Week 3 – continued review of The Vital Question by Nick Lane
Nick Lane takes a look at the evolution of life on earth with an eye to explaining large-scale patterns, from a perspective based on the energy metabolism. In the first week, we talked about the origin of life and the structue of the cell. In the second week, we looked at the differences between eukaryotes and what came before, and asked about mergers of widely differing species. In this third and final installment, I want to look at sex and death, and also to advocate for two important concepts that could broaden Lane’s perspective yet further.
Sex is the exchange of genetic material. It was invented long before the first eukaryote. Bacteria freely pass circular snippets of DNA called plasmids among themselves, with little regard to where they came from or what they are for. But in eukaryotes, sex became formalized, with exchange strictly limited to another of the same species (this is the definition of species), and it became compulsory, a prerequisite for reproduction in multi-celled species. Many plants and some animals are hermaphrodites, with both male and female in one individual. But most higher organisms have two separate sexes. Lane proposes to explain all these patterns based on the most fundamental observation: the mitochondria, having colonized the eukaryotic cell and brought with them their own DNA, have to remain healthy and work hormoniously with the host cell.
bacteria enjoy the benefits of sex (fluid chromosomes) along with the speed and simplicity of cloning. But they don’t fuse whole cells together, and they don’t have two sexes, and so they avoid many of the disadvantages of sex. They would seem to have the best of both worlds. So why did sex arise from lateral gene transfer in the earliest eukaryotes?
This is an (uncharacteristic, for Lane) understatement. For anyone who thinks in terms of the dominant paradigm of the 20th Century, evolution is all about individual competition and selfish genes. Plasmids, as selfish genes, make perfect sense. But the way that sex is implemented in eukaryotes makes no sense from the perspective of selfish gene theory. The most successful members of the community have combinations of genes that work better than anyone else’s. What incentive do they have to share genes with their competitors, bringing their fitness down and their competitors’ fitness up? And the biggest violation of selfish-gene logic is the “cost of males”. Hermaphrodites have twice the fitness compared to diecious sex (2 separate sexes).
The standard view is that this is a mystery, an isolated phenomenon that has yet to be reconciled with selfish gene theory. I prefer to think that diecious sex is an unequivocal refutation of selfish gene theory, that evolutionary theory must expand to embrace a notion of fitness more sophisticated than “every gene for itself”.
Origin of Sex
Eukaryotes were around for half a billion years as single-celled protists. Like bacteria and archaea before them, they were single cells, but the cells were 100,000 times larger and had a great deal of structure and mechanics that the prokaryotes didn’t have.
Lane says sex arose very early in the history of eukaryotes. He cites as evidence (1) that the long list of traits that all eukaryotes have in common (but that prokaryotes lack) could only have arisen in an inbreeding population; and (2) even the simplest eukaryotes today (giardia is the example that Lane cites) have the genes necessary for meiosis=cell mergers and gene exchange.
Cloning may produce identical copies, but ironically this ultimately drives divergence between populations as mutations accumulate. In contrast, sex pools traits in a population, forever mixing and matching, opposing divergence. The fact that eukaryotes share the same traits suggests that they arose in an interbreeding sexual population. This in turn implies that their population was small enough to interbreed.
In a diverse population sharing genes, it is possible for different lineages to evolve different features, and then these features come together in a single offspring when they mated.
An alternative hypothesis due to Margulis is that these diverse features were too different to have been encompassed in a single species (a single, interbreeding population). Rather, the the different features that came together in eukaryotes evolved separately and then the separate species combined in rare cell-merger events, a process she wrote about as “endosymbiosis”, or acquiring genomes.
(How different are these two pictures, really? We know that individuals with very different features must have shared genes; perhaps it is only a subtlety to ask whether these very different individuals were part of one wide-ranging inter-breding population, or of separate demes that might be called different species.)
Sex and Reproduction were Different Functions
In the one-celled eukaryotes, sex and reproduction were separate and unrelated functions. Reproduction occurred by mitosis, simple cell division, producing two clones. Sex occurs via conjugation, in which two individuals merge their cells, and merge the cell nuclei temporarily. Their chromosomes mix, and as each chromosome finds its opposite number, genes can cross over between the two chromosomes. When the merged cell comes apart, the two individuals that go their separate ways are no longer the same two individuals that came together an hour earlier. Instead, there are two new individuals, each a hybrid.
Could mitochondria have “agitated for sex”?
Lane sees the cellular invasion by mitochondria as the source of everything eukaryotic. Sex, as we have seen, is a particularly thorny problem—not just the mechanics, but the fact that (short-term) selective pressures should have been acting against it. But while sex would not be adaptive for the host cells (in the short run), it would have provided the only effective way for the mitochondrial “infection” to spread. There must have been a long transition period in which the mitochondria were not fully domesticated, and had their own ideas about what it means to be “adaptive”. After mitochondria learned to be endosymbionts, they would have trouble surviving outside the host cell, and trouble penetrating the cell walls of other cells, in order to spread from one host to another. So perhaps it was the genius of the mitochondria to induce some chemical change that would soften the host’s cell wall, and to promote behaviors that would seek other cells to merge with, giving the mitochondria a chance to spread.
My take: this hypothesis has the virtue of being “conservative” in the sense that it fits well within the predominant selfish gene paradigm. What could be more selfish than for the mitochondria to want to spread themselves? But at a slightly deeper level, the main thing that the selfish gene paradigm has going for it is that it is supposed to provide an explicit mechanism for natural selection, i.e., that the gene that makes the most copies of itself is the one that prevails. In this case, Lane’s hypothesis suffers for want of a mechanism how the mitochondria were able to take control of the cell’s behavior and override the interest of the genes in the nucleus for which sex was a liability.
Difference between plants and animals
Mitochondria reproduce within a cell so their DNA is copied many times for each one time that the nuclear DNA is copied. Furthermore, mitochondria exist in an environment of high-energy chemistry (ROS) that is a constant threat to the integrity of their DNA. So we expect high mutation rates in mitochondria, perhaps high enough to cause permanent damage and impaired performance. Somehow, in domesticating its mitochondrial guests, cells had to learn to culture the healthy ones and eliminate the damaged ones. Otherwise, mitochondria would gradually mutate and degrade over time.
This is a genuine conundrum, about which there are really no cogent ideas in the literature. If natural selection keeps populations healthy (and even improves them gradually) by filtering out the dysfunctional, where is the selection on mitochondria as they reproduce within a cell? Most dangerous of all would be the possibility of Darwinian competition within a cell among the different mitochondria. Some mitochondria might devote less of their metabolisms to serving the host cell and more to reproducing faster than their sisters. This could produce an evolutionary advantage within the cell for the slackers, the least useful mitochondria. Selfish evolution of mitochondria is an existential threat to the partnership between mitochondria and host.
Lane devotes a whole chapter to speculation about the resolution of this problem. We know that nature has managed to keep mitochondria healthy over billions of generations, in all surviving eukaryotes, but we weren’t around to watch how the mitochondria were tamed or convinced to submit to the hegemony of the cell nucleus. What we have to go on are surviving patterns that may bear the imprint of this ancient battle. The fact that mitochondria are inherited through the female line only is one piece of data. A difference in strategy between plants and animals may be another legacy of the battle: any cell of a plant’s meristem can grow into a seed that grows to a new plant, but in animals, the “germ line is segregated”, meaning that there is specialized reproductive tissue, protected from the earliest stage of embryonic development. Lane relates this difference to the fact that animals have a higher metabolic rate, with more mitochondria that are more active, thus a lower mitochondrial mutation rate. There may even be a connection to the reason that females lose their fertility earlier than men; the mitochondria become more highly mutated late in life, and it would be a risk to the offspring to launch them into life with a stock of mutated mitochondria. Males can afford to reproduce later in life because they don’t contribute mitochondria to the offspring.
Aging and death
Lane doesn’t have a lot to say about aging in this volume, but he does note that aging only really became an option once the germ line was segregated. Germ line cells need to have full capacity for regenerating everything (pluripotency) but cells of the soma have the luxury of specializing, and one option is to differentiate and grow once and for all, creating an organ that must last a lifetime (like a brain or heart).
In the end, Lane’s explanation of aging lands at a place very close to conventional theories based on tradeoffs. The somatic tissues of the body can’t be simultaneously good at everything, and they are specialized to their differentiated purpose, to the detriment of the ability of regenerate. Hence they are prone to wear out over a lifetime. I find this explanation less compelling than many of his other ventures, but this is probably inevitable, since evolution of aging is the area where my own thoughts are most highly developed.
Lane goes on to describe his own version of the mitochondrial free radical theory of aging, which is not an evolutionary theory. He elaborates why, despite the many well-known failures of this theory in its naive form, he nevertheless finds a core of truth in it.
Sex and Death in Protists Presages Sex and Death in Multicelled Plants and Animals
The mechanics of conjugation in protists looks strikingly like the mechanics of sex in later multi-celled organisms. The way in which the cells merge, the crossover of chromosomes, the particular genes that are involved all point to a close relationship. Most striking is the strange mechanism of doubling the chromosome population before dividing it in half, and then in half again. The very arbitrariness of this behavior, and the fact that we see it both in protist conjugation and in male-female sex, is attests to the fact that latter evolved from the former.
I’ve said that sex and reproduction in one-celled eukaryotes are separate, unrelated functions. But there does exist one connection in ciliates, an advanced group of protists including the paramecium. Telomeres get shorter and shorter with each cell division. This is cellular senescence. It is permitted to continue, threatening the cell’s viability, because telomerase is repressed, and only comes out to restore the telomere when two individuals conjugate.
Thus, already in the early ciliates, cellular senescence has the purpose of enforcing conjugation. This ancient form of aging evolved to protect population diversity. And in higher organisms to this day, cellular senescence contributes to the death of the individual, assuring that the population continues to be enriched by new combinations of genes. The rationing of telomerase in protists presages the rationing of telomerase in you and me.
(William Clark tells this story in his very readable book, A Means to an End. My current project is a computer model demonstrating how telomerase rationing evolved on this basis.)
Where to go from here? Two suggestions
I am an enthusiastic supporter of Lane’s program, trying to understand the broad outlines of evolution, and why life is the way it is. I offer, from my own experience, two more themes that might complement his program.
- the conflict between what is adaptive for the individual and what is adaptive for the community, and how evolution has ways to suppress individual competition in order to create cohesive communities that are powerful competitors.
- adaptations at every level from chromosome structure to ecosystem structure that contribute to evolvability. It seems that natural selection has been a bootstrapping process, constantly increasing its own efficiency in the long term, even as it is selecting higher fitness in the short term.
Suppression of individual competition has been necessary for evolution to be able to find long-term solutions. This happens in somas that have the same genome as the germ line, and so their allegience to the germ line is not in question, and even in eusocial insects, where close kin selection helps to support division of labor in a functional community at a higher level of organization than the individual soma. David Sloan Wilson has devoted his career to the theory of multi-level selection, the ways in which natural selection operates simultaneously at the level of the individual and larger units of families, populations, and entire ecosystems. Often there are conflicts between what is good for the individual and what is good for the community, and the striking thing (taking the large perspective) is how consistently the communal interest has managed to take precedence, suppressing selfishness.
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Lane doesn’t mention “evolvability” by name, and tends to see it as random, chance event. “Adaptive” is the operant word, which signifies a Darwinian process,
changes to the genome itself, which might take the form of large deletions, duplications, transpositions or abrupt rewiring as a result of regulatory genes being inappropriately switched on or off. But such changes are not adaptive; like endosymbioses, they merely alter the starting point from which selection acts.
But I would suggest that there are too many of these properties of eukaryotic life that seem to serve not the gene or the individual carrying it, but the long-term viability of the community. We should expand our notion of a “Darwinian” process, if necessary, to accommodate the reality that evolvability has evolved. To be explicit: “Fitness” is the ability to survive and reproduce copiously and robustly. “Evolvability” is the ability to increase in fitness. Evolvability is the rate of change of fitness. We all agree that there is natural selection for fitness. The controversial idea is that there can also be natural selection for its rate of increase.
I have a personal relation to this idea. Harvard astrophysicist David Layzer wrote the first modern paper proposing the evolution of evolvability in 1980 when I was his student. Layzer’s analysis was ignored by the biology community for 16 years, until the time was ripe, and the same idea was re-cast into language more familiar to evolutionists by a prominent evolutionary theorist who teamed up with a creative and versatile computer scientist. Wagner and Altenberg generated a discussion that has developed and expanded to this day, but the revolutionary implications of this idea for evolutionary theory have yet to be assimilated. When the central importance of evolvability is fully appreciated, I predict that it will alter the foundations of evolutionary science.
Examples of evolvability adaptations include:
- Sex imposes a huge cost in individual fitness, but promotes evolvability. In fact, sex has benefits both for evolvability and for expanding the level of selection. As practiced by eukaryotes, sex gives each gene a stake in survival of the entire breeding community, and thereby promotes cooperation over selfishness [ref]
- Hierarchical signaling cascades, “command and control” with HOX genes controlling transcription factors and transcription factors controlling expression of many genes at once.
- Eukaryotic proteins are modular, with modules that are re-used in different combinations for different purposes. “Exons” are areas of the chromosome that code for pieces of protein.“Why do eukaryotes have genes in pieces? There are a few known benefits. Different proteins can be pieced together from the same gene by differential splicing…”
- Aging is an evolvability adaptation. This idea has a checkered history that goes back to August Weismann, but has recently been put on a firm mechanistic footing.
Though he never uses the word “evolvability”, Lane gets the message clearly about the benefit of sex, “fending off debilitating parasites, as well as adapting to changing environments, and maintaining necessary variation in a population.” In my view, he has yet to realize the profound implications of the fact the sex evolved for the sake of its contribution not to fitness but to evolvability. The fact that natural selection can favor not just fitness itself but also the rate at which fitness increases carries a deep message. “Evolvability” is not an individual trait of immediate value, but a property of an entire breeding community (a deme), spread through evolutionary time. The implication is that natural selection can enhance collective fitness, not just individual fitness, and that the long-term health of the community can be favored over the short-term advantage of the individual.
Evolvability is both a result and a cause of natural selection for traits (like aging) that benefit the community over the individual, even at a substantial cost to individual fitness. Evolution of evolvability is a bootstrap, a self-reinforcing process, a positive feedback system.
Sex in particular helps to elevate the level of selection from the individual to the community, because sex gives each gene a stake in survival of the entire breeding community, and thereby promotes cooperation over selfishness [ref].
This is a further clue, a connection between multilevel selection and evolvability.
I am full of admiration for Lane’s ambition to explain the broad properties of eukaryotic life, and he has made impressive progress pulling together diverse evidence into coherent theories. Lane is a biochemist and a “strict constructionist”, working within the predominant school of evolutionary theory, sometimes called the “New Synthesis” or “Population Genetics” or “neo-Darwinism”. My opinion is that to make further progress, he will find it necessary to venture beyond the neo-Darwinian framework to think about levels of selection, evolvability, and evolutionary ecology.