Evolution 

Evolution is a hot topic in science. The idea is that the organisms living on Earth today are not the same as those that existed millions of years ago. Jean-Baptiste Lamarck (1744-1829) and Charles Darwin (1809-1882) both thought about how different species appeared and had different ideas about how life on earth got to be the way it is now. 

Unlike most other people at that time, Darwin and Lamarck both thought that life had changed gradually over time and was still changing, that living things change to be better suited and adapted to their environments, and that all organisms are related. Darwin and Lamarck also agreed that life evolved from fewer, simpler organisms to many, more complex organisms. 

Lamarck is best known for his Theory of Inheritance of Acquired Characteristics, first presented in 1801 (Darwin's first book dealing with natural selection was published in 1859): If an organism changes during life in order to adapt to its environment, those changes are passed on to its offspring. He said that change is made by what the organisms want or need. 

Darwin believed that changes in an organism during its life do not affect the evolution of the species. He said that organisms, even of the same species, are all different and that those which happen to have variations that help them to survive in their environments survive and have more offspring. The offspring are born with their parents' helpful traits, and as they reproduce, individuals with that trait make up more of the population. Other individuals that are not so well adapted die off. Therefore, only the ones who best fit the environment survive (“the survival of the fittest”). Nature selects the fittest, a process known as natural selection. Natural selection operating through long periods of time gives rise to new species. Darwin also believed that evolution does not happen according to any sort of plan. 

Charles Darwin championed the theory of common descent and evolution by natural selection among descendants with slight variations on the ancestors' features. The concept of natural selection springs from artificial selection, a procedure breeders use to enhance desired characteristics such as stamina, color, size, yield, and so forth, in animals and plants. Darwin thought that a similar process happens in nature. 

Darwin actually knew very little about genetics. The great pioneer of that field was Gregor Mendel, whose work was contemporary with Darwin's. Now the theory of evolution incorporates Mendel's genetics into Darwin's framework; the combined theory was called "neo-Darwinism." 

According to this paradigm, evolution is driven by chance. Chance mutations affect one or a few nucleotides of DNA per occurrence. Bigger changes come from recombination, a genetic process in which longer strands of DNA are swapped and transferred. These two processes, mutation and recombination, create new meaning in DNA by lucky accidents. According to the prevailing paradigm, this is the mechanism behind evolution. 

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What the fossil record says about evolution 

Darwin wrote that evolution was a gradual process, with infinitesimal changes accumulating over the ages to eventually yield major differences in living things. If evolution advances as Darwin says it must, only tiny steps would ever happen. He states in The Origin of Species: “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down”. 

Evidence from fossils does not bear out Darwin's theory of gradual change. Instead, species remain relatively unchanged for long periods, and then suddenly, new kinds arise. Many bacteria today have apparently changed very little since they first appeared. Some archaebacterial species appear to be as old as life on Earth; they haven't evolved very far in almost four billion years. We know that bacteria were the only inhabitants of the earth until about 1.7 billion years ago. Apparently, no major evolutionary developments (multicellularity, cell specialization, etc.) happened among the bacteria for the first two billion years of life — more than half of the time life has existed on Earth. By contrast, the entire Cambrian Explosion of about 570 million years ago took only five to nine million years. All kinds of multicelled creatures, in astonishing variety, seemed to come at once out of nowhere. Similar discontinuities can be seen on a finer scale in the individual histories of species. In fact, the sudden appearance of new kinds of creatures, without evidence of intermediate kinds, is more the rule than the exception. 

Punctuated equilibrium (also called punctuated equilibria) in evolutionary biology proposes that once species appear in the fossil record they will become stable, showing little net evolutionary change for most of their geological history. This state is called stasis. When significant evolutionary change occurs, the theory proposes that it is generally restricted to rare and geologically rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which a species splits into two distinct species, rather than one species gradually transforming into another. Today there is still considerable discord over punctuated equilibrium¹⁰. How real is stasis (the period without appreciable change), how gradual is punctuation, and how can neo-Darwinists account for them¹¹?. 

Ernst Mayr's 1988 classic, Toward a New Philosophy of Biology, asks the question, "Does Microevolution (A change in the gene pool of a population over a sucession of generations) Explain Macroevolution (Evolutionary change on a grand scale, encompassing the origin of novel designs)?". Microevolution would occur during stasis, and macroevolution at the punctuation points. This scenario is inconsistent with neo-Darwinian gradualism, according to which macroevolution is simply cumulative microevolution over long periods of time. The question challenges standard neo-Darwinism at its heart. 

¹⁰ Perhaps punctuated equilibrium is a clue that the genetic mechanism underlying evolutionary progress is altogether different from the one currently in favour. 

¹¹ The new idea is that big evolutionary steps occur gradually in small, isolated populations. When the evolutionary steps are complete, the small population with its new advantage quickly expands and replaces the bigger population. Thus, in the geological record the change looks instantaneous 

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Neo-Darwinism adequately accounts for microevolution. Changes in existing allele frequencies are already known to cause microevolution in many species. However, macroevolutionary progress such as the evolution of photosynthesis, on the other hand, requires wholly new genes with lengthy new instruction sequences. There is scant evidence that new genes can be originated by Darwinian random point mutations and recombination events. 

Currently, the Darwinian theory of evolution is generally accepted as the explanation of the Earth's present biodiversity. However, since Darwin first proposed natural selection as the leading mechanism of evolution, a series of other mechanisms have been periodically advanced to explain the observed variability. Some of these are proposed as complementary to natural selection but others constitute alternative explanations. 

Genome dynamism is providing new, and previously unanticipated, sources of variability. New evidence of gene transfer is forcing us to redefine the concept of biological species. There is no doubt that some principles will have to be reshaped or even removed, introducing new concepts in a new theory of evolution beyond Darwin. 

Beyond dispute: all life is related 

Leaving aside the controversy about what the mechanisms that explain evolution are, the basic idea that all scientist agree on when talking about evolution is that life has existed for billions of years and has changed over time. Overwhelming evidence supports this fact. The history of living things is documented through multiple lines of evidence that converge to tell the story of life through time. These lines of evidence include: 

● Fossil evidence 

The fossil record provides snapshots of the past that, when assembled, illustrate a panorama of evolutionary change over the past four billion years. The picture may be smudged in places and may have bits missing, but fossil evidence clearly shows that life is old and has changed over time. 

● Transitional forms 

Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms. There are numerous examples of transitional forms in the fossil record, providing an abundance of evidence for change over time. 

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● Homologies 

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Evolutionary theory predicts that related organisms will share similarities that are derived from common ancestors. Similar characteristics due to relatedness are known as homologies. Homologies can be revealed by comparing the anatomies of different living things, looking at cellular similarities and differences, studying embryological development, and studying vestigial structures within individual organisms.¹⁴ 

● Cellular/molecular evidence 

All living things are fundamentally alike. At the cellular and molecular level living things are remarkably similar to each other. These fundamental similarities are most easily explained by evolutionary theory: life shares a common ancestor. 

The cellular level: all organisms are made of cells, which consist of membranes filled with water containing genetic material, proteins, lipids, carbohydrates, salts and other substances. The cells of most living things use sugar for fuel while producing proteins as building blocks and messengers. The typical animal and plant cells have very similar structures — only three structures are unique to one or the other (chloroplasts and cell walls in plants, centrioles in animals) 

The molecular level: different species share genetic homologies as well as anatomical ones. Roundworms, for example, share 25% of their genes with humans. These genes are slightly 

¹² Pakicetus (below left), is described as an early ancestor to modern whales. A skull of the gray whale that roams the seas today has its nostrils placed at the top of its skull. It would appear from these two specimens that the position of the nostril has changed over time and thus we would expect to see intermediate forms. Note that the nostril placement in Aetiocetus is intermediate between the ancestral form Pakicetus and the modern gray whale — an excellent example of a transitional form in the fossil record! 

¹³ Our understanding of the evolution of horse feet, so often depicted in textbooks, is derived from a scattered sampling of horse fossils within the multi-branched horse evolutionary tree. These fossil organisms represent branches on the tree and not a direct line of descent leading to modern horses. But, the standard diagram does clearly show transitional stages whereby the four-toed foot of Hyracotherium, otherwise known as Eohippus, became the single-toed foot of Equus. Fossils show that the transitional forms predicted by evolution did indeed exist. As you can see each branch tip on the tree of horse evolution indicates a different genus, though the feet of only a few genera are illustrated to show the reduction of toes through time. 

¹⁴ One example of homology is the forelimb of tetrapods (vertebrates with legs). Frogs, birds, rabbits and lizards all have different forelimbs, reflecting their different lifestyles. But those different forelimbs all share the same set of bones. These are the same bones seen in fossils of the extinct transitional animal, Eusthenopteron, which demonstrates their common ancestry. 25

different in each species, but their striking similarites nevertheless reveal their common ancestry. In fact, the DNA code itself is a homology that links all life on Earth to a common ancestor. DNA and RNA possess a simple four-base code that provides the recipe for all living things. In some cases, if we were to transfer genetic material from the cell of one living thing to the cell of another, the recipient would follow the new instructions as if they were its own. 

These characteristics of life demonstrate the fundamental sameness of all living things on Earth and serve as the basis of today's efforts at genetic engineering. 

Nested hierarchies 

Common ancestry is conspicuous. Evolution predicts 

that living things will be related to one another in 

what scientists refer to as nested hierarchies — 

rather like nested boxes. Groups of related 

organisms share suites of similar characteristics and 

the number of shared traits increases with 

relatedness. This is indeed what we observe in the 

living world and in the fossil record and these 

relationships can be illustrated as shown below. 

In this phylogeny, snakes and lizards share a large 

number of traits as they are more closely related to one another than to the other animals represented. The same can be said of crocodiles and birds, whales and camels, and humans and chimpanzees. However, at a more inclusive level, snakes, lizards, birds, crocodiles, whales, camels, chimpanzees and humans all share some common traits. 

Humans and chimpanzees are united by many shared inherited traits (such as 98,7% of their DNA). But at a more inclusive level of life's hierarchy, we share a smaller set of inherited traits in common with all primates. More inclusive still, we share traits in common with other mammals, other vertebrates, other animals. At the most inclusive level, we sit alongside sponges, petunias, diatoms and bacteria in a very large "box" entitled: living organisms.