British naturalist Charles Darwin (1809-1882) laid the foundations of evolutionary biology through the process of natural selection, which he outlined in two books, Origin of the Species and The Descent of Man.
Masatoshi Nei is Evan Pugh Professor of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics. He has written several books on molecular evolution including Molecular Evolutionary Genetics (1987), Molecular Evolution and Phylogenetics (2000), and more recently Mutation-Driven Evolution (2013). Nei was awarded the 2013 Kyoto Prize in Basic Sciences in recognition of his “research on the evolution of biological populations using quantitative analyses of genetic variation and evolutionary time.”
Simply Charly: You were recently awarded the 2013 Kyoto Prize in Basic Sciences for your pioneering work in molecular evolutionary biology, specifically for developing various statistical methods to determine the molecular mechanisms of biological diversity and evolution. Can you give us some insight into how you developed these methods and why you did it?
Masatoshi Nei: When I was a college student around 1950, I read a number of articles and books on evolution, but I did not like the subject because it was based on too much speculation. I then studied population genetics, which was formulated on the solid basis of Mendelian genetics. Unfortunately, there were not many Mendelian characters identified in wild populations at that time. This situation suddenly changed in the 1960s, when molecular techniques were introduced in the study of evolution and population genetics. At this time, it became clear that genetic variation can be studied by amino acid variation within and between species rather than allele frequency differences, as was done in population genetics. To facilitate these studies, I developed several statistical methods with which we could measure the extent of amino acid variation within and between populations, and relate these variations to mutation rate, evolutionary time, and other evolutionary factors. I also recognized the importance of gene duplication in evolution and investigated how duplicated genes are formed, and how they produce gene families of evolutionary significance. I conducted these studies because I wanted to make evolutionary biology a hypothesis-testing science.
SC: The idea for which you are probably best known is the eponymously named Nei’s Genetic Distance. Can you tell us what the idea behind it is?
MN: In evolutionary biology, it is important to know the extent of genetic divergence between populations to understand their evolutionary history. In the 1950s and 1960s, a number of different measures of genetic divergence were proposed, but none of them was related to the time after separation of the populations. Because I knew the general pattern of amino acid substitutions in proteins, I developed a new statistical measure, which is proportional to the number of amino acid substitutions between populations. This measure is now called Nei’s Genetic Distance. Since the rate of amino acid substitution is known to be approximately constant per year, it is possible to estimate the time of divergence between populations if we know the rate for the proteins used. Using this idea, I could estimate the times of divergence between African and non-African peoples (about 115,000 years ago) and between Europeans and Asians (about 55,000 years ago). This study represents the first indication of the Out-of-Africa theory of the origin of modern humans.
SC: Your latest book, Mutation-Driven Evolution, presents one of your most controversial views, which you’ve been developing over the last 40 years. As the title implies, you challenge Charles Darwin’s theory of natural selection head-on by asserting that mutation, not natural selection, drives evolution. While you don’t deny that natural selection plays a role, you consider it to be secondary to mutation as the real driver of evolution. How so?
MN: From the time of Charles Darwin, evolutionists have examined the temporal changes of phenotypic (visible) characters or paleontological data. However, because these changes are affected by both genetic and environmental factors, it was difficult to assess how new genetic variation was generated at each genetic locus, and how natural selection operated for individual genes. Darwin showed that organisms could change in time because artificial selection is effective, but he had difficulty in explaining how organisms can change in nature without human intervention. He then argued that struggle for life must exist in nature because the population size of an organism tends to increase geometrically while food supply increases arithmetically, according to an 18th/19th-century scholar, Thomas Malthus. However, Darwin never presented evidence that natural selection is really the factor of evolution. Actually, in his time it was almost impossible to show that natural selection rather than mutation is responsible because Mendelian inheritance and the mechanism of generation of new mutations were not known.
Experimental study of natural selection was initiated in the early 20th century after Mendelian genetics was established, and population genetics theory was developed. However, it was a difficult task to study the process of allele frequency changes by natural selection, because allele frequency changes were often affected by environmental factors and human life was too short to observe the entire process of allele frequency changes in natural populations. The mechanism of occurrence of new variations or mutations was also unclear in the first half of the 20th century.
The development of molecular biology in the latter half of the 20th century changed this situation dramatically. Because all processes of metabolism and reproduction have now been shown to be controlled by DNA or RNA molecules, we could study the evolutionary changes of organisms by examining the changes of DNA or RNA molecules. Initially, most investigators studied the evolutionary changes of DNA or RNA molecules themselves, and this study led to the conclusion that most nucleotide substitutions occur by mutation pressure, and the rate of nucleotide substitution is more or less constant per year. Because of this finding, biologists Motoo Kimura, Jack King, and Tom Jukes proposed the neutral theory of molecular evolution around 1968. However, they believed that the evolution of phenotypic characters occurs by natural selection as postulated by Darwin.
At this time, I thought that if most nucleotide substitutions occur in a neutral fashion, there must be a large component of neutral or near-neutral changes in phenotypic characters as well. I then examined the evolutionary changes of genes controlling many different phenotypic characters and found that the genes are evolving neutrally for most of the time. This has become clearer as developmental biology and genomics have advanced.
SC: What evidence and arguments do you adduce in support of this new mechanistic theory of mutation-driven evolution?
MN: Recent genomic studies have shown that there are many different kinds of mutations at the DNA level, including nucleotide substitution, deletion/insertion, gene duplication, gene loss, chromosomal change, genome duplication, horizontal gene transfer, symbiosis, etc.; these genomic mutations have been shown to affect various phenotypic characters. For this reason, the amount of genomic mutations occurring in one generation is now known to be enormous. At present or kept in the genome as neutral variations, but some mutations are advantageous, so that they spread through the population. These advantageous mutations are biochemically compatible with the pre-existing genes in the genome, and mutations that are not compatible are eliminated from the population. This is true even with a gene, which is composed of a sequence of hundreds or thousands of nucleotides. In almost all genes, the nucleotide sequence is far from random, and only a set of genes composed of specific arrangements of nucleotides is capable of having gene function.
In other words, each nucleotide sequence of a gene is under strong functional constraint. A genome composed of many genes is also under strong functional constraint, and it is not a random combination of different genes. For this reason, species with well-differentiated genomes cannot produce offspring; if offspring are produced, they are usually infertile. When we study the struggle for life in a species, we cannot see this because the traits for fighting are controlled by a large number of genes. However, the evolutionary pattern of underlying genes appears to be the same for all the traits. The genomic constraint apparently existed even when life originated. Therefore, it appears that genomic constraint is quite general and natural selection is generally for eliminating unfit genomes or genotypes; it also seems that innovative characters are generated when constraint-breaking mutations occur. This view conforms with the conclusion of recent genomic research.
Darwinians often state that adaptation of organisms occurs only by natural selection. Although it is very difficult to define adaptation quantitatively, there are many cases of adaptation of organisms that are triggered by the formation of very special proteins. For example, the flying ability of the bar-headed goose over the Himalayas is known to be due to the high level of oxygen affinity of hemoglobins. The bar-headed goose crosses the Himalayas twice a year at altitudes where oxygen (O2) levels are less than half those at sea level, and temperatures are below −20°C, whereas the closely related graylag goose can live only in the plains. It is known that there are four amino acid differences between the hemoglobins of the two species, and these differences are responsible for the bar-headed goose to be able to cross the Himalayas. This finding indicates that a small number of amino acid substitutions (mutations) enable bird species to adapt to a new environment. We now know that there are many examples of mutations that are responsible for adaptation of an organism to new environments.
Recently, we have come to know that there are many different kinds of mutations that cause phenotypic evolution more effectively than amino acid substitutions. They are genome duplication, chromosomal change, symbiosis, horizontal gene transfer, change in gene expression, transposon, etc. These DNA changes are obviously mutational events and do not belong to the realm of natural selection. It is now well established that genome duplication and chromosomal change have played important roles in generating a large number of new species in plants and fungi. Symbiosis is also known to have generated many new species.
MN: As mentioned above, I first came to suspect that if the number of amino acid substitutions increases in proportion to evolutionary time, most amino acid substitutions must be more or less neutral—even in genes controlling phenotypic characters—and that mutation rather than natural selection must be the driving factor of evolution. It was then discovered that a large portion of amino acid mutations are deleterious, and only a small proportion of the mutations generate innovative phenotypic characters. I then concluded that phenotypic characters must occur by constraint-breaking mutations.
SC: Why do you suppose the scientific community hasn’t caught up with your findings? Do you feel they’ve ignored your views because molecular biology is still a comparatively nascent field of study, despite the great strides that have been made in recent years?
MN: I believe that because most evolutionists are still working with phenotypic characters, they are not aware of the recent progress of developmental biology and genomics. Most of them still do not study mutational events and selection at the molecular level.
SC: If you’re correct that mutation drives evolution, then it would seem that there’s a fundamental bias against your way of thinking. It reminds me of the observational bias known as The Streetlight Effect encapsulated in the following humorous story:
A policeman sees a drunk man searching for something under a streetlight and asks what the drunk has lost. He says he lost his keys and they both look under the streetlight together. After a few minutes the policeman asks if he is sure he lost them here, and the drunk replies, no, that he lost them in the park. “Then why are you looking over here?” asks the policeman. And the drunk replies, “because the light’s better here.”
Do you think a lot of scientific inquiry is conducted in this manner, i.e., looking for answers where the light is better rather than where the truth is more likely to lie?
MN: Evolutionary biology is a broad science covering a large number of subjects and studying diverse groups of organisms, and only a few scientists are aware of the progress of the general principles applicable to diverse groups of organisms. Therefore, the streetlight effect is certainly an important factor hindering the acceptance of new theories. For example, many classical evolutionists are still unaware that the definition of mutation has recently been expanded enormously and that all mutational changes can be studied at the molecular level.
SC: Your view isn’t the only challenge to Darwin’s theory of natural selection. There have been others. For instance, the late evolutionary biologist, Lynn Margulis, argued, quite controversially, that symbiosis (or what she calls symbiogenesis) was the central force behind the evolution of new species, because natural selection is a process of elimination and cannot produce all the diversity we see around us. What do you make of her view?
MN: Lynn Margulis was a maverick proposing the importance of symbiosis in evolution. She indicated that symbiosis is an important evolutionary mechanism for generating species diversity. However, she attacked the traditional theory of species formation without understanding it very well. In my view, symbiosis is one form of mutational event, and although it generates a great deal of genetic variation, there are many other ways of generating new variation as mentioned above. For this reason, her theory is not a unified theory of evolution.
SC: Another, more recent, attack on the concept of natural selection was mounted by philosophers Jerry Fodor and Massimo Piatelli-Palmarini in their book What Darwin Got Wrong. They contend that the theory of natural selection “cannot predict/explain what traits the creatures in a population are selected-for” because how would one distinguish a trait that is selected from one that comes along with it. For example, a trait such as a heart evolved for pumping blood, but such traits usually come along with other features, such as making a heart-like noise. Therefore, they conclude that “the claim that selection is the mechanism of evolution cannot be true.” Do you find any merit in their argument?
MN: I disagree with them. If we study the entire developmental process of various characters, we should be able to tell which part of the organism has changed first by mutation and selection, and which part is of secondary or auxiliary changes. I am interested in understanding the coordinated evolution of different characters at the molecular and developmental level.
SC: What are some of the biggest hurdles still facing molecular evolutionary biology today?
MN: Although we have the basic knowledge of molecular and developmental biology, it is not easy to know the evolutionary process of organisms because it is very complicated. We now have the complete genome sequences of humans and chimpanzees, but we know very little about the molecular basis of phenotypic differences of the two species. This is true even with the physiological differences between two different bacterial species. This difficulty arises because all the genes in the genomes interact in intricate ways. The interaction between genomic expression and environmental factors is also very complicated. However, unless we know the molecular basis of phenotypic differences between different species, we cannot claim that we have understood the evolutionary process. To achieve this goal, enormous efforts would be necessary for many years.
At the present time, it is often stated that evolution occurs by mutation, selection, and genetic drift, and there is no need to do more work. This view is similar to the idea of creation by God, where we do not need to understand how different species are produced mechanistically. However, if we want to understand every step of evolution, we cannot avoid using the most fundamental approach that depends on developmental biology and genomics.