Evolution, Part II: Evolution in Action

Steve Vigdor, April 4, 2019

In Part I of this blog series, we introduced the central concepts of the modern synthesis of evolutionary theory and the development of opposition to it, through stages from religious fundamentalism through creation science to Intelligent Design (ID). In this part, we will present some of the extensive observational evidence that supports the theory of evolution, including: the direct observation of mutation and natural selection in action among bacteria and the development of antibodies; the fossil record of extinct species and their anatomical similarities to living species; biogeographical evidence for natural selection among humans and other species. In Part III, we will discuss the evidence for evolution provided by the enormous database now available from sequencing of the genome for many living, and even a few extinct, species. We will also discuss how mutations occur at the biomolecular level and how the advantages favored by natural selection can exert enough pressure to foster multi-generational developments that might otherwise seem naively improbable. Both the fossil and genomic evidence strongly support the concept of universal common descent. Along the way in our discussions, we will point out some of the flaws in objections ID proponents raise to aspects of this evidence.

6)   Bacterial Evolution in Action

When scientists expose species capable of rapid reproduction to controlled environmental conditions to which those species are not yet adapted, it becomes possible to observe evolution taking place in the laboratory. If the genomes of those species are furthermore easily mapped using modern technology, it becomes straightforward to identify where and when genetic mutations take place. Such experiments provide compelling evidence for the roles of genetic mutation and natural selection in evolution.

The largest number of experiments of this type have been performed on bacteria, which mostly reproduce asexually to produce clone descendants that are identical to the parents, unless mutations occur during reproduction. One class of experiments studies the development of bacterial resistance to particular antibiotics. A particularly clever realization of such a study has been carried out by researchers from the Harvard Medical School and the Technion Institute of Israel, and was reported in the journal Science in 2016. The experimenters prepared a large rectangular petri dish subdivided into nine rectangular bands, as seen in Fig. 6.1. They introduced E. coli bacteria in the outermost bands, where there was no antibiotic mixed with a gelatinous agar substrate through which the bacteria could move. In the next band going inward from the left and right, they mixed in just slightly more antibiotic concentration than the bacteria could, on average, survive. The subsequent bands, moving toward the center, then had successively 10, 100 and 1000 times that concentration of antibiotic.

The experimenters then observed the bacteria over a period of 12 days as they migrated toward the center of the petri dish in search of food and reproduced. Only bacteria born with beneficial mutations were able to survive traversal, and produce further clones capable of surviving traversal, across subsequent antibiotic concentration bands of the dish. New mutations were needed for survival at each gradation in antibiotic concentration, so that by the 11th day of observation, there were several descendants that had gained enough adaptive benefit from sequential mutations to survive at least briefly in antibiotic 1000 times stronger than their ancestors could have survived. A time-lapse video following the full E. coli colony through its migration and adaptation is available at https://youtu.be/plVk4NVIUh8. The paths of selected bacteria are traced by colored lines in Fig. 6.1. This experiment and a number of its precursors demonstrate the role played by natural selection in the development of bacterial resistance to antibiotics.

Evolution of antibiotic resistance
Figure 6.1. Illustration of succeeding generations of E. coli bacteria as they migrate and develop resistance, by the processes of mutation and natural selection, to progressively increasing concentrations of antibiotic going toward the central band in the picture. The level of local bacterial population within each initially black band is reflected in the opacity of the white covering layer. The colored lines trace several generations arising from three (among many) individual bacteria apiece introduced at the left and right edges of the multi-band plate used in the experiment. The different colors represent sequential mutations that occur during the cloning reproduction of the E. coli. When a line terminates, the corresponding bacterium has been killed by the antibiotic. The generations were observed by an experimental team from Harvard Medical School and the Technion Institute over a period of 12 days. A more impressive time-lapse video of the experiment is available at https://youtu.be/plVk4NVIUh8 .

An even more influential experiment, the Long-Term Experimental Evolution Project, has been carried out over a 30-year period in the Michigan State University laboratory of Richard Lenski, a MacArthur “genius” fellow and member of the National Academy of Sciences. Lenski and co-workers have tracked genetic changes in 12 isolated, but initially identical, populations of E. coli since February 1988, through nearly 70,000 generations! The goal of the experiment has been to study the dynamics and repeatability of evolution in environments characterized by limited availability of food. For E. coli the food supplied was a low concentration of glucose, just enough to support each initial population for one day. Each day – a period characterized by 6.6 generations in each of which the surviving population doubles – a representative 1% of each surviving population is transferred to a new flask with fresh growth medium.

What is truly unique about Lenski’s experiment is that every 75 days, or roughly 500 asexual reproduction generations, a sizable portion of each of the 12 cultures is frozen with glycerol. The bacteria in each of these cryogenically preserved samples remain viable and can be revived at future dates, for example, for complete genomic mapping. The frozen cultures thus provide a sort of “living fossil” record that allows the experimenters to identify the range of generations in which each observed mutation first occurred. Because the E. coli reproduce only asexually, evolution in the experiment’s populations occurs strictly by the core evolutionary processes of mutation passed along to later clones in the same line of descent, genetic drift, and natural selection. After 30 years of observation of 12 populations, every possible point mutation (i.e., mutation at a single location in the E. coli DNA) has most likely occurred multiple times, and it is fascinating to see which mutations survive the struggle for nourishment.

Lenski’s results to date have been illuminating. The genomic analyses on the living fossil cultures have revealed that, among hundreds of millions of individual mutations sampled in each population, fewer than 100 total point mutations were found to survive in each population through the first 20,000 generations. And of these, most were neutral mutations, with only 10 to 20 beneficial mutations improving fitness for the bacteria to survive in their scarce resource environment. Some of the beneficial mutations were common to all 12 populations. For example (see Fig. 6.2), all populations showed an increase in cell size, although after the first several hundred generations the different populations exhibited different rates of growth. The fitness for survival increased rapidly at first for all populations. Later generations continued to exhibit increased fitness, but the rate of increase decelerated in comparison to the early generations.

Lenski cell size growth
Figure 6.2. The growth in cell size for the 12 E. coli populations (each represented by a different colored line) tracked in Lenski’s experiment, through the first 10,000 generations.

While the common features of genomic change in all 12 populations reveal the influence of natural selection to improve fitness in equivalent environments, the differences among the populations reveal the important role played in the sequence of mutations by the element of chance. The rate of mutations during reproduction is normally quite small because DNA contains the inherent capability to repair errors that occur. It has been found that 6 of the 12 populations have developed mutations that impair this DNA self-repair mechanism, allowing those populations to sample mutations more rapidly than in the other populations. One of the populations was found to have developed, during its first 6000 generations, two distinct genetic variants that co-existed within that population thereafter. One of those variants was based on mutations that increased growth while glucose was still available for nutrition, while the other had developed an advantage for staying alive after the glucose had run out.

The most striking example of the role of chance in evolution among Lenski’s bacteria is that one among the 12 populations was discovered to have developed, after 31,000 generations, the ability to survive by using as a power source a different carbon-based molecule, called citrate, within the solution in each flask. This was a surprise because the inability to grow on citrate in the presence of oxygen is one of the defining characteristics of E. coli as a species. The population that developed this ability exhibited a growth spurt after the genomic change, since there was a large amount of citrate present in the growth medium.

In order to determine whether the change resulted from a single rare mutation or rather as the cumulative effect of a sequence of mutations, one of Lenski’s post-docs took some of the frozen cells from various earlier generations and attempted to grow them in a culture completely lacking glucose, with citrate as the only potential food source. He observed some growth only when he tested cells from the 20,000th generation onward, eventually producing a total of 19 mutants that could survive on citrate. The complete absence of growth observed from samples of earlier generations suggested that the citrate processing was the result of mutations built upon earlier sequences of mutations that developed over 20,000 generations. Genomic mapping among the new bacteria revealed multiple genetic differences from not only the ancestral strain, but also from the other 11 populations, differences that actually made the organisms less fit to survive in a glucose-only environment. One population had thus developed an entirely different natural selection route to thrive in its environment, and seemed to be developing into a distinct species.

Creationists and Intelligent Design advocates dismiss the types of experiments described here as evidence only for microevolution, the accumulation of small changes among primitive microscopic species. They seem to demand as proof of macroevolution – what they term “molecules-to-man” evolution – the actual observation of a single-celled organism evolving into a human, which obviously cannot occur over the time span of a single experimenter’s lifetime. But, in an especially bold co-option of the clear experimental evidence for the roles of mutation and natural selection, creationist Scott Whynot claims in a blog post on the site Answers in Genesis that “Lenski’s Bacteria Support Creation.”

Whynot’s claim is based on the standard, somewhat fuzzy, ID concept that “the idea of evolution from a simple common ancestor requires the accumulation of novel genetic information over a long period of time,” combined with an entitlement to define “novel genetic information” as he pleases. In particular, he asserts that “fitness improvements or even gains of protein function are not equivalent to a gain of novel information.” And in the specific case of Lenski’s E. coli population that evolved utilization of citrate as an energy source: “no novel information was gained in this instance as this ability was the result of previously existing information being rearranged and used in a different way.” Well, such “rearrangements” represent one of the standard mechanisms of DNA mutation, and in Lenski’s case they appear to be leading to speciation.

Even if one accepts that all the “information” – i.e., the enormous, but still finite, complete set of possible DNA mutations – was implanted at creation, that does not negate the existence, and indeed the observation in Lenski’s lab, of evolution leading even to the production of a new species. Sexually reproducing organisms that develop quite different paths to adapt to their environment – even if those distinct paths were all conceivable from the start – often evolve to a state where they can no longer cross-breed, and hence become distinct species. This was the discovery of Theodosius Dobzhansky’s experiments with fruit flies — described in Part I of this series and in Dobzhansky’s book Genetics and the Origin of Species – that completed the Modern Synthesis of evolutionary theory.

7)   Antibody Evolution

An example of rapid natural selection of beneficial mutation in humans is associated with the effect of immunization in generating antibodies that can successfully fight off a particular virus or bacterial infection. The biomolecular science and DNA rearrangements by which the vaccination builds up immunity are well understood as the result of research on the generation of antibody genes that led to and followed Susumu Tonegawa’s 1987 Nobel Prize in Physiology and Medicine.

Antibodies are specific proteins attached to the surface of particular white blood cells known as B lymphocytes, and which are capable of binding to the antigen molecules of a particular invading virus or bacterial infection. The body can produce an enormous variety of antibodies by random selection of gene segments within each lymphocyte cell, but each cell is capable of producing only one particular type of antibody. When antigen molecules bind to B lymphocyte cells, the antigens themselves become tagged for later recognition and destruction by other white blood cells, but they also trigger rapid multiplication of the lymphocyte cells into daughter clones, each of which expresses the same antibody, except for the effect of random mutations in the genes of the clone cells. The mutation rate in this cloning process has been found to be as much as a million times greater than the normal DNA mutation rate. It is this feature that allows the sampling of many mutations for increased antigen affinity in many fewer replication generations than would otherwise be needed.

Some antibodies found in blood samples prior to vaccination with a weakened form of a specific antigen may have a weak affinity for binding to the invaders even if they were not specifically optimized for that purpose. But effective antibodies grow rapidly in number, binding affinity, and, hence, efficacy, after vaccination. Both types of improvement occur even more rapidly after a subsequent booster vaccination with the same antigen. Analyses of the B lymphocyte gene structures in mice both before and at various times after immunization with a particular antigen have confirmed the central role played by random gene mutations in increasing an antibody’s affinity for antigens.

Clone lymphocyte cells for which random mutations lead to reduced antigen affinity, and hence to reduced subsequent stimulation, are programmed to die. Only a small fraction of observed gene mutations improve affinity, but it is the cells that experience such improvements that reproduce most rapidly. The natural selection pressure for these beneficial mutations increases progressively as the prior immune response reduces the concentration of antigens that can trigger the cloning process. By the time the antigen is finally cleared from the body, the antibodies tuned by multiple generations of mutation and selection may have a hundred times the affinity of the original slightly successful protein. Some fraction of the successful B-lymphocyte cells will remain in the body to launch a far more efficient battle against subsequent invasions by the same antigen. This explains, for example, why a child who recovers from measles develops immunity against subsequent bouts of measles.

8)   Fossil Evidence

The examples considered above demonstrate clearly the central roles of genetic mutation and natural selection in the adaptation of cells to survive and fulfill functions in a changing environment. It is natural, but far more socially controversial, to assume that they play analogous roles in the broader macroevolution and increasing diversity and complexity of the species that has played out over hundreds of millions of years. But it is far more difficult to provide clear biomolecular evidence as a function of time to demonstrate multigenerational evolution that may require thousands, or even millions, of years to gradually produce demonstrable beneficial effects on a major portion of a large population, or even the eventual transformation from one species to another.

Nonetheless, there is very strong and wide-ranging experimental support of a less direct nature for the central, and most stubbornly resisted, concept introduced by Charles Darwin: that of universal common descent. Much of that evidence has been documented in detail elsewhere: e.g., see Douglas Theobald’s 29+ Evidences for Macroevolution and Richard Dawkins’ The Blind Watchmaker. In the next few sections, we will present some examples of this evidence refuting objections raised by Intelligent Design advocates to the consensus “tree of life,” which we reproduce from Part I of this series in Fig. 8.1.

standard tree of life
Figure 8.1. The broad outlines of the consensus tree of all life on Earth, illustrating the concept of universal common descent. The figure is reproduced from Douglas Theobald’s 29+ Evidences for Macroevolution.

One of the most persistent claims of creationists opposing common descent has been a perceived absence of fossil evidence for transitional species that would have characterized life in the vicinity of one or another of the branch points (e.g., the red dots labeled A, B and C in Fig 8.1) where two evolutionary lines of species separated. For example, in the 1994 book Darwinism: Science or Philosophy?, Michael Behe asked “If random evolution is true, there must have been a large number of transitional species between the Mesonychid [a land-dwelling whale ancestor] and the ancient whale. Where are they?” Within a year after Behe raised the question, fossils of three transitional species between whales and land-dwelling Eocene Mesonychids were discovered. One of these is pictured in Fig. 8.2, the Ambulocetus natans or “walking whale that swims,” discovered in Pakistan in 1994 by Thewissen and colleagues [Science 263, 210 (1994)].  Yet another example of a four-legged amphibious whale from the middle Eocene period has just been discovered in Peru.

ambulocetus natans
Figure 8.2. Reconstruction of a skeleton found by Thewissen et al. of a whale precursor that was capable of both swimming and still walking on land.

Another fossil intermediate between land and sea mammals was discovered in Jamaica in 2001, the four-legged seacow pictured in Fig. 8.3, a precursor to today’s manatees.

seacow skeleton
Figure 8.3. Reconstructed skeleton of a seacow with legs, a precursor of manatees, discovered in 2001 in Jamaica. The parts in grey represent existing fossils, while those in white are partly conjectural.

Many fossils have been found of reptile-like flightless dinosaurs with feathers or of birdlike creatures with teeth and/or long reptilian tails—all indicative of transitional species around branch point A in Fig. 8.1. Perhaps the most famous is archaeopteryx, characterized by the reconstructed skeleton in Fig. 8.4, which lived in the late Jurassic period, about 150 million years ago. The earliest fossils were found during the second half of the 19th century in Germany. Archaeopteryx used to be classified as the oldest known bird species, leading many creationists to reject its identification as a transitional fossil. It did indeed have feathers and broad wings that should have made it able to fly or glide. But it also had features more in common with other small Mesozoic dinosaurs than with modern birds. Among these features were jaws with sharp teeth, three fingers with claws, a long bony tail, hyperextensible second toes, and various skeletal features. A similar, but distinct, species of dinosaur capable of flight were the microraptors, which lived slightly later and of which there are many existing fossil specimens.

archaeopteryx
Figure 8.4. Reconstructed skeleton of an archaeopteryx at the Academy of Natural Sciences of Drexel University.

Yet another rough contemporary of the archaeopteryx and microraptor was the sinosauropteryx, for which fossils have been found in northeastern China. This was another transitional species, a flightless dinosaur that appears to have been covered with a coat of simple filament-like feathers, precursors to modern bird feathers.

Similarly, there is an extensive fossil record indicative of branch point B in Fig. 8.1 of species transitional between reptiles and mammals. This fossil record is described in detail here and in book form in The Evolution of Mammalian Characters by D.M. Kermack and K.A. Kermack. Quoting from the Talk Origins site: “This list [of transitional fossils] starts with pelycosaurs (early synapsid reptiles) and continues with therapsids and cynodonts up to the first unarguable “mammal”. Most of the changes in this transition involved elaborate repackaging of an expanded brain and special sense organs, remodeling of the jaws & teeth for more efficient eating, and changes in the limbs & vertebrae related to active, legs-under-the-body locomotion.” For example, the transitional species exhibited combined-function jaw and ear bones that have evolved since into the distinct bone patterns of reptiles (four lower jawbones and one middle ear bone) and mammals (one lower jawbone and three middle ear bones).

The most complete and impressive fossil evidence maps the ancestry of humans over the past several million years, since the human branch separated from that for chimpanzees and bonobos. There are fossil specimens from over 100 individuals in each of multiple precursor species to homo sapiens. A possible timeline and branching of human evolution, based on that fossil record, is indicated in Fig. 8.5. The fossil evidence documents gradual changes in the structure of the skull and teeth (see Fig. 8.6), in brain size, and in the evolution of walking from four to two limbs.

hominid evolution
Figure 8.5. A possible timeline and branching diagram emerging from the fossil evidence of human evolution.
hominid skulls
Figure 8.6. Fossil skulls of a variety of hominid species, showing the evolution leading to homo sapiens.

The transition in these characteristics is especially telling in the various discovered species of Australopithecus, from the more apelike A. ramidus (species A in Fig. 8.5), to the intermediate A. afarensis (species C), to the more human-like A. africanus (species D) and A. robustus (species F), which lived more than a million years ago. While the leg and pelvis bones of Lucy (see Fig. 8.7), the most celebrated example of A. afarensis, clearly indicate that this species walked upright on two feet in a fashion close to the way humans walk, the species also had a bony forearm ridge that may well have been a vestigial remnant from earlier ancestors that used knuckles for walking support.

Lucy
Figure 8.7. A reconstruction of “Lucy“, a female Australopithecus afarensis on exhibit in the National Museum of Natural History, Washington, D.C., U.S.

The existence of vestigial features, by the way, provides another strong piece of supporting evidence for the phylogeny of Fig. 8.1. These features include anatomical or biomolecular remnants of structures developed in ancestral species to perform essential functions that are no longer needed by the descendants. Vestigial examples abound in nature, from the wings of flightless birds and beetles, to the rudimentary eyes of sightless animals, to the human coccyx remnant of external tails in ancestral species. In some cases, the vestiges now serve inessential functions, while in other cases they have no remaining function at all.

The fossil record furthermore supports the relative chronology implicit in the tree of life in Fig. 8.1. For example, geological dating of fossils intermediate between mammals and reptiles, associated with branch point B in Fig. 8.1, shows them to be roughly twice as old (~300 million vs. ~150 million years) as those associated with the bird-reptile branch at point A. The geological dating is carried out by analysis of the rock layers (strata) containing the fossils and the layers above and below them. (Most of the fossils are too old to be subjected themselves to successful radiocarbon dating.) Analyses of large samples of such stratigraphic evidence for relative timelines show those timelines to be very strongly correlated with those implicit in the phylogeny.

Furthermore, no fossils have been discovered that would suggest intermediate species not associated with a specific branch point in Fig. 8.1. For example, there is no fossil record of species transitional between birds and mammals. A convincing discovery of such an unexpected transitional fossil would go a long way toward falsifying the concept of a single tree of common descent. The theory of evolution is a scientific theory and, as such, is subject to falsification by any number of potential discoveries. But no falsifying evidence has been found to date.

9)   Biogeographical Evidence

Since natural selection favors adaptation to the local environment in a species’ habitat, it stands to reason that geography also influences the arc of evolution. For example, his perception that species on isolated islands would develop unique characteristics is what led Charles Darwin to devote particular attention to animals on the Galapagos Islands. Geography has also been the driver behind some of the branch points in Fig. 8.1. For example, with very few exceptions, marsupials such as the kangaroo and the wallaby only inhabit Australia, while placental mammals are not native to Australia (although humans have transported many to Australia).

This appreciation for the important role of geography also informed Darwin’s guesses about human origins, expressed in The Descent of Man: “In each great region of the world the living mammals are closely related to the extinct species of the same region. It is therefore probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man’s nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere.” Darwin offered this speculation in 1871, long before any hominid fossils had been discovered. Indeed, the subsequent discoveries of fossil remains of the earliest precursors of homo sapiens in Fig. 8.5, the australopithecus and homo habilus species that lived up to perhaps two million years ago, have all been made in Africa.

The fossil record of species in genus homo indicates that our ancestors began to migrate out of Africa to Eurasia nearly two million years ago, presumably moving over land bridges. Figure 9.1 shows a model deduced from the fossil record illustrating how human species have spread over time and across lands during the past two million years. Note that it is only over the past 70,000 years or so that homo sapiens have emerged from Africa to spread across the globe, occasionally (and with some difficulty in spawning successful offspring) interbreeding there with contemporaries who preceded them, such as Neanderthals and Denisovans. Indeed, DNA studies have suggested that several percent of current humans’ genetic makeup has arisen from Neanderthals.

human migration patterns
Figure 9.1. A model of the evolution and migration of the genus Homo over the last 2 million years (vertical axis). The rapid “Out of Africa” expansion of homo sapiens is indicated at the top of the diagram, with some admixture indicated with Neanderthals, Denisovans, and unspecified archaic African hominins. The purple area at the lower right reflects the late survival of australopithecus robustus (Paranthropus) in Africa alongside homo until about 1.2 million years ago.

A full evaluation of the fossil evidence supporting the phylogeny of Fig. 8.1 thus also requires an understanding of the migratory paths that were available to land-based and some freshwater-based species as a function of geologic time. A crucial development in that evaluation was the theory of continental drift introduced by Alfred Wegener in 1912. The theory was not widely accepted until the 1960s, when it was understood that plate tectonics below Earth’s surface had indeed caused continents that were formerly joined together in one large land mass to slowly drift apart over geologic time. Wegener named this ancestral land mass Pangaea and deduced its existence in part from comparisons of fossils from different continents (see Fig. 9.2), along with geological similarities and suggestive continental shapes.

Wegener migration through Pangaea
Figure 9.2. The southern continents and sub-continents that Wegener speculated had been joined in Pangaea, showing the schematic migratory paths he deduced from various pieces of fossil evidence.

In modern usage, Pangaea refers to the even more massive supercontinent that resulted from the temporary merger of the northern land mass Laurasia and the southern land mass Gondwanaland, the latter of which comprises the present day continents and sub-continents shown in Fig. 9.2. Gondwanaland existed as a supercontinent from roughly 550 to 175 million years ago, while the merger with Laurasia lasted from 335 to 175 million years ago. Those geologic timelines are then consistent with numerous features of the fossil record of ancient species, and they help to explain certain commonalities among species which have evolved from them and are now found on separate continents.

For example, the southern parts of South America and Africa and all of Australia are home to lungfish, ostrich-like birds and leptodactylid frogs that are found nowhere else on Earth. There are a few marsupial species in South America, in addition to the abundance of marsupials in Australia, suggesting that marsupial ancestors should have migrated across Gondwanaland. Indeed, marsupial fossils have been found in both South America and Antarctica, even though no marsupials have survived the Antarctic environment to live there today. In contrast, the australopithecus ancestors of humans lived long after the supercontinents had broken up, so that their fossils are found only in Africa, but not in Australia, South America or Antarctica. Similarly, fossils of other recently evolved animals, such as apes and elephants, found in Africa have never been found in South America, Antarctica or Australia.

The role of random genetic mutation and genetic drift in fueling evolution is apparent in the fact that some species that have developed in one location are not found in other locations where they are capable of thriving, but did not originally develop. For example, although the American, Saharan and Australian deserts are similar habitats, indigenous cacti are only found in the Americas. Humans have since introduced cacti in the Australian outback, where they grow quite well. But the vegetation native to the Saharan and Australian deserts are only very distantly related to American cacti. Pineapples are found in diverse habitats in the American tropics, but not in similar habitats in Africa or Asia.

Biogeographical considerations also help to explain the occurrence of some diseases that would not seem to have been generated within a natural selection framework. The increased rate of occurrence of sickle-cell anemia among Americans with African ancestry is an apt example. Sickle cell disease is an inherited condition that occurs in people who receive from each parent abnormal genes that govern hemoglobin production in red blood cells. The mutated sickle cell allele causes red blood cells to develop a crescent shape that acts to block blood flow. Individuals who have only one, rather than both, of their 11th chromosomes affected by this allele have a greater resistance to the mosquito-borne disease malaria. The mutation was thus favored by natural selection in populations where exposure to malaria-bearing mosquitos was prevalent. This is clear in Fig. 9.3, which compares the geographical distributions of malaria incidence with those for occurrence of the sickle cell allele.

sickle cell geography
Figure 9.3. The green areas in the left frame show the distribution of malaria in southern Europe, southwest Asia, and Africa around 1920, prior to mosquito eradication programs. The blue areas in the right frame show the distribution of the sickle-cell allele within the same area. The darker the blue, the greater the percentage of people carrying the allele. Note the correlation between these maps.

However, when two individuals who each carry a naturally selected single copy of the sickle cell allele mate, there is a 25% probability that their offspring will carry two copies and be subjected to sickle cell disease. The condition can then be inherited by future generations, even after migration to geographical areas, such as the U.S., which were never themselves subject to malaria. The prevalence of sickle cell anemia among people of African ancestry in the U.S. is now about 0.25%, much lower than the 4% occurrence rate in West Africa. That U.S. incidence rate is still notable, but is now declining due to some combination of cross-breeding with individuals of non-African descent, prenatal genetic screening, and natural selection over multiple generations, since the mutation no longer serves a beneficial purpose.

10)   Objections to Fossil Evidence from Intelligent Design Advocates

Creationists and ID proponents dismiss the fossil evidence supporting common descent by a variety of arguments, ranging from biblical fundamentalism and philosophy to claims of fraud and a paucity of evidence, disbelief in scientific methods, and emphasis on as yet unexplained phenomena. The many creationist claims against evolution are compiled and debunked, one by one, on the talkorigins site.

The fundamentalist objection is best exemplified by young Earth creationist Kenneth Ham’s question “Were You There?” Ham puts his argument this way: “We need to ask ourselves this question: ‘Where do we put our faith and trust? In the words of scientists who don’t know everything, who were not there? Or in the Word of God—the God who does know everything—and who was there?’” This attitude clearly dismisses the possibility that scientists can infer the mechanisms of past events from a combination of the remnants they have left behind and deductions of the laws governing natural processes from laboratory observations. In the view of Ham’s followers, all scientific claims about past events are merely speculation and story-telling. One is tempted to ask Ham if he was there when the Bible was written, so that he can provide evidence that its account of Earth’s origins is more than human story-telling. We have described the problem with this fundamentalist viewpoint in detail in our posts on young Earth creationism: insistence on a literal reading of the Bible leaves one unable to account coherently for observations scientists make today, without either invoking supernatural occurrences that would have caused catastrophic consequences or painting God as a “showman” who set up nature to deceive humans.

Claims that discovered transitional fossils are frauds are often stimulated by reference to the Piltdown Man hoax. Piltdown man was a claim by amateur archaeologist Charles Dawson to have discovered the missing link between apes and man in Sussex, England in 1912. Although skepticism was expressed from the outset, it was not until 1953 that the claim was definitively exposed as a hoax, based on a fossil assembled from a medieval human skull, a 500-year old orangutan’s lower jaw and chimpanzee fossil teeth. The experience in dealing with that hoax led a number of scientists, including famed astrophysicist and Big Bang denier Fred Hoyle, to claim that archaeopteryx was also a forgery. The focus was specifically on the claim that the feather impressions in the fossils were faked, by adding them to the fossil of a flying reptile, the pterosaur. However, the archaeopteryx fossil does not share the skeletal structure of the pterosaurs. As explained in detail here, the forgery claims have been disproved, but that has not stopped evolution deniers from continuing to claim that archaeopteryx, and hence many other transitional fossils found since, are frauds. When they do accept their authenticity, they typically claim that they are not truly transitional, ignoring the anatomical features they share with one subsequent evolutionary branch to claim that the fossils belong to the other subsequent branch.

Creationists disbelieve the accuracy of radiometric and stratigraphic dating techniques and therefore dismiss the support the fossil evidence provides for the chronology of common descent. However, as we have again detailed in our posts on young Earth creationism, independent dating techniques are in agreement for specimens where multiple techniques are applicable, and in the case of radiometric dating, are validated by an extensive laboratory database. Creationist “theories” proposing sudden dramatic changes in radioactive decay rates during Earth’s history are fantastical and incapable of accounting for even their own implications. While trying to debunk those transitional fossils that have been discovered, evolution deniers also claim that many more transitional fossils should have been discovered, and that gaps in the fossil record render them unconvincing as scientific evidence. In other words, they demand more evidence while rejecting any evidence that is presented, as is typical of science deniers across the many topics we deal with on this blog site.

For those who believe in the fossil record and its chronology, the most interesting, and still unsettled, question it raises for evolutionary theory concerns the so-called Cambrian Explosion. This refers to the apparently “sudden” burst of evolution that occurred about 540 million years ago, when most major animal phyla (i.e., groupings of animals that share the same general body plan) that we know today first appeared in the fossil record. I put “sudden” in quotation marks, because the “explosion” seems to have unfolded over 20-25 million years. Prior to this period the majority of living species appear to have been single-celled organisms, or colonies of such cells, although there is some fossil evidence for moderately complex animals. But during the Cambrian era there was a boom in the rate of evolutionary diversity. Creationists often overstate this boom as evidence for intelligent design (albeit some four billion years after Earth first appeared), by claiming erroneously that all major animal groups then appeared together in the fossil record fully formed, instead of branching from a common ancestor.

Although several possible explanations for the Cambrian explosion have been proposed, there is not yet consensus or definitive evidence supporting one correct account. Since natural selection favors adaptation to the environment, one class of explanations attributes the burst to a rapidly changing Earth environment. The proposals are characterized by one or more of the following: the increase in originally absent oxygen molecules in the atmosphere, emitted over billions of years as a product of photosynthesis by microscopic early organisms; the original formation of the atmospheric ozone layer that shields Earth’s surface from fatal deep ultraviolet radiation from the Sun; the emergence from an ice age during which most of Earth’s surface was covered in ice; enormous volcanic activity that dramatically increased calcium concentrations in the oceans, facilitating the development of skeletons.

There is evidence that rapid environmental changes in the opposite direction led to the most calamitous mass extinction event in Earth’s history, at the end of the Permian and beginning of the Triassic periods, some 250 million years ago. That “Great Dying” is correlated with long-term massive volcanic activity in Siberia, which led to rapid heating and oxygen depletion in Earth’s oceans and a thinning of the atmospheric ozone layer. As a result of those environmental changes, more than 90% of all marine species and up to 70% of all land vertebrate species were killed off.

Other possible explanations for the Cambrian explosion focus on developmental biology or ecology. Some argue that relatively minor modifications in the development of embryos to adult form could have triggered large changes. Others suggest that the nature of the relationship between predators and prey would have changed dramatically after eyesight evolved. Still others propose that the development of genetic complexity may exhibit threshold behavior, with a threshold passed during the Cambrian as a result of the appearance of sufficient oxygen to support more energetic metabolism.

The Cambrian explosion is one of the features of the fossil record that prompted Niles Eldredge and Stephen Jay Gould to propose in 1972 the theory of punctuated equilibrium. According to their theory the history of evolution among sexually reproducing organisms is characterized by long intervals of near stasis, with only minor evolutionary advance in most species, punctuated by short periods of rapid change. The theory remains controversial, although some more modern research in developmental biology has suggested dynamic and physical mechanisms in tissue growth that could, in principle, be responsible for rather abrupt changes in animal body plans.

The bottom line is that evolutionary biology remains a living science. Not all phenomena are yet explained, not all mechanisms are understood. The open questions do not falsify the theory, but rather stimulate attempts to introduce more detail to it and to accounting for the highly complex interactions of biology with the history of Earth’s changing environment. While those attempts proceed, the evidence for the roles of genetic mutation, natural selection and common descent is continually growing and becoming more convincing. In the next part of this series, we will discuss perhaps the most compelling evidence, which comes from the biomolecular mapping of the genome of many species.

To be continued in Part III

References:

T.M. Conrad, N.E. Lewis and B.O. Palsson, Microbial Laboratory Evolution in the Era of Genome-Scale Science, Molecular Systems Biology 7, 509 (2011) (http://msb.embopress.org/content/7/1/509)

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https://www.sciencealert.com/one-of-longest-evolution-experiments-overthrowing-previous-assumptions

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https://en.wikipedia.org/wiki/Microevolution

https://en.wikipedia.org/wiki/Speciation

https://en.wikipedia.org/wiki/Phylogenetic_tree

http://www.talkorigins.org/faqs/comdesc

http://www.talkorigins.org/faqs/comdesc/section1.html

https://trueorigin.org/theobald1b.php

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R. Dawkins, The Blind Watchmaker (Norton, 1987) (https://www.amazon.com/Blind-Watchmaker-Evidence-Evolution-Universe/dp/0393351491)

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D.M. Kermack and K.A. Kermack, The Evolution of Mammalian Characters (Springer, 1984) (https://www.amazon.com/Evolution-Mammalian-Characters-D-Kermack-ebook/dp/B00FB724EM)

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https://en.wikipedia.org/wiki/History_of_human_migration

https://en.wikipedia.org/wiki/Biogeography

https://www.thoughtco.com/how-biogeography-supports-evolution-249883

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https://en.wikipedia.org/wiki/Piltdown_Man

http://www.talkorigins.org/faqs/archaeopteryx/forgery.html

https://iconsofevolution.com/icons-of-evolution/

https://en.wikipedia.org/wiki/Cambrian_explosion#Uniqueness_of_the_explosion

https://en.wikipedia.org/wiki/Punctuated_equilibrium