(Note: All previous parts in the Complexity Explained series by Dr. Vinod Wadhawan can be accessed through the ‘Related Posts’ listed below the article.)
In any evolutionary process, what evolves is complexity. Chemical complexity evolved till some of it became indistinguishable from biological complexity. Evolution of biological complexity is determined by two main factors: natural selection (made famous by Charles Darwin), and self-organization. I focus on the natural-selection aspect of biological evolution in this article.
13.1 Darwinian Evolution
The greatest single contribution to the subject of complexity was made (unwittingly, perhaps) by Charles Darwin. The year 2009 marked the second birth centenary of Darwin, as also 150 years of the publication of his celebrated book On the Origin of Species by Means of Natural Selection.
Living organisms are open systems, i.e. they are constantly exchanging matter and energy with the environment. There is a fair amount of dynamic equilibrium between a living organism and its surroundings. The organism cannot survive if this equilibrium is disturbed too much, or for too long. The fact that an organism survives implies that, in its present form, it has been able to adapt itself to the environment. If the environment changes slowly enough, living entities can evolve (over a long enough time period) a new set of capabilities or features which enable them to survive even under the changed conditions. Over long periods of such evolutionary change, creatures may even develop into new species. This was the message of Charles Darwin’s (1859) bold theory of evolution through cumulative natural selection. He demonstrated that adaptation to the environment was a necessary outcome of the exchange processes going on between organisms and their surroundings. A consequence of his theory was that all living organisms are the descendants of one or a few simple ancestral forms.
Darwin started with the observation that, given enough time, food, space, and safety from predators and disease etc., the size of the population of any species can increase in each generation. But this indefinite (exponential) increase does not actually occur, i.e. the so-called ‘biotic potential’ of a species is actually never realized. In fact, usually only a very tiny fraction of the biotic potential is realized, meaning that only a small minority of the offspring reach maturity to produce the next generation of offspring; the rest die prematurely.
Thus, there must be limiting factors in operation. Influenced by Malthusian ideas, Darwin imagined that if, for example, available food is limited, only a fraction of the population can survive and propagate itself. [Of course, it is now known that limited resources are seldom the primary factor influencing the course of evolution.] What decides who will survive and who will not?
Darwin’s answer was that, since not all individuals in a species are exactly alike (i.e. there is variation in the population), those which are better suited to cope with the prevailing conditions will stand a better chance of survival (survival of the fittest). The fittest individuals not only have a better chance of survival, they are also more likely to procreate. Thus, attributes conducive to survival get ‘naturally selected’ at the expense of less conducive attributes. And the effects of this natural selection accumulate over time. This is the process of cumulative natural selection recognized by Darwin.
It is also observed that children tend to resemble their parents to a substantial extent. The progeny of better-adapted individuals in each generation, which survive and leave behind more offspring than others, acquire more and more of those features which are suitable for good adaptation to the existing or changing environment. A species perfects itself, or adjusts itself, for the environment in which it must survive, through the processes of both cumulative natural selection and inheritance.
Thus there are four basic features of Darwinian evolution:
- Variability and variety in members of a population in the matter of coping with a given environment.
- Inheritance of this variation by the next generation, with random modifications.
- Differential survival and reproductive success of individual members of this new generation in the given environment.
- Establishment of a new population more adapted to the environment, possessing new variations to pass onto the next generation.
Darwin’s main postulate was that a species evolves because natural selection acts on small inheritable variations in the members of the species. But it was argued by his opponents that, since a species is also characterized by interbreeding among its members, such small variations should get averaged away. Darwin had no answer to counter this because the actual mechanism of inheritance was not known at that time. The answer in fact had been provided in 1865 (i.e. during the lifetime of Darwin, but apparently unknown to him) by the work of Gregor Mendel, the founder of the subject of genetics. We now know that the genotype or genome of an organism is its genetic blueprint. It is present in every cell of the body of the organism. The phenotype, on the other hand, is the end-product (the organism) which emerges through execution of the instructions carried by the genotype. It is the phenotype that is subjected to the battle for survival, but it is the genotype which carries the accumulated evolutionary benefits to succeeding generations. The phenotypes compete, and the fittest among them have a higher chance of exchanging genes among themselves.
Mendel’s laws of genetics were rediscovered independently by quite a few workers. One of them was the Dutch botanist Hugo de Vries, who not only rediscovered Mendel’s laws for the inheritance of dominant and recessive characteristics, but also genetic mutations. These were sudden (unexplained) changes of form which could be inherited by the offspring.
The present, post-Darwinian picture is that the inherited characteristics of the progeny are caused by genes. In sexually reproducing organisms, each parent provides one complete set of genes to the offspring. Genes are portions of molecules of DNA, and their specificity is governed by the sequences in which their four bases (adenine (A), thymine (T), guanine (G), and cytosine (C)) are arranged. The double-helix structure of DNA, together with the restriction on the pairing of bases comprising the DNA molecule to only A-T and G-C, provides a mechanism for the exact replication of DNA molecules. The DNA sequence on a gene determines the sequence of amino acids in the specific proteins created by the live organism.
Genes programme embryos to develop into adults with certain characteristics, and these characteristics are not entirely identical among the individuals in the population. Genes of individuals with characteristics that enable them to reproduce successfully tend to survive in the gene pool, at the expense of genes that tend to fail. This feature of natural selection at the gene level has consequences which become manifest at the organism or phenotype level. Cumulative natural selection is not a random process.
If like begets like (through inheritance of characteristics), by what mechanism do slight differences arise in the gene pool of successive generations so that the species evolves towards evolutionary novelty? Apart from crossover (where applicable), one mechanism is that of mutations. Mutations, brought about by radiation or by chemicals in the environment, or by any other agents causing replication errors, change the sequence of bases in the DNA molecules comprising the genes.
In organisms in which sexual reproduction has been adopted as the means for procreation, since the genetic material has two sources instead of one (namely, the two parents), the occurrence of variations in the offspring is higher. The genes from the parents are reshuffled in each new generation. This increases the evolutionary plasticity of the species. However, not all differences in individuals in a population are due to the genetic makeup. Factors such as nutrition also play a role. The observable characteristics of an organism, i.e. its phenotype, are determined both by the genetic potentiality and by the environment.
If all living beings have the same or only a few ancestors, how have the various species arisen? The Darwinistic answer lies in isolation and branching, aided by evolution. Migrations of populations also play a role in the evolutionary development of species. If there are barriers to interbreeding, geographical or otherwise, single populations can branch and evolve into distinct species over long enough periods of time. Each such branching event is a speciation: A population accidentally separates into two, and they evolve independently. When separate evolution has reached a stage that no interbreeding is possible even when there is no longer any geographical or other barrier, a new species is said to have originated.
The term neo-Darwinism essentially connotes a modification of the original ideas of Darwin in the light of later knowledge about the mechanism of transmittal of genetic information from one generation to the next. Margulis and Sagan (2003), who disagree with this neo-Darwinistic view of the origin of species, have summed up neo-Darwinism as follows (in their book Acquiring Genomes: A Theory of the Origins of Species): ‘All organisms derive from common ancestors by natural selection. Random mutations (heritable changes) appear in the genes, the DNA of organisms, and the best “mutants” (individuals bearing the mutations) in competition with the others, are naturally selected to survive and persist. The unsuited offspring die – they tend to be called “unfit” – with fitness, a technical term, referring to the relative numbers of offspring left by an individual to the next generation. The most fit, by definition, produce the largest number of offspring. The mutant variations then leave more offspring, and populations evolve; that is, they change through time. When the number of changes in the offspring accumulates to recognizable proportions, in geographically isolated populations, new species gradually emerge. When sufficient numbers of changes in offspring populations accumulate, higher (more inclusive) taxa gradually appear. Over geological periods of time new species and higher taxa (genera, families, orders, classes, phyla, and so on) are easily distinguished from their ancestors.’
When Darwin published his theory of biological evolution, the field of genetics had not yet taken shape. Naturally, Lamarck, whose work on biological evolution preceded that of Darwin, was also unaware of the crucial role of the genetic mechanism in the evolution of species. We now have the familiar concepts of genotype and phenotype. The term genotype (or genome) refers to the genetic constitution of an organism. It is the genetic blueprint encoded in its strings of DNA chains. Phenotype, on the other hand, signifies the characteristics manifested by an organism; it is the structure created by the organism from the instructions in its genotype. The phenotype is the organism itself. Genotypes correspond to the ‘search space,’ and phenotypes to the ‘solution space.’
Biological evolution is generally believed to be all Darwinian. Namely, variety in a population means that some individuals have a slight evolutionary advantage with respect to a particular characteristic, which is therefore more likely to be passed on to the next generation if it helps in the survival and propagation of the species. Over time, this characteristic gets strengthened and is easily noticeable in the phenotype. Lamarck’s theory of evolution, or Lamarckism, on the other hand, was based on two premises: the principle of use and disuse; and the principle of inheritance of acquired characteristics (without involving the genotype).
But can the environmental conditions in which the parents live indeed affect the genetic characteristics of the offspring? ‘No’ according to the neo-Darwinian theory of evolution, and ‘Yes’ according to the theory of Lamarck. The Lamarckian viewpoint of inheritance of acquired characteristics is not acceptable in modern biology because it runs counter to the central dogma of modern molecular genetics, according to which information can flow from DNA to proteins (or from genotype to phenotype), but not from proteins to DNA (or from phenotype to genotype).
Although Lamarckism is unacceptable for explaining biological evolution, nothing prevents us from using it in artificial evolution (i.e. inside a computer) and exploiting the much higher speed it may offer for reaching an end-goal.
The new (or rather currently hotting up) field of research called epigenetics has brought us dangerously close to Lamarckism, without violating the central dogma of molecular biology. It is now clear that changes other than those in the sequence of nucleic acids in DNA, acquired during the lifetime of parents or grand-parents, can indeed be inherited. Gene expression or interpretation can be influenced by molecules hitchhiking on genes. This heritable non-genetic hitchhiking is called epigenetic inheritance.
The DNA in the cell of an organism carries the genetic blueprint for the synthesis of various proteins needed by the organism. Some of these proteins even help in the synthesis of other proteins via the instructions embodied in the nucleotide sequence along the DNA chain. But there is no way proteins by themselves can engineer the synthesis of the nucleic acids comprising the DNA. Thence the central dogma of molecular biology that information can flow from nucleic acids to proteins, but not from proteins to nucleic acids. Lamarckism in its original form is unacceptable in the theory of biological evolution because it implies that the information acquired by an organism during its life time, and therefore incorporated in its phenotype only (e.g. as proteins), can be somehow transmitted to the offspring via the genotype.
But there is a ‘loophole’ in this argument! Genes, which are nothing but portions of the long sequence of nucleic acids in the DNA chain, contain the coded information for synthesizing various proteins. And we have known since the days of Mendel that not all genes are active all the time. Some genes are dominant, while others are recessive. One of the Mendelian laws of genetics is that it is the combination of dominant and recessive genes inherited from the parents that dictates the characteristics (phenotype) of an offspring. The dominant genes are the active or ‘switched on’ genes, and recessive genes are the ‘switched off’ genes. We saw in Section 12.3 (Part 12) how the presence of certain hormones can influence gene expression, and once a gene has been switched on by the presence of a hormone, it acts as a switch which can alter the ‘on’ or ‘off’ states of other genes. So hormones are one example of what can influence gene activity.
But hormones, after all, are nothing but chemical compounds. Can other chemicals, for example those in the diet of an organism, also influence gene expression? The answer is ‘Yes’. And not just food, but even the mental state of an animal can be responsible for the secretion of chemicals which can influence gene expression. From the point of view of genetics and transmittal of acquired characteristics, the influence on the genotype of a parent should be of an irreversible nature; only then can it affect the progeny in a permanent manner; then only can we have an inheritance of acquired characteristics by the progeny. This is the subject matter of the field of epigenetics.
Epigenetics is the study of changes in gene function that do not depend on changes in the primary DNA sequence, and depend on stable, heritable marking of DNA. Epigenetic effects influence the phenotype, without changing the genotype.
One particular heritable marking of DNA that has been investigated substantially is that of methylation, i.e. attachment of the -CH3 group to one or more nucleic acids along the DNA chain. It has been found, for example, that methylation is quite frequent in cancer cells and it is difficult to distinguish from mutations. Methylation affects gene expression, and, as a feedforward mechanism, can have serious transgenerational effects. Epigenetic changes can be passed through the germ line for many generations. And epigenetic changes can occur throughout the life time of an individual: Methylation can turn some genes off, and demethylation can turn other genes on.
The Human Genome Project was completed a few years ago. It has mapped out the sequence of all the three billion nucleotide pairs comprising the human DNA. And the Human Epigenome Project has been already started. Its goal is to add an indicator to every spot on the DNA where methyl markers can attach and change the gene expression there.
13.5 Theories of the Origins of Species
Ironically the popular evolutionist’s view that organisms evolve by the accumulation of random mutation best describes the evolutionary process in bacteria. All of the larger, more familiar organisms originated by symbiont integration that led to permanent associations.
Margulis and Sagan (2002)
Indeed, as Wallin wrote in 1927, ‘It is a rather startling proposal that bacteria, the organisms which are popularly associated with disease, may represent the fundamental causative factor in the origins of species.’ We agree.
Margulis and Sagan (2002)
The classical viewpoint that speciation occurs, i.e. new species arise, as a result of the cumulative effect of mutations, has been strongly contested by Lynn Margulis. According to Margulis and Sagan (2002), ‘No evidence in the vast literature of heredity change shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation. Then how do new species come into being? How do cauliflowers descend from tiny, Mediterranean cabbagelike plants, or pigs from wild boars?’ Their answer is that species arise largely by the acquisition of entire genomes through symbiogenesis.
Margulis’s stance has raised debate. Ernst Mayr wrote an appreciative foreword to the book by Margulis and Sagan (2002). But the foreword also said this: ‘Speciation – the multiplication of species – and symbiogenesis are two independent, superimposed processes. There is no indication that any of the 10,000 species of birds or the 4,500 species of mammals originated by symbiogenesis.’ Contrast this with the statement of Rachel Nowak (2005): ‘Symbiosis has popped up so frequently during evolution that it is safe to say that it’s the rule, not the exception.’
Life appeared on Earth during what F. Niele (2005) calls the thermophilic regime of energy in the history of the Earth. This form of life comprised of microorganisms that thrived in hot conditions. Chemical evolution and diversification of molecular structure had occurred, and closed-loop autocatalytic reactions had led to the creation of life-like molecules of increasing complexity. Things progressed to a point where the forebears of DNA started appearing, which had potential for replication. The biological prokaryotic cell emerged in due course. This energy regime also saw the emergence and establishment of a metabolism mechanism for the supply of energy, with ATP as the principal ‘cellular energy currency.’ The living organisms of this period used nucleotides for synthesising DNA, and amino acids for synthesising proteins. There was practically no free oxygen in the atmosphere of the Earth.
The next energy regime, namely the phototrophic regime, was dominated by the exploitation of solar energy. It came about because some of the living organisms of the thermophilic regime reached the surface of the sea, where they encountered sunlight. In due course they developed a new metabolism which used solar energy through photosynthesis. Fixing of carbon dioxide, as also the stripping of hydrogen from water (resulting in the creation of free oxygen), originated in this energy regime. The new microorganisms which achieved this were cyanobacteria or blue-greens. They stripped electrons from water molecules, thus releasing hydrogen for use, along with carbon dioxide, in the production of carbohydrates. This gradually built up the molecular-oxygen content of the Earth. Within a few hundred thousand years the atmospheric oxygen levels rose from less than 1% to ~15% of present-day levels.
Abundant availability of solar light made the population of the blue-greens to grow, producing more and more oxygen. But oxygen itself was poison to them. Therefore evolutionary adaptation led to the development of a new kind of cell, namely the eukaryotic cell, which had ‘organelles’ limited by membranes. Let us see how this resolved the crisis.
The atmospheric oxygen in the phototrophic regime was conducive to the aerobes, but poison for the anaerobic blue-greens. However, the blue-greens did not simply fade away in such a situation, as they were instrumental, not only in the production of molecular oxygen, but also in the production of food for the respiring aerobes. Therefore the build-up of oxygen in the atmosphere was really a threat to both these types of organisms. They responded by evolving a symbiogenesis of the two, resulting in the emergence of the eukaryotic cell. Such a cell has an outer membrane which protects its contents from the harsh conditions outside. It also has internal membranes housing the organelles. Lynn Margulis pointed out that the organelles called mitochondria of a green plant cell are descended from an oxygen-respiring bacterium. Similarly, the chloroplasts are descended from another free-living bacterium, namely a cyanobacterium. The first aerobic eukaryotes had the enzymatic tools to detoxify reactive oxygen products. This is how they could ensure the survival of the symbiont blue-greens. In a photosynthesizing eukaryotic cell, the chloroplasts store solar energy in sugars and supply it to the host. The host, in turn, supplies the sugar to the mitochondria, which then supply the host with ATP, the cell fuel.
This symbiogenesis between oxygenic photosynthesis and aerobic respiration was at the heart of the oxo-energy revolution (Niele 2005), resulting in the emergence of the aerobic energy regime. The emergence of the eukaryotic cell embodied sunlight-harvesting photosynthesis, and protection against oxygen toxicity. Its highly efficient metabolic combustion via aerobic respiration triggered the appearance of multicellular life forms which, in turn, led to the emergence of still more complex life forms and ecosystems. Humans appeared on the scene in due course.
Of course, the eukaryotic organisms have continued to coexist with the prokaryotic organisms (namely the bacteria and the archaea) in several schemes. In fact, as Knoll said, the prokaryotes ‘maintain the foundation of all functioning ecosystems on this planet.’ An example is the nitrogen that bacteria make available for biological processes.
Emergence of new species
Life originated with bacteria. Bacteria do not speciate the way eukaryotic organisms do. The idea of a species does not apply to them. Bacteria can pass genes back and forth. There is no fixed genome to define the species of any bacteria. Bacteria are prokaryotes.
The first eukaryote emerged by the symbiogenesis of two prokaryotes. The concept of a species can apply only to eukaryotes. It follows that the origin of species occurred long after the origin of life in the form of bacteria. Therefore, the species of all the larger organisms (protoctists, fungi, animals, plants) originated symbiogenetically in the beginning. Nucleated organisms emerged on Earth some 1200 million years ago.
However, there is no reason to believe that symbiogenesis is the only way in which new species can arise. It is characteristic of complex systems that, often, small changes can have unexpectedly large consequences, including the emergence of new species. Effects of mutations can gradually build up to a stage wherein a sudden bifurcation occurs in phase space, and a new species arises. Speciation may well be an emergent phenomenon. This is in disagreement with the statement of Margulis and Sagan (2002) that ‘intraspecific variation never seems to lead, by itself, to new species.’
13.6 Concluding Remarks
Any entities that can replicate, and that have a variation both in their specific features and in their reproductive success, are candidates for Darwinian selection and evolution.
Darwin changed the way we humans look at ourselves and our place in the world. The basic idea of evolution by natural selection has gone far beyond the precincts of biology, and has permeated the human psyche in all sorts of ways. Apart from biological Darwinism, we speak of chemical Darwinism, quantum Darwinism, neural Darwinism, and what not. Deep down under, what evolves in any system is complexity.
Evolution of biological complexity is determined by two factors: natural selection, and self-organization. Self-organization creates order in any complex system. Darwinian natural selection acts on this existing order and hones it further. I shall dwell on the self-organization aspect of biological complexity in the next article in this series. Symbiogenesis is not the only way in which new species can arise. Often, small changes in complex adaptive systems can have unexpectedly large consequences, including the emergence of new species. Effects of mutations can gradually build up to a stage wherein a sudden bifurcation occurs and a new species arises. Speciation may well be an emergent phenomenon in a complex adaptive system.