Several issues in Chao's related paper J. theor. Biol. (1991, 153, 229-246) are revisited... more Several issues in Chao's related paper J. theor. Biol. (1991, 153, 229-246) are revisited. It is argued that mixes of segments from different viral coinfection groups cannot be regarded as sex, unless one is willing to accept that these groups are replicators and individuals. But, because selection in coinfection groups is dynamically analogous to that in trait groups in structured demes, one should also regard these latter groups as replicators. This approach is unacceptable since the groups in question have irregular ploidies, an unfixed number of parents, and no rules analogous to those of meiosis. It is emphasized, however, that the effective presence of neighbour-modulated fitness can ensure dynamical coexistence of covirus segments, even if the equal net reproduction rate within groups is not warranted. It seems that during the origin of coviruses from complete viruses, a higher-level evolutionary unit has become disintegrated, whereas during the origin of life a higher-level unit, the protocell, has emerged from lower-level ones, i.e. unlinked, replicating genes. These two gene-level systems are not homologous, but analogous. Although it is true that the resistance to parasites and the need to avoid a mutational collapse of the genome are likely to have called for some compartmentation in precellular stages of evolution, no clear demonstration, that the proposed mechanisms (the compartmentalized hypercycle and the stochastic corrector model) do in fact solve the error threshold problem, exists. Neither has a plausible mode of protocellular sex been suggested.
New levels of evolutionary units have emerged a number of times. One major pathway of emergence i... more New levels of evolutionary units have emerged a number of times. One major pathway of emergence is the integration of information dispersed in originally competitive lower-level units. Such a transition is thought to have occurred during the origin of life, leading from RNA replicators to protocells. Recent alternative ideas, and some of their connections with population biology, are reviewed.
By sex in eukaryotes, we understand a more-or-less regular succession of meiosis and syngamy. A n... more By sex in eukaryotes, we understand a more-or-less regular succession of meiosis and syngamy. A natural consequence of this is the alternation of haploid and diploid phases in the life cycle. Eukaryotic sex significantly differs from prokaryotic sex in two crucial respects: the cellular mechanisms are quite different, and the transfer of genetic material in prokaryotes is less frequent and more localized (Maynard Smith et al., 1991). However, there seems to be significant continuity in the molecular mechanisms: sex in either case requires recombination enzymes, many of which are active in repair of damaged DNA as well. Thus, it seems plausible that recombinational repair was a preadaptation for sexual recombination. We mention in passing that there is a theory that selection for the recombinational repair of doublestrand DNA damage is responsible for the current maintenance of eukaryotic sex (Bernstein et al., 1981, 1988), but there are severe theoretical as well as factual problems with this theory; we will mention some factual difficulties later. Although an alternation of haploid and diploid phases follows from sex, a clue to the origin problem may lie in the idea that this alternation existed before the evolution of sexual recombination proper. The first hint that this may have been so comes from the classic paper by Cleveland (1947), where he proposed that the haploid-diploid cycle may have started with a spontaneous diploidization by endomitosis: that is, without syngamy. His suggestions were based on original observations on primitive flagellates (hypermastigotes and polymastigotes). Among them, Barbulanympha has a regular endomitosis-meiosis cycle. Margulis & Sagan (1986) called renewed attention to Cleveland’s ideas. In particular, they argued that the alternation of ploidy phases could have a primarily ecological explanation: if the environment alternates in some important factors, this may drive a haploid-diploid cycle, provided the phases are adaptations to different environments. For example, diploids have a smaller relative surface area than haploids, which may confer higher metabolic efficiency. We shall come back to such ideas soon. We focus first on the possible cellular mechanisms connecting the two phases. It is important that some protists have a one-step rather than a two-step meiosis: after syngamy, the two homologous chromosomes become disjunct without premeiotic doubling.
The idea that there may be a conflict between different genetic elements—for example, between chr... more The idea that there may be a conflict between different genetic elements—for example, between chromosomal and mitochondrial genes—is a natural one. A wide range of phenomena, from distorted sex ratios and male sterility in plants to the evolution of chromosome form, may best be understood in terms of such conflict. Before discussing examples, however, it is useful to define ‘genomic conflict’. Suppose that two genetic elements, A and B, influence some phenotypic trait, T. Suppose, further, that some value of the trait, TA, would evolve if only genetic elements A were effective, and an alternative value, TB, if only elements B were effective. If TA and TB are not the same, then there is a potentiality for genomic conflict between elements A and B. In this chapter, we are mainly concerned with cases in which the two genetic elements are present in the same cell: hence the term ‘intragenomic’ conflict. However, the definition can be applied when the elements are in different cells in the same organism, or in different organisms: ‘parent-offspring conflict’ (Trivers, 1974; Parker & MacNair, 1978) is a case in which there is a conflict between genes expressed in different organisms. The occurrence of intragenomic conflict depends on how the genes are transmitted. Imagine a single-celled asexual haploid organism, with a single chromosome containing no transposable elements, one copy of which is transmitted to each daughter cell. Suppose further that the cell contains no symbionts or accessory genetic elements. There would then be no possibility of intragenomic conflict. In practice, conflict arises because cells contain transposons, plasmids, organelles and symbionts, and are sexual. Most biologists find the phenomena of intragenomic conflict unfamiliar and unexpected. It might seem that a good way of making sense of the subject would be to classify the genes concerned according to whether they are in parasites, mutualists, organelles or chromosomes. The snag is that parasites can evolve into mutualists and vice versa, symbionts can become organelles, genes can transfer from organelles to chromosomes, and chromosomal genes may be well behaved, transposable or ‘driving’. For these reasons, we will discuss intragenomic conflict under four heads, according to the different ways in which genes can obtain an unfair advantage over their fellows.
The origin of humans and human society is linked to the appearance of a unique mechanism for cult... more The origin of humans and human society is linked to the appearance of a unique mechanism for cultural inheritance, namely language. Earlier major evolutionary transitions can shed light on the latest transition. Keywords: major transitions; language; society; cultural evolution; cooperation
Philosophical Transactions of the Royal Society B: Biological Sciences
Human societies are no doubt complex. They are characterized by division of labour, multiple hier... more Human societies are no doubt complex. They are characterized by division of labour, multiple hierarchies, intricate communication networks and transport systems. These phenomena and others have led scholars to propose that human society may be, or may become, a new hierarchical level that may dominate the individual humans within it, similar to the relations between an organism and its cells, or an ant colony and its members. Recent discussions of the possibility of this major evolutionary transition in individuality (ETI) raise interesting and controversial questions that are explored in the present issue from four different complementary perspectives. (i) The general theory of ETIs. (ii) The unique aspects of cultural evolution. (iii) The evolutionary history and pre-history of humans. (iv) Specific routes of a possible human ETI. Each perspective uses different tools provided by different disciplines: biology, anthropology, cultural evolution, systems theory, psychology, economy,...
Discriminating, extracting and encoding temporal regularities is a critical requirement in the br... more Discriminating, extracting and encoding temporal regularities is a critical requirement in the brain, relevant to sensory-motor processing and learning. However, the cellular mechanisms responsible remain enigmatic; for example, whether such abilities require specific, elaborately organized neural networks or arise from more fundamental, inherent properties of neurons. Here, using multi-electrode array technology, and focusing on interval learning, we demonstrate that sparse reconstituted rat hippocampal neural circuits are intrinsically capable of encoding and storing sub-second-order time intervals for over an hour timescale, represented in changes in the spatial-temporal architecture of firing relationships among populations of neurons. This learning is accompanied by increases in mutual information and transfer entropy, formal measures related to information storage and flow. Moreover, temporal relationships derived from previously trained circuits can act as templates for copyi...
Complexity of life forms on the Earth has increased tremendously, primarily driven by subsequent ... more Complexity of life forms on the Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted sub-solutions in the framework of learning theory, no general mathematical formalization of this analogy has been provided yet. Here we show, building on former results connecting replicator dynamics and Bayesian update, that (i) evolution of a hierarchical population under multilevel selection is equivalent to Bayesian inference in hierarchical Bayesian models and (ii) evolutionary transitions in individuality, driven by synergistic fitness interactions, is equivalent to learning the structure of hierarchical models via Bayesian model comparison. These correspondences support a learning theory-oriented narrative of evolutionary complexific...
Complexity of life forms on Earth has increased tremendously, primarily driven by subsequent evol... more Complexity of life forms on Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted subsolutions in the framework of learning theory, no general mathematical formalization of this analogy has been provided yet. Here we show, building on former results connecting replicator dynamics and Bayesian update, that (i) evolution of a hierarchical population under multilevel selection is equivalent to Bayesian inference in hierarchical Bayesian models, and (ii) evolutionary transitions in individuality, driven by synergistic fitness interactions, is equivalent to learning the structure of hierarchical models via Bayesian model comparison. These correspondences support a learning theory oriented narrative of evolutionary complexificatio...
Several issues in Chao's related paper J. theor. Biol. (1991, 153, 229-246) are revisited... more Several issues in Chao's related paper J. theor. Biol. (1991, 153, 229-246) are revisited. It is argued that mixes of segments from different viral coinfection groups cannot be regarded as sex, unless one is willing to accept that these groups are replicators and individuals. But, because selection in coinfection groups is dynamically analogous to that in trait groups in structured demes, one should also regard these latter groups as replicators. This approach is unacceptable since the groups in question have irregular ploidies, an unfixed number of parents, and no rules analogous to those of meiosis. It is emphasized, however, that the effective presence of neighbour-modulated fitness can ensure dynamical coexistence of covirus segments, even if the equal net reproduction rate within groups is not warranted. It seems that during the origin of coviruses from complete viruses, a higher-level evolutionary unit has become disintegrated, whereas during the origin of life a higher-level unit, the protocell, has emerged from lower-level ones, i.e. unlinked, replicating genes. These two gene-level systems are not homologous, but analogous. Although it is true that the resistance to parasites and the need to avoid a mutational collapse of the genome are likely to have called for some compartmentation in precellular stages of evolution, no clear demonstration, that the proposed mechanisms (the compartmentalized hypercycle and the stochastic corrector model) do in fact solve the error threshold problem, exists. Neither has a plausible mode of protocellular sex been suggested.
New levels of evolutionary units have emerged a number of times. One major pathway of emergence i... more New levels of evolutionary units have emerged a number of times. One major pathway of emergence is the integration of information dispersed in originally competitive lower-level units. Such a transition is thought to have occurred during the origin of life, leading from RNA replicators to protocells. Recent alternative ideas, and some of their connections with population biology, are reviewed.
By sex in eukaryotes, we understand a more-or-less regular succession of meiosis and syngamy. A n... more By sex in eukaryotes, we understand a more-or-less regular succession of meiosis and syngamy. A natural consequence of this is the alternation of haploid and diploid phases in the life cycle. Eukaryotic sex significantly differs from prokaryotic sex in two crucial respects: the cellular mechanisms are quite different, and the transfer of genetic material in prokaryotes is less frequent and more localized (Maynard Smith et al., 1991). However, there seems to be significant continuity in the molecular mechanisms: sex in either case requires recombination enzymes, many of which are active in repair of damaged DNA as well. Thus, it seems plausible that recombinational repair was a preadaptation for sexual recombination. We mention in passing that there is a theory that selection for the recombinational repair of doublestrand DNA damage is responsible for the current maintenance of eukaryotic sex (Bernstein et al., 1981, 1988), but there are severe theoretical as well as factual problems with this theory; we will mention some factual difficulties later. Although an alternation of haploid and diploid phases follows from sex, a clue to the origin problem may lie in the idea that this alternation existed before the evolution of sexual recombination proper. The first hint that this may have been so comes from the classic paper by Cleveland (1947), where he proposed that the haploid-diploid cycle may have started with a spontaneous diploidization by endomitosis: that is, without syngamy. His suggestions were based on original observations on primitive flagellates (hypermastigotes and polymastigotes). Among them, Barbulanympha has a regular endomitosis-meiosis cycle. Margulis & Sagan (1986) called renewed attention to Cleveland’s ideas. In particular, they argued that the alternation of ploidy phases could have a primarily ecological explanation: if the environment alternates in some important factors, this may drive a haploid-diploid cycle, provided the phases are adaptations to different environments. For example, diploids have a smaller relative surface area than haploids, which may confer higher metabolic efficiency. We shall come back to such ideas soon. We focus first on the possible cellular mechanisms connecting the two phases. It is important that some protists have a one-step rather than a two-step meiosis: after syngamy, the two homologous chromosomes become disjunct without premeiotic doubling.
The idea that there may be a conflict between different genetic elements—for example, between chr... more The idea that there may be a conflict between different genetic elements—for example, between chromosomal and mitochondrial genes—is a natural one. A wide range of phenomena, from distorted sex ratios and male sterility in plants to the evolution of chromosome form, may best be understood in terms of such conflict. Before discussing examples, however, it is useful to define ‘genomic conflict’. Suppose that two genetic elements, A and B, influence some phenotypic trait, T. Suppose, further, that some value of the trait, TA, would evolve if only genetic elements A were effective, and an alternative value, TB, if only elements B were effective. If TA and TB are not the same, then there is a potentiality for genomic conflict between elements A and B. In this chapter, we are mainly concerned with cases in which the two genetic elements are present in the same cell: hence the term ‘intragenomic’ conflict. However, the definition can be applied when the elements are in different cells in the same organism, or in different organisms: ‘parent-offspring conflict’ (Trivers, 1974; Parker & MacNair, 1978) is a case in which there is a conflict between genes expressed in different organisms. The occurrence of intragenomic conflict depends on how the genes are transmitted. Imagine a single-celled asexual haploid organism, with a single chromosome containing no transposable elements, one copy of which is transmitted to each daughter cell. Suppose further that the cell contains no symbionts or accessory genetic elements. There would then be no possibility of intragenomic conflict. In practice, conflict arises because cells contain transposons, plasmids, organelles and symbionts, and are sexual. Most biologists find the phenomena of intragenomic conflict unfamiliar and unexpected. It might seem that a good way of making sense of the subject would be to classify the genes concerned according to whether they are in parasites, mutualists, organelles or chromosomes. The snag is that parasites can evolve into mutualists and vice versa, symbionts can become organelles, genes can transfer from organelles to chromosomes, and chromosomal genes may be well behaved, transposable or ‘driving’. For these reasons, we will discuss intragenomic conflict under four heads, according to the different ways in which genes can obtain an unfair advantage over their fellows.
The origin of humans and human society is linked to the appearance of a unique mechanism for cult... more The origin of humans and human society is linked to the appearance of a unique mechanism for cultural inheritance, namely language. Earlier major evolutionary transitions can shed light on the latest transition. Keywords: major transitions; language; society; cultural evolution; cooperation
Philosophical Transactions of the Royal Society B: Biological Sciences
Human societies are no doubt complex. They are characterized by division of labour, multiple hier... more Human societies are no doubt complex. They are characterized by division of labour, multiple hierarchies, intricate communication networks and transport systems. These phenomena and others have led scholars to propose that human society may be, or may become, a new hierarchical level that may dominate the individual humans within it, similar to the relations between an organism and its cells, or an ant colony and its members. Recent discussions of the possibility of this major evolutionary transition in individuality (ETI) raise interesting and controversial questions that are explored in the present issue from four different complementary perspectives. (i) The general theory of ETIs. (ii) The unique aspects of cultural evolution. (iii) The evolutionary history and pre-history of humans. (iv) Specific routes of a possible human ETI. Each perspective uses different tools provided by different disciplines: biology, anthropology, cultural evolution, systems theory, psychology, economy,...
Discriminating, extracting and encoding temporal regularities is a critical requirement in the br... more Discriminating, extracting and encoding temporal regularities is a critical requirement in the brain, relevant to sensory-motor processing and learning. However, the cellular mechanisms responsible remain enigmatic; for example, whether such abilities require specific, elaborately organized neural networks or arise from more fundamental, inherent properties of neurons. Here, using multi-electrode array technology, and focusing on interval learning, we demonstrate that sparse reconstituted rat hippocampal neural circuits are intrinsically capable of encoding and storing sub-second-order time intervals for over an hour timescale, represented in changes in the spatial-temporal architecture of firing relationships among populations of neurons. This learning is accompanied by increases in mutual information and transfer entropy, formal measures related to information storage and flow. Moreover, temporal relationships derived from previously trained circuits can act as templates for copyi...
Complexity of life forms on the Earth has increased tremendously, primarily driven by subsequent ... more Complexity of life forms on the Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted sub-solutions in the framework of learning theory, no general mathematical formalization of this analogy has been provided yet. Here we show, building on former results connecting replicator dynamics and Bayesian update, that (i) evolution of a hierarchical population under multilevel selection is equivalent to Bayesian inference in hierarchical Bayesian models and (ii) evolutionary transitions in individuality, driven by synergistic fitness interactions, is equivalent to learning the structure of hierarchical models via Bayesian model comparison. These correspondences support a learning theory-oriented narrative of evolutionary complexific...
Complexity of life forms on Earth has increased tremendously, primarily driven by subsequent evol... more Complexity of life forms on Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted subsolutions in the framework of learning theory, no general mathematical formalization of this analogy has been provided yet. Here we show, building on former results connecting replicator dynamics and Bayesian update, that (i) evolution of a hierarchical population under multilevel selection is equivalent to Bayesian inference in hierarchical Bayesian models, and (ii) evolutionary transitions in individuality, driven by synergistic fitness interactions, is equivalent to learning the structure of hierarchical models via Bayesian model comparison. These correspondences support a learning theory oriented narrative of evolutionary complexificatio...
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