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Introduction

Specific examples of evolutionary novelty

1. The Hall-Hartl E. coli experiment. In a 1974 paper Barry Hall and Daniel Hartl identified a gene in the bacterium E. coli that is responsible for metabolizing lactose, using a complicated three-part process. They removed this gene, and then permitted the bacteria to multiply in a stressed environment containing lactose. Within 24 hours the bacteria had evolved a capability to utilize lactose, by means of a similar but distinct three-part biochemical pathway, involving two mutated genes [Hall1974; Miller1999, pg. 145-147]. Biologist Douglas Futumya described this discovery as follows: "One could not wish for a better demonstration of the neo-Darwinian principle that mutation and natural selection in concert are the source of complex adaptations." [Futumya1986]. Biologist Kenneth Miller points out that not only is it a valid example of evolutionary novelty, it is also an example of a multi-part biochemical system that intelligent design writer Michael Behe has insisted could not be produced by natural evolution [Miller2004].

2. Lenski's long-running E. coli experiment. Biologist Richard Lenski and his colleagues have been conducting a long-running experiment on bacterial evolution that began in 1988. Starting with 12 flasks of E. coli bacteria, identical except for some neutral markers, and then each day inserting 1/100 of the flask's liquid (which contained glucose and citrate, among other materials) into a new flask. In this way they followed the course of these bacteria for 45,000 generations. As the generations continued, each of the 12 lines grew progressively better at processing glucose, although each took a different trajectory. Examining the results after 20,000 generations, the experimenters found that for two of the 12 lines, 59 genes had changed their levels of expression, and that all 59 had changed in the same direction in each line -- in other words, the two lines had independently "discovered" virtually the same improved scheme for glucose metabolism. Later in the experiment, shortly after generation 33,000, the average population of one of the lines shot up by a factor of six above the others. The investigators found that this line had developed the ability to utilize citrate, which bacteria normally cannot use, by means of a remarkable combination of two distinct mutations [Lenski1994; Dawkins2009, pg. 116-132].

   In a new result from Lenski's long-running experiment, in June 2015 Lenski's team found that that a second strain of E. coli has arisen within the same flask as the citrate-eating strain. This second strain, although lacking the ability to utilize citrate, has evolved the ability to utilize some by-products of the first strain. Thus the two strains together have formed a cross-feeding ecosystem, all within a flask [Turner2015]. Lenski's fascinating career and experiment are recounted in a November 2013 article in Science [Pennisi2013].

3. Lenski's 2012 virus/E. coli experiment. In a separate experimental study, announced in 2012, a research team led by Richard Lenski demonstrated how colonies of viruses were able to evolve a new trait in as little as 15 days. The researchers studied a virus, known as "lambda," which infects only the bacterium E. coli. They engineered a strain of E. coli that had almost none of the molecules that this virus normally attaches to, then released them into the virus colony. In 24 of 96 separate experimental lines, the viruses evolved a strain that enabled them able to attach to E. coli, using a new molecule (a channel in E. coli known as "OmpF") that they had never before been observed to utilize. All of the successful runs utilized essentially the same set of four distinct mutations. Justin Meyer, a member of the research team, estimated that the chance of all four mutations arising "at random" is roughly one in 10²⁷ (one thousand trillion trillion). Yet these lambda viruses acquired all four mutations in a matter of weeks [Zimmer2012].

4. Doebeli's E. coli experiment. Michael Doebeli, a mathematical biologist at the University of British Columbia in Canada, ran experiments with E. coli, wherein the bacteria were provided both glucose (E. coli's preferred food) and acetate. In multiple runs of the experiment, the bacteria often split into two lines, one specialized to use glucose, and the other specialized to use acetate. When the researchers sequenced the genomes of the two resulting lines from various experimental runs, they found that the bacteria had evolved in remarkably similar ways, involving many of the same mutated genes from run to run. In other words, the evolutionary result was remarkably consistent [Zimmer2014c].

5. Japanese nylon-eating bacteria. Japanese biologists recently discovered a bacterial species that thrives in nylon waste. It turns out that these bacteria had undergone a "frame shift" mutation, where an extra base pair had been inserted into the bacteria's DNA. This mutation significantly changed the bacteria's biology, since a long series of amino acids were altered, but by remarkable chance this alteration endowed the bacteria with the facility to metabolize nylon, albeit not very efficiently [Negoro1994].

6. The Milano mutation. Scientists recently discovered that certain persons in an Italian community, all descended from a single individual several generations back, possess a genetic mutation that increases "good" cholesterol and provides an effective antioxidant, thus resulting in measurably improved cardiovascular health [Krotz2002; Musgrave2003].

7. Antibiotic-resistant diseases. Perhaps the best-known examples are the recent evolution of new strains of tuberculosis that are resistant to all known anti-TB drugs. By analyzing DNA sequences, researchers have identified at least six different families of tuberculosis, at least one of which appears to be evolving on an unexpected and potentially very dangerous path [Lehrman2013]. Another example is drug-resistant strains of HIV that in many cases evolve within the body of a single patient [Coyne2009, pg. 130-131; Mason2009]. For instance, researchers now fear that HIV, which has been largely kept in check by antiretroviral drugs in first-world countries, is now poised for a rapid upsurge, due to the emergence of multi-drug-resistant strains of HIV that have been documented in several large U.S. and European cities.

   Sadly, even these regimes are now failing, as "pan-resistant" genes, which defeat all available antibiotics" are now spreading around the globe [MacKenzie2015]. This was brought to the fore by the announcement on 27 May 2016 that a Pennsylvania woman, who was diagnosed with a urinary tract infection, was in fact infected with a strain of bacteria that was resistant to colistin, an antibiotic "of last resort" -- used only when all other antibiotics have failed. This was the first instance of this strain in the U.S. More are feared [Moyer2016].

8. Tibetan high-altitude genes. In 2010, researchers at the University of Utah and Qinghai University in China have found that natives of the Tibetan highlands have evolved ten unique genes that permit them to live well at very high altitudes. Because of these genes, Tibetans have more efficient metabolisms, do not overproduce red blood cells in response to thin air, and have higher levels of nitric oxide, which helps get oxygen to tissue [SD2010b]. A even more recent study found a total of 30 genes that were distinct in the Tibetan population, and concluded that this change constitutes the fastest documented case of human evolution [Wade2010b].

9. Other recent human genetic changes. In addition to the Tibetan high-altitude genes noted in the previous item, several other examples of human genetic changes have recently been discovered, mostly by comparison of DNA sequences, that appear to have occurred very recently in human history (within the past 50,000 years or so). These include: (a) a genetic adaptation has arisen among Southern Chinese that makes them more resistant to alcohol, at the cost of turning red in the face; (b) gene changes in Eskimo populations that help them better cope with bitter cold; (c) genetic changes have been identified among certain primitive farming people that enhance folic acid (vitamin B9) production, which is absent in the tuber plant diet they rely on; (d) two different genetic mechanisms have arisen for the lightened skin color, which among higher-latitude people promotes vitamin D production -- Europeans have one, while East Asians have another; (e) a version of a gene that promotes hair with thicker shafts has arisen in East Asians, possibly as added protection against cold [Wade2010c].

10. New York City fauna. Present-day "before your very eyes" evolution is not restricted to distant lands. In 2011 researchers at the New York University Medical center noted that tomcod in the Hudson River appeared to have acquired resistance to PCBs, which otherwise cause deformities in fish larvae. As it turns out, almost all of these fish share a mutation known as AHR2, which inhibits PCB action and thus shields the fish from harm. This mutation is completely missing from tomcod that live in northern New England and Canada. In a similar vein, researchers at the City University of New York recently identified a set of mutations spanning more than 1000 genes that are present in all white-footed mice in New York City, but which are missing from mice in Harriman State Park, just 45 miles north. Many of these genes are involved in fighting bacteria, while others appear to aid in coping with exposure to chemicals [Zimmer2011].

11. Trinidad guppies. In 2008 study, biologist David Reznick removed guppies from streams in Trinidad that had predators and released them into some new streams above the falls, where predators were absent. After just 11 years, the guppies released in the new streams had evolved to mature later and have fewer (but larger) offspring, just like guppies that naturally occur in Trinidad streams lacking predators [Zuk2013, pg. 71-72].

12. Hawaiian crickets. In the 1800s, a species of cricket was introduced to the Hawaiian Islands, where they became quite common in grassy areas. Males attract mates with their chirps, and females select males based on their songs. However, unlike their counterparts in other Pacific islands, the Hawaiian crickets have a fearsome predator -- dive-bombing flies that target chirping crickets, then implant their larvae in them. In the 1990s, researchers noted that a field in Kauai that previously was the home to many crickets now seemed silent. However, a nighttime search found that in fact there were lots of crickets there, but very few of the males now chirped -- in just five years, or roughly 20 generations, a mutation had arisen in a single gene that inhibited many of the males from chirping [Zuk2013, pg. 81-82].

13. Snakes and Australian cane toads. Originally introduced to Queensland, Australia in 1935 to control sugar cane pests, cane toads both poison their predators (such as snakes) and also out-compete native frogs, resulting in a significant ecological problem. Among other impacts noted in the region, researchers found that over just a few decades, several species of snakes in the area had evolved smaller heads and differently shaped bodies, so that they could no longer swallow cane toads, thus protecting themselves from toads' poison [Zuk2013, pg. 84].

14. Tasmanian devils. Tasmanian devils, a rodent-like creature with impressive fangs, have been seriously threatened by an unusual cancer, namely "facial tumor disease," which is typically transmitted when one individual bites an infected animal. The condition, first observed in 1996, has caused the devil population to plummet by roughly 80% overall, 95% in certain locations. Now genomic analysis has confirmed that a gene has arisen that confers partial immunity, and in only ten generation has spread very widely in the population [Klein2016].

15. Evolution of the coronavirus. The Covid-19 pandemic of 2020-2022, which as of June 2022 has claimed the lives of over 18,000,000 worldwide, including over 1,000,000 Americans, has underscored the reality of evolutionary novelty in a way that affects every person on the planet. The rise of the delta and omicron variants of the virus, which are significantly more transmissible than earlier variants, is a particularly striking case of "evolution before our eyes" [Achenbach2021; Adam2022; Schumaker2021]. No one "designed" these deadly virus variants.

Mathematical and computer models of evolution

Computer simulations have been utilized to study the nature of biological evolution itself. One recent study utilized "digital organisms" -- i.e., computer programs that can mutate, compete, evolve and replicate. Numerous features of natural evolution were seen in these studies, including mutations that were temporarily deleterious, but which served as "stepping-stones" to the evolution of more complex features [Lenski2003; Isaak2007, pg. 64]. Along this line, a 2013 study found, based on extensive computer simulations, that "evolvability," namely the tendency of organisms to develop increasing diversity and evolutionary potential, appears to be a fundamental feature of evolution, not requiring pressure to adapt [Lehman2013].

Along this line, the present author has done a study wherein a computer program, which mimics many of the features of natural evolution, was used to "compose" strings of English text that are reminiscent of the writings of Charles Dickens. Details of this study, as well as an overview of mathematical and computer models that have been used to study evolution, are available in another article on this site: English text.

In short, while it is not yet possible to simulate, on a computer, in full detail, the entire panorama of evolution over the multi-billion history of the Earth, computer-based studies affirm the basic features of evolution, including the generation of novelty. There is certainly no suggestion in the results of these studies that there is some fundamental "showstopper" obstacle to the process of biological evolution as we currently understand it.

Conclusions

On the other hand, such phenomena underscore the remarkable, awe-inspiring nature of the biological world. As astronomer Carl Sagan once wrote [Sagan1994, pg. 52]:

How is it that hardly any major religion has looked at science and concluded, "This is better than we thought! The Universe is much bigger than our prophets said, grander, more subtle, more elegant?" Instead they say, "No, no, no! My god is a little god, and I want him to stay that way." A religion old or new, that stressed the magnificence of the universe as revealed by modern science, might be able to draw forth reserves of reverence and awe hardly tapped by the conventional faiths. Sooner or later, such a religion will emerge.