15.5 hours.

Over two working days.

In this comment colewd says: “Let’s start with this overview.”

An “overview” that according to this tool contains 187153 words.

Where those words according to this tool will take over 15 hours to read.

15 hours for an “overview”. 15 hours.

If only there was some way to take a sprawling set of claims and refine them down into a core that could then be reviewed by others and feedback given until it is a reasonable size (typically 3,000 to 10,000 words on the average scientific paper) where all claims have been tested by other experts and errors removed.

It seems to be it’s a strategy. Never get pinned down on anything too specific and you never have to be wrong. Hence the sprawl.

colewd, do you seriously expect people to spend 15 hours reading an “overview”? How long is the main argument? A million or two words?

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90 thoughts on “15.5 hours.

  1. Rumraket: But it’s essentially gibberish. Don’t be fooled, Bill is not really responding in a sensible way as much as keeping up the pretense that he is.

    Keep in mind Bill’s goal is not to convince anyone else. Bill couldn’t care less about the actual science. His goal is to convince himself science proves his Christian God.

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  2. I’m not so sure it makes too much sense to talk in terms of ‘optima’. In my E3 search, most primates showed 100% alignment; more distant relatives dropped into the 99%s. But if I’d started there – with the bears for instance – I’d probably see 100% at the family level there too. This pattern would hold elsewhere I’m sure. But which, of these groups that have been subject to much the same amount of evolution, is the ‘optimal’ sequence? For systems that are pinned in place by multiple interactions, and hence widely conserved, I think we may often just be looking at frozen accidents and restricted degrees of freedom rather than ‘optimality’.

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  3. Joe Felsenstein:
    Alas, to explore the space thoroughly for 10 amino acids would require a 30-base stretch of DNA […]

    I don’t think we need to treat amino acids as 20 completely different things though. As discussed in my OP, and elsewhere, simply subdividing the amino acid set on property can give fair coverage without being exhaustive to the letter.

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  4. Adapa: Keep in mind Bill’s goal is not to convince anyone else.Bill couldn’t care less about the actual science.His goal is to convince himself science proves his Christian God.

    And he still hasn’t managed that? 🤔

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  5. colewd:
    Allan Miller,

    We have a good explanation for money disappearing so I would not use the design hypothesis is this case.

    There’s a better reason not to use the Design hypothesis. Until it is demonstrated that the postulated entity has the capacity to do that which it needs to do, it is a pure fantasy.

    The gaps are no longer an accepted consequence once we observed the organized complexity of the cell.

    You still can’t rule it out. But your objections tend to be much further down the line than that, in groups whose cellular organisation is much the same – humans and chimps, f’rexample.

    Can you name any two non-interbreeding species that you regard as commonly descended?

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  6. Allan Miller: I’m not so sure it makes too much sense to talk in terms of ‘optima’. In my E3 search, most primates showed 100% alignment; more distant relatives dropped into the 99%s. But if I’d started there – with the bears for instance – I’d probably see 100% at the family level there too. This pattern would hold elsewhere I’m sure. But which, of these groups that have been subject to much the same amount of evolution, is the ‘optimal’ sequence? For systems that are pinned in place by multiple interactions, and hence widely conserved, I think we may often just be looking at frozen accidents and restricted degrees of freedom rather than ‘optimality’.

    I understand but that betrays a misunderstanding of what is meant by ‘optima’. It is not asserted that the current system is the best of all conceivable solutions to some given problem, merely that within the sequence-neighborhood, it is the one with highest fitness. And as we know, fitness is always contextually defined. Given it’s local constraints and interactions, this particular one seems to have higher fitness than all 1-mutant versions of it.

    My understanding is that any local optimum is defined as such by there being no higher-fitness sequences within a hamming distance of 1.

    That’s doesn’t make it “optimal” of course in that sense you alluded to, just better at what it is currently doing, given it’s constraints and interactions(aka all else held constant) than all other variants of it with 1 mutation.

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  7. Rumraket,

    Yes, that seems fair. However I suspect Bill will be thinking in terms of optimal designs. That somehow the bear sequence is ideal for bears, the primate sequence ideal for primates etc. Whereas the differences may well have nothing to do with selection.

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  8. colewd:
    Allan Miller,

    While common descent is certainly an explanation it is at best a partial explanation as it can explain similarities but not differences. A question remains.

    As far as a clade with 100% sequence identity is concerned, there are no differences needing explanation. And as far as two clades with 99% mutual identity is concerned, Design too is completely silent on the 1%, while common descent remains the explanation of choice for the 99.

    Further, differences themselves are phylogenetically informative.

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  9. Allan Miller: It’s a common idiomatic approach, like ‘to be fair’ or ‘frankly’ or ‘honestly’, which you’ve picked me up on before.

    Is it commonly used at the annual shareholder meetings, perhaps?

    How many votes would you get, if you used ” to be honest or frankly” at the end of your presentation at the selection of the company’s board of directors?

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  10. J-Mac: Is it commonly used at the annual shareholder meetings, perhaps?

    How many votes would you get, if you used ” to be honest or frankly” at the end of your presentationat the selection of the company’s board of directors?

    I didn’t realise this was a presentation to the company’s board of directors.

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  11. colewd,
    The hypothesis that zebras can breed with donkeys and produce offspring but that the offspring is infertile? The experiment has been done.

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  12. Alan Fox,

    The hypothesis that zebras can breed with donkeys and produce offspring but that the offspring is infertile? The experiment has been done.

    The hypothesis is if two animals that cannot breed share a common ancestor.

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  13. colewd: The hypothesis is if two animals that cannot breed share a common ancestor.

    All life on Earth descends from a common ancestor. Molecular phylogenetics makes this hard to reject.

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  14. colewd:
    Alan Fox,

    The hypothesis is if two animals that cannot breed share a common ancestor.

    The test of the hypothesis is the extent of sequence alignment. Given that genetic identity (diminishing with divergence) is an expectation of a bifurcating process of descent, then finding it supports the hypothesis.

    Even if they can breed … the final ‘checkpoint’ of fertility is successful meiosis. That is in fact a proxy test of sequence alignment – meiosis fails because the haploid genomes are too divergent; their common ancestor was too long ago, even though the genomes can work together in a life. You allow biology to perform this test, and tentatively agree that it is likely common descent even when meiosis fails. Yet you don’t accept it when we do it, for species whose hybridisation fails at the zygotic stage or earlier..

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  15. Allan Miller: The test of the hypothesis is the extent of sequence alignment. Given that genetic identity (diminishing with divergence) is an expectation of a bifurcating process of descent, then finding it supports the hypothesis.

    Of course this test has already been done hundreds if not thousands of times. The branching nested hierarchy indicative of common descent has been found every last time. Here’s but one of many examples

    Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae

    Watch Bill ignore the scientific evidence just like he ignores all scientific evidence.

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  16. Allan Miller,

    The test of the hypothesis is the extent of sequence alignment. Given that genetic identity (diminishing with divergence) is an expectation of a bifurcating process of descent, then finding it supports the hypothesis.

    How do you determine the pass/fail points of the test?

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  17. Allan Miller,

    What would you suggest?

    I would start with genetic profiling of species that share ancestry and see the tolerated variation. I would also try and isolate the sources of the variation to try and identify a mechanism. Genetic recombination comes to mind as something to explore. VDJ recombination study may help here.

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  18. colewd: I would start with genetic profiling of species that share ancestry and see the tolerated variation.

    (facepalm) Bill the idea is we’re using the data to confirm common ancestry. How are you going to start with species of known common ancestry to establish common ancestry?

    I would also try and isolate the sources of the variation to try and identify a mechanism.

    FFS Bill science did that more than half a century ago.

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  19. J-Mac: I’ll be honest, I don’t know which language is my first…
    I know few…

    Allan Miller: I know fewer.

    You do pretty damned well with at least one. That’s a well written OP. (I don’t mean to downplay the content.)

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  20. colewd:
    Allan Miller,

    I would start with genetic profiling of species that share ancestry and see the tolerated variation.

    And you would find that the variation between species differs only by degree from that observed within, as expected.

    I would also try and isolate the sources of the variation to try and identify a mechanism.Genetic recombination comes to mind as something to explore.VDJ recombination study may help here.

    Point mutation, insertion, deletion, transposition, inversion, duplication, homologous recombination, gene conversion …

    All the above transformations, observed as polymorphisms within species, also characterise the kinds of difference observed between. Furthermore, the biases observed or expected – silent or conservative substitution, transition-transversion bias, mutational/recombinational ‘hotspots’ – also appear on analysis of interspecies data.

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  21. colewd: I would also try and isolate the sources of the variation to try and identify a mechanism.

    Why?

    colewd: Genetic recombination comes to mind as something to explore. VDJ recombination study may help here.

    Nothing about disembodied intelligences manipulating reality? I mean, that’s what you think actually happens right? So why bother pretending otherwise?

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  22. Alan Fox: You pose an interesting question.Do you think we could form a testable hypothesis?

    You could start with Wikipedia.

    We can form a testable hypothesis for a devolution within a kind. .
    Dwarfism and the disruptions of meiosis are similar side effects to the devolution of wolf to chihuahua, as Behe has exposed it in his recent book…

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  23. Tom English: Tom English
    . said:
    J-Mac: I’ll be honest, I don’t know which language is my first…
    I know few…

    Allan Miller: I know fewer.

    You do pretty damned well with at least one. That’s a well written OP. (I don’t mean to downplay the content.)

    You both shouldn’t…
    To be perfectly honest, OMagain hasn’t disappointed, again…😂
    I guess Tom and Allan have some kind of code variant written into the everyday English???

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  24. Allan Miller:
    colewd: I would start with genetic profiling of species that share ancestry and see the tolerated variation.

    Allan: And you would find that the variation between species differs only by degree from that observed within, as expected.

    If you guys are still discussing equines: there will be a LOT of variation. Neither zebra’s nor donkeys are a single species. Both have multiple species and subspecies. Where does common ancestry stop, I wonder?

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  25. Allan Miller,

    And you would find that the variation between species differs only by degree from that observed within, as expected.

    You are falling back to a working hypothesis vs a tested hypothesis. Degree is a vague quantity you cannot use it as a pass/fail entity. How much variation do we know at this point signifies common ancestry. Expected human variation is about .1%.

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  26. colewd:
    Allan Miller,

    You are falling back to a working hypothesis vs a tested hypothesis.

    The working hypothesis is a tested hypothesis so … whatevs.

    Degree is a vague quantity you cannot use it as a pass/fail entity.

    Obviously, I would add a little more of a rigorous threshold if I was doing something other than chatting on the internet.

    When was the last time you measured the FI of an organism, by the way?

    How much variation do we know at this point signifies common ancestry.Expected human variation is about .1%.

    And that’s the only organism on the planet is it? 🤔 The chimps are hurt.

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  27. Allan Miller,

    And that’s the only organism on the planet is it? 🤔 The chimps are hurt.

    It’s where we can correlate variation with common descent. Other species will also work. Dogs have been reported to have a .5% variation. Here we have a case of strong artificial selection.

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  28. Adapa: Of course this test has already been done hundreds if not thousands of times. The branching nested hierarchy indicative of common descent has been found every last time. Here’s but one of many examples

    Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae

    Watch Bill ignore the scientific evidence just like he ignores all scientific evidence.

    Exactly as predicted Bill completely ignored this example of how a genetic phylogeny was determined.

    Bill is all about the science doncha know. 😀

    Hey Bill, tigers and house cats share 96.5% commonality in their coding DNA. Are they related by common descent?

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  29. colewd:
    Allan Miller,

    It’s where we can correlate variation with common descent.Other species will also work.Dogs have been reported to have a .5% variation.Here we have a case of strong artificial selection.

    Humans and dogs are terrible proxies for variation estimates in the wild! It’s like you’re trying to game things or something, turning your detector’s sensitivity down to zero.

    Chimp/bonobo would be interesting. They don’t appear to interbreed now, but there is evidence of introgression or incomplete lineage sorting (look ’em up). How do you think that got there?

    Also, bonobo lie within the variation range of chimps. That’s curious, if they don’t share a common ancestor.

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  30. Allan Miller,

    Chimp/bonobo would be interesting. They don’t appear to interbreed now, but there is evidence of introgression or incomplete lineage sorting (look ’em up). How do you think that got there?

    Also, bonobo lie within the variation range of chimps. That’s curious, if they don’t share a common ancestor.

    This is a very good proposal at first blush. If we set the test point as tight as .5% this would work given the sequence similarity appears to be better then this.

    The things I can think of to look at in addition would be
    -chromosome count (probably the same)
    -gene sets
    -alternative splicing
    -gene expression.

    The other great think here is we could possibly find the common ancestor.

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  31. Bill once again puts on his IDiot hat, starts posting random scientific terms he doesn’t understand to give the appearance he had a meaningful response.

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