An intriguing analysis of the consequences of the genotype/phenotype, or soma/germ separation.

Personal summary (2005-12-17)

• We see development as an elegantly orchestrated cooperative among cells, created clonally from a zygote, in order to generate an individual. While this view may be appropriate for extant organisms, it is hardly so for their ancestors. Rather before the advent of metazoa, each cell in a clonal lineage retained the capacity for cell division; thus each cell propagated its own germ line. This is seen in extant unicellular taxa, e.g. bacteria, some protists, and yeast.
• One major limitation to many unicellular lineages was the possession of only a single microtubule organizing center, which constrained each cell to decide between somatic growth or division. Thus we have the classic life history trait. In this case the state of growth includes motility as a general ability.
• Existence of this constraint permitted its resolution via natural selection of variant cell linages which cooperated at some level to reduce and eventually eliminate this constraint. Such pacts (which can be seen in sponges and slime molds, e.g.) allowed a collection of diverse cell linages to grow and divide together, performing both simultaneously, through blastular cleavage. The result is the process of gastrulation, or the separation of animal (motile) and vegetal (dividing) cells.
• The evolutionary significance of this cooperation is apparent: behold the diverse array of existing individuals that have evolved.
• In the face of clonal cooperation, a new constraint arose, due to the fact that each cell could potentially contribute to the germ line of the individual. Thus the lineages compete for resources internal to the individual, and whichever out-replicates the other lineages will dominate the population. Mutation operating on lineages generated variants within the individual. Such mutations can be categorized into two classes: those that promote the fitness of both lineage and individual; those that promote the fitness of the lineage at a cost to the individual.
• Subsequent variants had an ability to positively, neutrally, or negatively affect the rate of advent of additional variants, and thus acted to differentially preserve the effects of preceding variants.
• Evidently selection for the individual was strong, so that the general effect of subsequent variants was to limit the ability for additional variants to contribute to the germ line. Thus some variants were selected for their ability to limit the replication rate of other variants. (Notably these variants arose in the course of ontogeny and those favorable contributed to the germ line. i.e., inheritance of characteristics acquired through development.) These explicit attempts to hold cells back led to the processes of induction, competence, cell death, and finally commitment to alternative cell fates, prohibiting a role in germ line formation.
• Thus the conservation of early ontogeny arose due to selection both at the level of the cell lineage and at the level of the individual constituted by the lineages.
• Striking a balance between these two antagonistic processes led (and still leads) to a temporal range, before the fates of cells are sealed, in which cells may affect the germ line. Thus the existence of general modes of devlopment: somatic embryogenesis (a cell can both divide and grow, i.e. a totipotent stem cell); epigenesis (antagonistic interactions among cells to outcompete each other); and maternal preformation (factors deposited by the parent determine a priori the fates of daughter lineages).
• Variation in the timing and magnitude of the interactions among cells is a general phenomenon called heterochrony, seen to be responsible for the generation of the thirty some different metazoan body plans, representative of the major animal phyla.
• Just as the advent of individuality introduced the need to stabilize the process itself of generating the individual, the advent of a particular body plan introduced the need to stabilize the production of that plan in descendents.
• The diversity of late ontogeny inextricably led to its control and regulation, with selected variants arising via differential heterochrony.
• The generative process of ontogeny is responsible for the inheritance and modification of individuality through differential regulation of genetic transmission.

Weismann’s theory of individuality (2005-10-28)

• the modern synthesis of evolution assumes the individual as the basic unit of genetic transmission and inheritance
• the equivalence ‘organism = individual’ was developed first by August Weismann in the late 1800s. he assumed the mechanism of reproduction always separated gametes from somites.
• this assumption found its way into the modern synthesis with the idea that genetics only and not ontogeny was necessary and sufficient for Darwinian evolution.
• it turns out that equating organism with individual is only approximate, and flat out inaccurate for most forms of life
  • specifically, only higher animals such as vertebrates, which feature multicellular cell differentiation and epigenetic or preformatic modes of development, closely approximate the ideal of the individual.
  • clonal invertebrates, viz bacteria, protists, fungi, have the ability to pass on developmentally acquired genetic variation, due to asexual reproduction.
  • eg in some organisms, eg Hydra and yeast, which reproduce both sexually and asexually, development is tightly coupled to genetic trnasmission. Thus acquired life history traits may be passed on in a Lamarckian fashion.
• Buss claims that individuality is evidently a derived character, having evolved from “non-individual” organisms.
• the question now is why has the individuality of higher organisms evolved
  • this suggests specifically that the modern synthesis lacks a theory of ontogeny, which realization brings evo devo to the forefront of investigation

The Evolution of Development

Conservation of early ontogeny

I

• It is apparent that after an ontogenetic pattern is formed and inherited, especially early in development, it becomes difficult for an organism to change the pattern without affecting severely downstream developmental events. The fact that the patterns of blastulation and gastrulation are homologous throughout metazoans is apparent. However the causal reason for why these patterns became fixed is unclear.
• Although many ciliated species overcame the constraint of having a single microtubule organizing center (MTOC), it appears that metazoa originated from those constrained protists. Thus no ciliated metazoa are able to divide when ciliated.
• As a possible link between protists and sponges, Proterospongia haeckli (a colonial choanoflagellate) is surrounded by flagellated, covered, and nondividing cells, with nonciliated dividing amoeboid cells kept towards the interior.
• Res Addendum: Would metazoa have been constrained if each cell retained more than one MTOC? ie, if there was no conflict between movement and division, what would happen? Would there be a similar drive towards complexity?

III

• The patterns of cleavage, blastulation, and gastrulation appear as we see them because of the conflict between movement and division.
• If a bunch of cells are dividing, then ciliate, division is halted. So an organism must halt movement in order to reproduce. The solution is to overcome the constraint to move and divide in parallel. Most metazoa accomplish this first by ciliating a subset of cells, retaining others for division. This divides a blastula into animal and vegetal poles.
• Now there is another conflict. Division of vegetal cells would elongate a spheroid blastocyst into an ellipsoid, thus inhibiting movement in water by increasing viscosity. One common solution is to direct the dividing cells inward, allowing the blastocyst to retain a spherical shape. Thus the existence of gastrulation as unipolar invagination. Variants of this pattern occur when selection for motility is not as strong, e.g. maternally brooded or yolk sac embroys, which do not need motility as early in life.

IV

• The evolution of gastrulation created another conflict, one among the now inhomogeneous population of cells in a blasocyst, the vegetal cells and the animal cells. These lineages will compete for resources, and whichever has a faster overall replication rate will will dominate the environment and its resources. The environment at hand is the gastrulating blastocyst. To resolve this conflict, controls were developed both to limit the division rate of vegetal cells; this was perhaps in part accomplished by forcing a subset of these cells to ciliate (and thus stop dividing).
• Such a control must have developed precisely because selection at the level of the organism became more important than selection at the level of the cell lineage.

Res Addendum

• Perhaps selection at the level of the individual became a dominant force because a blastocyst composed of multiple cell lineages working without conflict created a rather stable microenvironment for growth of all of the cell lineages. Once some of the cells were made terminal, the replicating lineages were safe from harm’s way due to the motility provided by vegetal cells, and retained sufficient resources in a microenvironment to sustain replication.
• What made the vegetal cells stop dividing so easily? Was there some sort of dupe, or were they just less fit in some sense, and became “subjugated” to the animal cells?

Diversity of late ontogeny (2005-12-17)

Lots of cool stuff about heterochrony in annelids, molluscs, and flies

Life Cycle Evolution (2005-12-18)

Summary

II

• Sexuality is pervasive, and is highly correlated with cellular differentiation.
• The question is whether this relationship is causal.
• The implication would indicate practical limits to particular life cycles.
• Buss suggests that sexuality is a limiting prerequisite for cellular differentiation, without which any variants in an asexual population (i.e. clone) will inevitably revert the population to a homogeneously non-somatic character, via Muller’s ratchet.
• Thus sex was a necessary precondition for the evolutionary fixation of cellular differentiation.
• Not just any of the myriad possible life cycles is realizable.

III (2006-01-08)

• If we are to understand life cycle evolution, we must first account for the life cycles we observe. This begins by characterizing the differences among the kingdoms and phyla of life.

IV

• Life cycles are repetitions of sex and development, but alone these two characteristics fail to explain the variety of extant life cycles. Life cycle choices are made which permit the intracellular conditions of an organism (the intrasomatic ecology) to mediate conflicts between cell lineage and organism, and its extracellular conditions (the extrasomatic ecology) to mediate conflicts among individuals. The two ecologies do not operate independently.
• Any life cycle trait will be accepted, rejected or modified under the condition that it faithfully resolves conflicts between lineage and individual (else the cycle will never fix).
• Many plant and fungal life cycles include asexual clonal reproduction (e..g aspen trees, coral). This choice requires active ontogenetic maintenance of a totipotent cell lineages, which can be packaged off into a new clone, extrasomatic ecology permitting.
• However active totipotent lineages were precluded in metazoa upon fixation of secondary somatic differentiation, which was necessary or germ-line sequestration and stability of epigenetic processes, all important because, unlike the other kingdoms, animals allow free movement of cells.
• This demand inevitably results in the much shorter life time (both genetic and zygotic) of metazoa, whereas plant and fungal clones may be very old zygotically.

While evolution may often result from the control of ecology on development, the converse may also be true.

• Development exhibited control over ecology during the progression towards germ-line sequestration, thus constraining possible life cycle modes. Environmental contexts, however, favored asexuality in some cases, allowing selection of more complex life cycles which interleave sexual and asexual modes, and which expand on the number of heritable divisions between mitoses. Such life cyycles are found in all but higher metazoans, because the germ-line sequestration is very much at odds with sexuality.

Historecognition

• Sedentary life stules resulted in local population densities leading into increased heterogametic fusion events. To prevent parasitism, histo/allo/xeno-recognition systems evolved. However fusion has benefits such as immediate increase in cell size, promoting survival, and genetic redundancy. Thus the theory of diploidy.
• Eventually recognition systems became tuned to offer the best of all worlds: individuality, attack recognition, size, redundancy in kin recognition, all benefits during asexual life.
• On the other hand, there is a need for fusion of gametes, and their spread from local homogenetic densities. Systems evolved them to prohibit clonal growth of the foreign component following syngamy. Fungal examples include hyphal septic systems and controlled cellularization, a possibility since fungi are coenocytic.
• “Competition within organisms for access to the germ line arises not only through mutation but also through fusion between conspecifics. The potential consequences of fusion for the integrity of the individual varied as a function of the primitive conditions of the plant, animal, and fungal kingdoms with respect to cell membrane architecture and cellularization. Plants were not challenged. Those animal groups that were challenged responded by evolving sensitive mechanisms of self-recognition. The fungi turned the challenge to their own advantage, inventing from it novel life cycles.”
• Fusibility is a life cycle trait.

Ploidy

• Why are most fungi haploid, higher metazoans diploid, and plants a mix?
• Animals: Morphologies are constrained in space by distance and volume. Structures must be filled with cells. Fewer cell division for diploids are required to fill the space than for haploids. Alternatively, proliferative ability may correlate wtih surface area as it allows for more growth factor receptors, and a diploidic genome provides more potential to express these receptors.
• Fungi: This spatial correlation does not exist for fungi, because they are coenocytic. There are also possible structural limitations to fruiting with diploid cells.
• Plants: In plants the correlation is not as strong beacuse rigid cell walls force growth aplically only (distanec). As in fungi absense of a somatic advantage allows for a persistently vegetatively haploid condition. More importantly however is the possibillyt of separate diploidic elaborations, e..g the default decision in many unfertilized cells is intercalation and projection into a multicellular diploid stage. This allows for diploid specific variants to arise, e..g kelp.
• To summarize plants have rigid membranes and cellularization. Fungi have rigid membranes and no cellularization. Animals have flexible membranes and cellularization.

V

• Buss summarizes the preclusions in life cycles, resulting from evolution of certain life cycle traits.
• Life Cycle Traits (from p166, Table 4.3)
  1. Cell Architecture
     • Coenocytic (common cells)
     • Cellularized with rigid walls
     • Cellularized with non-rigid walls
  2. Sexuality
     • Sexual
     • Asexual
  3. Asexuality
     • Primitively asexual
     • Secondarily asexual
     • Absent
  4. Division of Labor
     • Unicellular
     • Multicellular lacking cellular differentiation
     • Multicellular with cellular differentiation
  5. Germ-line Sequestration
     • Present
     • Absent
  6. Historecognition System
     • Fuse if similar
     • Fuse if different
     • Absent
  7. Ploidy
     • Haploid vegetative phase
     • Diploid vegetative phase
     • Alternating
• Buss calculates a possible 972 life cycles from combinations of these traits. However empirically we observe only 27. Thus not all life cycle is possible, because certain traits preclude others from evolving. This is how phylogenetic precedent is established.

The Evolution of Hierarchical Organization (2006-01-19)

Summary

• Before I proceed, I want to link this document with Stuart Kauffman, whose goal, as far as I am aware, is similarly to identify and define the property that permits life to exist and organize itself, in a thermodynamic sense.
• The transition from lineage to individual is clearly not the only such selective transition in the course of evolution. Origin of molecular replication, replication of molecular complexes, replication of organelles, groups of organelles, and cells preceded it. Replication of tissues, organs, and organ systems proceeded it, within the scope of selection on a unified entity, in the sense that one may classify any individual.
• Beyond this arguably lie the selection on kin groups, as well as selection on the variation and replication of neuronal activities (i.e. memes). Communication and culture have evolved as vehicles to facilitate the transport of and selfish interests of memes, just as individuals evolved to facilitate the selfish replicative interests of the encapsulated cell lineages.
• Evolution is punctuated because innovation arises at the points in time where selection transitions its focus from one unit to another, in a hierarchical fashion.
• Evolution is thus hierarchical because selection acts like a machine feeding on variation of a particular unit (at the time the most prevalent unit). This results in the optimization, or standardization, of that unit, after which the majority of variation is lost. However a new unit of selection opens up, that results from synergisms among the now standardized units. Such synergisms increae the variation available to selection, and it thus feeds again.

I

• Truth is subjective. As an example, science as a community appears to “make progress”, simply because it utilizes tools of language that allow heritable variation and selection, just as evolution operates on life to “make progress”. Heritable variation is inherent to the minds of humans, and the analog of natural selection is the scientific peer review process.
• It is clear that the synthetic theory of evolution is on the brink of a major theoretical expansion. What is unclear is the language that must develop to carry the innovations forward.
• The gene selectionist point of view is equivalent to the group selectionist one, both of which are equivalent to the hierarchical one espoused by Buss. All three views offer theoretically the same abilities to describe the empirically observable consequences of evolution.

II

• Buss contends that his hierarchical language is better equipped to carry on the evolution of the synthetic theory. He states that where the various selectionist views differ is in their ability to serve as predictive theories, beyond a merely descriptive one. Thus the gene selectionist view identifies evolution of the organelle as the result of the selfish actions of genes, who want increased replication. However this view provides no predictive insight as to where evolution will turn next, as an implication, consequence, or effect of this action. Buss argues that the hierarchichal view indeed offers predictive power because it acknowledges the existence of both gene and organelle, e.g., as units of selection, and accordingly can generate predictions from studying the synergisms between these units.

III

IV

V