to the body of animals and plants, respectively.
How did two photosystems develop in chloroplasts? The author argues that photosystem I and photosystem II were initially separate; photosystem I used to extract electrons from easy sources such as iron and hydrogen sulphide and pass them down to carbon dioxide to form sugars, and photosystem II captures light energy to send electrons to high energy levels and collect energy in the form of ATP as electrons cascade back down to its original level. Bacteria came to possess both photosystems to respond better to changing environments, turning on and off each photosystem when necessary. In the time of high UV radiation, photosystem II received too much electrons from the environment, so a mutation developed that could pass on electrons to photosystem I. The oxygen evolving complex mainly comprised of manganese atoms facilitated the removal of oxygen from water.
The Complex Cell
How did prokaryotes develop into eukaryotes? The one defining characteristic of eukaryotes, phagocytosis, requires large cell size and high energy output, both of which were made possible by absorbing mitochondria. This was made possible by a fateful union of two prokaryotes in a symbiotic relationship. Also, the nucleus developed to provide a buffer between the slow paced RNA transcription and the fast paced RNA translation, allowing introns to develop and the DNA to diversify.
At first, it is puzzling why sex evolved at all. Sexual reproduction is costly compared to asexual reproduction; it requires mates to spend energy in finding mates and transmits diseases like syphilis and AIDS. Yet it must have had even bigger advantages since it evolved after all. Indeed, sex allows organisms to combine beneficial mutations from different parents into offsprings while eliminating harmful mutations (by weak offsprings dying out).
Movement was responsible for the sudden increase in diversity after the Permian extinction. Motility allows organisms to survive in rapidly changing environments, to interact with each other more often, and to fasten the pace of evolution. Motility in turn was made possible by the development of the muscle, which act by myosin filaments sliding across actin filaments. The primitive forms of muscle can be traced back to the cytoskeleton, in which actin filaments themselves allow movement in and out of the cell by their building blocks to attach at one end and detach at the other end.
Traditionally, the evolution of the eye has been one of the main arguments of the opponents of evolution who claimed that the eye is too perfect, and that incremental changes would not have benefitted the organisms. However, Darwin claimed that if some eyes are more complex than others, if differences in eyesight can be inherited, and if poor eyesight is a liability, eyes can evolve.
Indeed, there is a range of complexity of eyes in different organisms. The most primitive form of eyes developed in algae, which used rhodopsin to detect light and photosynthesise. The site where the retinal binds to the protein contains sections that are exactly the same as both the invertebrate and vertebrate opsins. Naked retina is then found on vent shrimps, which use the retina to detect green light in the pitch dark areas near the ocean vents. Further, rhodopsin is not just used for detecting light, but also to function as a circadian clock; it was observed that human circadian rhodopsin is closer in structure to the rhodopsin in the naked retina of vent shrimps than to the rhodopsin found in the human retina. Clearly, the invertebrate and vertebrate photocells sprang from the same source that goes beyond the vent shrimps in the evolutionary tree.
The lens is a specialised tissue that is transparent and flexible; this would seem to require a very specific protein. Yet this lens is formed by a protein called crystalline that happen to be found in many parts of the body, such as in the brain, liver, skin, etc. Once the raw materials were there, it was not that difficult to form a lens, which would have made a great difference in the survival rates of organisms, since blurred image is better than no image.
All this, i.e. the development of naked retina to a functional image forming eye, like that found on fish, are calculated to have taken place within half a million years, given that each generation of fish usually breeds in one year. Each step is an improvement, such as a slightly deeper eyeball and more lens.
It is at first puzzling to observe why cold-blooded creatures evolved to become hot-blooded creatures. Hot-blooded creatures have high metabolic rates even at rest, so they need to consume much more nutrients than cold-blooded creatures. This was probably because high metabolic rates gave hot-blooded creatures much more stamina than their cold-blooded counterparts: a lizard can make a quick escape to a hiding place, but needs a lot of time to recover from that rapid movement. It is also interesting to ponder about whether dinosaurs were hot-blooded or cold-blooded; it is widely thought that although they had high resting metabolism, they were not true hot-blooded creatures.
There are more questions than answers when we come to the nature of consciousness. What is consciousness? Antonio Damacio claims that consciousness is feeling and knowing our own feeling. What does it mean then to feel? Feelings exert physical effects, yet current physics can't explain what they are. The best answer we have is that a pattern of neuron firing entails a feeling that is inseparable from it. Further, are such feelings limited to humans alone? Emotional centers of the brain are located in the ancient parts of the brain, which are share by almost all vertebrates. Indeed, feelings play a significant role in evolution, since organisms who feel good when advancing their chances of survival (orgasm for example) are more likely to survive.
Death makes evolution and multicellular life possible, since in multicellular organisms, cells are specialized; only some cells can be germ cells, while supporting roles are played by other cells, which die out according to the needs of the germ cells. However, death of cells and death of organisms are different. Peter Medawar states that old age is the decline caused by harmful genes that are immune to selection, since the genes are activated after the reproductive stage has long passed. The solution, then, is to slow down aging, and the author argues that calorie restriction can do just that by inducing reduced leakage of free radical signals in the mitochondria.