Why this creationist flocking likes this 2019 evolution video!

on another blog called pandas Thumb Joe Felsenstein directed readers to the 2019 evolution videos. i canned them, watch numerous summeries, and a few whole programs.

Added by moderator: This appears to be the Panda’s Thumb post that is being referenced. The videos appear to be HERE.

The only one i gave thumbs up to was by a dude called Bowen. It was called adaptative radiations. What the flock is going on?

I really like this as a creationist. He talks about flocks of specification that turns up everywhere now in the sees. they find, like in the cichlid fishes of africa, clusters/flocking of dozens of species from a parent one.

This is not what evolutionists should expect and Bowen suggests there must be some NEW evolutionary rule guiding this. He finds it everywhere.

The reason a creationist loves this is because it does show a sudden speciation of something that fills every niche it possibly can. including changing bodyp[lan as needed.I would add this happemns on the dry land and in the fossil record. This is very predicted by creationist models to show speciation fast and furious and done and no time needed. that it hardly changes bodyplans after the initial explosion of flocking. And its very likely the morm for speciation and not the exception. Flocking is the normal common way how diversity in biology happened. iThis is unwelcome in evolutionist circles. They want very chance happening that coupled withy mutations and selection make trees/nests of relationships.They want PE concepts with start and stop events creating lineages.indeed randomness. Yet investigation shows speciation is a explosion every time. It doesn’t need to wait for mutations. i think from this flocking can be why theropod dinosaurs had so much variety because they were just a flocking of flightless ground birrs. lIkewise marsupials and placentals and others are just a flocking episode fast and furious. So the evolution talks of 2019 really do have something to offer progress.

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299 thoughts on “Why this creationist flocking likes this 2019 evolution video!

  1. DNA_Jock:

    CharlieM: Does this mean that you think gametes do have incentives to increase their representation?

    Yes. And there’s some really cool examples of the scuzzy tactics they may use…check out “meiotic drive”…

    Thanks for that helpful piece of advise.

    I read a few articles and watched a few videos to do with meiotic drive and they are full of the same type of language that you have used above. “Scuzzy tactics” is a phrase that would normally apply to agents who are trying to achieve particular ends.

    Similar wording is found here

    How chromosomes ‘cheat’ for the chance to get into an egg

    “If you’re a selfish centromere and you’re facing the wrong way, you need to let go so you can face the other way,” Lampson said. “That’s how you ‘win.'”

    In future work, Lampson and his team hope to further explore what characteristics of the centromeres make them strong or weak.

    “This work gave us some good information about biased transmission of centromeres, but it also brings up a ton of other questions,” Lampson said. “Why do our centromeres look the way they do, and how do they evolve to win these competitions? These are fundamental biological questions that we still don’t know a lot about.”

    Certain chromosomes use molecular motors* to ensure that they have a more than average chance to being passed on as explained in this video:
    R. Kelly Dawe: Meiotic Drive: A chromosome movement phenomenon.

    *I have argued that instead of seeing these entities as molecular machines a more apt description of them would be as ‘nano-beings’ or ‘nano-creatures’. The use of language such as incentive, tactic, winning competitions; suggests to me that I have a valid point.

    The chromosome Ab10 intends to insert itself on the right pole of the cell and it achieves this with the help of a kinesin protein complex which attaches to a neo-centromere and pulls it in the correct direction faster than the actual centromere moves. They don’t yet understand how it “knows” which is the right direction to travel but it never gets it wrong according to R. Kelly Dawe.

    Ab10 is similar to us humans in that it has motives and drives. The difference is that we are consciously aware of some (but by no means all) of our motives and drives

    Finally, I came across this article where they said:

    A research team led by an Oregon State University biophysicist and a plant biologist from University of California, Davis has discovered a novel motor protein that significantly expands current understanding of the evolution and design principle of motor proteins…

    And some land plants, if not all, have evolved novel kinesin-14 motors to potentially compensate for the loss of dynein.”

    With language such as “design principle of motor proteins”, we are back to machine metaphors. But if we want to stick with this language we must admit that these proteins are intelligently, if not consciously, designed. They can pick up a load and transport it to a specific destination. An important difference between these complexes and mules is that they never show any signs of stubbornly resisting carrying out what is required of them.

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  2. CharlieM: But if we want to stick with this language we must admit that these proteins are intelligently, if not consciously, designed. They can pick up a load and transport it to a specific destination.

    Sure. The ‘blind watchmaker’ did it. Nobody disputes these things are designed, it’s just they were designed by evolutionary processes over very long periods of time in very large populations.

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  3. OMagain: Sure. The ‘blind watchmaker’ did it. Nobody disputes these things are designed, it’s just they were designed by evolutionary processes over very long periods of time in very large populations.

    How do you know how long it took from the time when there were purportedly no “molecular motors” to the time when cells contained such entities? How do you justify your belief that it took a very long period of time for them to evolve? How did these “very large populations” function without them?

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  4. CharlieM: How do you know how long it took from the time when there were purportedly no “molecular motors” to the time when cells contained such entities?

    Most flagellar genes originated very early on. A lot is known about the origin of these genes, and how co-option seems to be involved in the flagellum’s construction.

    CharlieM: How do you justify your belief that it took a very long period of time for them to evolve? How did these “very large populations” function without them?

    Evolution is a slow process involving gradual change over many generations. It’s a safe bet that any particular mechanism took “a long time” to evolve.

    And how did these “very large populations” function without them?

    https://en.wikipedia.org/wiki/Non-motile_bacteria

    Non-motile bacterial are still doing just fine.

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  5. Flint,

    Right, right. Random mutations with respect to fitness means its unguided.

    Not random with respect to fitness also means unguided.

    Apparently skeptics definitions are pointless.

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  6. phoodoo:
    Flint,

    Right, right.Random mutations with respect to fitness means its unguided.

    Not random with respect to fitness also means unguided.

    Apparently skeptics definitions are pointless.

    Feel free to define terms then.

    For example, is ‘guided evolution’ something you think your designer takes an active part in?

    i.e. something happens other than what would have been expected from chemistry?

    What is guided evolution phoodoo? When and where is the guidance put in?

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  7. CharlieM: “Scuzzy tactics” is a phrase that would normally apply to agents who are trying to achieve particular ends.

    I am glad to see that you are willing to ascribe agency to a piece of DNA. This was the thesis of a couple of books by that Dawkins chap.
    😉
    Your “has agency, therefore designed” argument interests me. Are you saying that anything that shows agency must be designed?

    1+
  8. phoodoo:
    Flint,

    Right, right.Random mutations with respect to fitness means its unguided.

    Not random with respect to fitness also means unguided.

    Apparently skeptics definitions are pointless.

    “Guided” really has nothing to do with this, but I see you cannot understand your reality without assigning a “guided/not guided” label to everything.

    Once again, “random” doesn’t mean unguided, it means random”. Non-random does NOT mean guided. Not in any way. If you wish to make any non-risible contribution to this discussion, you must discard the notion of “guided” and instead focus on what actually happens. Can you do this?

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  9. Flint: “Guided” really has nothing to do with this, but I see you cannot understand your reality without assigning a “guided/not guided” label to everything.

    Once again, “random” doesn’t mean unguided, it means random”. Non-random does NOT mean guided. Not in any way. If you wish to make any non-risible contribution to this discussion, you must discard the notion of “guided” and instead focus on what actually happens. Can you do this?

    Flint, please refrain from making fun of Jock’s use of definitions.

    DNA_Jock: Unguided evolution posits that mutations are random with respect to fitness.

    Unguided evolution also posits that they might be non-random with respect to fitness.

    The wondrous joy of being a skeptic.

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  10. phoodoo: The wondrous joy of being a skeptic.

    It’s ironic that despite evolution being, according to you, incoherent, you’ve not been able to suggest anything better with more explanatory power.

    So whatever your particular worldview is you already know it can be defeated by something that makes no sense and explains nothing. How poor must your version be then?

    For example, you cannot say the simplest thing about your version of events.

    Mutations are:

    a) Baked in at the start of the universe
    b) Adjusted in real time

    You can’t say even that, nor explain how you might be able to say it one day. And logically if you cannot speak to that issue you cannot speak to the actual source of the mutations and therefore the ‘plan’ you believe exists.

    Attacking is your only defense, as you cannot defend your own position and you know it. So it’s attack attack attack but never say anything about how you would solve the problem.

    And you don’t think this has been noticed?

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  11. phoodoo: Unguided evolution also posits that they might be non-random with respect to fitness.

    Odd how you managed not quote somebody saying that, but could provider other quotes.

    I wonder why…..

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  12. OMagain:

    CharlieM: How do you know how long it took from the time when there were purportedly no “molecular motors” to the time when cells contained such entities?

    Most flagellar genes originated very early on. A lot is known about the origin of these genes, and how co-option seems to be involved in the flagellum’s construction.

    I’m not talking about flagellar genes, I’m talking about internal “motors” involved in the processes of prokaryote cellular growth and division.
    From here

    Abstract
    Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.

    Technology is advancing at such a rate that we are only now beginning to be able to observe the processes within bacterial cells but we’re still very much in the dark.

    CharlieM: How do you justify your belief that it took a very long period of time for them to evolve? How did these “very large populations” function without them?

    Evolution is a slow process involving gradual change over many generations. It’s a safe bet that any particular mechanism took “a long time” to evolve.

    Would you say that the evolution of antibiotic resistance is a very slow process?

    And how did these “very large populations” function without them?

    https://en.wikipedia.org/wiki/Non-motile_bacteria

    Non-motile bacterial are still doing just fine.

    But non-motile bacteria still rely on internal “motors”

    This video is worth watching.

    It was thought for many, many years that the bacterial cell was too small to require proteins that help things move. It was too small to have particular protein complexes in specific places. Its DNA was not wrapped up in a nucleus. So people thought, “Well the cell is so little that proteins and pieces of DNA could be anywhere in the cell in milliseconds by diffusion.” In fact, this is not true. Bacterial cells have proteins that control movement. They have localization of complexes at different places in the cell. And one of the candidates for helping this happen is an actin-like protein. Now actin has been well known for many, many years in eukaryote cells beng involved in functions and movement. Bacterial cells have an actin homolog, And that’s called MreB.

    More on bacterial “motors”. From Science Direct

    The single-filament event in Fig. 2 E illustrates a noncontinuous transport with both stop-and-go and reversal of direction during the observed time window of 105 s. This behavior can be well explained by a mechanistic model in which multiple motors acting in both directions are attached to MreB filaments, as discussed further below…

    These dynamics can be explained by the cooperative work of several synthesis motors transporting MreB as cargos, which is similar to the collective behavior known for eukaryotic cells. Our mechanistic bidirectional, multimotor model is able to explain all of our observed data, which, apart from the variable filament lengths, agree with observations from other groups. The allure of the model is that it only assumes that PG-synthesis motors are stochastically connected and disconnected to MreB, and that motors are equally distributed over the cell periphery.

    Lots of directed activity and purposeful activity coming to light in these relatively “simple” cells. Flagellar motors aren’t required for every type bacteria but these internal motors are essential for all.

    So my question still stands: How did these “very large populations” function without them?

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  13. phoodoo,

    That is not a definition. I wrote:

    Unguided evolution posits that mutations are random with respect to fitness.
    You are welcome to try to disprove this proposition; but your first step should probably be understanding it.
    [Emphasis in original]

    The point being that mutations are not “random” in your “equiprobable” sense. They are random with respect to fitness.
    I included the word “unguided” in order to make it clear that I was referring to MES, rather than the God-guided “evolution” of theistic evolutionists, YECs, & JoeG…

    Note that guided/unguided is pretty much orthogonal to the question of whether mutations are random with respect to fitness: a deity could achieve ‘guided’ evolution merely by messing with who procreates, leaving mutations utterly random. Hypothetically, evolution could be utterly ‘unguided’ and yet still have the vast majority of mutations be non-random with respect to fitness. The reality, however, is that the vast, vast majority of mutations are random with respect to fitness, and no evidence has been found to support the idea that evolution is ‘guided’ by anything except the environment.
    I know you think you are doing a killer job destroying opposing arguments. Unfortunately, I see no indication that you even understand the term “random with respect to fitness”, as evidenced by your cluelessness regarding ‘Mutations that increase fur length’. I even provided you with some handy counter-examples — salmonella, trypanosomes and plasmodium — all human pathogens (I had a good giggle about that) but out of kindness I did also offer up yeast mating type switching, which is a Good Thing, and a personal favorite of mine.

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  14. CharlieM: Would you say that the evolution of antibiotic resistance is a very slow process?

    Slow processes can be sped up by running them in parallel. As Behe found out to his cost at Dover.

    CharlieM: So my question still stands: How did these “very large populations” function without them?

    The same way they do right now? As I already noted?

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  15. DNA_Jock: I know you think you are doing a killer job destroying opposing arguments. Unfortunately, I see no indication that you even understand the term “random with respect to fitness”

    Actually phoodoo disputes the entirely of the concept of “fitness” and yet now he’s using it directly. How very strange. It’s almost as if he does not care how consistent he is as long has he can attack.

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  16. phoodoo: Unguided evolution also posits that they might be non-random with respect to fitness.

    In what sense are you using “fitness” there? Are you using your own definition?

    Previously you have disputed the very concept. Have you come around now?

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  17. DNA_Jock: I am glad to see that you are willing to ascribe agency to a piece of DNA. This was the thesis of a couple of books by that Dawkins chap.
    😉

    It’s not the pieces of DNA that are the agents. The agents are the protein complexes that are carrying out specific functions in the cell. Agents make use of the DNA.

    Your “has agency, therefore designed” argument interests me. Are you saying that anything that shows agency must be designed?

    No I’m saying that we can look at these protein complexes, work out how they carry out a certain function and work out how the function is achieved by the way they have been arranged (designed). We can look at structures, say a pigeon’s wing, and work out the design principles that allow it to produce lift and so enable the bird to fly.

    These internal “motors” are agents working on behalf of the cell which enable it to function. DNA does not work, it is worked upon.

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  18. CharlieM: These internal “motors” are agents working on behalf of the cell which enable it to function.

    And yet, without them, they still function.

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  19. OMagain:

    CharlieM: So my question still stands: How did these “very large populations” function without them?

    The same way they do right now? As I already noted?

    But as far as I’m aware there are no bacteria in existence without them.

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  20. OMagain: In what sense are you using “fitness” there? Are you using your own definition?

    Previously you have disputed the very concept. Have you come around now?

    There’s fitness and phitness. He’ll be talking about the latter.

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  21. Just to make it clear that I’m not talking about flagellar “motors”, see here

    MreB is a bacterial actin that is important for cell shape and cell wall biosynthesis in many bacterial species. MreB also plays crucial roles in Myxococcus xanthus gliding motility, but the underlying mechanism remains unknown. Here we tracked the dynamics of single MreB particles in M. xanthus using single-particle tracking photoactivated localization microscopy. We found that a subpopulation of MreB particles moves rapidly along helical trajectories, similar to the movements of the MotAB-like gliding motors. The rapid MreB motion was stalled in the mutants that carried truncated gliding motors. Remarkably, M. xanthus MreB moves one to two orders of magnitude faster than its homologs that move along with the cell wall synthesis machinery in Bacillus subtilis and Escherichia coli, and this rapid movement was not affected by the inhibitors of cell wall biosynthesis. Our results show that in M. xanthus, MreB provides a scaffold for the gliding motors while the gliding machinery drives the movement of MreB filaments, analogous to the interdependent movements of myosin motors and actin in eukaryotic cells.

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  22. CharlieM: It’s not the pieces of DNA that are the agents… DNA does not work, it is worked upon.

    And yet, as I noted, you are willing to ascribe agency to the DNA:

    The chromosome Ab10 intends to insert itself on the right pole of the cell

    and the truly awesome

    Ab10 is similar to us humans in that it has motives and drives.

    In other news, the fact that you are not aware of any bacteria that lack “molecular motors” is not indicative of anything…I’ll let OMagain deal with that one.

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  23. I do find this deliberately arse-about-face approach to the DNA-protein relationship to be obtuse. If we talk about DNA-RNA the foolishness becomes more apparent. They are virtually indistinguishable but for a 2′ oxygen and a methyl group on one of the 4 bases. Would we talk about rRNA ‘using’ the DNA that specifies it? Effectively, they have the same sequence – or rather, the rRNA has the same sequence as the antisense strand of the specifying DNA. But no, the template has to be a ‘tool’ of the product … for some reason.

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  24. DNA_Jock:

    CharlieM: It’s not the pieces of DNA that are the agents… DNA does not work, it is worked upon.

    And yet, as I noted, you are willing to ascribe agency to the DNA:

    CharlieM: The chromosome Ab10 intends to insert itself on the right pole of the cell

    There is a vast difference between a chromosome and a section of bare DNA. Chromosomes are observed to be very dynamic, complex arrangements of various molecules, DNA being just one among many..
    From Wikipedia

    Most eukaryotic chromosomes include packaging proteins which, aided by chaperone proteins, bind to and condense the DNA molecule to prevent it from becoming an unmanageable tangle

    That is why IMO Ab10 does not equate to DNA and your criticism does not stand.

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  25. Allan Miller:
    I do find this deliberately arse-about-face approach to the DNA-protein relationship to be obtuse. If we talk about DNA-RNA the foolishness becomes more apparent. They are virtually indistinguishable but for a 2′ oxygen and a methyl group on one of the 4 bases. Would we talk about rRNA ‘using’ the DNA that specifies it? Effectively, they have the same sequence – or rather, the rRNA has the same sequence as the antisense strand of the specifying DNA. But no, thetemplate has to be a ‘tool’ of the product … for some reason.

    Templates are tools.

    The biological world does not consist of basic molecules existing in isolation. If researchers do isolate chemicals such as protein, DNA, or RNA these molecules will just behave like any inorganic chemical. It is not until the chemicals are combined into complex entities that they become active and creative. But any living entity that has ever been observed has consisted of such complexity. Isolating the basic molecules results in only one outcome, any living substance becomes dead substance. And the only way to bring life back is to recombine it with complex living systems, but this recombination can only be achieved by complex living systems.

    Can you tell us what you think is the most elementary, basic living process that has ever been observed or studied and what molecules or substances are involved?

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  26. CharlieM: There is a vast difference between a chromosome and a section of bare DNA. Chromosomes are observed to be very dynamic, complex arrangements of various molecules, DNA being just one among many..

    What a delightfully vague back-pedal: you were ascribing agency to the DNA elements (in your example the TR-1 repeats and 180bp repeats) that use “scuzzy tactics” to assure their preferential segregation.
    Furthermore, you can take a piece of bare DNA and stick it in a eukaryotic cell and it becomes a fully functioning chromosome.
    Well, I can (with a bit of help from the wife).

    CharlieM: That is why IMO Ab10 does not equate to DNA and your criticism does not stand.

    Well, that’s your opinion. I encourage you to examine yours constantly and thoroughly.

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  27. CharlieM,

    No-one is denying that a living cell is an integrated, interacting system. But you are making a categorical statement that phenotype sits ‘above’ genotype in the overall scheme. That somehow, the product of a gene is the ‘actor’ and the gene itself a mere tool of this actor. That makes no biological sense, even if it appeals to some philosophical itch you evidently feel the need to scratch.

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  28. DNA_Jock:

    CharlieM: There is a vast difference between a chromosome and a section of bare DNA. Chromosomes are observed to be very dynamic, complex arrangements of various molecules, DNA being just one among many..

    What a delightfully vague back-pedal: you were ascribing agency to the DNA elements (in your example the TR-1 repeats and 180bp repeats) that use “scuzzy tactics” to assure their preferential segregation.
    Furthermore, you can take a piece of bare DNA and stick it in a eukaryotic cell and it becomes a fully functioning chromosome.
    Well, I can (with a bit of help from the wife).

    But Ab10 is much more than a string of nucleotide repeats. It is a chromosome and the entity which gets preferentially inserted is a chromatid. This is a complex molecule which consists of much more than DNA.

    We don’t speak of legs winning races, we speak of individual athletes winning races. So why have you isolated TR-1 repeats and 180bp repeats from the whole inserted chromatid? You were the one who brought up “scuzzy tactics”, so if you want to insist that there is something which uses these tactics why not the the thing which carrying out the activity and that is the chromatid.

    CharlieM: That is why IMO Ab10 does not equate to DNA and your criticism does not stand.

    Well, that’s your opinion. I encourage you to examine yours constantly and thoroughly.

    Nice video. I would amend your advice to be more inclusive. I think we should all examine our opinions.

    From the video

    Science is not a body of knowledge nor a belief system, it is just a term which describes human-kinds incremental acquisition of understanding through observation. Science is awesome. The arts and sciences need to work together to improve how knowledge is communicated.

    I have given my opinion on why I think it is more realistic to see this action as an activity of the whole complex molecule. I would like you to give your opinion as to why we should see it more as the actions of strings of DNA. What is it that is actually observed under the microscope, active molecules or bare DNA?

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  29. CharlieM: But Ab10 is much more than a string of nucleotide repeats. It is a chromosome and the entity which gets preferentially inserted is a chromatid. This is a complex molecule which consists of much more than DNA.

    The entity that benefits from the scuzzy tactics is the string of nucleotide repeats (and, importantly, the adjacent DNA sequences), NOT THE CHROMATID. The chromatid is going to get disassembled at the next S-phase anyway.
    The DNA sequence needs a living organism to reap that benefit, sure. This was Dawkins point: the living organism is simply a vehicle for that DNA. You can try to obscure this simple fact with all the “it’s so complicated” woo and deranged analogies that you can come up with, if that makes you feel better about yourself.
    Ascribing motives to the chromatid is epic.

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  30. Allan Miller:

    No-one is denying that a living cell is an integrated, interacting system. But you are making a categorical statement that phenotype sits ‘above’ genotype in the overall scheme. That somehow, the product of a gene is the ‘actor’ and the gene itself a mere tool of this actor. That makes no biological sense, even if it appeals to some philosophical itch you evidently feel the need to scratch.

    We are not the product of our genes, we are the product of a living cell complete with organelles, cytoplasm, nucleus, proteins, DNA, RNA, lipids and various other chemicals mostly interacting in meaningful ways. I am a product of a zygote which is a phenotype in its own right.

    Please explain, without all of these other constituents, how the gene acts to do anything?

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  31. CharlieM: We are not the product of our genes, we are the product of a living cell complete with organelles, cytoplasm, nucleus, proteins, DNA, RNA, lipids and various other chemicals mostly interacting in meaningful ways. I am a product of a zygote which is a phenotype in its own right.

    Please explain, without all of these other constituents, how the gene acts to do anything?

    All the things you mention are gene products, or the product of gene products. No gene, no product. It is true that many gene products have DNA as substrate. That does not negate the fundamental principle that phenotype flows from genotype, not the other way round. I really have no idea why this seems so objectionable to people. I wonder if it stems in part from a knee-jerk reaction to Dawkins.

    Nonethess, you’re just wrong. Nucleic acids are at the centre of this jigsaw. The aren’t just some ‘tool’ for the real string-pullers, which you rather bizarrely deem to be proteins (and, presumably, functional RNAs). You are hampered in comprehending this by a rather simplistic view of biochemistry.

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  32. My favourite trick to distort segregation involves the homing endonuclease. The substrate for this is its own flanking sequence. It is inhibited if that flanking sequence is interrupted, for example if the sequence contains the gene itself. All it does, if it can bind, is nick the chromosome it binds to. This then triggers the homologous repair pathway, which uses the homologous chromosome as template – the opposite chromosome just happens to possess the endonuclease gene at that point, so it gets copied. By this subterfuge, the endonuclease gene gains a copy, bypassing the more normal means of increase by a positive effect on organismal fitness. It would be absurd to view the endonuclease gene as a ‘tool’ of the endonuclease enzyme. The endonuclease gene increases by virtue of production of the endonuclease enzyme.

    This pattern is not restricted to genes of this class. Proteins are discarded, though they may last a cell cycle or two; genotypes are copied and persist indefinitely. They increase by virtue of the effects of their products or the binding reactions they participate in.

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  33. DNA_Jock: The entity that benefits from the scuzzy tactics is the string of nucleotide repeats (and, importantly, the adjacent DNA sequences), NOT THE CHROMATID. The chromatid is going to get disassembled at the next S-phase anyway.

    It’s not the physical processes that we should be spending time arguing over. It is the fact that you and Corneel have claimed that these molecules use “scuzzy tactics” to achieve an end and that they are given “incentives” to do so.

    The DNA sequence needs a living organism to reap that benefit, sure. This was Dawkins point: the living organism is simply a vehicle for that DNA. You can try to obscure this simple fact with all the “it’s so complicated” woo and deranged analogies that you can come up with, if that makes you feel better about yourself.
    Ascribing motives to the chromatid is epic.

    I was using the same sort of language that you and Corneel have been using to see what the reaction would be. What do you think the difference is between having an incentive and having a motive to perform some act?

    What incentive or motivation do you think a kinesin-14 “motor” has to walk along a microtubule taking the neo-centromere with it?

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  34. Allan Miller: All the things you mention are gene products, or the product of gene products. No gene, no product. It is true that many gene products have DNA as substrate. That does not negate the fundamental principle that phenotype flows from genotype, not the other way round. I really have no idea why this seems so objectionable to people. I wonder if it stems in part from a knee-jerk reaction to Dawkins.

    Nonethess, you’re just wrong. Nucleic acids are at the centre of this jigsaw. The aren’t just some ‘tool’ for the real string-pullers, which you rather bizarrely deem to be proteins (and, presumably, functional RNAs). You are hampered in comprehending this by a rather simplistic view of biochemistry.

    I don’t think that proteins or functional RNAs are the instigators of anything. It is the active entities of which proteins are a part that are the things that can be seen to be doing the work. The molecular “motors”and all the other nano “machines” that are the only entities that can be said to be actually doing anything. Where would the DNA in the zygote be without the rest of the cell’s “machinary” that has been ever present working on it from before conception?

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  35. CharlieM: I don’t think that proteins or functional RNAs are the instigators of anything. It is the active entities of which proteins are a part that are the things that can be seen to be doing the work. The molecular “motors”and all the other nano “machines” that are the only entities that can be said to be actually doing anything. Where would the DNA in the zygote be without the rest of the cell’s “machinary” that has been ever present working on it from before conception?

    This makes no sense. Suddenly one must look at ‘the whole telly’, which directs its constituent parts? Of course, reductionism and holism both have a role. No-one, including Dawkins, is proposing a gene-centred reductionist approach to physiology, for example. A position is taken for its utility, not because it fits with one’s fuzzy philosophy. Or at least, that is a preferable way to do science.

    When it comes to evolution, it remains the case that genes – using Dawkins’s sense: stretches of DNA – are the ultimate beneficiaries of their action, increasing or decreasing in frequency in the population accordingly. Your zygote is of course furnished with proteins that enable transcription and translation to take place (mainly from the egg, or ovule if you’re a plant). But they come from genes, and the developing embryo is soon furnished with a host of proteins from postzygotic copies of the genome. The primordial egg/ovule proteins are long gone. And so, before long, is the soma. It’s only there for one life. Meantime the genes persist, wrapping themselves in a succession of somas – a Cheshire-cat smile, ever and ever, amen.

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  36. CharlieM: It’s not the physical processes that we should be spending time arguing over. It is the fact that you and Corneel have claimed that these molecules use “scuzzy tactics” to achieve an end and that they are given “incentives” to do so.

    Wrong, and rather revealing. What matters, is what actually happens: the physical processes. Whether Someone On The Internet wrote something that you find misleading is neither here nor there.

    I was using the same sort of language that you and Corneel have been using to see what the reaction would be.

    And I was a little naughty. I used anthropomorphic language, ascribing “scuzziness” to a piece of DNA. You jumped straight into the trap, and decided to treat the obviously metaphorical language literally in an effort to score a lame-ass rhetorical point, writing — “Scuzzy tactics” is a phrase that would normally apply to agents who are trying to achieve particular ends. — Hence my response, citing Dawkins… with a winky face.

    What do you think the difference is between having an incentive and having a motive to perform some act?
    What incentive or motivation do you think a kinesin-14 “motor” has to walk along a microtubule taking the neo-centromere with it?

    None whatsoever.
    It does what it does. Selfish DNA is “motivated” to act selfishly because that’s what gets it into the next generation. Transposons transpose. Homing endonucleases gene convert. What’s the “motivation”? It works, that’s all. We observe these behaviors because the DNA that codes for them is successful at propagating itself. Safe to say that DNA that codes for an enzyme that destroys itself is created on a daily basis. We don’t get to observe it, however.
    [i.e. restriction-positive, modification-negative]

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  37. CharlieM: I would like you to give your opinion as to why we should see it more as the actions of strings of DNA. What is it that is actually observed under the microscope, active molecules or bare DNA?

    CharlieM: It’s not the physical processes that we should be spending time arguing over.

    Uh-huh.

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  38. DNA_Jock: CharlieM: I would like you to give your opinion as to why we should see it more as the actions of strings of DNA. What is it that is actually observed under the microscope, active molecules or bare DNA?

    CharlieM: It’s not the physical processes that we should be spending time arguing over.

    Uh-huh.

    Hey, we have a point of agreement, that’s good 🙂

    So what is it about life that sets it above the merely physical processes of inanimate matter. In living systems there is intrinsic intentionality. We observe goal directed activity throughout life from the microscopic level to the migrations of vast numbers of animals we see purposeful activity.

    And I hope both agree that throughout life, there are abundant selfish and selfless activities, both metaphorical and actual. We could say that evolution proceeds by maintaining a dynamic balance between constructive and destructive forces, growth and decay, anabolic and catabolic processes.

    Life is not about static strings of molecules or coded sequences. It is about ceaselessly active, directed, fluidic, creative processes. Not so much about the physical substances but about how these substances are combined and manipulated. And the properties of substances such as water, carbon, nucleic acids, fatty acids and proteins are very well suited to being used in this way.

    So what is seen as selfish with regards to the part is very often beneficial for the whole.

    I’m not sure how anyone would want to argue against something so obvious as this.

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  39. CharlieM: Not so much about the physical substances but about how these substances are combined and manipulated.

    So, in theory, the Sun could be conscious?

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  40. CharlieM,

    So what is seen as selfish with regards to the part is very often beneficial for the whole

    Which is pretty much the thesis of one R. Dawkins, if one reads past the title.

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  41. OMagain: So, in theory, the Sun could be conscious?

    Well stars are born and they die, so they could at least be classed as living.

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  42. Allan Miller: So what is seen as selfish with regards to the part is very often beneficial for the whole

    Which is pretty much the thesis of one R. Dawkins, if one reads past the title.

    I own and have read several of his books. He tells a good story.

    But genes, as in strings of nucleotides, cannnot act in a selfish manner because they do not act at all. They are acted upon. They can be used in the carrying out of a “selfish” act. When it comes to genetic processes anyone who tries trace ultimate causes will end up chasing their own tail (metaphorically speaking).

    If a load of counterfeit bank notes flooded the market we would not say that the notes were acting in a selfish manner.

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  43. CharlieM: I own and have read several of his books. He tells a good story.

    But genes, as in strings of nucleotides, cannnot act in a selfish manner because they do not act at all. They are acted upon. They can be used in the carrying out of a “selfish” act. When it comes to genetic processes anyone who tries trace ultimate causes will end up chasing their own tail (metaphorically speaking).

    If a load of counterfeit bank notes flooded the market we would not say that the notes were acting in a selfish manner.

    We do need an explanation as to why certain alleles or genes are found more often than others in a population. If we make all things equal except for changing one gene we can see different and consistent outcomes in the two groups. It isn’t unfair to explain these different outcomes in terms of that one changed variable.

    We could also talk about transposons whose only inherent function is to create more copies of themselves in the genome. Sure, they may secondarily change gene expression, but that is more happenstance compared to the inherent function of those gene sequences.

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  44. CharlieM: I own and have read several of his books. He tells a good story.

    But genes, as in strings of nucleotides, cannnot act in a selfish manner because they do not act at all.

    Ah, geez. Despite reading the books, you still come across all Mary Midgely. It’s a metaphor

    They are acted upon. They can be used in the carrying out of a “selfish” act. When it comes to genetic processes anyone who tries trace ultimate causes will end up chasing their own tail (metaphorically speaking).

    Only up to a point. If you think you have pointed up an unsolvable chicken-egg paradox by pointing to an organism born yesterday with transcription enzymes already in place, you are not saying anything significant, merely pointing out the known fact that the modern genome acts mainly through being transcribed. Was it always thus? In a hypothetical protein-free genome would nucleic acids suddenly change their role from actor to inert ‘tool’ the day one produced the first protein enzyme?

    Regardless, none of this negates the fact that what persists over evolutionary time are genes, not proteins nor bodies nor cells. They persist by virtue of their effects – which it pleases me to call actions – in multiple lives. These actions are mediated by the transcription/translation system, also produced by genes. The objection that they don’t catalyse reactions (even that’s not true) does not change this.

    If a load of counterfeit bank notes flooded the market we would not say that the notes were acting in a selfish manner.

    Wha? I’ve mentioned this before; your analogies illustrate little more than your own confusion.

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  45. T_aquaticus: We do need an explanation as to why certain alleles or genes are found more often than others in a population. If we make all things equal except for changing one gene we can see different and consistent outcomes in the two groups. It isn’t unfair to explain these different outcomes in terms of that one changed variable..

    Yes, single changes can have no effect, one effect or multiple effects. But genes don’t change themselves. So we need to look further. Was the change due to an external source or was it intrinsic to the system? There will be a reason why the gene changed. Can you think of a reason that lies within the gene itself?

    We could also talk about transposons whose only inherent function is to create more copies of themselves in the genome. Sure, they may secondarily change gene expression, but that is more happenstance compared to the inherent function of those gene sequences.

    It’s not just transposons, the inherent function of any gene expression is to create copies of the gene. The viability of the system depends on how this copying process is controlled. It is up to the system to maintain the correct balance between growth and decay within it. Loss of control of either will result in disorder and disease.

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  46. Allan Miller:

    CharlieM: I own and have read several of his books. He tells a good story.

    But genes, as in strings of nucleotides, cannnot act in a selfish manner because they do not act at all.

    Ah, geez. Despite reading the books, you still come across all Mary Midgely. It’s a metaphor

    I also have a copy of, “Evolution as a Religion”. It’s a fact.

    They are acted upon. They can be used in the carrying out of a “selfish” act. When it comes to genetic processes anyone who tries trace ultimate causes will end up chasing their own tail (metaphorically speaking).

    Only up to a point. If you think you have pointed up an unsolvable chicken-egg paradox by pointing to an organism born yesterday with transcription enzymes already in place, you are not saying anything significant, merely pointing out the known fact that the modern genome acts mainly through being transcribed. Was it always thus? In a hypothetical protein-free genome would nucleic acids suddenly change their role from actor to inert ‘tool’ the day one produced the first protein enzyme?

    I would prefer to discuss what we can observe without bringing any speculations as to what might or might not have been into the discussion.

    Regardless, none of this negates the fact that what persists over evolutionary time are genes, not proteins nor bodies nor cells. They persist by virtue of their effects – which it pleases me to call actions – in multiple lives. These actions are mediated by the transcription/translation system, also produced by genes.

    Are you saying that genes are immutable over evolutionary time? That entities such as cell membranes and cytoplasm do not persist over evolutionary time?

    The objection that they don’t catalyse reactions (even that’s not true) does not change this.

    Why stop at the gene? Carbon, oxygen, hydrogen and the like persist over evolutionary time. And even metals can catalyse reactions.

    If a load of counterfeit bank notes flooded the market we would not say that the notes were acting in a selfish manner.

    Wha? I’ve mentioned this before; your analogies illustrate little more than your own confusion.

    Hopefully I am becoming less confused by participating here. Learning is an enjoyable experience.

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  47. CharlieM:
    I also have a copy of, “Evolution as a Religion”. It’s a fact.

    No, that’s a metaphor too. It has none of the trappings more normally associated with a religion. That you find such a title persuasive indicates a certain lack of receptiveness to the science.

    I would prefer to discuss what we can observe without bringing any speculations as to what might or might not have been into the discussion.

    Haha. You would prefer not to consider scenarios that would render your attempts to subordinate the role of genes moot. Good one.

    Are you saying that genes are immutable over evolutionary time?

    Nope.

    That entities such as cell membranes and cytoplasm do not persist over evolutionary time?

    There is a turnover of the molecules in membranes and cytoplasm. Indeed, there is a turnover of the molecules in DNA. But what is conserved – albeit with some modification – is nucleotide sequence. Every atom of a given nucleic acid sequence can disappear, but still the sequence survives – what I termed the ‘Cheshire-cat smile’. In membranes and cytoplasm, while they form a repository for new molecules (synthesised from genes), they have no informatic persistence.

    The key currency of evolution is the nucleic acid linkage unit. This can be covalently linked, as in a chromosome, or encapsulated, as in a cell with multiple chromosomes. What matters is the common future for sub-stretches of such units. They can benefit (by increase) or suffer detriment (by decrease) due to the genes they contain. Sometimes the picture is more complex, because a unit may contain both benefit and detriment at various points along its length. Recombination and independent segregation can have an effect here, allowing subunits (‘selfish genes’) to propagate and integrate in a quasi-independent manner. But even with such independence, there is significant persistence of combinations. A gene can increase because it finds itself in a succession of better genomes due to its effects. It is linked in, but can integrate into other units. This is where the evolutionary logic of gene-centrism derives: a linkage unit physically hangs on to all its members, and so they are all in it together. This encourages a (sometimes uneasy) co-operation.

    Why stop at the gene? Carbon, oxygen, hydrogen and the like persist over evolutionary time. And even metals can catalyse reactions.

    Hopefully, if you have digested the above, you can see why.

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  48. Allan Miller:

    CharlieM:
    I also have a copy of, “Evolution as a Religion”. It’s a fact.

    No, that’s a metaphor too. It has none of the trappings more normally associated with a religion. That you find such a title persuasive indicates a certain lack of receptiveness to the science..

    Sorry, I was being ambiguous. In your previous post your sentence, “It’s a metaphor” didn’t specify what the “it’s” was referring to. It could have been referring to either “selfish” or “Mary Midgely”, as you were using both metaphorically. It is a fact that I have a copy of “Evolution as Religion”. I have never thought of evolution as a religion. I think that evolution is a fact. Although I do think that certain people have a religious attitude towards their beliefs about evolution.

    I would prefer to discuss what we can observe without bringing any speculations as to what might or might not have been into the discussion.

    Haha. You would prefer not to consider scenarios that would render your attempts to subordinate the role of genes moot. Good one.

    No. I do think that these scenarios are worth a great deal of thought. But until any of them can be backed up with more than just speculation then they cannot be used to argue for any position

    Are you saying that genes are immutable over evolutionary time?

    Nope.

    That entities such as cell membranes and cytoplasm do not persist over evolutionary time?

    There is a turnover of the molecules in membranes and cytoplasm. Indeed, there is a turnover of the molecules in DNA. But what is conserved – albeit with some modification – is nucleotide sequence. Every atom of a given nucleic acid sequence can disappear, but still the sequence survives – what I termed the ‘Cheshire-cat smile’. In membranes and cytoplasm, while they form a repository for new molecules (synthesised from genes), they have no informatic persistence.

    I’m not arguing that there is no information in the strings of DNA. But this information has to be used by something in order to be of anything more than an unread book. The parents provide the “book” along with the equipment required to read the book, take what is read, and alter it in meaningful ways in order to maintain the viability of the whole. Life requires whole organisms be passed on from genetation to generation, and the zygote is a whole organism suited to the environment in which it finds itself.

    The key currency of evolution is the nucleic acid linkage unit. This can be covalently linked, as in a chromosome, or encapsulated, as in a cell with multiple chromosomes. What matters is the common future for sub-stretches of such units. They can benefit (by increase) or suffer detriment (by decrease) due to the genes they contain.

    Currency is something that is used in the exchange of goods. It is of no value unless it is being used, so your metaphor is apt.

    Sometimes the picture is more complex, because a unit may contain both benefit and detriment at various points along its length. Recombination and independent segregation can have an effect here, allowing subunits (‘selfish genes’) to propagate and integrate in a quasi-independent manner. But even with such independence, there is significant persistence of combinations. A gene can increase because it finds itself in a succession of better genomes due to its effects. It is linked in, but can integrate into other units. This is where the evolutionary logic of gene-centrism derives: a linkage unit physically hangs on to all its members, and so they are all in it together. This encourages a (sometimes uneasy) co-operation.

    And the danger here is in abstracting the gene by ignoring the context of its existence. We witness meaningful activity, both constructive and destructive at all levels of life. Within cells there are structures being built up and broken down, as there are in the organs of an individual organism, as there are in groups such as the social insects. There is danger from destructive forces such as to cells from pathogenic viruses and bacteria which penetrate and multiply within, to organisms from invaders such as insects which lay their eggs via ovipositors and multiply within. As above, so below. The whole reflected in the parts.

    Why stop at the gene? Carbon, oxygen, hydrogen and the like persist over evolutionary time. And even metals can catalyse reactions.

    Hopefully, if you have digested the above, you can see why.

    Well I can see that there is no end directed activity at the level of the gene and below. But there is such activity above the level of the gene. Unless that is you consider the gene to include all the active complexes associated with the DNA.

    (Sorry about the time it took me to reply, computer problems.)

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