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  Topic: Synthesis: Origins of Complexity, Towards a Biocomplexity FAQ< Next Oldest | Next Newest >  

Posts: 319
Joined: May 2002

(Permalink) Posted: Feb. 02 2003,06:43   

Originally posted over at ARN, perhaps this could serve as starting material for an overall "progressive case for the origins of complexity" FAQ, i.e. that starts with the small processes and then builds them up.

Feel free to add relevant links, posts, etc., especially to threads that better document specific points, e.g. adaptive radiation, transitional fossils, IC, etc.

Original thread:


Berthajane, Vivid, et al.,

I've often thought that there should be a FAQ somewhere specifically on the evolution of complexity, since that is what is the sticking point for a lot of people.

I don't really have the time to write a FAQ or even do more than hit-and-run post, but perhaps I can communicate how I think it might go.  Perhaps you can comment if you think all of this is old hat and would be pointless and unconvincing to you in a FAQ or if you think it would be worth reading.

OK, here goes.

The case for RM & NS producing complexity is cumulative.  You start from small-scale processes and then work up.

1) "Microevolution" -- local adaptation: drug resistance, peppered moths, pesticide resistance, guppy size change, etc.  Presumably everyone accepts this.level of evolution.

It is worth considering, for a moment, some of the implications of even this minor level of evolution:

a) Microevolutionary forces can, in short order, take a single mutation in a single individual and spread it to fixation, so that it exists in every member of a population of millions.  All of the millions of bad mutations don't matter a bit, they rarely made it further than a generation or two.  That one-in-a-million lucky mutation is the one that natural selection picks (even if it is lost by chance the first few times, sooner or later it or an equivalent mutation will spread far enough that its success becomes guarenteed).

Also, note that even at this minor level we have a fair bit of design-mimicking occurring.  Peppered moths, for example, don't change color in any random direction, they change color to match the color of tree bark (please refer to the Wells FAQ before critiquing the peppered moth example).  Modern militaries only got around to producing decent camoflague in the mid-1900's.

Now think about all the other amazing instances of camoflague in the animal (and plant!;) world.

A few examples:

A frog in Madagascar:

Those were fairly modest examples.

Look for the plants in this picture, they're in plain view:

The well-named Lithops:

And here, which one is the ant and which one is the ant-mimicking spider?

(hint: count legs)

Here is a fairly decent webpage on mimicry (Kimballs pages are about the best online pseudo-bio text I've seen, decent pictures etc)

Camoflague and prey-mimicry combined in this one:

(Click here for an II thread discussing anglerfish evolution BTW)

Anyhow, I went on a tangent with camoflague and mimicry.  My point: I submit that all of these cases are rather easily explained by "microevolution" of the peppered moth type (and there are many other studies of natural selection for camoflague BTW) -- indeed, many of these impressive designs are specific to species in genera or families with completely different coloration...e.g. anglerfish that live so deep that no light reaches them don't bother with camoflague.

If this kind of thing is conceeded, then we've already allowed that microevolution has a rather substantial ability for "creativity" and acheiving very specific "designs".

(b) Returning to the population-genetics-level processes described at the top of (a)...Now think about them happening continually (many different mutations will be under the influence of selection in any given species at any given point in time) for millions of years.  Here we add in speciation, both due to geographical separation (allopatric) and niche partitioning (sympatric).  Many species going in many different directions.  Many recent adaptive radiations of species, where very-closely related species are morphologically very different and "designed" for very different niches, could be cited.  Here are a few:

Kimball's speciation page

Darwin's Finches (Darwin did not even realize they were all finches for years after he collected them; they fill the niches fufilled by various birds on continents -- seed eaters, insect eaters, woodpecker, warbler, etc.):

(this, BTW, is the most important point about Darwin's Finches, although Peter & Rosemary Grant's studies of recent natural selection are also interesting)

The Hawaiian honeycreepers are even better examples.  These are all closely related (well, were, some were driven extinct when Europeans and their pets invaded):

And be sure to check out Art's post on the Hawaiian Silversword Alliance (sounds like an army in an online wargame, I know...):

Some of these Silverswords are trees, some are little herbs, and yet they are all closely related and many are even interfertile

© If it is conceeded that RM & NS can account for the rather astounding diversity of the above groups, then we've agreed that natural evolutionary processes can account for family-level diversity.  Now, if the same processes produced orders (e.g. the various mammal groups) and classes (e.g., reptiles, amphibians, etc.), we should see some fossil evidence of this, and we do.  In the case of vertebrates, rather a lot, and a bunch of new ones in the last 10 years.  Just to review what we've got intermediates or close-offshoots for:

walking sirienians (manatees etc., forget what they're descended from)
...and of course, humans.

Why any of these should exist, except on the hypothesis that all modern organisms originated by modification of previous organisms by a process limited to fairly gradual changes (like RM&NS) is a useful question to consider.

2) Turning from morphology to molecules: while the lower levels of evolution and adaptation might be explained basically by selection of point mutations, at some point new genetic information has to be created.  There is a mechanism for this, namely the combination of gene duplication (and variations on this, e.g. deletions, rearrangments, etc.) with the mutation-and-selection processes discussed back in 1a.

Even unmodified gene duplications are often selected; e.g., some DDT resistant mosquitos have 100+ copies of a DDT-resistance gene (see Weiner, Beak of the Finch).  Plus we have genome duplications, duplication of whole segments of chromosomes, etc.  These kinds of processes give evolution a lot of material to play with, and there are numerous documented and published cases of observed or recent origins of novel genes by various combinations of the above processes.

Lots of them are described in this origin of information thread

And of course the same kinds of adaptive radiation patterns found in morphology can be found in molecules, and here we even have hard-and-fast evidence that directional natural selection was operating millions of years back in the unobservable past, in the form of substitution biases, e.g.:


Gene 2000 Dec 30;261(1):43-52
Adaptive evolution of animal toxin multigene families.

Kordis D, Gubensek F.

Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.

Animal toxins comprise a diverse array of proteins that have a variety of biochemical and pharmacological functions. A large number of animal toxins are encoded by multigene families. From studies of several toxin multigene families at the gene level the picture is emerging that most have been functionally diversified by gene duplication and adaptive evolution. The number of pharmacological activities in most toxin multigene families results from their adaptive evolution. The molecular evolution of animal toxins has been analysed in some multigene families, at both the intraspecies and interspecies levels. In most toxin multigene families, the rate of non-synonymous to synonymous substitutions (dN/dS) is higher than one. Thus natural selection has acted to diversify coding sequences and consequently the toxin functions. The selection pressure for the rapid adaptive evolution of animal toxins is the need for quick immobilization of the prey in classical predator and prey interactions. Currently available evidence for adaptive evolution in animal toxin multigene families will be considered in this review.
And here is the tip of the iceberg (Drosophila is always the tip of the iceberg) for the molecules giving us an even better handle on just how important a force directional natural selection is on genomes:


Adaptive protein evolution in Drosophila.

Nature 2002 Feb 28;415(6875):1022-4
Smith NG, Eyre-Walker A.

Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK.

For over 30 years a central question in molecular evolution has been whether natural selection plays a substantial role in evolution at the DNA sequence level. Evidence has accumulated over the last decade that adaptive evolution does occur at the protein level, but it has remained unclear how prevalent adaptive evolution is. Here we present a simple method by which the number of adaptive substitutions can be estimated and apply it to data from Drosophila simulans and D. yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species.
If this is not impressive enough, think about what the population of a species of fruit fly must be (billions? trillions?).

As for the origin of new morphology, the combination of the origins-of-genes processes described above, with recent knowledge of the genes patterning development, has made this much clearer.  E.g.:


Philos Trans R Soc Lond B Biol Sci 1995 Sep 29;349(1329):313-9

Hox genes and the evolution of diverse body plans.

Akam M.

Wellcome/CRC Institute and Department of Genetics, Cambridge, U.K.

Homeobox genes encode transcription factors that carry out diverse roles during development. They are widely distributed among eukaryotes, but appear to have undergone an extensive radiation in the earliest metazoa, to generate a range of homeobox subclasses now shared between diverse metazoan phyla. The Hox genes comprise one of these subfamilies, defined as much by conserved chromosomal organization and expression as by sequence characteristics. These Hox genes act as markers of position along the antero-posterior axis of the body in nematodes, arthropods, chordates, and by implication, most other triploblastic phyla. In the arthropods this role is visualized most clearly in the control of segment identity. Exactly how Hox genes control the structure of segments is not yet understood, but their differential deployment between segments provides a model for the basis of segment diversity. Within the arthropods, distantly related taxonomic groups with very different body plans (insects, crustaceans) may share the same set of Hox genes. The expression of these Hox genes provides a new character to define the homology of different body regions. Comparisons of Hox gene deployment between insects and a branchiopod crustacean suggest a novel model for the derivation of the insect body plan.

Annu Rev Cell Dev Biol 2002;18:53-80
Gene co-option in physiological and morphological evolution.

True JR, Carroll SB.

Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, New York 11794-5245, e-mail:

Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.
In fact, right now we are living through the merging of developmental biology with the modern synthesis, e.g.:


Genetica 2001;112-113:45-58

Toward a new synthesis: population genetics and evolutionary developmental biology.

Johnson NA, Porter AH.

Department of Entomology and Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst 01003, USA.

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.
I have put the above articles and some others over in this thread.

3) OK, so at this point we perhaps have reached the amount of evolution that Mike Behe accepts or at least doesn't argue about, that is: a heck of a lot.  I tend to be of the opinion that if natural evolutionary processes can produce new genes, novel morphological traits, and even body plans, we ought to expect that it's powerful enough to do just about anything that that we see in biology today.  But, some will raise IC at this point, arguing that, sure, evolution could have produced mammals, humans, wings, whales, innumerable new genes and adaptations, but that a designer still intervened to produce a certain class of system (*really* complex or rather simple-but-irreducible, depending on who you talk to...) that Behe calls IC.

This has been discussed to death in numerous places, but suffice it to say that for the most complicated of Behe's IC systems, namely the vertebrate immune system, Behe's claims about lack of evidence for an evolutionary origin, and lack of scientific publications on the topic of the origin of the immune system, he has been decisively refuted.


Read this: Evolving Immunity by Matt Inlay

Then read: This ISCID thread where IDists were hapless in their attempt to defend Behe

If natural processes can produce even ridiculously complex IC like this, then there is no particular reason to invoke ID to explain IC.

4) Finally, once all of the above is accepted or considered probable, we are in a position to consider the origin of eukaryotes and prokaryotes.  In my opinion, if RM&NS processes can create something like the metazoan phyla and the immune system, there's no reason to suspect that anything else was responsible for earlier events.

We are however getting into events that occurred on a microscopic scale 1+ billion years ago, so details are necessarily much more speculative.  All I can recommend is some of the better reading I've found on these topics:

Maynard Smith and Szathmary, Major Transitions in Evolution, 1995.  Here is a brief review by someone.

The short version of the above is their 1998 Origins of Life but it is pretty much pointless compared to the bigger book.

The other good source is pretty much anything written by Cavalier-Smith (type his name in here), e.g. this series of articles:


J Mol Evol 2001 Oct-Nov;53(4-5):555-95
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis.

Cavalier-Smith T.

Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom.

I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex autotrophic, anaerobic green bacterium.

Int J Syst Evol Microbiol 2002 Jan;52(Pt 1):7-76
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier-Smith T.

Department of Zoology, University of Oxford, UK.

Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.

Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

Cavalier-Smith T.

Department of Zoology, University of Oxford, UK.

Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. [...abstract too long... (!!!;)]

Heredity 2002 Feb;88(2):125-41
Origins of the machinery of recombination and sex.

Cavalier-Smith T.

Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.

Mutation plays the primary role in evolution that Weismann mistakenly attributed to sex. Homologous recombination, as in sex, is important for population genetics--shuffling of minor variants, but relatively insignificant for large-scale evolution. Major evolutionary innovations depend much more on illegitimate recombination, which makes novel genes by gene duplication and by gene chimaerisation--essentially mutational forces. The machinery of recombination and sex evolved in two distinct bouts of quantum evolution separated by nearly 3 Gy of stasis; I discuss their nature and causes. The dominant selective force in the evolution of recombination and sex has been selection for replicational fidelity and viability; without the recombination machinery, accurate reproduction, stasis, resistance to radical deleterious evolutionary change and preservation of evolutionary innovations would be impossible. Recombination proteins betray in their phylogeny and domain structure a key role for gene duplication and chimaerisation in their own origin. They arose about 3.8 Gy ago to enable faithful replication and segregation of the first circular DNA genomes in precellular ancestors of Gram-negative eubacteria. Then they were recruited and modified by selfish genetic parasites (viruses; transposons) to help them spread from host to host. Bacteria differ fundamentally from eukaryotes in that gene transfer between cells, whether incidental to their absorptive feeding on DNA and virus infection or directly by plasmids, involves only genomic fragments. This was radically changed by the neomuran revolution about 850 million years ago when a posibacterium evolved into the thermophilic cenancestor of eukaryotes and archaebacteria (jointly called neomurans), radically modifying or substituting its DNA-handling enzymes (those responsible for transcription as well as for replication, repair and recombination) as a coadaptive consequence of the origin of core histones to stabilise its chromosome. Substitution of glycoprotein for peptidoglycan walls in the neomuran ancestor and the evolution of an endoskeleton and endomembrane system in eukaryotes alone required the origin of nuclei, mitosis and novel cell cycle controls and enabled them to evolve cell fusion and thereby the combination of whole genomes from different cells. Meiosis evolved because of resulting selection for periodic ploidy reduction, with incidental consequences for intrapopulation genetic exchange. Little modification was needed to recombination enzymes or to the ancient bacterial catalysts of homology search by spontaneous base pairing to mediate chromosome pairing. The key innovation was the origin of meiotic cohesins delaying centromere splitting to allow two successive divisions before reversion to vegetative growth and replication, necessarily yielding two-step meiosis. Also significant was the evolution of synaptonemal complexes to stabilise bivalents and of monopolins to orient sister centromeres to one spindle pole. The primary significance of sex was not to promote evolutionary change but to limit it by facilitating ploidy cycles to balance the conflicting selective forces acting on rapidly growing phagotrophic protozoa and starved dormant cysts subject to radiation and other damage.
Even if one disagrees with TCS on certain issues (his late-dating of the origin of eukaryotes and archaeabacteria is certainly a minority position), this gives one some vague idea (read the 200+ pages of articles to get a somewhat improved but still incomplete idea) of the kind of background knowledge level one must be at to even begin to discuss the Really Long Ago issues of evolution in an informed fashion.

Hope that helps,

Reposting this to AE...

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