Evolutionary processes

Background: The Plenum.
The geologists first embraced the idea of geological time and of a world that gradually came to assume its current form. Biologists were aware of their work and its implications for their field, but were constrained by theological doctrine.
Whereas Bishop Ussher actually had to perform research and make logical inferences in order to draw his conclusions about the age of the Earth, anyone who wondered about the mutability of living things, had only to read Ecclesiastes 3:14 to be set straight:

"I know that whatever God does endures for ever; nothing can be added to it, nor anything taken from it;..."

From this emerged the notion of the Plenum [Latin "fullness"]. I.e. that God had populated the Earth with every conceivable variety of creature, and that He would never allow any of His creations to become extinct. Likewise from the creation forward there was nothing new that could possibly be added. Thus the idea of organismal extinction was considered anti-biblical. Indeed, many early paleontologists such as Thomas Jefferson assumed that living specimens of the animals whose remains they were finding must exist somewhere.

Extinctions: The concept of the plenum received a one-two punch.

Evolution

Definition: Before proceeding, evolution = "Descent with modification". The central tenet of the theory of evolution is, "The diversity of living things is the product of descent with modification." Note that this definition says nothing about how evolution occurs. Evolution is foremost a pattern. Before we discuss it, let's mention...

The reality of the pattern of evolution.

Prior to the discovery of geological time, it was reasonable to assume that all organisms had appeared recently. Since there had not, it was thought, been enough time for organisms to accumulate a serious history, the idea that their form reflected their history was meaningless.


Illustration for Agassiz' treatise on fossil fish
The discovery of geological time, however, added an extra dimension to the organization of organismal form. Specifically, when fossil and living organisms were organized according to their similarity of form and their occurance in time, it began to seem as if lineages had slowly been modified through time, and even as if different lineages had branched from the same ancestor. Indeed, as soon as geological was discovered, biologists began speculating that species had evolved, ie, has been modified during their descent. Even biologists like Louis Agassiz, who openly rejected evolution couldn't help but organize the history of organisms in a way suggestive of change throught time and shared common ancestry.

The pattern of evolution was readily visible to many investigators by the early 19th cent. All it took was the recognition of geological time, and some familiarity with the fossil record. The problem was that no one could propose a convincing mechanism by which this might happen. Several people tried, but were unable to propose anything that did not at some point resort to unfalsifiable propositions, typically a notion of "driving forces of nature" impelling organisms toward "improvement".


Jean-Baptiste Pierre Antoine de Monet,
Chevalier de Lamarck - UC Berkeley Museum of Paleontology
Jean Baptiste Lamarck was foremost among the "transmutationists" of the early 19th century. He is remembered for the idea of the acquisition of new characters through use and disuse, although this idea wasn't uniquely his. (Note, if we accepted this idea, then what would the newborn offspring of this man and this woman look like?) In fact, Lamarck maintained that:

Problem: None Lamarck's tenets were subject to falsification. Nevertheless, people were searching, and the stage was set for a major intellectual revolution. It was a matter of time before someone put it all together.


Charles Darwin - Omniscopic
How it happened: Charles Darwin (1809-1882)

Darwin was the son of Robert Darwin, a physician, and grandson of anti-monarchist abolitionist natural philosopher Erasmus Darwin. Originally planned a career in medicine until witnessing his first surgery, he developed a great love of natural history, including geology and zoology. Planned an undemanding career as a clergyman to allow time for natural history avocation. In 1839 he obtained an unusual job: "Captain's companion" for the captain of the naval research vessel HMS Beagle. (Not a standard position. Capt. Robert FitzRoy, himself a capable naturalist, had a tendency toward severe depression which was made worse by the isolation of life at sea. To make life more pleasant, he hired Darwin to simply be his confidante) Darwin took advantage of the opportunity to become a proper naturalist. His three year voyage around the world changed his life and set the stage for his later career. (cf. The Voyage of the Beagle, Charles Darwin for a highly readable account).


Bartolomé, Galápagos Islands
Before departure, Darwin obtained Vol. I of The Principles of Geology by Charles Lyell, advocate of Hutton's idea of uniformitarianism. Darwin read it on the way to South America. There, he encountered the fossils of ancient unknown mammals. By the time the Beagle reached the Galápagos Islands, Darwin seems to have been thinking about uniformitarianism in a biological context. On the Galápagos, (Geologically young volcanic islands) he noted paradoxes:

Thomas Malthus Eumed.net
Back in England, Darwin encountered the ideas of Thomas Malthus on reproductive excess. Malthus noted that generally human populations left unchecked increased exponentially while the resource base on which they depended increased linearly.



Population Economics and Thomas Robert Malthus

What resulted was not a stable situation and one had only to look at human history to see how cruelly these two accounts were balanced. Of course, what was true for humans might also be true in nature.

No one knows when the lightbulb appeared above Darwin's head, but by 1842, he had begun a notebook on the "transmutation of species". And yet, for 24 years after the voyage, he kept the idea to himself.


He was not idle during this time. Note also that Darwin wasn't an intellectual lightweight. Had he never published on evolution, he would have made it into the history books on the basis of his work on marine biology and the geology of coral atolls.

Darwin, seems to have wanted to publish a large work on evolution late in life, to be his "crowning achievement". Problem: I said before that the evolutionary intellectual revolution was waiting for someone to connect the dots. If Darwin wouldn't do it, someone else would.


Alfred Russel Wallace
In fact, in 1858, Alfred Russel Wallace, a naturalist stationed in Indonesia, wrote to Darwin, asking his opinion of some new ideas that he had. Darwin was alarmed to see that Wallace had independently reached the same conclusions he had about evolution. The two agreed to co-author a small paper presented at the Linnean Society in 1858.


In 1859, Darwin hastily published The Origin of Species by Means of Natural Selection, or the Preservation of favored Races in the Struggle for Survival. (AKA The Origin of Species). First edition sold out first day.

In the Origin, Darwin advanced two concepts.

These were illuminated by a large volume of observations.

By the time of his death (1882), the academic community had largely been won over.

Problem:


What evolution is not:


We've seen how Natural Selection operates. Now we'll look at additional aspects of evolutionary phenomena. Some are other forms of descent with modification beyond the "differential survival and reproduction of variants in a population." Others are patterns produced by any and all of these changes as they manifest on levels above the species: so-called macroevolutionary patterns.

The problem: Every few months, one hears something like this from a prominent politician, journalist, or cultural figure:

"Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science -- that is, not believed in the scientific community to be as infallible as it once was." - Ronald Reagan, 1980

Is it true, or have they naively misinterpreted advances in science? Let's see.

The New Synthesis - the Second Evolutionary Revolution: Mendel's work on genetics was rediscovered by the scientific community in 1900. When this occurred, biologists began synthesizing the fields of genetics and evolution in a movement called the New Synthesis. In this synthesis, several other evolutionary processes besides natural selection were discovered.

Genetic drift

Evolution (descent with modification) can occur as a result of purely random events. Cf. that every individual has a unique combination of genes. When an individual is added to or removed from the gene pool, that gene pool is changed. In large populations, the effect is negligible, but in small populations, the addition or removal of an individual has noticeable effects. Consider the prevalence of brachydactyly among the Amish. This gene was brought to the community by a single member of the founding population but because the Amish population is small and members generally marry within their group, it has, by chance proliferated.


TMDU

Genetic linkage:

The evolutionary interactions of genes that are close together on a chromosome. Remember meiosis, the process by which gametes (reproductive cells) are created:

Thus, genetic information gets shuffled during both meiosis and crossing over. Note, however that:

Suppose that a particular gene is highly favored by natural selection. Genes with no particular selective advantage that are close to it on the same chromosome are likely to be favored simply because they are fellow-travelers of the selectively favored gene. This "genetic parasitism" is termed genetic linkage. An example in humans is the linkage of nail-patella syndrome (a condition causing abnormalities of the limbs and kidney disease) and type-B blood.


The Word Warrior

Sexual selection

Really a subset of natural selection - evolution based on the selective advantage of traits that improve reproductive success, even if otherwise deleterious.

Genetic linkage sometimes manifests itself during sexual selection. Suppose there were a human population in which females possessed a gene that cause a compulsive attraction to men with red hair? Clearly we would get a general shift across generations toward a kind of genetic linkage:

And, any individual passing on the red-hair-attraction gene would likely pass on the red-hair as well. This particular concatenation of genes can lead to "runaway sexual selection" in which bizarre and otherwise maladaptive structures and behaviors evolve.

Mate selection choice is usually exercised by the limiting gender - whichever gender is the limiting factor for reproduction. In vertebrates this is usually the female. In some species, however, the opposite is true. examples:

Pleiotropy

When a single gene has many independent phenotypic manifestations. Not surprising. Genes code for proteins, and a protein may interact differently with different tissues. A recent example in the news involves the linkage of iris shape and personality through the action of the PAX6 gene. Even if one phenotypic effect of a gene is neutral or slightly deleterious, it may be selected for if another is highly advantageous.


Axolotl - axolotl.org

Heterchrony:

Subtle changes over evolutionary time in an organism's developmental timetable are a potent source of overall evolutionary change. This is an idea with a history as long as the study of evolution.

General patterns of heterochrony:


A single orgamisn can incorporate both paedomorphic and peramorphic change. Consider humans:


History of the Shell logo from Royal Dutch Shell plc.com
Cultural "evolution": Note that paedomorphosis and peramorphosis occur in popular cultural figures.