Sex – a matter of perspective

I am sure that many readers have already concluded that I do not understand the role of sex in either organic or biotic evolution. At least I can claim, on the basis of the conflicting views in the recent literature, the consolation of abundant company.

– George C. Williams, Sex and Evolution, 1975

What’s sex all about? This question has been exercising biologists since well before Williams’s time, but in the 1970’s, with the rise of ‘gene-centrism’ and the related controversy over group selection, a succession of prominent authors grappled with the problem, trying to fit it with current evolutionary theory to no-one’s particular satisfaction. Males were deemed an impediment to a female’s efforts to maximise her reproductive output, time wasted on these feckless types resulting in her only passing on 50% of her genes per offspring. From the perspective of a ‘selfish gene’, meanwhile, getting into every offspring seems a preferable fate to only getting into half of them. On the basis of these apparent large costs, a cryptic offsetting benefit of corresponding magnitude was assumed. Like Godot, it is yet to appear.

Yet sex is widespread. All eukaryotes either do it now, or possess tell-tale signs that their recent ancestors did. Given that it appears costly to individuals, and genes, how did it evolve and why does it persist?

Terminology.

In asexual reproduction the entire genetic complement of cells or individuals – all of their chromosomes – is duplicated during mitosis. Two new cells are produced per complete division, giving exponential increase where unrestrained.

Mitosis occurs in sexual lineages too, but the defining characteristic of eukaryotic sexual reproduction is a cyclic alternation of ‘ploidy’, or chromosome number, interrupting the mitotic series. A haploid cell has one set of chromosomes, a diploid two, and so on, and in sex, two haploid gametes merge to form a diploid zygote in which each chromosome has a similar partner – a homologue – in the other haploid set.

At some future point, the reduction division of meiosis generates more haploid sets from the diploid, by pairing then segregating these homologous copies into new haploid cells. Additionally, during haploid separation there may be reciprocal swap of entire chromosomes or segments: recombination. By this process, previously linked genes end up in different individuals, while previously separate genes end up linked.

While in the diploid state, at any segment held in common between a pair of homologous chromosomes, the genetic sequence may be identical (homozygous) or not (heterozygous). Where heterozygous, the genome has two different alleles (sequence variants) at that locus, one of which may be dominant (expressed) and the other recessive (suppressed).

The problem

Consider an organism … with equal numbers of males and females … In females, a gene A suppresses meiosis, and causes the production of diploid eggs that develop without fertilization into females genetically identical to the parent. … when rare, such a gene would double in frequency in each generation. This result has been expressed by saying that there is a ‘twofold cost of sex’, arising from the needless production of males. It is clearer, however, to take a ‘gene’s eye view’: a gene A that suppresses meiosis is certain to be transmitted to all the eggs produced by a female, whereas a gene a that permits meiosis is transmitted to only half.

John Maynard Smith, Evolutionary Genetics 2nd Ed 1998.

The issue tends to be framed in population-genetic terms, by reduction to mathematical abstractions or computer models based on the diploid phase. When applying such simple models, the following drawbacks appear, when comparing sex to perpetual asexuality:

  • Sex breaks up adaptive gene combinations (costs of recombination/segregation).
  • Sex halves the genetic contribution of an individual to the next generation (‘twofold cost’ of meiosis).
  • Sex halves the chance of a given allele getting into the next generation (cost of meiosis, gene’s eye view).
  • For an organism with separate genders, sex may halve the number of grandchildren produced (twofold cost of males).
  • The need to locate a mate.
  • Time costs.

Sex does have accepted benefits. As Fisher and Muller noted in the 1930’s, sex, largely through recombination, can enable populations to concentrate beneficial alleles and purge detrimental ones independently, and to generate beneficial combined genotypes more rapidly than serial mutation in an asexual lineage. Sexual populations also tend to have more standing variation, which can assist in withstanding environmental change, disease, or parasites. These benefits, however, are at population level. This kind of ‘group selective’, good-of-the-species idea has a problem: how do you get from low frequency to become common enough to reap the group benefit? Especially when, on cost-driven thinking, individuals (or, if you’re a gene-centrist, genes) suffer such a high cost?

The solution (!)

My heretical contention is that the costs are largely illusory: an artefact of perspective and model. Sex doesn’t start with the diploid chicken, but the haploid egg. Regarding diploid somas as the central entity in biology is natural enough. It’s what we are, and is how most eukaryotic organisms spend most of their life cycles, and therefore forms the basis of much of population genetics itself. But in the matter of sex, it’s the wrong start point. Choosing to start with diploidy begs an erroneous view of the transaction. We will never find that elusive benefit for the diploid; there isn’t one. I argue that the entity for whose benefit sex exists is not the diploid organism at all, nor individual genetic loci, but the haploid genomes that nowadays slip almost unnoticed from instance to instance of the larger bodies they often form in diploid partnership, now thoroughly shuffled by the transaction. One might say that haploids don’t exist for the propagation of diploids; it is the other way round.

If we start with fusing haploids, the diploid cell they form is a temporary union, no more an indivisible unit with superior ‘interests’ than a human couple. Despite the superficial elaborations and apparent asymmetries in modern organisms, genetically sex remains a symmetric and mutually beneficial cycle of haploid fusion and division, and looks much the same to haploids as it always did. Diploidy is haploid symbiosis: a marriage of convenience.

While such diploid unions can and do become permanent, they inevitably appear in a background of an established sexual competitor and ecosystem; their repetitive genomes are rarely up to the challenge, while tending to suffer genetic degradation if their paired haploid genomes spend too long in harness. The tools of population genetics, with their inevitable simplifications, tend to obscure rather than illuminate the respective dynamics of the two modes – they overestimate the frequency of asexuals’ occurrence, and over-count their relative production.

The argument should hopefully become clearer if we follow the trajectory of sex from its probable start point: haploid fusion.

The most likely evolutionary sequence is:

  1. Haploid fusion – sex originated among haploids, not diploids
  2. Division – return to the haploid state via the ‘back end’ of mitosis
  3. Independent segregation – gives primitive, coarse recombination
  4. Speciation – steadily broadens the sexual clade and ecosystem
  5. Crossover – helps tensioning in meiosis, with far-reaching side-effects
  6. Multicellularity – nurtures and amplifies paired haploid genomes
  7. Gender – gamete asymmetry, only possible in multicellular forms.

To start at the very beginning …

1) Haploid Fusion.

The ancestral population in which sex arose, more ancient even than the most recent common ancestor of all modern eukaryotes (being itself sexual), must have been haploid. To get two similar chromosome sets in the first place, they must be copies of a single template in their most recent common ancestor, since duplicated through mitosis in separate haploid lineages. Thus, immediately we can see the that the ‘haploid-centric’ perspective is fundamental, and not merely arbitrary. Diploidy is more usually chosen as the starting point only for reasons of convention and a ‘diplocentric’ bias, rather than evolutionary logic.

There has to be a reason why such fused-haploid cells could prosper of course, but we don’t have to explain everything at once. The following are suggested possibilities for selective advantage, not mutually exclusive:

  • Fusion generates an immediate increase in unit size, without going to the trouble of conventional growth. Whether predator or prey, this has the clear potential to be advantageous, to both partners equally.
  • It is commonly observed that hybrids exhibit ‘vigour’, being frequently more robust than either parent even if sterile. The cause is related to heterozygosity – deleterious recessives can be masked by their dominant allele, the heterozygote may be ‘fitter’ than either homozygote, and nonoverlapping loci can ‘complement’ each other. There is no reason to suppose that this phenomenon is recent.

2) Division. 

Of course, we have an immediate problem – sex as defined is a cycle, alternating haploidy and diploidy. Whatever benefits derive from fusion are discarded on division, yet without a return to the haploid stage, it’s not a sexual system. However, it is not essential that we provide a positive advantage to division. For example:

  • Having fused, the cell has been pushed rapidly along its growth phase. If one recalls high school biology, Interphase, where growth and replication take place, is divided into G1, S and G2. Chromosome copies are made during S, so it is certainly possible that a fusion diploid would resemble, to the machinery of mitosis, a normal asexual cell at G2. The cell has grown, and contains approximate chromosome duplicates. Rather than needing a rationale to trigger separation, an early difficulty may have been actually to defer this automated cell division to preserve any benefits of diploidy.
  • It is not a given that such early eukaryotes could actually perform mitosis in the diploid state. If they couldn’t fully mitose as diploids, then however beneficial that diploid state may have been, it could only be temporary if such a lineage were to persist.
  • Genomes in diploids can suffer attrition from gene conversion events. These occur during recombinational repair, in which one haploid chromosome provides a ‘patch’ to fix breaks in its homologue. In doing so, that region can become homozygous, if it wasn’t already, potentially exposing deleterious recessive alleles to selection, or reducing any benefit derived from complementation at nonoverlapping loci. Additionally these ‘masks’ can themselves increase in number, due to further mutation. Thus, a lineage of haploids which fuses but then never divides may lack evolutionary staying power, ‘selecting for’ the capacity of division as avoidance of a problem rather than exploitation of an advantage.

On both of the latter two points, even if fusion was common and division rare, surviving lineages would be biased in favour of those with the capacity of division. On all three points, no explicit advantage to division itself is suggested. From these early ‘fusers’, it may be the case that only ‘dividers’ have left descendants to the present due to this bias in lineage survival, rather than direct adaptive advantage.

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Intermission 1 – The Basic Transaction.

Cartoon view of a sexual system. Curved arrows indicate possible mitosis in either phase; H’s represent haploid genomes.

Even with this minimal system, we have all the basic components of modern sex: haploid cells fuse, form a diploid for a period and then reduce back to haploids. At this stage, diploidy need only provide a relatively minor benefit, shared by both haploid genomes, to allow it to compete in a background ecosystem of perpetually asexual haploids. Secondary asexual diploids, meanwhile, always find themselves in direct competition with a parent population already in residence, and will only be ‘average’, on average.

Let’s examine the costs in this primitive system.

Cost of meiosis

The diploid here is nothing more than a pair of haploid genomes sharing a cell, and each haploid is not obviously worse off after the transaction than another parallel pair that remained independent throughout. It is not even necessary that fusion be complete initially – the nuclei may have remained separate, as in Giardia and some fungi today. But either way, one would not view this transaction as a puzzling halving of the diploid’s genetic complement. Any benefits of diploidy accrue to both partners equally; the diploid has no say in the matter. The twofold cost of meiosis is an illusion of perspective.

The costs of meiosis and of males are often conflated. It should be clear that they are in fact distinct, despite taking the same numerical value. John Maynard Smith appears to commit precisely this error in the quote with which I headed ‘The Problem’, though he immediately points out that the cost is not applicable to isogamous organisms – those where both gametes make an equal contribution to the next generation. (Indeed, if sex really did provide a mysterious twofold benefit, as it is commonly assumed it must to cope with males, this stage of isogamy should be an absolute breeze to establish!).

Segregation load.

Segregation load is again a cost viewed from the perspective of the diploid, when comparing a population of perpetual diploids that do not return haploids to similar rivals that do. If a particular diploid combination of alleles is beneficial, sex as depicted may break that beneficial combination due to segregation. However, on this scenario it was sex that brought them together in the first place. An asexual clone will ‘freeze’ and repeat a particular combination, but it simply represents a random draw of two genomes from the wider haploid pool. The sexual population, meanwhile, continues to make random draws. There is no reason to suppose that the asexual’s luck is any better, on the average, than the sexual’s.

There is a rather puzzling assumption implicit in the genetic load arguments, that sex is fine for generating combinations, but should be abandoned the instant it has done so. Yet something better may be just around the corner – there is no reason to prefer ‘stick’ over ‘twist’. If we only count severance of adaptive combinations, without recognising the contribution of the process to their creation, we are guilty of incomplete accounting. As long as net creation exceeds net loss, sex still wins.

Variation

Gradually, as mutations accumulate, the sexual population of diploids may be expected to hold a greater degree of standing variation, even with no recombination, because its genomes circulate in ‘halves’, both uncoupling the diploid and permitting more combinations. This variation may assist local adaptation, and provide a buffer against environmental change – and, indeed, invasion by clonal asexuals.

Ongoing evolution

By circulating as, effectively, ‘half-genome’ fragments (from the diploid perspective), haploids can be tuned more readily by iteration than when locked in harness in a perpetual diploid. A beneficial mutation in the diploid state is interfered with by the other allele at its locus – if recessive, it is not even expressed. The same mutation circulating in bare haploids, however, can increase through drift, then when it begins to encounter copies of itself in diploids, can be further promoted by selection.

Gene conversion

As already noted, homologous repair can expose deleterious recessives to selection. This is an ongoing and growing problem for a perpetual diploid, which exacerbates the problems already mentioned, further diminishing the probability that secondary asexuality will extinguish sexuality. The famous rotifers – ‘an evolutionary scandal’, being a notable exception to the rule that asexual lineages are short-lived – appear to avoid this problem. Their genomes are barely distinguishable as ‘diploid’ at all. If we can’t identify homologues, the repair mechanism is unlikely to do any better. (An afterthought: that may be putting the cart before the horse. The original diploid genome may have been permitted to diverge by suppression of the use of homologues in repair).

In the sexual diploid, conversely, the negative aspects of gene conversion are diminished, since partners don’t stick together long enough for it to become an inconvenience. Additionally, it serves as an incidental mechanism of generating variation, by placing alleles into novel backgrounds.

Networking.

The sexual population of diploids is ‘networked’ by virtue of its haploid vectors. Different solutions to environmental challenges are worked on independently and combined and tested in diploids. Improved versions of the haploid genome can ultimately find themselves shared by every diploid in the future population, a luxury unavailable to the cloned asexual population except by competitive replacement of the entire species.

Asexual diploids

Of course, even at this stage there is nothing in principle to stop the diploid failing to separate, and so forming a diploid asexual lineage. However, such asexual mutants always arise within an established sexual population. A given asexual derivative has committed for better or worse to a single genome out of the myriad of possible variants available to the sexual equivalent. Armed with that single repetitive genome, we are invited to believe that, as a universal principle, this asexual genome would outcompete all variants, throughout a range, in every such contest, if sex is to retain its mystery. This seems a stretch. While the asexual might possess the fittest variant of one genotype (corresponding to a whole chromosome at this pre-crossover stage) it would be unlikely to possess the fittest variant of every single one. The resident sexual has, somewhere, an answer to every competitive challenge the clonal asexual can throw at it, it can evolve more quickly, and within it gene conversion tends to be more a blessing than a curse

In my view, secondary asexuals (those derived from an ancestrally sexual line) are better viewed as a kind of ‘species cancer’ – diploid overproduction which may eliminate the parent ‘body’ in some circumstances, but needs to do so in all to generate a ‘mystery of sex’. Cancer does not cause us to ask ‘Why People?’; likewise, secondary asexuality should not automatically lead us to ask ‘Why Sex?’. Without sex, such presumed diploid threats to it would not even exist, a neat paradox.

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By such marginal degrees, then, a sexual clade may slowly rumble into life, largely untroubled, at this stage at least, by the threat of secondary asexuals, which may briefly flicker but are not up to the task required of them in preserving a ‘mystery of sex’: universal extinction of parent populations.

At what point in subsequent elaboration does the mystery commence? Does sex really have to ‘try harder’ once it discovers multicellular males?

3) Independent segregation.

Eukaryotic sexual recombination generates novel genomes by swapping segments of chromosome in the diploid. Indeed most ‘theories of sex’ are actually theories of recombination. It certainly gives rise to its most far-reaching consequences, yet the active mechanism, crossover, is complex, and its consequences seem to be at population level, requiring certain assumptions both to get it from low to high frequency, and to keep it there. Furthermore, when genetically controlled, a recombining locus may become detached from any benefit it causes.

It is not necessary to evolve something new, however. We have already touched on a mechanism by which limited recombination is achieved as a byproduct of another process: gene conversion in homologous repair. But even with this grossly simplified proto-sexual system, another form of recombination is available ‘for free’: if the haploid chromosome number exceeds 1, we see independent segregation of those multiple chromosomes, shuffling the haploid inputs. The parental haploid chromosomes are not labelled as such; the machinery of segregation simply lines pairs up at random on either side of the metaphase plate and hauls them apart. There is a 50% chance that any given former cell-mates will be separated on division: {A, B} and {a, b} ‘parents’ can produce {A,B}+{a,b} or {A,b}+{a,B} outputs with equal probability. This further increases the variation that the population can sustain.

A chromosomal break can readily drift into a population, if neutral or even if mildly deleterious. While rare, it encounters unbroken versions in meiosis, and there is no independent segregation. But when more common, it will start to encounter copies of itself, and chromosome ‘swaps’ will occur at the break point, purely by chance. As a consequence, beneficial alleles on the one are uncoupled from detrimental alleles on the other, allowing the former to increase in frequency and the latter to decrease, somewhat independently. Additionally, new beneficial combinations can arise through such swaps without the need for serial mutation in one lineage.

Note that this is precisely what Fisher and Muller proposed, but without any necessity for either elaborate mechanism or adaptive benefit to drive its fixation. Such chromosomal breaks form an ‘ideal’ recombining locus, since they do not suffer detachment from any benefit they may promote. They can drift in or out, additionally being sometimes promoted by and sometimes opposed by selection, according to the extent to which the break tends to have net negative or net positive effects. The fragments so formed, meanwhile, can increase or decrease independently of each other. The population is enriched in beneficial alleles, and similarly depleted in detriment, a comparative fine tuning not possible when alleles are chained in indivisible lumps.

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Intermission 2 – On Recombination.

11112222333344445555

An idealised chromosome, each 4-character stretch representing the span of a separate gene.

Cost of recombination

Contrast the above flexible, responsive but accidental mechanism with the assumption underlying the ‘cost of recombination’: that breaking combinations is ‘always bad’. Whether it is or isn’t depends upon current circumstances. Suppose that genes 1111 and 5555 interact – in the jargon, they exhibit epistasis. This means that, in the presence of the other, each experiences either enhanced (positive) or diminished (negative) selection. If a breàk appears between them, potentially swapping 1111 and 5555 into a different background, this could be detrimental if the interaction is positive. However, if the interaction is negative, the break would be favoured.

Additionally, irrespective of interaction, genes may contribute additively to adaptation. If 2222 and 4444 are both locally adapted genes, a break between them may disrupt them, particularly in the face of a stream of less well-adapted alleles migrating in from the wider population. The combined genotype 222233334444 is assumed locally fitter than both 22223333xxxx and xxxx33334444.

In reality, though, there are thousands of genes on a chromosome, thousands times thousands of potential interactions either side of a chromosomal ‘break’, and a great reservoir of combinations to explore available in the wider population. As we saw with segregation load, recombination does not merely break combinations, it creates them in the first place. Migrants don’t merely import locally detrimental alleles; beneficial ones come in on the same tide. Thus whether a particular break point is net detrimental or net beneficial depends upon integration of a great number of variables, which the naive ‘cost of recombination’ serves only to obscure.

Selfish Genes.

The twofold cost is often portrayed from a gene’s perspective, as a halving of its chances to get into any given offspring. Richard Dawkins goes so far as to imagine genes ‘dragged kicking and screaming into the second anaphase of meiosis’ (The Extended Phenotype). His intellectual predecessor John Maynard Smith framed it less dramatically (see ‘The Problem’ above), but both are guilty of exporting their own ‘gene-centric’ conception beyond the boundary of its application.

This needs some unpacking.

By shortening the recombining units involved in the basic transaction, we have dropped down to a new, subgenome level of selection. In a perpetual diploid, the entire paired genome is subject to repeat testing en bloc. But by continuing to reduce to haploids in sex, each chromosome is selected independently, for combinations that work together along its length but in competition with other such chromosomes segregating in the diploid population. Even though we have not yet introduced intrachromosomal segmentation by crossover, we have all the conditions required for ‘selfish genes’.

Dawkins’s catchphrase is frequently misunderstood, in both its parts, though he takes great pains to explain himself. ‘Selfish’ sets up the paradox of his most famous book: how to explain altruism in a competitive, Darwinian framework. His ‘Gene’, meanwhile, is not the molecular biologist’s or the geneticist’s, but a shorthand for a recombinant unit – a stretch of genome bounded by the extent to which it independently recombines. Maynard Smith’s ‘gene A‘ is not a recombinant unit; such things do not exist in asexuals.

Selfish genes integrate into the genomes of the future diploid population; that integration depends entirely upon recombination, and hence upon sex. Along their length, shorter stretches are selected to co-operate, because their futures are linked. While in the diploid state, all genes again have a common interest in co-operation. However, on separation, selfish genes are supposed to oppose that separation. But this is to misunderstand the causal mechanism underlying the metaphor. How can they do so while still remaining selfish genes? While it can be helpful to think in terms of a gene’s ‘wishes’, the metaphor breaks down the moment their means of population integration is removed, and becomes misleading. Paradoxically, a selfish gene cannot ‘wish’ to stop being a selfish gene!

Further, genetic loci themselves are not omnipotent. Most genes supply proteins or RNA tasked with performing some biochemical function or another. This is not readily modified to do something completely different – to ‘plug up the works’ of meiosis in some way. It is simply not mechanically possible for most genes to directly influence their transmission. They must do so through their effects on fitness, in whatever genetic system they find themselves. Indeed genes – the majority – which are at high frequency in the population gain no copies by abandoning sex, since they will generally be homozygous most of the time in any case.

Therefore only a handful of genes have even the notional capacity to effect or benefit from the switch to asexuality. Such genes would leave the sexual population, taking everything else with them – they become de facto a separate species, imprisoning a genome which can compete as a lumpen diploid whole, but whose parts can no longer integrate ‘selfishly’.

This is not to say that mutation to asexuality cannot occur, but it is an error to see this as a genetic competition between genome subunits, when it completely removes the sense in which such subunits have ‘interests’. It is an ecological competition between species.

The only lever available to recombining genetic stretches is to distort their transmission in meiosis, by tinkering with its machinery or attacking their homologue, rather than abandoning meiosis completely. Even here, mechanisms are dissipative. While such drive may distort transmission from an equitable 50/50 for a period, when a distorter becomes common it starts to encounter copies of itself, and either transmission returns to 50/50, or the distorter suffers from attacks upon itself in homozygotes.

Advocates of selfish gene viewpoints sometimes imbue them with a reach that exceeds their grasp. Far from being ‘dragged kicking and screaming’ into meiosis, they file obediently in, as they have always done.

Genetic algorithms

These are computational search heuristics inspired by biological population processes. Digital chromosomes representing varying solutions to a problem are copied and varied further, and the ‘fitness’ of the population members evaluated to determine which persist into the next round. Adding recombination to such programs can have a dramatic effect on search times, and aid escape from local fitness maxima. Recombination is gentler, less ‘speculative’ than mutation, since both parts have already survived in the population.

Even though evolution is not a search as such, the effects of recombination on rate and connectedness in GAs must surely have an analogue in the evolutionary behaviour of the natural populations from which they take their inspiration.

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4) Speciation

So far we have dealt with a single species – the only ‘true species’ on earth under the Biological Species Concept, everything else being an asexual prokaryote or eukaryote. Over time, any persistent reduction in free gene flow around such a population would be expected to lead to divergence between the subpopulations so formed – ultimately to the point at which the subpopulations would be incompatible, due to biological isolating mechanisms. At such a point, the sexual clade would have broadened, and the supposed broad-scale threat of asexuality, to extinguish all parent species, reduced. If there is a probability p that any one species will be eliminated by its secondary asexuals in a given time, with two species the probability they both go is p x p, with 3 species p x p x p and so on. The longer sex survives, the more resilient it becomes, simply by putting its eggs in multiple baskets.

Furthermore, once the growing clade had acquired a degree of ecological divergence, new asexuals would have more than just the resident competing sexual parent species to deal with. The sexual clade may begin to throw up predators, prey, parasites and interspecific competitors, all of which possess greater variation and evolutionary fleet-footedness compared to each new clonal variant. This is termed the Red Queen effect – it takes all your running just to stand still! – and further serves to cement the sexual clade’s position. Secondary asexuals surely arise from time to time, but most either fail to supplant the resident, or succumb to extinction by the several forces ranged against them after replacing the parent species.

As to the original haploid populations from which sex sprang, they too suffer from attrition by the sexual clade. The dynamics provided by sex are not only manifest in the diploid phase. The sexual clade can tune haploid genomes at chromosome level (or lower, given crossover). It can generate beneficial combinations of genes, and possess greater variation even within the haploid phase of its cycle than is available to perpetually asexual haploids. All of these, when added to advantages in the diploid phase, would tend to see gradual extinction of the ancestral asexual haploids.

5) Crossover

Some of the effects of recombination are available passively through independent segregation of chromosomes, discussed above. A distinctive feature of modern sex, however, is further segmentation of chromosomes through crossover. This involves reciprocal swapping of segments of homologous chromosomes during separation in meiosis. A nick is made in one chromosome, the homologue is recruited to provide a bridging patch, just as in repair of accidental breakage, and the resulting interlinked structure is resolved to yield separate chromosomes. There are four different ways to resolve, two of which yield recombinant chromosomes and two return the chromosomes unchanged (but for the patch, which results in gene conversion).

In the ancient repair system from which this derives, the random swap/no-swap result made no difference – the input chromosomes were the identical sisters freshly duplicated during the S phase of mitosis. But with nonidentical homologues from separate parents, and independent futures for the outputs, the consequences are profound.

Because crossover sites are not fixed, it has the effect over multiple generations of exposing yet shorter genetic stretches to independent selection – fully unmasking Dawkins’s ‘selfish genes’, each locus uncoupled from its neighbours and tested independently, over evolutionary time. As with segregational recombination, we get

  • Increase of beneficial alleles and decrease of detrimental with reduced interference between loci.
  • More rapid creation of novel combinations
  • An increase in variation, promoting both local adaptation and evolutionary resilience

These are arguably the most significant consequences of sex, which indeed cause many authors to regard it as the whole ‘point’ of the enterprise; the reason it exists. However, on the argument presented here, this need not be the case. After all, if the gene conversion and segregational recombination above were purely incidental, might it not be the case here too? 50% of crossover sites resolve to a recombinant product, but genes are blind to this. No gene is fundamentally bothered whether it remains linked to the same or to different chromosome-mates, provided the result works.

Population effects are important for lineages, but we do need to get active recombination from low to high frequency before its population consequences can be manifest. Felsenstein (yes, that Felsenstein) considers the case in which that may be mediated initially by drift, subsequently cemented by the resilience of such populations to environmental change. My own preference is to appeal to cellular mechanics. Crossovers assist in the equal tensioning of homologues as they are hauled apart during meiosis. Without them, there is a tendency to damaging asymmetry – one haploid output may lack an entire chromosome, the other having two copies giving potentially damaging trisomies on subsequent fusion. This gives a sufficient reason for crossover to become common in a sexual population without appeal to circumstantial issues such as environmental fluctuation or the extent of negative epistasis in the population. While recombination has significant population effects, which play a substantial role in the success of the clade, those consequences may be arguably a side-effect of its cytological role – an example of what Stephen Jay Gould termed a ‘spandrel‘.

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Intermission 3macroevolutionary trends

As a result of these various dynamics, we might expect gradual elimination of the ancestral asexual haploid lineages, possibly complete even prior to our Last Eukaryote Common Ancestor. Certainly, there are no known asexual haploid lineages today.

Since sex has its roots in the prehistory of the entire eukaryote clade, it probably played a significant role in eukaryogenesis itself, that mysterious and probably extended sequence of amendments separating eukaryotes from prokaryotes. We see that as a singularity because we have no surviving intermediates. But sex – serial diploidy – may be at least as important as endosymbiosis, the origin of mitochondria, in the overall sequence. In mitochondria, we are familiar with two genomes in a cell, but in reality, in the diploid phase, there are three.

Subsequent to LECA, the constraints on invasion by asexual diploids and the greater capacity of sexual lineages for anagenesis and cladogenesis would lead us to expect to find a eukaryote clade consisting mostly of sexual forms, with few if any purely asexual haploids, and comparatively few secondarily asexual diploid species. Which is handy, because that’s exactly what we find! All of this was achieved without going anywhere near any ‘twofold cost’. Isogamy can get us a long way.

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6) Multicellularity

Multicellular organisms, featuring multiple tissues in one genetic ‘individual’, have arisen independently a dozen or more times in eukaryotes, but never in prokaryotes. Because the eukaryote clade is built upon sexual roots, there is a close relationship between multicellularity and sex. After all, taking the ‘haploids’-eye-view’, what is a multicellular body other than a vehicle to protect and amplify both genomes, before returning haploid copies in profusion?

Of course there is a little more to it than that.

A multicellular eukaryote forms from either or both of the haploid or the diploid state, according to life cycle, by repeated mitosis of the genome of one or a few cells. The multicellular mode gives advantages of size and of ‘division of labour’ – by differential gene expression, different cell types can perform different functions despite possessing identical genomes. Among those specialised functions is reproduction itself. The cells of a body, or the genes within them, forego their direct reproduction in favour of the reproduction of identical gene copies in the specialised reproductive tissues. Freed of the need to reproduce directly, other tissue cells can concentrate on their own function.

While haploid individuals do occur – for example male social bees – the predominant mode is to form a multicellular soma from the diploid. Even fungal fruiting bodies, which avoid true diploidy until spore formation, have cells that contain both haploid nuclei: dikaryons. Enforcing a reproductive dead-end on diploid cells (or fungal dikaryons) may be easier to orchestrate, since reproduction is performed via production of a non-diploid cell type, a specialism not easily accessed by cells specialised for other functions. (Male bees may be exceptional because they are functionally the sperm of a ‘superorganism’: the hive).

Thus , as a general pattern, the co-operation of all cells in transmission of their shared genome appears to be secured by the specialised exit; opportunities for rogue cell lines to ‘go it alone’ are reduced. Conversely, a hypothetical asexual lineage exploring the first steps towards multicellularity has no equivalent mechanism ensuring intercellular co-operation and specialisation of the reproductive function. Multicellular bodies, I would contend, are an invention of sexual lineages.

7) Gender

The key distinction of ‘male’ vs ‘female’ is relative gamete size, rather than the organs, tissues and bodies with which we are more familiar. Females have the larger gametes, males the smaller. Note that, genetically, there is still little or no distinction between the haploid gametes; it is purely a matter of cellular packaging, with female gametes getting the lion’s share of cytoplasm. For this reason, it is unlikely that gender so defined can arise in unicellular organisms, by asymmetric division; the smaller would suffer disproportionate losses, and any genetic conflict would appear to centre on equal division. By generating male gametes in multicellular organisms from the end of a series of diploid mitoses, however, we get massive amplification of the genome, compensating losses by sheer weight of number. Female gametes, meanwhile, can be nourished, and furnished with additional cytoplasm to kick-start the next generation. Male gametes, being smaller, do most of the dispersing. Being cheaper to produce, they can be generated in greater numbers, but ultimately offspring numbers are limited by females.

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Intermission 4

Cost of Males

Leaving aside, for want of space, the reasons why gamete asymmetry is more stable than isogamy in multicellular organisms, we are finally in a position to examine the ‘twofold cost of males’. Note that this is a long way down the evolutionary trajectory. We have managed to get almost every feature of a modern sexual system, without a whisper of a roadblock from that twofold cost which is supposed to render sex itself a mystery. Even now, it is only an issue for dioecious organisms – those with separate male and female individuals. So the ‘mystery of sex’ resolves to a mere ‘mystery of dioecy’.

Imagine first a multicellular species with slight asymmetry: ‘male’ gametes are fractionally smaller than ‘female’. Fertilisation takes place externally. An asexual offshoot of the female version could, by abandoning fusion, produce asexual diploid offspring directly. But what would such a lineage gain? As in the primitive scenario, all asexual mutations occur against a background of a resident sexual, having variation and faster evolution at its disposal. The asexual is not helped in this conflict by the supposed ‘twofold cost’. We can incrementally increase the cytoplasmic asymmetry, but there is no clear point at which the need for an individual twofold benefit to sex arises. Nor does it arise incrementally, in proportion to the increase in gamete asymmetry. The relative benefit of sex is ‘smeared out’ among the population members, residing in variation already generated, in future capacity for tuning, and in the minimisation of gene conversion-induced homozygous effects.

Finally, we can add resource asymmetry in the embryo to the picture. Females often provide far more to the next generation than males, much more than just a bit of cytoplasm. While males continue to offer nothing more than haploid genome copies, as sperm, spores or pollen, the developing embryo may remain part of the female, as a baby, a maturing fertilised egg or a ripening seed. Half of those babies, eggs or seeds are male. The opportunity finally arises to increase ‘twofold’, by producing only female offspring. This would result in twice as many grandchildren, and exponential increase, compared to the sexual. However, again asexuality happens, when it happens, against a varied sexual background. It is still by no means certain that asexuality should be expected to win this contest a sufficient amount of time to eliminate all parent populations.

The gene’s perspective, again.

Gender is about resource asymmetry, not genetic asymmetry. Most genes reside on autosomes, and as such spend half of their existence in each body, investing equally in two complementary strategies. While in a male, they get inserted into large numbers of mobile gametes, widely dispersed. While in a female, they get inserted into fewer, less mobile but larger and better-provisioned gametes.

Despite several added complexities, from the perspective of any given gene the situation has still not changed from the single-celled state sketched above. In that sketch, individual genes feel no ‘force’ compelling them to remain paired indefinitely – to become asexual diploids. They come together for a period, then part. Even with full recombination, as long as the upstream and downstream companions of any gene constitute a viable haploid, it doesn’t matter whether those companions came from the same or different input haploids. In adding crossover, multicellularity and gender, we have changed nothing in terms of the dynamic between the haploid and diploid states. A given gene in the simple cartoon cycle above will appear in 50% of haploids, deterministically. In the more complex state we are now considering, a gene has exactly the same odds, now offered stochastically.

Haploids go in two by two, haploids come out two by two. Their roles as units are somewhat obscured by their loss of individual integrity as a consequence of the amplification and ‘randomisation’ of the input genomes. With independent segregation and crossover, output haploids are scrambled versions of the inputs – every one of the sometimes billions of outputs is unique; a sexual snowflake. But there is no gene in the haploid which is fundamentally motivated to ‘object’ to this scrambling. Throughout, it remains a genetically symmetrical transaction of pairing and parting.

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Population Genetics.

The ‘twofold cost’, along with other proposed costs of sex, such as recombination and segregation loads, is an argument derived initially from population genetics rather than observation.

Population genetics attempts to model populations in terms of mathematical or computational abstractions – necessarily, simplifications. The population in a simple equation is considered to be panmictic – all individuals are equidistant from all others, and equally likely to mate. Note here that sex is built into the very fabric of the assumptions. The panmictic population is stirred by, among other things, sex itself, through mate search and gamete dispersal. Such populations are also bounded by sex. If an obligate sexual, the range is determined in part by the need for a partner. A male can wander freely, but his genes cannot be passed on if he wanders too far from the available females. The same applies to an unfertilised female.

Now, population genetic models can be applied to asexuals. But there’s a bit of a difficulty there, because they lack both the stirring and bounding effects of sex. We artificially assume they are stirred and bounded, even though a significant cause of these is absent: sex itself. This is OK(ish) until we try and use the same model to compare sex and no-sex. Maynard Smith makes the same error in his textual argument above.

Consider what we’re doing when we use an equation to model a population. In essence, we are putting the population into a massive corral and giving it a good old stir. Individuals can leave the corral – it’s more a line in the sand than a fence – but they can only breed within it. Now, we add a few hypothetical asexuals. But implicitly we keep stirring at the same rate – despite the asexuals not being subject to those ‘stirring’ vectors related to sex. We also keep the same ‘breeding boundary’ – despite the asexuals not being constrained by it.

In a real population in which you bodily moved every new asexual individual to a different location, and kept them corralled, and eliminated all variation in the parent sexuals … then yes, the ‘cost of males’ might be an issue! The simplification is equivalent to metastasis in cancer. If cancer cells were always spread evenly around the body, cancer would kill in far greater numbers.

Because asexual individuals do not disperse in the same way as sexual genes, it is misleading to count their numbers as if they did. If an asexual colony arose within the ‘corral’, partially displacing the resident sexual locally, many of its offspring would be competing not with sexuals, but with other asexuals, reducing the impact of asexuality from that in a maximally-mixed model.

Asexuals are also free to leave the ‘corral’ entirely – here they find no competition with sexuals. Yet the model metaphorically rounds up such individuals and shoves them back inside, efficiently and artificially mixing each such individual to a different location within.

Using a simple model substantially over-counts asexuals.

How easy is it?

A fundamental assumption of ‘cost’ models is that the mutation to asexuality is freely available. This may not be the case. Clearly, to be costly, something must exist that can cash in on the saving. In a land without predators, it costs nothing for a zebra to browse leisurely and alone. Likewise, sex is only costly in the face of an existent asexual.

Firstly, mutation rate is proportional to population size. Small populations are most at risk from asexual invasion, as they lack variation, but equally they are less likely to suffer the mutation(s) in the first place.

Secondly, there is not a uniform susceptibility to the mutation across the tree of life. There are, for example, no known asexual mammals. There may be several reasons for this, but difficulty of mutation may certainly be one. Sperm import imprinted genes which have a profound effect on embryogenesis, while female meiosis is geared towards sperm reception. For a female mammal, it may not be a simple matter of ‘turning off meiosis’. She cannot perform autogamy either, fusing her own gametes, since 3 of the 4 outputs of meiosis are shrivelled ‘polar bodies’. Female mammals, with internal fertilisation, embryo retention and post-partum nurturing might seem to have the most to gain from asexuality, but they may also, as a group, find that amendment the hardest to achieve. This, rather than cryptic twofold benefit, may account for its absence.

I am only aware of one asexual bird, the turkey. And those offspring are all male, and so can’t form a lineage.

Asexuality becomes commoner as we go through the reptiles, and on to fish. However, even there, many of the examples arise from a process known as hybridogenesis rather than mutation. A significant competitive difficulty facing hybridogenesis is the replacement of both parental species, if they are ecologically distinct. Therefore, such mechanisms don’t pose a great threat to sex on the grand scale.

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To summarise, sex is woven into the fabric of the whole of eukaryote biology. It is an error to view asexuality as if it were a simple adaptation for diploids; much of the ongoing puzzlement derives from adherence to that standpoint. Contingency, side-effect, central stability and exaptation play at least as great a part as adaptation in the prevalence of sex, while the expectation that a twofold benefit is still required is an artefact of the diploid stance in oversimplified models. Sex and diploidy are fundamentally an adaptation for haploids, with far-reaching consequences.

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227 thoughts on “Sex – a matter of perspective

  1. CharlieM:
    Fair enough. But do you believe that the distinct, separable, independent, minuscule, elementary entities posited by some physicists are more fundamentally real than consciousness?

    No.

    I may be wrong but I would say that, just as my prior belief tends towards spiritism and psychism, your prior belief tends towards materialism and physicalism.

    I don’t know what’s achieved by playing the ‘prior belief’ card, though I see it a lot. Its sole merit seems to be in bringing someone else’s arguments down to your level. Well, I reject your equivalence, so there you go.

    Convergence doesn’t necessitate a feature or attribute appearing in separate lines at the same time. So in this respect a single instance is not an odd choice.

    It does necessitate multiple appearances eventually. You are extrapolating from a few instances to a very general principle with little justification. For a convergence to occur there has to be both a directional selective force and the capacity for response in a lineage. Where was the reward for consciousness in the days when we were worm-like, pulling us inexorably in that direction? Can the fly agaric lineage respond in the necessary manner? “Only time will tell”? 🤣

    But you are correct in one respect.

    I’m correct in all respects!

    Organisms that hadn’t maintained a generalised flexibility but had hardened into a narrow niche too early in their progressive evolution could never achieve the stage of being a rational self-conscious organism.

    Well, what a stroke of massively contingent luck our lineage remained suitably ‘generalist’ right the way from LUCA, then.

    An analogy would be …

    oh, Gawd! 🤣

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  2. CharlieM,

    Do you think the similarity between single development and the development of life as a whole is just an illusion or is there some reality to it? Do not both of these progress from single cells through multicellular differentiation?

    Bit of a glaring difference there, since the former goes back to single cells every time. “Oh, that. Yeah, apart from that…”. That’s the trouble with analogies.

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  3. Allan Miller:

    CharlieM,

    Me: It’s effectively a sequence of genetic code, yes. Just because it can change does not mean that a configuration cannot aid its own persistence***. Those changes that hinder are weeded out.

    Charlie: So if it’s not the sequence that persists, what is it that does persist? You say it’s a configuration that persists.

    It is the sequence that persists. Of course, if it changes, then that, slightly modified, sequence persists. One could say it’s the lineage that persists. Fusers leave more (haploid) descendants.

    But the fusers and descendants you are referring to are not just sequences of DNA, they are cells.

    Both you and Dawkins share the same reasoning. For Dawkins organisms are just, “survival machines – robot vehicles blindly programmed to preserve the selfish molecules known as genes” And for you we are just here in order to preserve the selfish molecules known as haploid genomes.

    I don’t use the term ‘selfish’ much. But arguing from first principles, diploids are instances of haploid fusion, not entities with evolutionary ‘interests’. The diploid lasts one generation.

    And the haploid genomes within the cells that get passed on are a mixture from two separate lines. So what does have evolutionary ‘interests’?

    What’s to stop others joining in this game? Perhaps we are just here in order to preserve our selfish mitochondria.

    It’s no more a ‘game’ than your attempt to make everything about humans and their peculiarities. My reasoning on costs and beneficiaries is aimed at biologists who are familiar with these approaches, rather than an attempt to persuade anyone to adopt these approaches. To those people who think in gene’s-eye terms (cost of meiosis), and others who think at organismal level (cost of males/segregation/recombination), I suggest that the intermediate perspective might be more appropriate in this instance: understanding the biological role of sex.

    Mitochondria get copied down the line more faithfully than nuclear haploid chromosomes. Sex is a means by which organisms can gain intra-species individuality.

    So are you saying that, say in humans, the individual entities that benefit are the mature sex cell genomes? But surely the genome in my sperm cells is not the same entity as the genome that my father carried nor the same as my son carries?

    Imagine a pair of haploids going into an early fusion, with a single chromosome each. While diploid, some benefit accrues to the haploid genomes. On separation, the same haploid genomes are recovered intact. No problem there. Now imagine two chromosomes in the haploid. Half the time, due to random segregation, the result is two recombinant genomes – not the original haploids. But it still is a question of haploid genomes in, haploid genomes out. Every locus on every chromosome still survives. They have simply – and accidentally – swapped partners. The ‘benefit’ has, in one sense, dropped a level. If one is looking at lineage continuity of linked genes, one could say that it’s now chromosomes that benefit. But it’s equally valid to say that the input haploid genomes have benefited. They have simply been separated on output. Their sequence still exists.

    So would you say it drops a further level in processes where crossing over occurs? And I’m still unsure of what the benefit is. If it is continued survival then I would say the ovum that gets fertilised is the main beneficiary.

    A genome provides what is needed to build and maintain the body of the creature to which it belongs and is an integral part of.

    So in my minimalist sex picture, where two single-chromosome haploid cells fuse for a period then separate, does a new ‘creature’ form on fusion, to which the two genomes ‘belong’? What happens to that creature when they go their separate ways?

    Yes, an individual creature begins its existence at conception when the sperm penetrates the ovum and the two cells fuse. When the cells separate then the creature is on the road to becoming multicellular.

    Benefits and costs are human economic terms which in my opinion lead us into a view of the natural world which is an abstraction.

    I argue quite strenuously against ‘cost-based’ thinking in my piece. But your view of the natural world is every bit as abstract, additionally importing a force with no evidence beyond its results, which have alternative explanations.

    What force? Apart from the earthly gravitational forces and the opposing heavenly levitational forces, the formative forces on living beings are all integral to that being. No external ‘hand’ shapes their form.

    There is a short piece by Stephen L. Talbott entitled, ‘Of Machines, Organisms, and Agency’ which I have linked to before which should be read in full.

    Here is an excerpt:

    The “design work” accounting for the organism is an activity inseparable from the organism’s own life. It is an expression of that life rather than a cause of it.

    Machines and organisms, therefore, have this in common: whatever is responsible for orchestrating causal arrangements — initially, in the case of machines, or continually, in the case of organisms — cannot itself be explained by those arrangements. This single fact calls into question the entire habit within biology of trying to explain the present purely as the consequence of material forces playing out of the past.

    It’s true that biologists speak incessantly of mechanisms and of machine-like or programmed activity in organisms. But this is empty rhetoric. No one has ever pointed to a computer-like program in DNA, or in a cell, or in any larger structure. Nor has anyone shown us any physical machinery for executing such program instructions. Nor, for that matter, has anyone ever explained what constrains diffusible molecules in a watery medium to carry out elaborate operations, such as DNA replication or RNA splicing.

    The complexity of these operations, the ever-shifting patterns of cooperation required from the molecules, the sequencing of steps in a prolonged narrative, and the attention to an ever-shifting context that says, “Head in this direction” under one set of conditions and “Head in that direction” under a slightly different set of conditions — none of this is governed by machine-like controls that coerce the molecules into their essential, infinitely varying, and context-sensitive roles in the larger narrative. Yet, despite the lack of controlling mechanisms, the achievement is vastly more sophisticated than any intricately choreographed, well rehearsed performance by a ballet troupe.

    Picture in your head what is going on during the process of meiosis, how all the molecules expand and condense, and purposefully move around within the cell. Don’t just look at cartoon images of the various stages but imagine you are a “protein on the wall” witnessing this coordinated activity. Each and every actor in this process instincively knows its role and how to carry it out.

    And this can be an obstruction and restrict us from getting to the reality that is all around and within us.

    Reality, huh? 🤔 Well, why do you think sex is so common among eukaryotes?

    Sex allows for variation and variation leads to individuality. It is a process whereby individual beings can separate off from the clonal mass.

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  4. Allan Miller:

    CharlieM:Me: No it doesn’t. All you have done is utter a trite truism. If you wish to assert some extra force shepherding our Chosen Lineage ever-Charliewards, you’re going to have to do better than “well, I’m here aren’t I?”.

    Charlie: Well let’s have a look at a necessary step on the way to the arrival of humans. You wrote:
    [multicellularity]
    This is one of the convergences I was talking about.

    I am hardly denying the existence of convergence. But when you talk of an entire trajectory from LUCA to us being one massive ‘convergence’, yet only resulting in a singular instance of us-style consciousness, I am unconvinced by your reasoning. Red algae or basidiomycetes appear not to be headed towards consciousness, despite sharing the possible ‘convergence’ of multicellular organisation.

    Divergence and convergence are the polarities by which life progresses towards a point where individual consciousnesses can appear. The plant world has prepared the way for mobile animal life to diversify. Plants have diversified in so many ways but the fact that they have remained at their sessile stage of existence has allowed animals to evolve and diversify.

    And there are many convergences, such as bipedality, eyes, endothermy, egg laying, live birth, flight. All these to do with reaching a certain loosening of ties to the environment.

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  5. dazz:

    CharlieM: I may be wrong but I would say that, just as my prior belief tends towards spiritism and psychism, your prior belief tends towards materialism and physicalism.

    Do you have psychic powers?

    We all do. The fact that you can move through the power of your own will and thinking is a psychic power. It is you who will make the decision to either ignore or respond to this post, and to make decisions as to the way in which you respond if that is what you decide. You do this through the power of your psyche.

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  6. CharlieM:
    But the fusers and descendants you are referring to are not just sequences of DNA, they are cells.

    ‘Fusers’ would possess the DNA which promoted fusing, and would pass that on to their descendant cells. Non-fusers would lack it, and hence the two strategies would have potentially different outcomes, based solely upon this genetic distinction. I shouldn’t have to keep saying this. Your refusal to see the role of DNA in evolution, to cling to some vague and uninformative ‘holism’ informed by individual physiologies, is getting tiresome.

    And the haploid genomes within the cells that get passed on are a mixture from two separate lines. So what does have evolutionary ‘interests’?

    That depends on the level of segmentation. If there’s only one chromosome, it’s the entire genome. If there’s more than one, it’s chromosomes. If there’s crossover too, it’s haplotypes (‘ selfish genes’). But whichever way you slice it, it isn’t diploids.

    Mitochondria get copied down the line more faithfully than nuclear haploid chromosomes.

    Who/what cares about that? Mitochondria reproduce asexually. Haploid genomes reproduce sexually, by fusion in diploids then subsequent segregation. The fact that homologous sequences may have been swapped is not a problem for any individual locus. As long as inputs and outputs are viable haploid genomes, nothing is troubled by this shuffling, nor even ‘aware’ of it, to take the gene’s stance.

    Sex is a means by which organisms can gain intra-species individuality.

    I don’t know what use that is.

    So would you say it drops a further level in processes where crossing over occurs?

    Indeed. That’s where Dawkins comes in. But my point is that you don’t need an active mechanism to get ‘selfish haplotypes’, which is important in discussions about selection on recombination.

    And I’m still unsure of what the benefit is. If it is continued survival then I would saythe ovum that gets fertilised is the main beneficiary.

    You should stop thinking about modern sex (and your obsession over ‘The Cell’). Primitive sex involved isogamous unions – the same amount of DNA and cytoplasm from each haploid, and going into each subsequent one on division. Asymmetry – which even then is only cytoplasmic asymmetry, and only in multicellular organisms – comes much later.

    Yes, an individual creature begins its existence at conception when the sperm penetrates the ovum and the two cells fuse. When the cells separate then the creature is on the road to becoming multicellular.

    Like I say, forget about us. I was using an illustration of a primitive unicellular diploid to illustrate the difficulty of placing the diploid at the centre. You seem to have ignored most of what you were responding to.

    What force? Apart from the earthly gravitational forces and the opposing heavenly levitational forces, the formative forces on living beings are all integral to that being. No external ‘hand’ shapes their form.

    Whatever you choose to call it, you are adding something to biology beyond simple differential survival – something that is alert to future asteroids, the need to avoid ‘specialism’ in our sainted lineage, and shepherds every precious mutation from single copy to fixation.

    Me: Reality, huh? Well, why do you think sex is so common among eukaryotes?
    Charlie: Sex allows for variation and variation leads to individuality. It is a process whereby individual beings can separate off from the clonal mass.

    And why does that matter?

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  7. CharlieM:
    Divergence and convergence are the polarities by which life progresses towards a point where individual consciousnesses can appear.

    You are using ‘convergence’ in a very non-standard way. Stop helping yourself to concepts!

    And there are many convergences, such as bipedality, eyes, endothermy, egg laying, live birth, flight. All these to do with reaching a certain loosening of ties to the environment.

    Like I say, I am not denying convergences. But far from ‘loosening ties’, conventionally the environment, rather the niche, drives them. Why do so many aquatic animals tend to be streamlined?

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  8. Allan Miller:

    CharlieM:
    Fair enough. But do you believe that the distinct, separable, independent, minuscule, elementary entities posited by some physicists are more fundamentally real than consciousness?

    No.

    So you don’t believe that consciousness is a product of the interaction of these elementary elements? If that is the case, I’m glad to hear it.

    I may be wrong but I would say that, just as my prior belief tends towards spiritism and psychism, your prior belief tends towards materialism and physicalism.

    I don’t know what’s achieved by playing the ‘prior belief’ card, though I see it a lot. Its sole merit seems to be in bringing someone else’s arguments down to your level. Well, I reject your equivalence, so there you go.

    So you believe is that you have no prior beliefs. You are indeed a true sceptic 🙂

    Convergence doesn’t necessitate a feature or attribute appearing in separate lines at the same time. So in this respect a single instance is not an odd choice.

    It does necessitate multiple appearances eventually. You are extrapolating from a few instances to a very general principle with little justification. For a convergence to occur there has to be both a directional selective force and the capacity for response in a lineage. Where was the reward for consciousness in the days when we were worm-like, pulling us inexorably in that direction? Can the fly agaric lineage respond in the necessary manner? “Only time will tell”? 🤣

    You are giving your reasons for believing how convergence happens. I was noting that we can observe convergences and see a repeated pattern. This is in the same way I can observe a tree and see a repeated pattern in the way that individual branches and branchlets reflect the same pattern as the whole observed tree.

    The rudimentary nervous system of our worm-like ancestors had the potential to develop further which they obviously did hence the subsequent appearance of our advanced nervous system. Not all worm-like creatures achieved this potential. But the onward progress of life relies on worm-like creatures remaining at the stage they have reached as they form a necessary part of ecosystems.

    But you are correct in one respect.

    I’m correct in all respects!

    I bow to your omniscience 🙂

    Organisms that hadn’t maintained a generalised flexibility but had hardened into a narrow niche too early in their progressive evolution could never achieve the stage of being a rational self-conscious organism.

    Well, what a stroke of massively contingent luck our lineage remained suitably ‘generalist’ right the way from LUCA, then.

    It’s not just a case of remaining generalist and being able to cope with change. There has to be progression towards novel attributes and abilities along with this.

    An analogy would be …

    oh, Gawd! 🤣

    And now you’ve started talking to yourself 🙂

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  9. Allan Miller:

    CharlieM,

    Do you think the similarity between single development and the development of life as a whole is just an illusion or is there some reality to it? Do not both of these progress from single cells through multicellular differentiation?

    Bit of a glaring difference there, since the former goes back to single cells every time. “Oh, that. Yeah, apart from that…”. That’s the trouble with analogies.

    With the former we can observe individuals being conceived, living and dying. In other words the whole of their lives within time. Because we exist in the middle of life as a whole we are not in a position to witness an end point and beyond.

    Unless of course we are omniscient 🙂

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  10. CharlieM: No.

    So you don’t believe that consciousness is a product of the interaction of these elementary elements? If that is the case, I’m glad to hear it.

    That wasn’t the question you asked to which my answer was ‘No’.

    So you believe is that you have no prior beliefs.

    Hmmm. When you have to slip into misrepresentation mode … I believe that the ‘prior belief’ card is a cheap rhetorical trick, invariably coming from the ID-inclined side, which effectively says “I know I’m on shaky ground here, but I’m no worse off than you”. Other than that, it serves no real purpose. It certainly doesn’t advance a discussion. If your interlocutor fails to see the relevance of ‘prior belief’ to a particular argument that can be subject to reason, what’s the point of continuing to bang that drum? It’s like ‘That’s just your opinion’; a conversation stopper rather than a meaningful rejoinder.

    You are giving your reasons for believing how convergence happens.

    No, I’m saying what convergence is. It is restricted to lineages with the capacity to follow the path, is highly correlated with common ecological constraint, and comes (like Tarzan’s legs in the Cook & Moore sketch) with a minimum instance requirement of two. If you don’t mean the biological phenomenon, find a different word, and give up the biological examples.

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  11. CharlieM:
    With the former we can observe individuals being conceived, living and dying. In other words the whole of their lives within time. Because we exist in the middle of life as a whole we are not in a position to witness an end point and beyond.

    You think we’ll evolve back to single cells eventually? Your analogies just confuse matters.

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  12. newton: How about genetic mutations?

    Mutations are not “evolution”. This has been discussed.

    Alan Fox: And proof is for math not science.

    Actually, you can disprove false hypotheses in science. Why would you claim something clearly false?

    Entropy: That’s the point you little-minded imbecile. They’ve changed. They’re modified.

    Why do I continue to address cretins like Entropy? For the one in a million nugget. Not this time though.

    Allan Miller: Repeatedly asserted is hardly ‘proven’.

    Absolutely right.

    Allan Miller: Genetics covers the ‘modification’ part of ‘descent with modification’, via mutation and recombination.

    False. As discussed. You’re going in circles.

    Allan Miller: I demonstrated why your separation of mutation and recombination in modification was false.

    Your conclusion was:

    “Clearly, ‘eggs and flour’ notwithstanding, recombination is every bit as capable as mutation of generating heritable change.”

    OK. So? Mutation, recombination, modification are three different things. I don’t see how you link them. Perhaps you want to clarify.

    Allan Miller: If you understood genetics, you wouldn’t need to use such baby-talk terms, but could instead discuss the actual phenomena.

    I am not sure YOU understand genetics. Better start with something clear and simple. Now, would you answer that question?

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  13. Allan Miller:

    CharlieM:
    But the fusers and descendants you are referring to are not just sequences of DNA, they are cells.

    Allan Miller: ‘Fusers’ would possess the DNA which promoted fusing, and would pass that on to their descendant cells. Non-fusers would lack it, and hence the two strategies would have potentially different outcomes, based solely upon this genetic distinction. I shouldn’t have to keep saying this. Your refusal to see the role of DNA in evolution, to cling to some vague and uninformative ‘holism’ informed by individual physiologies, is getting tiresome.

    I do see that DNA is a vital component of cells. It is by means by which all the various proteins can be made. But the amounts and timing of gene expression is achieved by the coordinated effort of a vast number of players acting on and within the cell. From Science Daily “Defining the centromere: Roles of kinetochores in cell division”:

    The division of cells is highly-regulated and complex process which requires the organised collaboration of a multitude of different cellular components…

    Dr Lermontova let us know: “There are more than 100 different kinetochore proteins and only few of them have been described and characterised functionally in plants. In the group, we are focussing on elucidating the mechanism of kinetochore assembly and function.”

    And that is just one small area of the process of cell division.

    Some would say that your refusal to see the cell as the unit of heredity is getting tiresome. It is only in the case of viruses where this is not the case. But even here cells are required to be present.

    CharlieM: And the haploid genomes within the cells that get passed on are a mixture from two separate lines. So what does have evolutionary ‘interests’?

    Allan Miller: That depends on the level of segmentation. If there’s only one chromosome, it’s the entire genome. If there’s more than one, it’s chromosomes. If there’s crossover too, it’s haplotypes (‘ selfish genes’). But whichever way you slice it, it isn’t diploids.

    From prokaryotes to mammals in relation to vertical lines of descent, the basic entity that passes down the generations is the cell. This review, “Preformed cell structure and cell heredity” discusses cortical inheritance.

    Our understanding of biological processes is constrained within a circular relationship resembling the “hen-egg dilemma” which might be called the “DNA-cell dilemma”: if all the information necessary to make a cell (or a tyrannosaurus, as the fiction goes) is stored in DNA sequences, why does a cell only arise from a preexisting cell?

    This is what is observed, cells arising from cells.

    CharlieM: Mitochondria get copied down the line more faithfully than nuclear haploid chromosomes.

    Allan Miller: Who/what cares about that? Mitochondria reproduce asexually. Haploid genomes reproduce sexually, by fusion in diploids then subsequent segregation. The fact that homologous sequences may have been swapped is a problem for no individual locus. As long as inputs and outputs are viable haploid genomes, nothing is troubled by this shuffling, nor even ‘aware’ of it, to take the gene’s stance.

    I don’t have a problem with the fact that it is haploid genomes and not diploid genomes that get passed down. My argument is it is not just the bare genome that gets passed down. You cannot just ignore everything but the genome.

    CharlieM: Sex is a means by which organisms can gain intra-species individuality.

    Allan Miller: I don’t know what use that is.

    Well do you feel that you are an individual or do you feel more like a Borg collective? Sex produces offspring with an individual identity that clones do not have.

    CharlieM: So would you say it drops a further level in processes where crossing over occurs?

    Allan Miller: Indeed. That’s where Dawkins comes in. But my point is that you don’t need an active mechanism to get ‘selfish haplotypes’, which is important in discussions about selection on recombination.

    And my point is that pair orientation ensures one level of variation and crossing over produces a further level of variation. And this leads to greater individuality of the offspring. So from prokaryotes which mainly reproduce by cloning to higher eukaryotes such as mammals there is an ever increasing path to individualisation.

    CharlieM: And I’m still unsure of what the benefit is. If it is continued survival then I would say the ovum that gets fertilised is the main beneficiary.

    Allan Miller: You should stop thinking about modern sex (and your obsession over ‘The Cell’). Primitive sex involved isogamous unions – the same amount of DNA and cytoplasm from each haploid, and going into each subsequent one on division. Asymmetry – which even then is only cytoplasmic asymmetry, and only in multicellular organisms – comes much later.

    Yes, the more primitive the greater similarity. There is an advancement towards
    dissimilarity between individuals.

    CharlieM: Yes, an individual creature begins its existence at conception when the sperm penetrates the ovum and the two cells fuse. When the cells separate then the creature is on the road to becoming multicellular.

    Allan Miller: Like I say, forget about us. I was using an illustration of a primitive unicellular diploid to illustrate the difficulty of placing the diploid at the centre. You seem to have ignored most of what you were responding to.

    Like I said, I’m happy putting haploids at the centre. But either way they are always within a cell. New life begins with a cell and not a bare chromosome or chromatid..

    CharlieM: What force? Apart from the earthly gravitational forces and the opposing heavenly levitational forces, the formative forces on living beings are all integral to that being. No external ‘hand’ shapes their form.

    Allan Miller: Whatever you choose to call it, you are adding something to biology beyond simple differential survival – something that is alert to future asteroids, the need to avoid ‘specialism’ in our sainted lineage, and shepherds every precious mutation from single copy to fixation.

    Well life has reached the point where individuals can be alert to future asteroids. We don’t see all changes being guided, but we do see purposeful processes within cells, coordinated orchestrated activity working against unforeseen external disruptions in the same way that we see social insects working in a similar manner. There appears to be a group wisdom that cannot be explained by the individual parts. These parts work together not as in a machine but as in a team which can adapt to circumstances.

    Allan Miller: : Reality, huh? Well, why do you think sex is so common among eukaryotes?
    CharlieM: Sex allows for variation and variation leads to individuality. It is a process whereby individual beings can separate off from the clonal mass.

    Allan Miller: And why does that matter?

    If you come with the prior opinion that everything is just molecules in motion ten it doesn’t matter in the slightest. If you come with the prior opinion that consciousness is fundamental then it matters a great deal.

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  14. Allan Miller:

    CharlieM:
    Divergence and convergence are the polarities by which life progresses towards a point where individual consciousnesses can appear.

    You are using ‘convergence’ in a very non-standard way. Stop helping yourself to concepts!

    I’ve given examples of convergences. I don’t see how this is non-standard.

    And there are many convergences, such as bipedality, eyes, endothermy, egg laying, live birth, flight. All these to do with reaching a certain loosening of ties to the environment.

    Like I say, I am not denying convergences. But far from ‘loosening ties’, conventionally the environment, rather the niche, drives them. Why do so many aquatic animals tend to be streamlined?

    Because it allows them to move efficiently through the water. But this very process of streamlining has altered their limbs to such an extent that their further adaption for a wide range of functions becomes so unlikely that we might as well call it impossible.

    But taking things to extremes comes at a cost. Dolphins are more streamlined than otters. But otters can use its limbs for a wide variety of tasks and have a more free lifestyle because of this.

    So I agree with you. Convergences related to the environment can lead creatures down an ever narrowing path that becomes increasingly difficult to escape from.

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  15. Nonlin.org: Why do I continue to address cretins like Entropy? For the one in a million nugget. Not this time though.

    You cannot address my comments because you’re too obviously wrong. I won the argument you poor excuse of an elementary schooler. Go back to kindergarten. Pay much better attention this time around.

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  16. Allan Miller:

    CharlieM:
    So you don’t believe that consciousness is a product of the interaction of these elementary elements? If that is the case, I’m glad to hear it.

    That wasn’t the question you asked to which my answer was ‘No’.

    Of course it wasn’t. I asked this further question so that I could get a better understanding on your position in regards to the relationship between matter and consciousness. As to which in your opinion is more fundamental.

    So you believe is that you have no prior beliefs.

    Hmmm. When you have to slip into misrepresentation mode … I believe that the ‘prior belief’ card is a cheap rhetorical trick, invariably coming from the ID-inclined side, which effectively says “I know I’m on shaky ground here, but I’m no worse off than you”. Other than that, it serves no real purpose. It certainly doesn’t advance a discussion. If your interlocutor fails to see the relevance of ‘prior belief’ to a particular argument that can be subject to reason, what’s the point of continuing to bang that drum? It’s like ‘That’s just your opinion’; a conversation stopper rather than a meaningful rejoinder.

    We all have biases towards core beliefs to which we are attracted. Any one of the positions we take can be justified depending on the context. It is not just a case of arguing that because a person I am debating is arguing from a position diametrically opposed to mine then that person must be wrong and my position right.

    Mario Betti wrote a book inspired by a lecture by Steiner dealing with various philosophical positions and how they can be justified.

    In his book, Twelve Ways of Seeing the World, Mario Betti strives to make sense of the world through different lenses framed as twelve archetypes; Phenomonalism, Sensualism, Materialism, Mathematism, Rationalism, Idealism, Psychism, Pneumatism, Monadism, Dynamism, Realism and Humanus. Betti draws on the research of Rudolph (sic) Steiner and his twelvefold typology of human and cosmic thought to explore and validate each world view from its own unique perspective. In this way he means to transform dogmatism and enable a deeper dialogue.

    Twelve main positions are given but, as seconds and minutes can be inserted between the hours on a clock face, there are many more nuanced positioned that have a place within this circle of beliefs.

    So it is not a matter of trying to stifle conversation, it is a matter of recognising our own position and trying to see things from the position of others and in trying to understand where they are coming from.

    You are giving your reasons for believing how convergence happens.

    No, I’m saying what convergence is. It is restricted to lineages with the capacity to follow the path, is highly correlated with common ecological constraint, and comes (like Tarzan’s legs in the Cook & Moore sketch) with a minimum instance requirement of two. If you don’t mean the biological phenomenon, find a different word, and give up the biological examples.

    But I have never said that all life forms are converging on human type rational, self-consciousness. In fact I’ve stressed the divergence. And you agree that some organisms have diverged in a way that blocks their path to individual self-consciousness, as in your red algae and basidiomycete examples.

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  17. The veins on a leaf can converge on the same bifurcation pattern as in the pattern of the whole tree to which they belong but they will never converge in such a way that they become part of the main branching from the trunk. Their converging pattern is fractal in nature.

    The natural world is replete with fractal patterns. Chromatids are fractal.

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  18. Allan Miller:

    CharlieM:
    With the former we can observe individuals being conceived, living and dying. In other words the whole of their lives within time. Because we exist in the middle of life as a whole we are not in a position to witness an end point and beyond.

    You think we’ll evolve back to single cells eventually? Your analogies just confuse matters.

    No I don’t think that. Life and death are cyclic in nature at all levels. I get on my bike and cycle down the road. The valve on each wheel completes one revolution and returns to its starting point. But in reality it is not the same point because the bike has moved a distance along the road. If life was to disappear completely from the earth and then begin again from scratch it would not be the same because in the mean time the earth has moved on and changed considerably.

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  19. CharlieM: But this very process of streamlining has altered their limbs to such an extent that their further adaption for a wide range of functions becomes so unlikely that we might as well call it impossible.

    This is a global problem for organisms highly adapted to particular niches. Rapid change or loss of habitat results in extinction.

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  20. Alan Fox:

    CharlieM: But this very process of streamlining has altered their limbs to such an extent that their further adaption for a wide range of functions becomes so unlikely that we might as well call it impossible.

    This is a global problem for organisms highly adapted to particular niches. Rapid change or loss of habitat results in extinction.

    Quite right. For, “highly adapted to particular niches” we can say they are extremely specialised in a way which reduces their options of further independence from a particular environment or lifestyle.

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  21. Nonlin.org,

    Allan Miller: Genetics covers the ‘modification’ part of ‘descent with modification’, via mutation and recombination.
    Nonlin: False. As discussed. You’re going in circles.

    True. As not really ‘discussed’; you are merely repeating your ignorant assertions, so I feel free to counter by simply repeating my well-informed ones.

    Allan Miller: I demonstrated why your separation of mutation and recombination in modification was false.

    Nonlin: Your conclusion was:

    “Clearly, ‘eggs and flour’ notwithstanding, recombination is every bit as capable as mutation of generating heritable change.”

    OK. So? Mutation, recombination, modification are three different things. I don’t see how you link them. Perhaps you want to clarify.

    I explained above how mutation and recombination both result in heritable genetic change, which I, as a native English speaker, am happy to call ‘modification’. In one of my examples, they produced exactly the same effect. Go on, equivocate your way out of that one.

    Allan Miller: If you understood genetics, you wouldn’t need to use such baby-talk terms, but could instead discuss the actual phenomena.

    Nonlin: I am not sure YOU understand genetics.

    So you can point out where I’ve gone wrong, without resort to silly analogy then, can’t you?

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  22. CharlieM,

    I do see that DNA is a vital component of cells. It is by means by which all the various proteins can be made. But the amounts and timing of gene expression is achieved by the coordinated effort of a vast number of players acting on and within the cell.

    ALL of them have their root in DNA. All the control sequences, the proteins themselves, promoters and repressors: all trace back to a segment of DNA somewhere. All are susceptible to alteration by mutation of the DNA; you can’t achieve evolutionary change by changing anything else. I know I’ve said this before, but you keep ignoring it, banging on for all you’re worth about ‘the system’. The system is rooted in DNA.

    From Science Daily “Defining the centromere: Roles of kinetochores in cell division”.
    […]
    And that is just one small area of the process of cell division.

    Gosh. Cells are complex you say? Well, I never.

    Are any of those many proteins not transcribed from DNA, then?

    Some would say that your refusal to see the cell as the unit of heredity is getting tiresome. It is only in the case of viruses where this is not the case. But even here cells are required to be present.

    Why make an exception for inconvenient viruses? The same applies to any stretch of nucleic acid that gains copies through its consequences, in a system where copies are made.

    Any chromosome that does not possess a DNA polymerase is hitchhiking on the efforts of those that do. Likewise any that lack transcription/translation. Examples abound of supernumerary chromosomes, selfish haplotypes etc – even the centromeres you mentioned above can behave ‘selfishly‘. None of this makes sense from your obtusely one-sided viewpoint. It is simply the case that, given replication, different DNA sequences can be differentially replicated.

    From prokaryotes to mammals in relation to vertical lines of descent, the basic entity that passes down the generations is the cell. 

    ‘The cell’… that’s a bit of a sleight-hand way of ignoring the crucial difference I’ve been banging on about from the OP onwards. ‘The cell’ in a sexual diploid is sliced down the middle. It becomes two cells, which in most species cannot even replicate alone. In mammals, one of the cells is furnished with more cytoplasmic components than the other, but that’s not a universal.

    Our understanding of biological processes is constrained within a circular relationship resembling the “hen-egg dilemma” which might be called the “DNA-cell dilemma”: if all the information necessary to make a cell (or a tyrannosaurus, as the fiction goes) is stored in DNA sequences, why does a cell only arise from a preexisting cell?

    Not strictly relevant in discussions about sex, but I favour RNA world, with protein enzymes coming much later.

    I don’t have a problem with the fact that it is haploid genomes and not diploid genomes that get passed down. My argument is it is not just the bare genome that gets passed down. You cannot just ignore everything but the genome.

    For evolutionary considerations, you actually can. The cytoplasmic component of any cell is of recent origin, transcribed from DNA. What persists over the generations is DNA sequence, segmented, in sexual organisms, by recombinational shuffling.

    CharlieM: Sex is a means by which organisms can gain intra-species individuality.

    Allan Miller: I don’t know what use that is.

    Charlie: Well do you feel that you are an individual or do you feel more like a Borg collective? Sex produces offspring with an individual identity that clones do not have.

    I still don’t know what use that is. It’s relevant to my argument, but I don’t know why your ‘evolutionary unrolling’ needs to serve that end, given the vast diversity of sexual lineages that didn’t go that way. Nor do you offer any mechanistic means by which the future requirement is anticipated or implemented.

    And my point is that pair orientation ensures one level of variation and crossing over produces a further level of variation. And this leads to greater individuality of the offspring. So from prokaryotes which mainly reproduce by cloning to higher eukaryotes such as mammals there is an ever increasing path to individualisation.

    Still don’t see why it matters. I know why from an evolutionary point of view, but you are rejecting that point of view here, saying instead that it matters to whatever process you imagine operates (rather opaque) that you are different from me.

    Yes, the more primitive the greater similarity. There is an advancement towards dissimilarity between individuals.

    Yeah, ‘for some reason’. You’re confusing gamete asymmetry and diploid variation there, incidentally, unless you are agreeing with me that haploids are the true ‘individuals’.

    Like I said, I’m happy putting haploids at the centre. But either way they are always within a cell. New life begins with a cell and not a bare chromosome or chromatid..

    This doesn’t mean we can ignore their dynamics, simply because they are always encapsulated.

    Well life has reached the point where individuals can be alert to future asteroids.

    And is blindsided by viruses.

    If you come with the prior opinion that everything is just molecules in motion ten it doesn’t matter in the slightest. If you come with the prior opinion that consciousness is fundamental then it matters a great deal.

    Well, you can shove that ‘prior opinion’ strawman. Either you can make a case or you can’t. I realise the only bits of biology you care about are the ones that lead to you, but I see a vast eukaryote tree, nearly all sexual, a fact demanding an explanation. ‘Toadstools vary cos we needed different people’ is a deeply unsatisfactory explanation.

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  23. CharlieM:
    I’ve given examples of convergences. I don’t see how this is non-standard.

    What’s non standard is applying the term to something that only has a single exemplar, achieved in multiple niches over a 4 billion year timescale.

    So I agree with you. Convergences related to the environment can lead creatures down an ever narrowing path that becomes increasingly difficult to escape from.

    That’s confusing, because on the one hand you are using convergence to indicate some kind of an inevitability to consciousness, and on the other that it has a tendency to produce over-specialised forms lacking staying power.

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  24. CharlieM:
    The veins on a leaf can converge on the same bifurcation pattern as in the pattern of the whole tree to which they belong but they will never converge in such a way that they become part of the main branching from the trunk. Their converging pattern is fractal in nature.

    That’s not convergence … the basic process is cell division (even more basically: DNA replication!). That one process, coupled with termination of some cell lineages, is responsible for all the branching patterns.

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  25. Nonlin.org: Your statements are demonstrably false.

    Your statements are not demonstrating that my statements (whichever ones you are contesting – that is not clear) are false. You simply make wild assertions and when challenged you repeat them. It’s not impressive.

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