The Modern Synthesis of Evolution with Genetics

By Wayne Douglas Smith, Ph.D.

In the beginning, there was only chemistry on the Earth. There were no minds, no creativity, and no intention. Nevertheless, once self-replicating chemicals had a chance to arise, there would have been an automatic tendency for more successful variants to increase in frequency at the expense of less successful variants. Success in chemical replicators is simply synonymous with frequency in circulation. A successful replicator molecule will be one that has what it takes to get duplicated. DNA, which is a self-replicating material present in nearly all living organisms, is so uniform that it consists of variations in sequence of the same four proteins: A, T, C, G. Although the products developed by DNA sequences are almost infinitely variable (creating brains for mammals, wings for birds, and leaves for plants), the recipes for building these products are just permutations of A, T, C, G. With DNA, there arose a self-copying system in which there was a form of hereditary variation, with occasional random mistakes in copying. The consequence was that the planet Earth came to have a mixed population, in which variants of life competed for resources.
Resources will be scarce, or will become scarce when the competition heats up. Some variant replicants will turn out to be relatively successful in competing for scarce resources. Others will be relatively unsuccessful. So now we have a basic form of natural selection. To begin with, success among rival replicators will be judged purely on the direct properties of the replicators themselves: for example, on how well their shape fits their template. But after many generations, replicators survive not by virtue of their own properties, but by virtue of causal effects on something else, called phenotype. Phenotypes are parts of animal and plant bodies that genes can influence. Phenotypes are the way replicators manipulate their way into the next generation. More generally, phenotypes may be defined as consequences of replicators that influence the replicators' success, but are not themselves replicated. The chemical world in which a gene (which is the heritable unit in DNA) does its work is not the unaided chemistry of the external environment. The necessary chemical world in which the DNA replicator has its being is a much smaller, more complicated bag: the cell. The chemical microcosm that is the cell is put together by a consortium of thousands of genes. The simplest of autonomous DNA copying systems on the Earth are bacterial cells, and they need at least a couple hundred genes to make the components they need. Cells that are not bacteria are called eukaryotic cells. Our own cells, and those of all animals, plants, and fungi, are eukaryotic cells. They typically have tens of thousands of genes, all working as a team. It seems probable that the eukaryotic cell itself began as a team of a few bacterial cells that joined up together. All genes do their work in a chemical environment put together by a consortium of genes in the cell.
The next threshold in life on Earth is an increase in the speed at which information is processed. In the animals, this is achieved by a special class of cells called neurons, or nerve cells. Predators can leap at their dinner and prey can dodge for their lives, using muscular and nervous organs that act at speeds hugely greater than the embryological machinations at which the genes put the apparatus together in the first place. Among the consequences of high-speed information processing may be the development of large aggregations of data-handling units, which we call brains. Brains are capable of processing complex patterns of data apprehended by the sense organs, and capable of storing records of them in memory. A more elaborate consequence of crossing the neuron threshold is a conscious awareness. Many philosophers believe that consciousness is crucially bound up with language.

• Language: English
• Publisher: BookBaby
• Release date: Jul 8, 2023
• ISBN: 9798350911077

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BK90079371.jpg

Wayne Douglas Smith, Ph.D.

Copyright 2023

Subjects: Biology, Evolution, Natural Selection, Genetics

The Modern Synthesis of Evolution with Genetics

can be found on Amazon Kindle, Apple iBooks, Kobe eBook, Barnes & Noble Nook,, Overdrive, eSentral, Scribd, Playster, Garner’s Books, Hoopla, Ciando, Bookshop, and Baker & Taylor.

No part of this book may be reproduced or transmitted by any means, electronic or mechanical, including photocopying, recording, or by any retrieval system without permission in writing from the author.

eBook ISBN: 979-8-35091-107-7

Table of Contents

Darwin’s Impact

Introduction

Chapter 1: Darwin’s Journey

Chapter 2: Inheritance

Chapter 3: Genetic Mutations

Chapter 4: Gene Flow

Chapter 5: Geology and Genes

Chapter 6: Genetic Drift

Chapter 7: Rapid Evolution

Chapter 8: Varieties to Species

Chapter 9: Cambrian Explosion

Chapter 10: The Tree of Life

Chapter 11: Human Evolution

Chapter 12: Convergent Evolution

Chapter 13: Extremophiles

Chapter 14: Complexity

Chapter 15: Coevolution

Chapter 16: Microbiomes

Chapter 17: Evolution of Brains

Chapter 18: Evolution of Sex

Chapter 19: Evolution of Aging

Chapter 20: Evolutionary Medicine

Appendix: Future Evolution

Postscript

Glossary

About the Author

Darwin’s Impact

If Darwin is right, we will have to date from 1859 (On the Origin of Species) as the beginning of modern thought. For what Charles Darwin did was to offer a world-picture totally different from that which had satisfied the mind of humankind before that date. We had supposed that it was a world of order, moving under divine guidance and omnipotent intelligence to a just and perfect fulfillment in which every virtue would find its fit reward. But Darwin, without attacking any creed, described what he had seen.

Suddenly the world and nature seemed to be only a place of slaughter and strife in which birth was an accident, and only death was a certainty. Nature became natural selection: that is, a struggle for existence. And not for existence only, but for mates and power, and a ruthless elimination of the unfit. The surface of the Earth seethed with warring species and competing individuals. Every organism was the prey of some larger beast, and every life was lived at the expense of some other life. Great natural catastrophes came, and millions of living things were weeded out and killed. This was evolution.

Darwin had reduced a human to an animal fighting for his transient mastery of the globe. Man was no longer the son of God; he was the son of strife. His wars made the fiercest brutes ashamed of their amateur cruelty. The human race was no longer the favored creation of a benev-olent deity. It was a species of apes, which the fortunes of variation and selection had raised to a precarious dignity, and which in its turn was destined to be surpassed and to disappear. Man was not immortal. He was condemned to death from the hour of his birth.

Imagine the strain upon the minds brought up with the tender ideas of youth and forced to adapt themselves to the harsh and bloody picture of a Darwinian world. Is it any wonder that the old faith is fighting fiercely for its life, and that the conflict between religion and science is more bitter than at any time since Galileo retracted his heliocentric beliefs and Bruno was burned at the stake? And do the victors (the evolutionist) sit sadly amid the ruins, secretly mourning their triumph, yearning for the old world which their victory has destroyed?

Introduction

We humans have purpose on our minds. We find it hard to look at anything without wondering what it is for. The desire to see purpose is a natural one in a human being, because we live surrounded by machines and other artifacts. If a rock in a stream happens to serve as a convenient stepping stone, we regard its usefulness as an accidental bonus, not a true purpose. But the old temptation comes back with a vengeance when tragedy strikes: Why did the hurricane have to hit us? Why did cancer have to strike my child? And the same temptation is often positively relished when the topic is the origin of the universe, or the fundamental laws of physics, culminating in the ultimate question, Why is there something rather than nothing?

Somewhere between a rock on the one hand and the cosmos on the other, lie the living creatures. Living bodies and their organs are objects that, unlike rocks, seem to have purpose written all over them. The apparent purposefulness of living bodies has dominated the classic argument from design, invoked by theologians from Thomas Aquinas to William Paley. The true process that has endowed wings and eyes, nesting instincts, and everything else about life with the strong illusion of purposeful design is now well understood. It is Darwinian natural selection.

Our understanding of this has come astonishingly recently, within the last two centuries. Before Darwin, even educated people who had abandoned why questions for rocks and eclipses, accepted the legiti-macy of the why question where living creatures were concerned. Today only the scientifically illiterate do. Yet, the unpalatable truth is that the absolute majority of the population of people on the planet Earth are still scientifically illiterate.

Nature’s Indifference

Nature is neither kind nor unkind. She is neither against suffering nor for it. Nature is not interested one way or the other in suffering, unless it affects the survival of DNA. The total amount of suffering in the natural world is beyond all decent contemplation. During the minute it takes me to compose this sentence, thousands of animals are being eaten alive and others are running for their lives in fear. Others are being slowly devoured from within by rasping parasites; and thousands are dying of starvation, thirst, and disease. If ever there was a time of plenty, it would automatically lead to an increase in population until the natural state of starvation and misery was once again restored.

Theologians worry about the problem of evil and the related problem of suffering: How can a loving, all-powerful God allow tragedies to happen to good people? But in a universe of elementary particles and selfish genes, meaningless tragedies and equally meaningless good fortune, are what we should expect. Such a universe is neither evil nor good in its intentions. It manifests no intentions of any kind. In a universe of blind physical forces and genetic replication, some people are going to get lucky and other people are going to get hurt, and you won’t find any rhyme or reason in it. The universe that physicists observe has precisely the properties we should expect if there is no design and no purpose. DNA neither knows nor cares. DNA just exists.

The Rise of Life

In the beginning, there was only chemistry on the Earth. There were no minds, no creativity, and no intention. Nevertheless, once self-replicating chemicals had a chance to arise, there would have been an automatic tendency for more successful variants to increase in frequency at the expense of less successful variants. Success in chemical replica-tors is simply synonymous with frequency in circulation. A successful replicator molecule will be one that has what it takes to get duplicated.

DNA, which is a self-replicating material present in nearly all living organisms, is so uniform that it consists of variations in sequence of the same four proteins: A, T, C, G. Although the products developed by DNA sequences are almost infinitely variable (creating brains for mammals, wings for birds, and leaves for plants), the recipes for building these products are just permutations of A, T, C, G. With DNA, there arose a self-copying system in which there was a form of hereditary variation, with occasional random mistakes in copying. The consequence was that the planet Earth came to have a mixed population, in which variants of life competed for resources.

Resources will be scarce, or will become scarce when the competition heats up. Some variant replicants will turn out to be relatively successful in competing for scarce resources. Others will be relatively unsuccessful. So now we have a basic form of natural selection. To begin with, success among rival replicators will be judged purely on the direct properties of the replicators themselves: for example, on how well their shape fits their template. But after many generations, replicators survive not by virtue of their own properties, but by virtue of causal effects on something else, called phenotype. Phenotypes are parts of animal and plant bodies that genes can influence. Phenotypes are the way replicators manipulate their way into the next generation. More generally, phenotypes may be defined as consequences of replicators that influence the replicators’ success, but are not themselves replicated.

The chemical world in which a gene (which is the heritable unit in DNA) does its work is not the unaided chemistry of the external envir-onment. The necessary chemical world in which the DNA replicator has its being is a much smaller, more complicated bag: the cell. The chemi-cal microcosm that is the cell is put together by a consortium of thou-sands of genes.

The simplest of autonomous DNA copying systems on the Earth are bacterial cells, and they need at least a couple hundred genes to make the components they need. Cells that are not bacteria are called eukaryotic cells. Our own cells, and those of all animals, plants, and fungi, are eukaryotic cells. They typically have tens of thousands of genes, all working as a team. It seems probable that the eukaryotic cell itself began as a team of a few bacterial cells that joined up together. All genes do their work in a chemical environment put together by a consortium of genes in the cell.

Any one cell in an organism is a local sea of chemicals in which a team of genes bathe. The cells themselves multiply by splitting in half, with each one growing to full size again. When this happens, all the members of the team of genes are duplicated. If the two cells do not separate fully, but remain attached to one another, large edifices can form, with cells playing the role of bricks. When the many-celled threshold has been crossed, phenotypes can arise whose shapes and functions are appreciated only on a scale hugely greater than the scale of a single cell. A leaf on tree, or the lens of an eye, or the heart in our chest — these shapes are all put together by cells.

But many-celled organs do not grow the way crystals do. They

grow more like buildings, which are not the shape of overgrown bricks. A hand has a characteristic shape, but it is not made of hand-made cells, as it would be if phenotypes grew like crystals. Again, like buildings, many-celled organs acquired their characteristic shapes and sizes because layers of cells (bricks) follow rules about when to stop growing.

Cells must also, in some sense, know where they sit in relation to other cells. Liver cells, for example, behave as if they know they are liver cells and where they should be located. How they do this is a difficult question and a much studied one. Whatever the details, the methods have been perfected by the same general process as all other improvements in life: the nonrandom survival of successful genes judged by their effects. In this case, it is the effects on cell behavior in relation to neighboring cells.

The Next Threshold

The next threshold in life on Earth is an increase in the speed at which information is processed. In the animals, this is achieved by a special class of cells called neurons, or nerve cells. Predators can leap at their dinner and prey can dodge for their lives, using muscular and nervous organs that act at speeds hugely greater than the embryological machinations at which the genes put the apparatus together in the first place. Among the consequences of high-speed information processing may be the development of large aggregations of data-handling units, which we call brains.

Brains are capable of processing complex patterns of data appre-hended by the sense organs, and capable of storing records of them in memory. A more elaborate consequence of crossing the neuron threshold is a conscious awareness. Many philosophers believe that consciousness is crucially bound up with language, which seems to have been achieved only once, by the ape species called Homo sapiens.

Language, from this point of view, is the networking system by which brains have come to exchange information with sufficient intimacy to allow the development of technology. Technology is the application of scientific knowledge for practical purposes. It began with the development of stone tools, and proceeded through the ages of metal-smelting, wheeled vehicles, steam power, and electronics. Human culture has fostered a genuinely new kind of self-replicating process.

Chapter 1:

Darwin’s Journey

The implication of Charles Darwin’s theory of evolution by natural selection, the idea that all living species are descended from a common ancestor, revolutionized our view of who we are and where we come from. Yet it took more than a century before natural selection was united with genetics, leading to the modern science of evolution. The biggest gap in Darwin’s knowledge — the