Wednesday, September 2, 2015

The Reality of Organic Evolution 

Since one of the crucial aspects of living systems is that they have the capacity to evolve, an understanding of the basic processes of evolution itself is necessary. Few subjects are more crucial to our understanding of the world, and few subjects require greater clarification. There is a great deal of confusion surrounding the concept of evolution. Because of the resistance of religious authorities (and certain others who are mistrustful of science) in many parts of the world, or because many people simply lack an education in the sciences, there are many humans who do not accept the tenets of evolutionary thought. Many of these people are outrightly dismissive of the idea itself, saying that organic evolution is “just a theory”, unmindful of the fact that the words hypothesis and theory are not synonyms. As we will see in Science, in a later volume, a theory is a set of interrelated propositions that, taken together, describe the characteristics and processes of a given phenomenon. All such propositions are based on either empirical or deductive evidence, or both, and are, by definition, facts in the human frame of reference. Quantum mechanics, relativity, plate tectonics, and heliocentrism are all theories. Organic evolution is an established fact, as fully proven and as completely demonstrated as the fact that the Earth orbits the Sun. Although scientists sometimes disagree about the details of this process, virtually all scientists (with extremely few exceptions) agree that the process itself is real, and is supported by massive amounts of evidence. It is by means of organic evolution that the earliest life forms ultimately gave rise, after an inconceivable number of steps and an incomprehensible length of time, to the genus Homo. We cannot assume, however, that the “objective” of organic evolution was the bringing forth of the human species.

The genetic make-up of an organism is known as its genotype. The physical traits of an organism, its structure, physiology, and biochemical composition, are known as its phenotype and are the product of its genotype. Evolution changes the distribution of genotypes present in a population of organisms. These changes, over time, are expressed as phenotypic changes. The change in a population’s genotypes affects its ability to successfully reproduce. So bearing these basic facts in mind, what are the chief methods by which evolution proceeds?

Natural Selection. The core of evolutionary ideas. Natural selection is concerned with those conditions which lead a species to be either reproductively successful or unsuccessful. What do we mean by reproductive success? In order to be reproductively successful, the members of a species must survive long enough in a given environment to reach reproductive maturity, and when they do, they must reproduce and give rise to fertile offspring similarly capable of surviving. Not all members of a population need to reproduce, but a certain number of them obviously must do so. Two factors above all drive the outcome of this process:

1.   The DNA which determines the physical traits of a species, when reproduced, does not always reproduce with total accuracy. Errors in reproduction, or recombination, are known as mutations. (See below.) Such errors can have only three possible outcomes. First, a mutation may be neutral, and have no effect on the reproductive success of the species. Second, the mutation can be harmful, meaning it lessens the ability of the species to reproduce. Third, the mutation may be beneficial, meaning it enhances the ability of the species to reproduce. (To be perfectly accurate, there are mutations which appear to have negative consequences but which act more broadly to ensure reproductive success.) And how can we judge whether a mutation is neutral, harmful, or beneficial? We have to consider the species in the context of its environment.

2.   All species exist in a particular physical environment. If that environment undergoes significant changes, it will affect the ability of animals or plants to survive long enough to reproduce, and will make certain mutations crucially important.  An example which was of particular importance to us was the rapidity with which the forest environments of our tree-dwelling ancestors changed. Mutations which would be neutral in a stable environment, such as a gene for color vision, would become beneficial in an environment in which new and deadly predators were now common. If color vision gives an animal the ability to detect such predators and take action to evade them, the chances of the animal surviving to reproductive maturity are significantly improved—as are the odds that the gene for color vision will be reproduced. This is the essence of natural selection. What is being “selected” (unconsciously) is genetic material. Natural selection alters the genetic characteristics of a given population when those alterations prove to be beneficial to the reproductive success of that species. If the genetic characteristics of the species do not change rapidly enough to deal with extreme environmental changes, the outcome is grim: extinction. The vast majority, more than 99%, of all species that have ever lived on the Earth are now extinct, but many of them have left modern day descendants. The earliest mammals and primates are all gone, but we are their inheritors.

Natural selection is therefore a deeply interactive process involving all of the variables that affect a population’s genetic composition and the environment in which the population lives. It is not “random” in the sense that it follows no rules, because the rules that govern this process have largely been elucidated, but it is random in the sense that changes in genetic material or the physical environment in which that material exists cannot be predicted. The process of natural selection is driven by…

Selection pressures. Selection pressures (sometimes called selective pressures) are those aspects of the natural environment that, unconsciously and without direction, tend to demand of those animal and plant species living in that environment the ability to conform themselves to the conditions of the environment. In regard to this, a key principle needs to be emphasized once again: if an environment changes extremely rapidly, the results are usually disastrous for those species that have evolved a high degree of specialization for that environment. On the other hand, species having, for whatever reason, greater biological “flexibility”, stand to gain. The massive reptilians that dominated the Earth until 65 million years ago were excellently adapted to a comparatively warm (although perhaps already cooling) environment. When that environment changed with jarring suddenness, their highly specialized adaptations were no longer suitable. The selection pressures, in other words, had radically changed. The mammalians, smaller but more adaptable, were given a tremendous competitive boost from the wiping out of the large dinosaurs. Selection pressures, therefore, are aspects of the natural environment that favor animals and plants that can meet them—and which mercilessly eliminate those that can’t. The forest environment in which our primate ancestors evolved was filled with particularly sharp selection pressures, ones which tested their abilities to the utmost, and winnowed out those who failed the test.  

A great many variables, therefore, influence natural selection. The net result of this phenomenon is life forms that come in an amazing array of sizes, colors, shapes, internal structures, and configurations, living in an astonishing range of habitats. The changes that brought these life forms about are examples of the inherent gradualism of evolution.40 This is not to say that all evolutionary change occurs at one, rigidly determined pace, nor is it to say that there cannot be long periods of relatively little change followed by periods of relatively greater change. But it does indicate that large evolutionary change is brought about by the accumulation of small changes, yet another example of emergence in nature.41

In one perspective, life forms can be thought of as packages that carry genes, genes whose “job” it is to see that they are reproduced. This job can be accomplished in a tremendous variety of different ways. I call the process of natural selection driven by selection pressures by a simple and stark name: The Law of Whatever Works. Whatever works does not have to be especially efficient, attractive, or appealing. As long as some of the life forms in a population succeed in perpetuating their genetic material, that’s all that is required. The life form may be lethal to other animals (as are the Anopheles mosquitoes that transmit malaria), it may be one that (to human eyes) is disgusting or repellent in appearance, it may use methods of reproduction that are very inefficient and time-consuming (such as the reproductive cycle of penguins), it may exist in environments that to humans appear harsh or extreme. None of this is important. There is only one criterion of biological “success”. The species must continue in some way. Nothing else matters.

Adaptation. An adaptation is a physical characteristic of a life form that helps it thrive in a particular environment. It can be thought of, in a sense, as a biological “solution” to an environmental challenge. It is the end result of the natural selection process. Adaptations (for a time) enhance the reproductive prospects of a population of life forms. Evolution by natural selection is therefore also referred to as adaptive evolution. Adaptations are not just external physical traits. They can also be biochemical features, such as the evolution of different varieties of hemoglobin (the molecule that carries oxygen to cells).42 Are adaptations always perfect or elegant? Not at all. Natural selection, in “looking” unconsciously for whatever works, uses the available materials and does with them what it can, all without direction or purposefulness. If an adaptation helps ensure an animal or plant’s reproductive success, it gets reproduced more and more consistently. If the environment changes, the adaptation may rapidly become useless—or worse.

DNA Replication, Mutation. Although it is somewhat of an oversimplification, it can be said that bodies are built out of proteins. Proteins also regulate and maintain bodies. Different kinds of protein are used to build different kinds of structures in an animal’s body, and distinct kinds of protein perform the various regulatory functions as well. Gene expression is also regulated by proteins. There are 20 amino acids in life forms, and specific kinds of proteins are built out of specific sequences and arrangements  of amino acids. (Not all amino acids can be synthesized in the body; some must be ingested.) The “instructions” for building a protein are found in genes, which are simply segments of DNA located along the bodies of chromosomes, found within cells. Some proteins require several genes to assemble them. Conversely, certain single genes can produce several different kinds of protein. A sequence of nucleotides in a gene assembles a specific sequence of amino acids in a protein.43  

As you know, a DNA molecule consists of nitrogenous bases linked in pairs, with a surrounding structure of phosphate and sugar groups, all arranged in a double helical shape. The base adenine always links with thymine, and the base cytosine always links with guanine. (In RNA thymine is replaced by uracil.) A triplet of bases, called a codon, carries the “instructions” for the building of a particular amino acid. The DNA code for an amino acid is copied and the copy is a molecule known as messenger RNA, or simply mRNA. The copying process is known as transcription, and in eukaryotes takes place in the cell nucleus. The “information” carried by the mRNA is taken out of the nucleus to structures known as ribosomes. Ribosomes, which are constructed out of a different kind of RNA, (rRNA) are where the actual proteins are assembled by yet other forms of RNA (tRNAs). This second phase of the construction process is called translation.44 As long as the DNA of a cell reproduces properly, everything goes well within this process, and proteins are assembled according to plan.

But sometimes, there are problems. When a DNA molecule replicates, there are errors of copying that pop up from time to time, Most of these errors are corrected by enzymes that detect and repair these errors. But some of the errors slip through. These errors are the mutations mentioned in the description of natural selection above. The mutation can alter the coding of a protein, which results in the production of a different kind of protein altogether. Point mutations change a base in the DNA sequence to another kind of base. Certain kinds of point mutations change amino acids, and hence protein production. A more drastic kind of mutation, known as a frameshift mutation, inserts a base into a DNA sequence, knocking the whole sequence of base pairs out of position and producing a useless, non-functioning protein. Mutations can also involve a process known as transposition, in which a section of DNA can copy itself and insert itself into an existing gene, altering its function. Finally, whole chromosomes can become entangled with each other, causing a phenomenon called translocation. In translocation, chromosomes which have crossed each other’s path can swap genetic information equally or one can do all or most of the exchanging. In discussing evolution, it is the mutations that occur in gametes—sex cells—that are most crucial. These mutations, if they are of the right kind, can have phenotypic consequences. They can bring forth a new variation of a living thing, one not seen before.45 Mutations, therefore, are of crucial significance in evolution. The deep basis of natural selection is found in the process by which the genome of an individual is reproduced. It is the variability of genetic material that gives natural selection something from which to select. 

Genetic Drift. A very precise definition of evolution is that it is “a change in the proportion of alleles (different forms of a gene) in a population.”46 In a relatively small population, with a great deal of intergroup mating, certain alleles can be lost over time simply by random chance, and certain other alleles can rise to 100% frequency. This is a less powerful form of evolution, one that cannot produce complex adaptations. In fact, it can be disastrous, leading to high incidences of genetic disorders in isolated populations.47 There is a variation of the genetic drift theory known as the Neutral Drift Hypothesis. In the 1960s a Japanese biologist, Motoo Kimura, argued that random genetic changes take place with great frequency, and are not usually driven by natural selection. The overwhelming majority of such changes, according to Kimura, are neutral, and changes in the genetic characteristics of a given population can occur entirely by chance. Kimura is not rejecting the idea of natural selection at the levels of form and function. He is arguing that at the molecular level, however, the majority of mutations result purely from stochastic processes. Nor is he saying that such changes occur at a regular, constant rate. He does not exclude selection as one of the factors in molecular change. He is, however, saying that selection-driven changes at the molecular level are in the minority. Kimura’s work has been widely debated, and it is not universally accepted by any means, but he has definitely influenced the examination of genetic change.48

Synergy and Evolution. In the chapter Synergy and Feedback Loops we examined the way in which evolutionary development is driven by synergistic processes, as successful innovations make possible the greater and more widespread expression of these innovations. We examined the proposition that only when all the conditions necessary for the evolutionary development of a species are working in concert with each other can true novelty emerge. So evolution may properly be thought of as a natural process that by bringing together a host of variables produces an outcome that none of those variables operating in isolation can produce.

Speciation. A species can be chiefly understood as a population whose members can successfully reproduce only with other members of the population. (There are indistinct boundaries between species that sometimes allow genetic flow to occur.)  By successfully reproduce, as we noted above, we mean give rise to fertile offspring who will be able to continue the process. Speciation occurs when a population has become genetically distinct from other populations descended from the same ancestral group. If a population has, through natural selection and genetic drift, lost “genetic contact” with another population over the centuries, it may lose the ability to produce fertile offspring with that population, or even to produce any offspring at all. Speciation is usually caused by populations living in distinct environments that call for distinct adaptations. Different physical features have different adaptational advantages in such environments. What “works” reproductively in one place might not “work” in another. Various species of baboon have evolved, for example, to adapt to widely divergent environments in Africa. Speciation may also be driven by the action of speciation genes, genes that contribute to reproductive isolation. Such genes are thought to vary in a purely stochastic (by random chance) manner and if favored by natural selection, to drive the process of speciation forward. This process is still not fully understood, but it is now being studied intensely.49

Convergence. Convergent evolution occurs when varieties of animals of different species, or even different classes or orders, become similar in appearance due to selection for certain traits that are advantageous in a given environment. The most spectacular example of convergence we have is found in the cetaceans, the mammalian order that includes whales, dolphins, and porpoises. Through relentless selection pressures, the successful members of the order have acquired extremely hydrodynamic bodies similar in key ways to those of the vertebrate fishes. But an examination of a cetacean skeleton will reveal a surprising fact: in their wonderfully effective fins there are vestigial limbs and digits, the remnants of their terrestrial ancestors.50

Parallelism. This is more properly called parallelophyly. As described by the eminent evolutionary biologist Ernst Mayr, this is “the independent emergence of the same character in two related lineages descended from the nearest common ancestor.”51 This phenomenon is seen clearly in the evolution of birds. It should be noted that every step in the parallel evolution of various species is not going to be identical, nor does it need to be. But the phenomenon has been carefully traced, and it is the process which is complementary to convergence.52

Stasis.  There are particular environments, such as areas of the world ocean, that are so isolated and stable that certain species of animals can occasionally survive in them essentially unchanged over many centuries. The discovery in 1938 of a coelacanth, a fish once thought to have died out with the dinosaurs, illustrates this phenomenon. Such environments are characterized by a lack of selection pressures. For example, there may be no predators in the region. Similarly, the region occupied by a species may be thermally stable or out of the migratory patterns of potentially disruptive animals. But for whatever reasons, certain areas of the Earth harbor these biological remnants of earlier eras.

There are many, many more aspects of evolution that we will touch on as we have need to, but these will suffice for now. Now it’s time for us to examine…

Misconceptions About Evolution

Misconceptions about evolution abound. There is great misunderstanding about the term “survival of the fittest”. Fittest does not necessarily mean biggest and strongest. Fitness  in this context refers to reproductive success. Most dinosaurs were huge and tremendously strong; the mosquitoes that existed along with them were small and easily crushed. Which one was more fit? The various mosquito species have an unconscious reproductive “strategy”. They reproduce in such vast numbers that even if 95% of their members die, they have plenty left to continue the lineage. In fact, as Jerry Coyne has pointed out, the “solutions” devised by natural selection aren’t ideal ones, so perhaps we should think in terms of survival of the fitter.53

Further, many people say that “I didn’t descend from monkeys”. Well, if those people are referring to the modern day prosimians, monkeys, and apes, they’re right. They didn’t. All of the modern primates, including humans, are descended from common ancestors, the founders of the primate order some 65,000,000 years ago (or perhaps longer). The ancestral primate groups evolved many branches, and eventually gave rise to the approximately 200 varieties of primate which exist in the modern world, one of which is us. As we will see in more detail later, the lines that were to become the modern chimpanzees and humans split from each other somewhere around 5-6 million ybp, and genetic information can be used to confirm this.

There are those who think the scientific community is deeply divided about whether evolution is a fact. Such is absolutely not the case. The vast majority of scientists are thoroughly convinced by the massive evidence in favor of evolution.54 And there are people who believe that the evidence for the reality of evolution is thin. Nothing could be farther from the truth. Virtually every area of the sciences gives irrefutable evidence for its major propositions and supports our estimates of the time frames in which it occurred. Here are just some examples:

-- In outer space, the Wilkinson Microwave Anisotropy Probe (WMAP) has examined the cosmic microwave background radiation, the aftermath of the Big Bang. This examination has allowed us to make an estimate of the age of the Universe, 13.83 billion years, that is accurate to within 1%.55 This utterly demolishes the preposterous arguments of those who contend the Universe is only a few thousand years old, and demonstrates that there was an enormous amount of time for nucleosynthesis to have occurred.

--Radiometric dating, based on the known decay rate of radioisotopes, has established reliable absolute dates for many, many samples of the Earth and the life forms fossilized within it. For example, Potassium-Argon dating (40K-40Ar) is used to reliably date fossil remains embedded in layers of solidified volcanic ash. G. Brent Dalrymple, perhaps the world’s foremost authority on the age of the Earth, has thoroughly explained why radiometric dating is accurate and has completely refuted the ludicrous contentions of “Young Earth Creationists” and their insistence that a “great flood” laid down all the layers of sedimentary rock in the geologic column:

There is also no doubt that the rocks now exposed on the surface of the Earth or accessible to scientists by drilling were deposited and emplaced over the geologic epochs, starting in the earliest Precambrian more than 3.8 billion years ago. There are more than 100,000 radiometric ages in the scientific literature that date rock formations and geologic events ranging in age from Holocene to earliest Precambrian. These data and all the accumulated knowledge from the science of geology show conclusively that the Earth we now see is the result of natural processes operating over vast periods and not the product of one or two worldwide catastrophic events.56

--Molecular evolutionists can measure the genetic “distance” between and among various kinds of organisms through an analysis of the sequences of nucleotides or amino acids in key macromolecules:

For example, in humans and chimpanzees the protein molecule called cytochrome-c, which serves a vital function in respiration within cells, consists of the same 104 amino acids in exactly the same order. [Emphasis added.] It differs, however, from the cytochrome-c of rhesus monkeys by 1 amino acid, from that of horses by 11 amino acids, and from that of tuna by 21 additional amino acids.57

The calculation of reliable genetic “distances” by such methods has allowed scientists to trace the phylogenies of numerous species. It has allowed geneticists to explain when various lines of animals diverged from one another as life forms evolved from the LUCA (although the existence of fossil evidence is often used to calibrate such measurements). And for those who deny any relationship between humans and chimpanzees: what are the odds that the amino acids in the cytochrome-c molecule of humans and chimpanzees ended up being identical to each other purely by coincidence?

--Paleontologists have uncovered a huge number of fossils which demonstrate transitions over time from one kind of animal to another. This documentation is very strong in the record of dinosaurs, and many transitional examples have been uncovered. Further, there are many examples of animals in the fossil record which suggest a biological relationship between reptilians and birds.58 

--In relation to transitional forms, in 2004 a fossil species named by scientists Tiktaalik roseae was discovered in the Canadian Arctic. Anatomically, it is absolutely a mixture of  fish and tetrapod (four-legged animal), exhibiting traits found in both groups, and it is almost exactly the age—375 million years old—that those who were looking for it predicted it would be.59 (We will examine this find further in the chapter The Animal Kingdom Begins to Colonize the Land.) This helps bury the absurd creationist argument that there are “no transitional varieties in the fossil record” even deeper than it already was. Even if Tiktaalik does not turn out to be the defining transitional animal, it gives us an excellent idea of what that animal was like.

And as far as assertions of “divine” or “intelligent” design go, anatomists and physiologists have uncovered numerous “design flaws” in the human body, and a great many features of our anatomy that are ancient in origin and which have been conserved across many species through time. (We will look at the various suboptimal “design” features of humans in a subsequent chapter.) [See the Addendum below.]

Few propositions in scientific history have been more thoroughly demonstrated than organic evolution. It is evolution that has driven life forward ever since the appearance of the first life forms, and it has produced the various life forms that permeate the surface of the Earth and the world ocean. And it is evolution that continues to operate in every corner of the biosphere, mindlessly hurling out the challenge it always has: adapt, reproduce, or die out. By its processes, it ultimately produced a life form that can study it and understand it. And the interesting thing is that were the process to start all over again from the beginning, there is no guarantee that that life form would ever come into existence again.

Life, as we have observed, is something that energy-matter is capable of doing in the right circumstances. When elements are arranged in a particular manner, they exhibit the properties we associate with life. It was the capacity of living things to undergo change that ultimately led to the emergence, from the fantastically complicated web of life, of our genus. The story of life’s emergence and evolution is still being pieced together, painstakingly and systematically. Not all questions have been resolved, by any means. But we must resist the temptation to assert that these questions cannot be answered, or that they can only be answered by invoking supernatural intervention. The appearance of life on our planet was, obviously, of the most central importance to us. And yet, in the scope of the Universe, it was not a particularly noteworthy or unique development. The advanced, consciousness-possessing life forms of the planet Earth may yet make their mark on the broader Universe, but as of yet they have not done so. They are, in fact, still struggling with their own incomplete understanding of themselves, and their failures to deal with their own tendencies and limitations may yet bring about their downfall.


The “Just Good Enough” Body

The human body is extraordinary in many ways, but it is still an example of the rough-and-ready processes of evolution, the “goal” of which is reproductive advantage. Structures and functions don’t have to be perfect—they just need to work. There are many features of the body that from a purely engineering standpoint are sub-optimal. The male urethra passes through the prostate gland, and as a consequence, urinary problems in older men are common. The female pelvis is just barely big enough to accommodate the large-brained infants of our species, and because of this childbirth can be a harrowingly painful ordeal. In reproduction, only about one-ten millionth of one per cent of all ejaculated sperm get anywhere near an ovum. Capillaries leak so much liquid that a parallel circulatory system is needed to get it back into the cardiovascular highway. The common passageway for air and food can cause a choking hazard. The proximity or even overlap of excretory and reproductive structures can lead to infection. Our own immune system can turn on us, causing untold suffering. The protection afforded by the skull and the vertebrae can be tragically incomplete. Knees and hips wear out simply from prolonged use. Perhaps 40% of all conceptions end in miscarriage. And we are vulnerable to a disturbingly long list of diseases—more than 100 types of cancer93, dozens of major heart and vascular conditions94, more than 40 major respiratory illnesses95, more than 100 autoimmune disorders96, and on and on. We learn a hard truth when we are young, and understand that truth more deeply every year we live—we are not built to last. No matter how lucky we are in avoiding injury, no matter how diligently we look after our health, we will deteriorate if we live long enough. The body—which is everything we are—will finally give out. So in the last chapter of this volume, we will consider the processes of aging and the length of the human lifespan, and seek to understand the finite and ephemeral nature of the lives we live on this planet.


Main Article

40.  Coyne, Why Evolution is True, p. 4
41.  Dawkins, The Blind Watchmaker, pp. 43-74
42.  Travis, Joseph, and David. N Reznick, “Adaptation” in Evolution: The First Four Billion Years, pp. 105-109
43.  Mark Ridley, Evolution, pp. 23-25
44.  Ridley, p. 25
45.  Ridley, pp. 27-30
46.  Coyne, p. 122
47.  Coyne, 122-124
48.  Kimura, Motoo, The Neutral Theory of Molecular Evolution, passim.
49.  Nosil, Patrik, and Schluter, Dolph, “The genes underlying the process of speciation” in Trends in Ecology and Evolution, 2011.
51.  Mayr, What Evolution Is, pp. 225-226
53.  Coyne, p. 13.
54. Some years ago, in the United States, the National Center for Science Education began a project, somewhat tongue-in-cheek, to deflate claims by creationists that there were many scientists who are creationists. Called Project Steve, it has shown that there are more pro-evolution scientists named Steve than there are creationists of all names put together in the scientific community. And only about 1% of all scientists are named Steve (or some variation of that name, like Stephen).
57.  Francisco J. Ayala, “Molecular Evolution” in Evolution, First Four Billion Years, p. 136.
58.  Donald R. Prothero, Evolution: What the Fossils Say and Why It Matters, pp 249-268.

59.  Coyne, 35-37




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