Is anything in biology , man, beast, plant, in millions etc of species evolving as we speak?

I say no but why do evolutionists?

This is a sly way to demonstrate how unlikely evolutionism is on a probability curve.when on thinks of the millions (billions?) of segregated populations in biology(species) then it should be a high, or respectable percentage, are evolving as we speak to create new populations with new bodyplans to survive in some niche. By high I mean millions, with a allowance for mere hundreds of thousands. YET I am confident there is none evolving today. further i suspect evolutionists would say there is none evolving today. WHY? If not today what about yesterday or 300 years ago? Why couldn’t creationists say its not happening today because it never happened? Its accurate sampling of todays non evolution for predicting none in the past!

i think the only hope (hope?) is if evolutionism said , under pE influence, that all biology today is in the stasis stage and just waiting for a sudden need to change, qickly done, then stasis again. Yet why would it be that stasis has been reached so perfectly today relative to the enormous claim of the need in the past for evolutionism?

Anyways i think creationists have a good point here but willing to be corrected.

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391 thoughts on “Is anything in biology , man, beast, plant, in millions etc of species evolving as we speak?

  1. Allan Miller: Of course it’s still a ‘succession of cells’. But from LUCA we have gone through significant transitions, including eukaryogenesis, in which mitochondria and probable other ‘cells’ have become domesticated, adding cytoskeletal transport and internal compartmentalisation, and achieving complexities undreamt of by LUCA, some 50,000 times smaller. And sex, where the ancestral ‘haploidy’ of LUCA has been supplanted by diploidy. And multicellularity, where differential gene expression is responsible for a multiplicity of cell types, none of which is remotely like LUCA, and all of which trace back to the genotype of the zygote.

    A couple of questions. How much difference would you say there was between our genotype and the genotype of our LUCA? Do you think that we have any cellular processes in common with our LUCA.

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  2. J-Mac: Nothing is lost. Just try to substitute – whatever the researchers are trying to prove, with how environment causes the evolutionary adaptation

    Or extinction, removing adaptations.

    ( you can apply any of the typical evolutionary narrative)

    As opposed to the design narrative? What is the design narrative on how organisms react to a changing environment? Wait for the designer to do something?

    with the evolution of poo using the examples how red deer poo evolves due to the same factors…

    Cause or side effect?

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  3. Allan Miller: The result is at least 3 genomes in the one cell. This creates numerous additional dynamics which the rather childlike “it’s still cells” picture pointlessly obscures.

    Dynamics which are required to produce higher levels of consciousness.

    The base of the tree of life is thought to have beginnings that are less complex than any of the primal forms of the separate domains. Why should this be? Because if everything springs from the material then this speculation is logical. But what if this material outlook is false? There are other philosophies in which the base does not require simpler convergences.

    I have this argument repeatedly, and I’m not really sure why. The central role of genes in evolution and developmemt is not in dispute, and yet an endless succession of amateurs rails against it. It’s as if ‘reductionism’ has no place in science, despite it being the means by which we got to understand the ‘system’. More sensible, to me, is a pluralist approach, but the central truth remains that genes build cells and bodies. It is definitely not the other way round.

    Anyone who wants to know what genes can do on their own just needs to look at viruses.

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  4. CharlieM: A couple of questions. How much difference would you say there was between our genotype and the genotype of our LUCA? Do you think that we have any cellular processes in common with our LUCA.

    Enormous differences, with a common scrambled core.
    Just from a quick dig, an analysis of 147 sequences (2004, there are loads more now) they found fewer than 50 genes identifiably conserved. But there are all sorts of reasons for that, so it is likely to be a gross underestimate. By logic, DNA polymerase, and transcription/translation proteins and RNAs must be ancient, predating LUCA, along with chunks of metabolism and basic biosynthesis.

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  5. Allan Miller: If you think that all individuals cooperate within a company and that all companies compete, then you are not looking at reality.

    If you see me as making absolutist statements, you’re probably going out of your way to miss the point. Some companies co-operate, likewise some organisms. Some within-company individuals compete, likewise some genes/cells. Making it an excellent analogy; these exceptions prove the respective rules.

    Look at any industry, motor, oil or whatever, and there will many different companies within it. There will be main companies and their sub-contractors, service companies, various manufacturing companies and such like all cooperating in a common aim. Is competition between companies the norm?

    There is normally a hierarchy of positions within companies and less positions available the higher the pay grade. How much individual competition is there? I’d say quite a bit.

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  6. CharlieM: Dynamics which are required to produce higher levels of consciousness.

    And the fruiting body of the fly agaric, and the pseudopodia of the amoeba, and the legs of a wasp …

    Anyone who wants to know what genes can do on their own just needs to look at viruses.

    Yeah, they don’t make their own DNA polymerase, or much else. Shrug. They don’t need to, they grab a cell that does it for them. Parasites are well known to have reduced genomes.

    Here’s a fun fact: some transposons make a protein coat, even though they never go outside. Are these domesticated viruses, or viruses-in-the-making? What does holism tell us?

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  7. CharlieM: Look at any industry, motor, oil or whatever, and there will many different companies within it. There will be main companies and their sub-contractors, service companies, various manufacturing companies and such like all cooperating in a common aim. Is competition between companies the norm?

    Yes. Assuming they occupy the same niche.

    There is normally a hierarchy of positions within companies and less positions available the higher the pay grade. How much individual competition is there? I’d say quite a bit.

    They still find common cause, by contrast to the separate vehicles themselves.

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  8. Allan Miller:

    Charlie: If the Darwinian account is to be believed then it is true that these systems must arise gradually from simple beginnings. What if we don’t start out with this Darwinian belief. What evidence do we have that these systems arise gradually from simple beginnings?

    The lengthy piece of mine that Jock linked details a plausible sequence which is pretty much within the ‘Darwinian’ paradigm, accounting for the modern state(s) by stepwise elaboration. Of course, something else entirely may have been the actual case, but it answers the challenge of achieving the modern state ‘gradually’. That is, if it appears possible, you can’t chuck Darwinism out on the grounds that it isn’t.

    Evidence abounds, insofar as we have a wide variety of different modes that all contain the same fundamental character, in a vast array of organisms both simple and complex. All eukaryotes appear descended from a sexual LECA. Looking at meiosis-specific genes, they appear to be homologues of each other. Spo11, for example which initiates double strand breaks in crossover, exhibits homology across the eukaryote world (and furthermore appears to be derived from an archaeal Type ll topoisomerase, which is interesting if not strictly relevant).

    One could imagine some reason other than common descent for the commonalities, but it suffers both from a lack of parsimony, and a lack of mechanism. We must suppose an unknown force having the capacity to repeatedly initiate the complementary machinery, in group after group, different in detail but using similar base proteins. I don’t really see how that would work, or why one would prefer it.

    I am slowly working my way through your lengthy piece and so I’m getting a bit behind engaging with the ongoing arguments.

    But through reading it I am getting a much better and deeper understanding of the processes involved in meiosis and mitosis. Processes which are both complex and intricately coordinated. An example I found while looking further into something that you had written is the way that the cell ensures the metaphase plate is precisely aligned centrally. I found the following articles: The equatorial position of the metaphase plate ensures symmetric cell divisions and Spatial Regulation of Kinetochore Microtubule Attachments by Destabilization The former begins:

    Chromosome alignment in the middle of the bipolar spindle is a hallmark of metazoan cell divisions. When we offset the metaphase plate position by creating an asymmetric centriole distribution on each pole, we find that metaphase plates relocate to the middle of the spindle before anaphase. The spindle assembly checkpoint enables this centering mechanism by providing cells enough time to correct metaphase plate position. The checkpoint responds to unstable kinetochore–microtubule attachments resulting from an imbalance in microtubule stability between the two half-spindles in cells with an asymmetric centriole distribution.at Spindle Poles in Meiosis I

    Both make interesting reading.

    This is just one example of how everything needs to happen in the right place at the right time for fidelity of cell division whether it is in mitosis or meiosis.

    One thing I was wondering about and would appreciate an answer if you or anyone else knows. How do the chromosomes line up along the metaphase plate? Do they follow a particular order along the line or is it just a case of filling the nearest available gap? In humans that would be 23 positions. Also by what mechanism do they move to their position on the line?

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  9. Allan Miller:

    Charlie: So how is the overall balance maintained? Bacterial genomes are far more successful at reproducing themselves than say mammals. Compared to bacteria mammal reproduction is a very slow and laborious way of copying. You would think that bacteria could out-compete any eukaryote on the planet.

    If they occupied the same niche … eukaryote cells are some 50,000 times the size of bacteria, and tend to have different modes of nutrition. I keep out of digesting nylon, they keep away from chewing steak, we get along just fine.

    Except when we don’t

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  10. faded_Glory:

    Of course the trouble with gradual macro evolution as it is usually envisioned is that’s it’s not really forward evolution. In essence It is just more of the same. By specialising organisms fill niches that become available and we get an overall red queen effect. Having to change to keep up but getting nowhere in the process.

    This is only a trouble if you think that evolution has, should have, or must have, a direction.

    Evolution is observed to have a direction. It is moving towards individual autonomy. The question remains as to why it took this direction. Did it just move away from the wall because it was the only way to go as in Gould. Or are we seeing a natural unfolding and condensation of consciousness to the level of the physical.

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  11. CharlieM: Evolution is observed to have a direction. It is moving towards individual autonomy.

    I’m not seeing that. Can you explain?

    As far as I can tell, bacteria are autonomous, worms are autonomous, fungi are autonomous, grasses are autonomous.

    Yes, some species such as homo sapiens depend more on cooperation within a society. I don’t see any move toward autonomy.

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  12. CharlieM: Or are we seeing a natural unfolding and condensation of consciousness to the level of the physical.

    *Insert batshit crazy themed meme*

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  13. CharlieM:
    Except when we don’t

    Quite. But I was talking of the competitive argument, that they produce soooo many more offspring than us.

    In one sense, the cells of a body can be seen as a closer match to the numbers of bacteria. Counting organisms is misleading: count cells. One, or a few, cell lineages survives from a body, which is not far off what happens in bacterial populations over a similar time frame. Look at a chemostat, for example.

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  14. CharlieM,

    The metaphase ‘plate’ is a notional locality rather than a physical structure. In a normal diploid state, each chromosome occupies a separate ‘territory’ in the nucleus, which may or may not have a functional role (I don’t know, rather than it isn’t known). During meiosis, homologous chromosomes ‘find’ each other, by partial sequence matching (a physical process!), while opposite poles of the cell give rise to spindle fibres which attach to the homologues. The metaphase plate is just the halfway point between the poles. I don’t think there’s any particular logic to how they line up, and which homologue goes to which pole is also random.

    The spindle fibres contract, and the homologues are hauled apart. The process of ‘crossing-over’ helps ensure equal tensioning – without it, homologues may ‘stick together’ and both end up in one cell.

    Both independent segregation and crossover give rise to the farthest-reaching consequences of sex. Most people think recombination is the reason sex arose, but I think it’s just an incidental consequence of cellular process.

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  15. CharlieM,

    This is just one example of how everything needs to happen in the right place at the right time for fidelity of cell division whether it is in mitosis or meiosis

    For sure, but I’d argue that we are seeing the tuned process now – tuned by evolution. To compete in the modern world, you have to be as good as everything else. To compete in a primitive world, you can get by with being primitive. You don’t need crossover to do a form of meiosis, for example, it just helps. You don’t really need anything other than the last few steps of mitosis, indeed, IMO, which you’ve already got if you’re not extinct. Evolution builds on the past, inevitably.

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  16. Allan Miller:

    CharlieM:
    So in what sense is the recombinant unit “selfish”?

    It is a metaphor. By being exposed separately by repeat rounds of recombination, a genetic unit acts ‘as if’ it has volition, by integrating more frequently into its locus within the wider population than ‘rival’ sequences. Sometimes its action is by benefitting the ‘host’, sometimes (e.g. transposons etc) it can generally be detrimental to the host, but spreads anyway, on its own account.
    It can be useful to turn things round in that way, to look at matters from the gene’s perspective.

    There is always a danger of labelling something as selfish because we don’t have all the facts. And although more is being discovered about the ins and outs of these processes, our knowledge is still very limited.

    Many people thought that all non-coding DNA was junk and selfishly used up resources without contributing anything. But as our knowledge increased this was found to be false. IMO many of us are too quick to judge going on too little facts.

    Yes, no genes are bothered about anything.

    It is a metaphor

    A misleading metaphor.

    They are passive pieces of genetic material which are used by cellular processes.

    Where do those ‘cellular processes’ come from?

    They are inherited from the mother cell. From A novel, dynein-independent mechanism focuses the endoplasmic reticulum around spindle poles in dividing Drosophila spermatocytes

    The endoplasmic reticulum (ER) cannot be formed by cells de novo and must be inherited during the process of cell division.

    That and much else besides is inherited from the mother cell. Chromatin doesn’t just consist of DNA. There is probably as much protein as DNA in chromosomes.

    It is as you say, genes get copied, they do not copy themselves.

    They kind of do. DNA polymerase is produced from a gene. Among the genes it copies is that for DNA polymerase. Ditto for transcription and translation.

    Copying is a process, it is a very complex activity within the cell. Genes do not spontaneously express themselves. Look at any cellular process whether it be gene expression, mitosis or meiosis and you will see thousands of nano beings pulling, pushing, transporting, assembling and disassembling all in a directed, purposeful manner.

    To attribute the activity of copying to the gene in the way you do is like saying that it is your skeleton that holds you up and instigates your movements.

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  17. Allan Miller:

    CharlieM

    Well, I can, so there you go. I see no reason to suppose that some mysterious force is ‘running the biosphere’. How, when and why does it operate? What would happen if it stopped?

    We don’t need to speculate about mysterious forces. Observation will do. As they write here

    The remains of dead plants and animals release nutrients into the soil and ocean. These nutrients are re-absorbed by growing plants. This exchange of food and energy makes the biosphere a self-supporting and self-regulating system.

    We can see that throughout all of earth’s history since life first appeared it has sustained itself. It has survived the earth experiencing impacts from without, upheavals from within, ice ages and the like, and it still grew and diversified.

    The book Life, Temperature, and the Earth; The Self-Organizing Biosphere by David Schwartzman deals with the same issue in depth.

    Whether we are looking at life as a whole, individual organisms, or cells, we see the same self sustaining activity, the continued maintenance of viability through the exchange of material with the environment. Cells respire, we respire, life respires.

    Do you believe that humans contribute significantly to modern global warming? Can you see the parallel between smoking at an individual level and humans pumping harmful emissions into the atmosphere?

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  18. CharlieM: Many people thought that all non-coding DNA was junk and selfishly used up resources without contributing anything. But as our knowledge increased this was found to be false. IMO many of us are too quick to judge going on too little facts.

    You’ve been around here long enough to know that’s not true. You simply believe that creationist lie because it fits your narrative, right?

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  19. Allan Miller:

    :
    You imply that any and every connection between entities must involve physical contact.

    Not necessarily, but physical linkage generates a shared and direct interest which is very important, from the genetic level outwards.

    And the fact that plants produce oxygen and we are constantly taking in oxygen that has been given out by plants: would you not call that a physical linkage? We all share the same atmosphere. Isn’t that a physical linkage? Or do liquids and gasses not count as they are too ephemeral and diaphanous whereas solids are reliably real?

    Yet here we are, us puny humans, connecting with each other over distances spanning the planet.

    And yet the further apart we are, the more competitive. I’ve just been reading about race riots; we aren’t that harmonious.

    Except when we are employed by the same company, then all is harmony 😉

    If its a cohesive whole of connected organisms that you seek take a look at the Amazon rain forest with its system of waterways merging into the Amazon and returning to the ocean like the blood flowing through an organ via its system of capillaries and veins finally through the vena cava back to the heart to be recycled. It just takes us to open our eyes and our minds to see the whole reflected in the parts.

    Nah. Analogy again. Not persuasive.

    It doesn’t persuade you. I know that. What about mycorrhizal connections in plants, forests interconnected by vast fungal networks? Would these be solid enough for you to count them as cohesive?

    An individual organism is not a cellular mass glued together, it comprises a constant flow of material […].

    Sure. And through all that churn, the shared genotype smirks like the Cheshire Cat’s smile (barring a Pedant’s Latitude arising from somatic mutation).

    And the shared processes, what about them?

    The rationale lies in the fact that the entity (the biosphere in this case) exists through maintaining a dynamic balance among its parts which come and go throughout its existence. These need not be conscious processes. We have very little conscious awareness of the processes that are keeping us in existence.

    No elan vital appears required to maintain individual organisms. But to give your analogy legs, such a force is required at the biosphere level, immediately disconnecting the two things you want linked. I see no need for such vague forces.

    Bodies unroll a program, encoded in the shared cellular genome, progressing cyclically from zygote to zygote. Ecological units don’t. Newcomers simply exploit a niche, either reaching a balance, or going extinct through their own overexploitation. The result is a set of interacting niches whose denizens have not (yet) gone extinct, and along people come and declare it must be the work of a Celestial Gardener, and couldn’t possibly happen unaided. I don’t see why not.

    There’s no hard problem of consciousness for you. It’s all achievable through the magic of matter spontaneously springing into life. Arrange matter in a specific way and life will result. We don’t know how it happened but we promise you that’s the way it did happen. Consciousness comes about incidentally because the matter in living things is arranged in a certain way. We don’t know how it happened but we promise you that’s all there is to it.

    The genetic code is not a program for building form. It is a collection of strings of nucleotides which need to be manipulated to produce complexes suitable for the organism. Manipulated by epigenetic marking, by packing and unpacking, by alternative splicing, by being brought into contact with other molecules, and by any other processes which I have overlooked or am unaware of. If you feel up to it, can you describe how eye colour (or any other trait that takes your fancy) is achieved via genetics? Run through the sequence of events from start to finish as you understand it.

    Your “Celestial Gardener” gives a totally false impression of what I am saying. I am not positing some external force moulding and shaping nature. The creativity is within nature. We exist and have our lives within the life of nature in the same way that grapes exist and have their lives within the vine. A grape is meaningless without the reality of the vine, and our existence is meaningless without the reality of nature as a whole.

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  20. Allan Miller: CharlieM: I think the distribution of life over the planet from some warm little pond, or whatever you take the beginning to be, is a good example which covers that one.

    No it doesn’t. There’s no cycle there, just lineage.

    And how would you know this? Where do you get the knowledge to be able to definitively state that nature has not been subject to some sort of cyclic process over the purported billions of years of earth’s existence?

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  21. Allan Miller:

    CharlieM: I don’t have an ‘anti-reductionist’ stance. Reducing processes to their component parts is necessary for understanding. The problem lies in going no further than this. Unless we then use this knowledge we have gained to understand how the parts relate to the whole in their actual context, then we have put self imposed limits on our understanding.

    By ignoring or subordinating the role of nucleic acids in processes, I think you have put self imposed limits on your understanding.

    I am simply viewing them in context.

    What is more reductionist than reducing the world to a grain of sand?

    Um, atoms?

    Good point. But my point is still valid although exaggerated.

    And do you see any similarity between moons orbiting planets, planets orbiting stars and stars orbiting a galactic centre and electrons orbiting a nucleus? The whole reflected …

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  22. CharlieM: And do you see any similarity between moons orbiting planets, planets orbiting stars and stars orbiting a galactic centre and electrons orbiting a nucleus?

    Charlie, if the orbit of earth around the sun was similar to an atomic orbital you’d be very unhappy. The whole is behaving completely different from the parts in this case.

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  23. Allan Miller:

    CharlieM: Yes, similar. As I explained earlier, life and death exist at many levels. The various forms of the dinosaurs gave way to the forms of modern birds. Individual forms come and go but life marches on.

    No, dinosaurs evolved into modern birds (a process well under way before they croaked). The arbitrary ‘end point’ you have decided to draw (coinciding with an asteroid collision) has no analogue in multicellular life cycles. Closer to vegetative growth, but still no banana.

    Everything is in a state of transformation.
    Heraclitus

    “The living and the dead,
    The awake and the sleeping,
    The young and the old are all one and the same.
    When the ones change, they become the others.
    When those shift again, they become these again.

    Dying is within the living and living within the dying.

    Transformations are more processes than single events and from what you write above you seem to be aware of this. The foetus ceases to exist as it is transformed into the new born baby, the baby ceases to exist when it is transformed into the infant and so on.

    Older forms give rise to new forms at many levels. Theropods and birds have the egg laying, the bipedalism, a similar bone structure, and talons in common. But there is one important difference. Modern birds have developed traits which meant that they were less tied to the earth. The theropods that became extinct had well developed hind limbs at the expense of fore limbs which atrophied, they were relatively more massive. On the other hand birds developed specialised fore limbs, sophisticated temperature regulation and a reduced bulk and size. This freedom allowed them to prosper as the dinosaurs declined.

    The most obvious analogues in multicellular life cycles are the transitional stages in the life cycles of insects and amphibians. The appearance of the frog spells the end for the tadpole. You believe that birds are transformed theropods. Well in relation to single organisms I am saying that a butterfly is a transformed caterpillar.

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  24. Corneel:

    CharlieM: Yes, which begs the question: Why all this complication for something it didn’t need?

    Fancy that. I was going to ask you the same thing. My explanation is that parthenogenic lineages all derive from sexual ancestors.

    that still doesn’t answer the question about the origin of sex in eukaryotes in the first place.

    It’s been said before: you are extremely focused on humans. All those “intricate networks of coordinated activity” in spermatogenesis and fertilisation turn out to be completely dispensable in many other species. Since they managed to get rid of those useless male bastards, one might even argue they are more highly evolved.

    Which species are you talking about that have eliminated males? I can only think of instances where males still are still produced only they may not feature in continuing the generations.

    You seem to think that producing exact copies would be an advantage over producing variation. Which species do you think would be able to adapt better to changing conditions and progress further in evolution, those that engage in sex or those that produce clones by parthenogenesis?

    I think nature is wiser than any single one of us.

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  25. Corneel:

    Me (Corneel): Now imagine something similar occurring in humans. Does that sound like gene regulation or does it sound like a pandemic?

    CharlieM: Both, it’s not either/or. Take the coronavirus of which there are fears that it could become a pandemic. The virus by itself can do nothing without the regulatory system of the host cell.

    You believe SARS, HIV and influenza to be part of human gene regulation? That should bring you lots of joy next time you come down with the flu.

    No but without a regulatory network they are inert and harmless.

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  26. Allan Miller:
    CharlieM,

    Yes, things are gearing up for the annual return of haploid genomes, the true ‘organism’ of which we are mere nurturers and amplifiers!

    The thing is chromosomes and chromatids are living entities. As you sett so much store by physical attachment, when have you ever witnessed genomes apart from when they are attached to protein complexes. Genomes as considered by themselves are either an abstraction or they are dead molecules.

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  27. CharlieM: that still doesn’t answer the question about the origin of sex in eukaryotes in the first place.

    It does…you just have to have faith…the blind one 😉

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  28. Allan Miller:

    CharlieM:Me: Ahem … They all contain the same genome. They don’t mind a bit. This is a crucial distinction. Relatedness of the soma is the reason it hangs together.

    Charlie: All the body cells are related because they are descended from the same zygote. The isolated genome is an abstraction. The whole cell, complete with genomes, cell walls, cytoplasm, mitochondria and other organelles, was the source of all subsequent cells.

    You keep beating this drum, and I keep saying ‘no’. How long can we keep this up? The fundamental process is semiconservative nucleic acid replication. That creates two copies where once there was one. Without it, there would be no ‘purpose’ to cellular fission. If it did something other than create two for one, most hypothetical fission products would be empty.

    Chromosomal crossover is a purposeful activity which ensures that a unique set of chromosomes will be passed to the next generation. You say yourself that it is a fundamental process. This process is a demonstrable example of the way that genomes are manipulated to achieve individual variation in populations.

    Genomes are like multi-faceted ticker tape. They are pushed and pulled, wrapped and unwrapped, cut and rejoined, read and copied, and repaired.

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  29. Allan Miller:

    CharlieM:It was through a certain type of reductionist thinking that lead to the false belief that humans would have at least one hundred thousand genes

    Not really, but anyway you can’t chuck out a viewpoint just because it was wrong once. What was that about chucking the baby out with the bathwater?

    The true number of genes wasn’t discovered by ‘holists’.

    The important point is knowing the actually facts, not on the philosophy of those who discovered them. And I don’t know the various philosophies on all those involved.

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  30. CharlieM: Which species are you talking about that have eliminated males? I can only think of instances where males still are still produced only they may not feature in continuing the generations.

    There are many parthenogenic species where males are extremely rare or not produced at all, especially in invertebrate groups. You’ll find examples in the wikipedia lemma I linked to previously.

    CharlieM: You seem to think that producing exact copies would be an advantage over producing variation. Which species do you think would be able to adapt better to changing conditions and progress further in evolution, those that engage in sex or those that produce clones by parthenogenesis?

    Which species do you think would be able to colonize and spread more quickly in a habitat it is already adapted to? Those that have their genomes continuously scrambled by sexual reproduction and cannot reproduce without a partner or those that can instantly reproduce upon sexual maturation and rapidly produce faithful copies from a highly succesful genome?

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  31. CharlieM: No but without a regulatory network they are inert and harmless.

    Tsunami’s are harmless if you don’t live at the coast. Earthquakes are harmless if they occur on another planet. And guess what, parasites are harmless if no host is around.

    Problem is: viruses are infectious. They will find a host with a “regulatory network” and multiply at the expense of said host. Sometimes that host will be you, and you will gain absolutely nothing from this involuntary encounter. Pathogens do not exist for our benefit. Why is that so hard to accept?

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  32. CharlieM: Genomes are like multi-faceted ticker tape. They are pushed and pulled, wrapped and unwrapped, cut and rejoined, read and copied, and repaired.

    And sometimes they are completely eliminated by murderous chromosomes.

    PSR (paternal sex ratio) chromosomes are a type of supernumerary (or B) chromosomes that occur in haplodiploid arthropods. They are transmitted through sperm but then cause loss of the paternal chromosomes (except themselves) early in development. As a result, PSR chromosomes convert diploid fertilized eggs (which would normally develop into females) into haploid males that carry a PSR chromosome. Because they act by completely eliminating the haploid genome of their ‘hosts’, PSR chromosomes are the most extreme form of selfish or parasitic DNA known.

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  33. Allan Miller:

    Charlie: It’s not the genes that make the organism, it ‘s the way they are manipulated that provides the suitable material to build the form and to allow the form to function.

    Sorry, it is the genes. Transplant a foreign genome into a cell and it starts making that genome’s proteins. Change a gene, you change the way the program runs – look at antennopedia, for one of a squillion examples.

    More importantly, over evolutionary time, genotype is all that persists. Yes, in cells, but cells made by genes.

    Drosophila limb development is a good area to study.

    From this review:

    Primitive insects develop appendages directly from embryonic limb buds that grow as external projections, while more derived insect species with complete metamorphosis, such as Drosophila, develop their appendages from imaginal precursors.

    When Goethe said of plants, “all is leaf”, he meant by this that all the structures stem from the same source but are transformed to serve different functions. A case in point is the human limb. Forelimbs spring from the same source as the lower limbs but they serve a higher purpose.

    And we see the same process at work in insects. Antenna are transformed limbs. So it is no surprise that by interfering with development the growth of antenna we find there is a reversion back to limb development. Have they ever tried to induce antenna development where limbs normally grow? Would it be just as easy to do this? I’d be interested in any relevant references.

    Andreas Suchantke talks about this. Here is an excerpt from a translation of his book:

    More significant, however, is the occurrence of limb primordia on the head, which also consists of several merged segments. Here they are recognizable by the fact that they are arranged in pairs and move by means of
    joints as feelers and as “chewing limbs” (in insects the upper and lower jaws move horizontally). The feelers are particularly interesting. In many cases they will be found to have kept their original limb-nature. This is especially clear in ants, which use them to exchange tactile vibrations, and even to milk aphids, i.e., by stimulating them to excrete a sugar-rich substance

    Limbs become sense organs, or combine the related functions of perception and movement in one structure. Crickets hear with the tympanic organs located on their long hindlegs; moths, as recent studies have shown, hear with their wings; houseflies taste with the soles of their feet, etc

    The general archetypal form of these organs is physically expressed in a multitude of ways, the course of which can be altered by manipulating genetic networks.

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  34. CharlieM: The thing is chromosomes and chromatids are living entities. As you sett so much store by physical attachment, when have you ever witnessed genomes apart from when they are attached to protein complexes. Genomes as considered by themselves are either an abstraction or they are dead molecules.

    Your ‘system’ is as much an abstraction as the genome. It exists only in your head, a model pieced together from diagrams in Sal Cordova posts … 😉 There’s something ‘real’ at the back of it, but then, the genome is real in the same sense.

    Regardless, given an environment where genes (DNA/RNA) are copied, genes compete to be copied. But you’re never going to understand the point of the gene-centric view, no matter how often I explain it, and I’m not sympathetic to your rather waffly mysticism, so I’ll withdraw.

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  35. Corneel: There are many parthenogenic species where males are extremely rare or not produced at all, especially in invertebrate groups. You’ll find examples in the wikipedia lemma I linked to previously.

    Worth mentioning that all such species have homologues of meiosis specific genes – their ancestors are always sexual. So something that can only form through sex shouldn’t be regarded as a blocker to its evolution.

    Which species do you think would be able to colonize and spread more quickly in a habitat it is already adapted to?

    There’s already something living there!

    Those that have their genomes continuously scrambled by sexual reproduction and cannot reproduce without a partner or those that can instantly reproduce upon sexual maturation and rapidly produce faithful copies from a highly succesful genome?

    Asexuals can extend a range easily, because their close ecological competitor isn’t there. Their task is harder where the sexual species is present – and I’d quibble on the ‘highly successful’ part. Each snowflake sexual genome gets tested once. Taking an average genome and repeating it ad nauseam tests it more accurately, exposing it to selection in numbers, and in competition with the varied resident. It will never have a better allele at any locus than its sexual competitor.

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  36. Allan Miller: There’s already something living there!

    Why? My ecology is a bit rusty, but I believe new habitats open up continuously because of disturbances and succession.

    Allan Miller: Asexuals can extend a range easily, because their close ecological competitor isn’t there.

    .. and colonization of a new habitat is more easy because parthenogens are not mate-limited.

    Allan Miller: I’d quibble on the ‘highly successful’ part. Each snowflake sexual genome gets tested once. Taking an average genome and repeating it ad nauseam tests it more accurately, exposing it to selection in numbers, and in competition with the varied resident. It will never have a better allele at any locus than its sexual competitor.

    If memory serves, parthenogenic species often have overlapping distributions with their sexual sister species. Hence, either competition isn’t that stiff, or is somehow avoided. Succesful parthenogens are more likely to come from sexual species with broad ecological niches and distributions, so there appears to be some safety in numbers. I suspect that the combination of generalist strategy with superior colonization capability is important in the persistence of parthenogenic lineages.

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  37. Corneel: Why? My ecology is a bit rusty, but I believe new habitats open up continuously because of disturbances and succession.

    Yes, but it is inevitable that, where a parthenogenetic mutation occurs, there is a sexual species nearby.

    .. and colonization of a new habitat is more easy because parthenogens are not mate-limited.

    For sure. Also, where dioecious, that 2-for-1 thing.

    If memory serves, parthenogenic species often have overlapping distributions with their sexual sister species. Hence, either competition isn’t that stiff, or is somehow avoided.

    Hard to be sure which way the contest is going in a snapshot. But competition can’t be avoided, for ‘Malthusian’ reasons – intraspecific competition is what drives NS, after all (sort of …). And niche-competitive interspecific competition, which this is, would eventually result in competitive exclusion, a higher-taxon analogue of drift.

    Succesful parthenogens are more likely to come from sexual species with broad ecological niches and distributions, so there appears to be some safety in numbers.

    Given that it requires a mutation, then the bigger the sexual population, the more likely it is. But then, the bigger the population, the more variation there is, and the harder the parthenogen’s task in replacement, since it has no variation (rather, much less).

    I suspect that the combination of generalist strategy with superior colonization capability is important in the persistence of parthenogenic lineages.

    Their strategy is one taken at random from the sexual population and repeated. Certainly it will work where the sexual has no current presence – the need for mates creates a kind of ‘surface tension’ effect at its perimeter, limiting extension. But I take issue with ‘mystery of sex’ thinking in the expectation that parthenogens should defeat their parent species a sufficent amount of the time to create a puzzle as to why the latter are still around.

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  38. Allan Miller: And niche-competitive interspecific competition, which this is, would eventually result in competitive exclusion, a higher-taxon analogue of drift.

    Parthenogens tend to have broader ranges and generalize to utilize broader niches, at least for the examples I am familiar with (haplodiploid arthropods). I guess that fits what you are claiming, and parthenogens simply avoid competition.

    Allan Miller: But then, the bigger the population, the more variation there is, and the harder the parthenogen’s task in replacement, since it has no variation (rather, much less).

    It doesn’t need to replace the sexual population (and I believe this doesn’t occur that often), it just needs to persist. Re. variation: you are assuming both populations start from a suboptimal situation and need to rapidly adapt. If this isn’t the case, then the larger variation in sexuals isn’t necessarily an advantage.

    Allan Miller: But I take issue with ‘mystery of sex’ thinking in the expectation that parthenogens should defeat their parent species a sufficent amount of the time to create a puzzle as to why the latter are still around.

    I haven’t argued for that. Rather, I have taken issue with the reverse claim that sexual species will purge asexual sister species because they can more rapidly adapt. This ignores the fact that sexual reproduction has significant drawbacks, i.e. mate-limitation and destruction of co-adapted allele combinations. Typically, the advantage of sex and recombination occurs when populations need to rapidly generate genotypic variation to deal with novel environmental challenges.

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  39. Corneel: Parthenogens tend to have broader ranges and generalize to utilize broader niches, at least for the examples I am familiar with (haplodiploid arthropods). I guess that fits what you are claiming, and parthenogens simply avoid competition.

    Or aren’t really up to it?

    It doesn’t need to replace the sexual population (and I believe this doesn’t occur that often), it just needs to persist.

    Yes, though there are obviously challenges to that. Muller’s ‘ratchet’ (coined, I believe, by our own Joe F), locus interference, the ‘red queen’ effect of a sexual biosphere, and my own favourite, gene conversion, which increases the expression of deleterious recessives.

    Re. variation: you are assuming both populations start from a suboptimal situation and need to rapidly adapt. If this isn’t the case, then the larger variation in sexuals isn’t necessarily an advantage.

    That’s not quite the argument. A large population has local adaptation – eg the temperature-correlated clines in body size observed across numerous groups, where heritable. This gives a clone a harder task.

    But the other issue relates to variation along the genome. If there is any fitness difference at any polymorphic locus, the asexual can have the ‘best’ variant, but it won’t have the best at every locus. It’s true of any given sexual individual too, but they are only tested once. Sexual populations are sorting at locus level; asexuals at full-genome. It doesn’t need an environmental change for a population to adapt; it just needs a beneficial mutation, and decoupling from other loci sure helps. I’m doubtful that there is any population which is not in the process of purging detriment and concentrating benefit (kinda the same thing) at any given moment. Asexuals start off on the back foot, and fall behind.

    I haven’t argued for that. Rather, I have taken issue with the reverse claim that sexual species will purge asexual sister species because they can more rapidly adapt.

    No, I don’t think that’s the whole story. It’s the whole sexual clade, and the deterioration of their own genomes, that gives the reason for the comparative rarity of parthenogens.

    This ignores the fact that sexual reproduction has significant drawbacks, i.e. mate-limitation and destruction of co-adapted allele combinations.

    The latter is only a problem if they arose by some other means. If recombination/segregation cause co-adapted combinations to arise, there’s only a problem if they break more than they form. Which they don’t!

    Typically, the advantage of sex and recombination occurs when populations need to rapidly generate genotypic variation to deal with novel environmental challenges.

    Such as competition from a novel parthenogen? 🤔

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  40. Allan Miller: Or aren’t really up to it?

    They still hang on, so I presume they went where the sexual species cannot follow 😉

    Allan Miller: Yes, though there are obviously challenges to that. Muller’s ‘ratchet’ (coined, I believe, by our own Joe F), locus interference, the ‘red queen’ effect of a sexual biosphere, and my own favourite, gene conversion, which increases the expression of deleterious recessives.

    This is something I can claim some expertise on, by virtue of having had an extremely knowledgeable roommate who studied exactly that. As I understand it, the main piece of evidence to support the claim that asexual lineages are evolutionary dead ends is the “twigginess” of asexual lineages on phylogenetic trees. This has been accepted as evidence that asexual lineages are short-lived, because of the reasons you mentioned above. My former colleague Tanja (Schwander) demonstrated that the observed phylogenetic distribution can be explained by factors that are independent of (mal)adaptive effects of reproductive mode. Hence, as far as I am aware, none of the challenges you mention have been observed to affect evolutionary persistence of asexual lineages. The paper is here. It touches on several topics we have been discussing.

    Allan Miller: The latter is only a problem if they arose by some other means. If recombination/segregation cause co-adapted combinations to arise, there’s only a problem if they break more than they form. Which they don’t!

    It is a problem. Suppose that your model holds up: there are multiple subpopulations connected by gene flow (essentially the island model), each with locally adapted populations. Then the sexual populations are constantly required to cope with influx of maladaptive alleles. In such cases, recombination is a curse, as it prevents the sexual population from adapting to the local environment.

    Allan Miller: Such as competition from a novel parthenogen?

    Why would that give them a fright? A new parthenogenic lineage is ecologically indistinguishable from its sexual compatriots, and if you are right it will only fall behind. 🙂

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  41. Corneel: They still hang on, so I presume they went where the sexual species cannot follow

    Well, clearly observed species exist! But it’s hard to determine if they are stable or on the way out.

    Hence, as far as I am aware, none of the challenges you mention have been observed to affect evolutionary persistence of asexual lineages.

    None? Well, the neutral ones haven’t been ‘observed’ either (to sound like a Creationist!). It’s certainly interesting that neutral models can generate the pattern, but I wouldn’t consider that grounds for dismissal of the rest. It’s notable for instance that rotifers have notionally ‘haploid’ genomes, which could support the contention that gene conversion was an issue more typically. Once a genome has passed a threshold of divergence, it can’t be used for recombinational repair, so gene conversion stops and dominance effects stop masking beneficial recessives, making them a touch more evolutionarily flexible.

    Another thought: the ‘geographical’ model would appear to support my contentions on competition – why are they in these poor habitats in the first place? ‘Cos they can’t compete! So, not all that neutral then!

    A third thought: the ‘history’ section of the paper is stuffed with the ‘twofold cost’ stuff that I (an internet crank, I know) find completely misplaced as a ‘mystery of sex’ issue! It’s a ‘mystery of dioecy’, at best.

    It is a problem. […] In such cases, recombination is a curse, as it prevents the sexual population from adapting to the local environment.

    And yet it provides the locus-level ‘tuning’ that enables such local adaptation in the first place – and allows access to benefit segregating in the wider population, flowing in on the same tide. Nonrecombining genomes might be able to hold onto a beneficial combination, but there might be a better one just round the corner! Plus, that local adaptation they’ve conserved only helps them locally – stopping recombination doesn’t generate a broad scale benefit, at least on that model.

    Why would that give them a fright? A new parthenogenic lineage is ecologically indistinguishable from its sexual compatriots, and if you are right it will only fall behind.

    Competition ‘selects for’ alleles that deal better with that competition. The sexual can network these alleles at locus level, raising the fitness of the population. The asexual can’t access these alleles, if it doesn’t already have them, so its subpopulation fitness can’t keep pace.

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  42. Allan Miller: Well, clearly observed species exist! But it’s hard to determine if they are stable or on the way out.

    So it is. As far as I know elevated extinction rates of asexual lineages have not been demonstrated. I also note that several long-term asexual lineages are known.

    Allan Miller: It’s notable for instance that rotifers have notionally ‘haploid’ genomes, which could support the contention that gene conversion was an issue more typically.

    I wasn’t aware of that. interesting, thanks.

    Allan Miller: Another thought: the ‘geographical’ model would appear to support my contentions on competition – why are they in these poor habitats in the first place? ‘Cos they can’t compete! So, not all that neutral then!

    Haha, what happened to the “Malthusian reasons” and the severe intraspecific competition? The sexuals dedided to gang up on those pesky asexuals and drove them away? No, if there are no sexuals in those habitats, they either can’t reach them or they cannot survive there. In either case, the asexuals compete just fine.

    Allan Miller: Nonrecombining genomes might be able to hold onto a beneficial combination, but there might be a better one just round the corner!


    I think you miss the significance: nonrecombining genomes can hold on to combinations of alleles. That is: they preserve association of beneficial alleles and beneficial epistatic interactions. Recombination destroys these.

    ETA: Misread your comment, sorry. Yes, there may be better one, but if it arises it cannot be reliably transmitted in a sexual population that experiences constant influx of maladaptive alleles.

    Allan Miller: Plus, that local adaptation they’ve conserved only helps them locally – stopping recombination doesn’t generate a broad scale benefit, at least on that model.

    I was actually arguing the opposite: having recombination doesn’t generate a broad scale benefit on that model.

    Allan Miller: Competition ‘selects for’ alleles that deal better with that competition. The sexual can network these alleles at locus level, raising the fitness of the population. The asexual can’t access these alleles, if it doesn’t already have them, so its subpopulation fitness can’t keep pace.

    Yes, the Red Queen scenario. I won’t deny that sex brings certain benefits. I merely point out drawbacks exist as well. The balance between pros and cons will depend on details of ecology, population structure and such. I don’t see any reason to suppose that sexuals will always have the upper hand.

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  43. Allan Miller:

    Charlie: Yes, which begs the question: Why all this complication for something it didn’t need?

    Heh heh. You haven’t read my paper then! All is revealed … my stance, however, is ‘reductionist’. 😉

    I’ve read some of it.

    That said, reductionism hasn’t been hugely successful in understanding sex either. A poorly-thought-out version of ‘selfish gene’ theory leads to an imaginary ‘twofold cost’ of meiosis. There is, however, a reductionist stance which does make sense, both of sex and of the multicellular bodies it builds. It’s not simple to expound, hence 55 pages.

    From what I can make out you believe that evolution is just the result of haploid genomes making copies of themselves. But the way I see it meiosis produces unique haploids not true copies. I’m sure we can both agree that present day humans with our 46 chromosomes have vastly different sets of genomes compared to our ancestors stretching back into the remote past.

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  44. Allan Miller:

    What I wrote above can be seen in another way. I did not inherit a functioning cell, In fact I was a functional single cellular organism.

    Before that, you were two haploid genomes.

    What, just floating freely in some ocean or whatever?

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  45. Allan Miller:

    I became multicellular, I became sentient, I became a rational thinking being. All these things are a part of who I am.

    I think the problem is that you are seduced by your analogy. Gene-centrism is not even intended as a stance for understanding physiology, but evolution. Genes integrate into the genomes of the future population, by recombination, and gene centrism views this ‘as if’ they have volition. In a life, it’s just one genome, differentially expressed. But because you want to get from physiology to the biosphere by analogy, you reject gene centrism in toto – chucking the baby out with the bathwater. And yet, it gives a good evolutionary explanation for a huge proportion of our genomes.

    As soon as it was discovered how close genetically we were to our nearest primate relatives it became obvious that our differences could not be accounted for by genes alone. It isn’t the genes that produce the differences it is the way in which they are manipulated.

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  46. Allan Miller:

    I agree that all the substances within me are either imported or made from genes. Does this mean that genes are the ultimate cause of form? No. To say that genes cause form is like saying that building materials cause the form of the house that has been built.

    No, it’s like saying the architect’s drawings [hears excited clattering from Design enthusiasts’ keyboards!] cause form. Shove things around in CAD, you change the form.

    So you agree with what I wrote above, that it’s not the genes but the way in which they are manipulated?

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  47. Allan Miller:

    The creativity comes from epigenetic marking, cascade instigation and suppression, alternative splicing and all the other ways in which genes are manipulated.

    All of which traces back to genes, from one diploid genome, with the ultimate result of returning haploid genomes in profusion.

    But there is never any point in which there exists bare genomes without the context of their accompanying protein coats within a cell and organism. The closest we see to this are viruses, but they remain inert without the context of cells.

    Bare genomes are an abstraction, never observed in reality.

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  48. Corneel:

    Allan Miller: Our genomes are littered with the scars of old infection, of course, some of which end up ‘getting with the program’. The rest lies there waiting for a ‘holist’ to come up with a DNA-as-system-tool explanation.

    Because of my unwavering devotion to “seeing things from the other side” I can actually see the logic behind that. But if Charlie fails to recognize dangerous infectious agents like SARS coronavirus as selfish pathogens, I am all out of arguments.

    Reality is littered with opposites, good and evil, selfishness and altuism, growth and decay, expansion and contraction, chaos and order.

    Life is a progression which steers a course between these opposites, but if they didn’t exist there would be no course to steer. There are many levels to consider and to progress at one level may take death and destruction at a lower level. Our hands could not form without massive death and destruction of individual cells. In fact we could not have any form of life as individuals without this constant cellular death and destruction.

    Many of these viruses are brought about by us humans failing to consider the wider context of our actions. Metaphorically speaking nature doesn’t care about individuals, she marches on regardless of the death and suffering of individuals. And I don’t see any problem with using the “selfish” metaphor for these viruses, but they still need the cellular processes in order to replicate.

    But none of that prevents us from marvelling at the complexities of the replication processes.

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  49. CharlieM:
    Charlie: I was a functional single cellular organism.

    Allan: Before that, you were two haploid genomes.

    Charlie: What, just floating freely in some ocean or whatever?

    You have no problem self-identifying with a single celled zygote, but you are baffled by the idea that you were the gametes that fused to produce it? What causes this hard boundary I wonder?

    CharlieM: So you agree with what I wrote above, that it’s not the genes but the way in which they are manipulated?

    You need to distinguish between the phenotype and the genotype. In this case, “the way in which they are manipulated” is a phenotype. What we are interested in is what part of the variation in “the way in which they are manipulated” gets inherited, because only that part contributes to resemblance between relatives (and ultimately between conspecifics)*. Genetics tells us that heritable variation is predominantly transmitted with the DNA.

    ETA: *assuming a common environment

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