The Fridge-o-matic Challenge

I once offered nonlin.org the ‘fridge-o-matic’ challenge. The idea was to give me a number from 1 to 9 (a shelf in my fridge/freezer), and a lateral location Left, Middle or Right, and a depth locator Front, Middle, Back. That gives 81 sectors. I go to the named sector and fumble for the nearest organism (he’d have to trust me not to cheat). If it’s a stew or pizza I’d need more info. Then I’d need a chromosome number in that organism, and a gene number on the chromosome. We could shortcut the back’n’forth by giving numbers 1-50 and 1-10,000 which I’d then normalise to the actual counts.

Armed with this target of a random gene in a random organism in my fridge, I’d go to a public database and (if it’s in) run a BLAST on the gene to find the sequence alignments, arranged by closeness of match. I offered high confidence that this would recover a reasonable approximation of the Linneaean hierarchy – closest matches in species, then genus, then Family etc. This, I feel, nicely fits with the hypothesis of Common Descent of taxonomic ranks.

Now, the Linnaean hierarchy was based on morphology. He did not have the technology to ‘see’ genes directly. So we’d have to wonder why I could stick my random thumb in and pull out a Linnaean plum pretty much every time, on genes invisible to him.

Nonlin declined to play (he is, frankly, no fun at all). “It’s expected”, he said. “Like organisms will have like genes”. But for that to be a relevant objection, every single genetic difference between every single species pair must be involved in every morphological distinction between them. That requires quite a lot of heavy lifting from a gene. Its job might be to … I dunno, ligate a strand break in DNA let’s say. But it’s also got to do it in a squid way, and a dandelion way, and a yeast way that feeds through to morphology for every gene. We’re always being told how brittly unchangeable genes are, yet we seem to have a huge range of latitude in genes that are notionally pinned in place both by primary function and by multiple morphological roles across species.

I bring this up now for two reasons related to nonlin’s ‘Sexual selection’ thread.

1) If every difference between every gene really were morphologically significant, there’d be a constant stream of mutants not possessed of the vital characteristics that render the sexes mutually attractive to each other but not to members of other species.

2) Sexual dimorphism is a particularly striking morphological difference, which, on the ‘genes=morphology’ view, would require similar genetic differences between the sexes to those observed between like species. But most genes, even those involved in sexual differences, reside on the autosomes, which pass through both genders of offspring.

The answer, of course, is that genetic differences on the broad scale are not the key to morphological difference. Those differences are under the control of relatively few genes, and a lot of regulation (itself genetic in origin). This is as true between species as it is within (don’t fight me on this; it’s an established fact!).

Anyway, anyone fancy taking the Fridge-o-matic for a spin?

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169 thoughts on “The Fridge-o-matic Challenge

  1. OK, I’ve run the numbers; let’s have a squint. As shown in the graphic, the nucleotide changes cluster around our Linnaean neighbourhood. You might expect that if the proteins do too, of course. Note there are a couple of differences with gorilla, though there were none on protein BLAST; they’re both silent.

    It is interesting that, in all amino acid substitution scenarios, the substitution is achieved by a single nucleotide difference. This applies much more widely than just this zoomed-in region. That’s quite peculiar, outside of the evolutionary paradigm (or a Design paradigm involving “change”). To explain: there is a lot of redundancy in the genetic code; most triplets are third-base-blind, the first two specifying the acid completely. If an acid isn’t being changed by evolution or Design, but the whole peptide is being cast afresh without cross-reference, I would expect the new acid to be underlain by a difference (not a change!) in 2 or 3 positions about as often as in 1. But no, it is almost always 1. As an example, alanine is GCx while valine is GUx, the x being any of the 4 bases in position 3. If you had alanine as GCA, you (almost) never see the substitution as GUG, 2 bases different. It’s always GCA-GUA. Still less do you ever see substitutions that can only be achieved by a swap in all 3 positions – eg UUU Phenylanine to GGG Glycine.

    Another expectation, if there is no ‘change’ involved in generating two sequences, is that silent substitution, involving no change in the acid, should appear a lot more often than it does. If the sequences aren’t (cor)related, they should be under no constraint to match at that fine level. But they do. Typically, where SS does occur, it is embedded in a ground of paired nonredundant assignments. A single peptide may contain all the possible alanine triplets, but at any given aligned position between two peptides in two species, we see the same one used much more often than not.

    A third expectation is that acid substitutions will tend to be chemically conservative more often than not – an acid of similar size and properties will be less disruptive to form and function. This is partly guaranteed by the apparent single-nucleotide rule – the arrangement of the code happens to make single-nucleotide swaps more likely to hit similar acids. This is often cited as a Design feature, to reduce misread errors during translation. OK, but why should we expect to see the same feature between species?

    All in all, the Designer seems to have hamstrung itself with a significant amount of constraint!

    So, to my predictions. For rapidity I’ll just include one species, the Northern White-cheeked Gibbon Nomascus leucogenys, to compare with us, with a sufficiency of differences without going mad. Let us see what conversions occur on – ahem – the road to Nomascus

    In each case, the human triplet is first.
    Base 7 CGG-CGC Silent transversion pos 3
    Base 10 GTG-GCG Val-Ala transition pos 2 cons
    Base 19 GCT-ACT Ala-Thr transition pos 1 semi cons
    Base 34 GCC-GCT Silent transition pos 3
    Base 55 CTT-CTG Silent transversion pos 3
    Base 58 CAA-CGA Gln-Arg transition pos 2 non cons
    Base 115 ACA-GCA Thr-Ala transition pos 1 semi cons
    Base 226 GCG-GTG Ala-Val transition pos 2 cons
    Base 304 TTG-CTG Silent transition pos 1
    Base 424 ATC-ATA Silent transversion pos 3
    Base 445 GTC-GTA Silent transversion pos 3 

    So I make that:
    – 7 transitions to 4 transversions.
    – 5/11 changes at base 3 vs 3/11 base 2 and 3/11 base 1***
    – 6 changes silent, 2 conservative, 2 semi conservative and 1 not conservative. Note that the even the changes are from a restricted set. The 5 substitions are made up of just 3 transformations, suggesting that ala-thr and ala-val could be quite common, in both directions.

    So, my predictions, based on evolutionary assumptions, are all borne out.  

    *** The base 3 prediction was due to the greater likelihood of silence at that position, but I forgot about Leucine which can be silent at pos 1, which is what we see at 304, so I’m counting that as well, which makes 6 that are silent, pos 3 or both. Bite me. 

    +2
  2. Alan Fox,

    No it hasn’t. I know you hope and believe this but you are not convincing anyone.

    A book club I am in read both the Blind Watchmaker and Darwins black box. Have the group was secular. All agreed Behe had the easier argument.

    All you are doing is categorical denial which is not an argument.

    More than hope and believe it the empirical evidence supports the design argument as being a viable way t to detect design in nature. One of the secular engineers in the group called it a good way to exercise Evolutionary theory.

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  3. colewd:
    More than hope and believe it the empirical evidence supports the design argument as being a viable way t to detect design in nature. One of the secular engineers in the group called it a good way to exercise Evolutionary theory.

    Dembski was, as I recall, also asked to identify natural phenomena which are NOT designed. After all, any “viable way to detect design in nature” has to have SOME way to differentiate between things that are and are not designed. If you simply take the policy position that everything is designed, you aren’t detecting anything, you are only making a useless claim.

    On the other hand, I will agree that claiming that everything is designed is a MUCH easier argument — one that requires no intelligence, knowledge, education, logic, etc. To make his argument, Dawkins must address messy reality, make statistical inferences, recognize exceptions, and delve into the sort of detail that makes eyes glaze over.

    I’m interested in this sort of thing, but I’m totally unqualified to comment on Allan Miller’s charts. I would need several college semesters to grasp what terms like conversion, translation, transversion, and transitions even mean. In contrast, POOF is simple because the poof mechanism is pure magic, couldn’t be simpler.

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  4. Allan Miller: You’ll be able to tell me what it’s for on the ID viewpoint, then. And why it varies among species the way it does.

    You’re the one writing an OP. It’s your burden to prove something. Which you failed to do so far.

    Allan Miller: Run the numbers and tell me how much waste (in your example).

    About 95% I’d say, given that you only really need the end sequences for neat excision, and assuming they aren’t self-splicing.

    Maybe that’s your problem, simple math. Let’s find your cure:
    If 5% is useful and another 95% on top of that is “junk”, then your waste is 95/5 = 19. This is a whopping 1900% waste. Not a “measly” 95%. Of course that has a cost! Imagine you had 40 hands only two of which were useful and the others just got in the way. Or your head was 20 times bigger with no increase brain power or visual, etc. acuity.

    This fact alone refutes “evolution”. For those smart enough to understand, that is.

    Allan Miller: Assuming a proposition’s truth in order to examine its entailments is so basic a part of logic and science, I don’t know why you have a problem with it, being a top logician and scientist an’ all.

    Only you fail to “examine its entailments”.

    Allan Miller: An example without change denies change in all scenarios.

    Blatantly false. You’re just stuck in your own falsehood.

    Allan Miller: It’s not affirming the consequent, it is affirming consistency with the hypothesis.

    Of course it is. If that’s your only claim. To NOT be affirming the consequent, you need the ‘only if’ on top of the ‘if’.

    IOW, you need:
    “only if “evolution” were true, we would observe ABC, which we do”.
    But you can support exactly ZERO such claims.

    And in truth, you don’t even have the ‘if’ given “evolution” predicts everything AND its opposite about genetics.

    Allan Miller: Because genes ‘should’ be optimised for function. If that function is independent of morphology, then ‘why not’ is a massive cop-out.

    I gave examples from design. FO.

    Allan Miller: Why do nonmorphological and unexpressed genes follow morphological ones, if a Designer is at work? “That’s what a Designer would do, so Design it is”.

    It’s your OP. When will you defend your so-far-bogus claims?

    Allan Miller: You don’t even have an explanation, beyond “Why not?”.

    Whose OP is this again?

    Allan Miller: Translation: “I got nuthin’”

    Why “translation”? What part of “look it up”, you don’t understand?

    Allan Miller: Can’t be arsed searching. If you have a question, ask away.

    Already did.

    OMagain: No, nonlin only does what evolution cannot do, not what ID can do.

    There’s an essay on ID. You can [still] comment there. This is Allan’s show… going down in flames.

    Allan Miller: “Why do ye elements combine in precise proportion, Mr Dalton?” “Why not?”.

    “Why not” is not an argument. It’s a counter to a stupid argument. Do you get the very important nuance?!?

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  5. Nonlin.org: t’s your burden to prove something. Which you failed to do so far.

    How many more times? Science doesn’t deal in proofs.

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  6. Nonlin.org: There’s an essay on ID.

    No there isn’t. There is no “Intelligent Design” theory or hypothesis that makes testable predictions.

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  7. Nonlin.org: Allan Miller: It’s not affirming the consequent, it is affirming consistency with the hypothesis.

    Of course it is. If that’s your only claim. To NOT be affirming the consequent, you need the ‘only if’ on top of the ‘if

    Say I decided to check the geographical location of the battle of Brunanburh. I could look at historical records to establish possible locations and then conduct an archeological search in those locations. On finding artefacts of the right age and type with the damage and distribution one finds at known sites, would I be affirming the consequent to provisionally declare I had found a likely site for the battle?

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  8. Nonlin.org: If 5% is useful and another 95% on top of that is “junk”, then your waste is 95/5 = 19. This is a whopping 1900% waste. Not a “measly” 95%.

    How did you get that 5%? Did you assume that the total number of base pairs in a gene add to 100%?!? DID YOU COUNT THEM?

    Now I want to play the creationist math game too. Lessee, according to that logic, 5/5 = 100% of all useful base pairs in a gene are useful. That is the bleedin’ maximum!

    This fact alone proves that evolution can account for ALL useful bases in a gene

    +4
  9. Flint: I’m totally unqualified to comment on Allan Miller’s charts.

    I agree the charts and their presentation is daunting but the underlying principle is, I think, fairly easy to grasp. When Linnaeus produced his tree of life, all he had available to base it on was similarities and differences between organisms, their shape and structure – morphology. Linnaeus’ tree has undergone many modifications and additions as our accumulated knowledge of life on Earth expands but the basic concept has remained valid.

    As offspring tend to resemble parents, the idea that traits are passed on, inherited, became an idea that Darwin articulated with such success.

    Mendelian genetics brought in the idea of transmissible units, genes.

    Discovery of what the vehicle of transmission is (DNA sequences in chromosomes) and the ability we now have to quickly and cheaply sequence whole genomes has added a huge database of knowledge. Simply by comparing and matching sequences and without any other information, it is possible to produce another tree of relatedness.

    https://www.biorxiv.org/content/biorxiv/early/2019/09/10/756155/F1.large.jpg?width=800&height=600&carousel=1

    I find it persuasive that the morphology tree and the sequence tree show huge similarity.

    +1
  10. Flint,

    Dembski was, as I recall, also asked to identify natural phenomena which are NOT designed. After all, any “viable way to detect design in nature” has to have SOME way to differentiate between things that are and are not designed. If you simply take the policy position that everything is designed, you aren’t detecting anything, you are only making a useless claim

    Everything is designed. ID is about design detection. Some artifacts exhibit a stronger design signal. ID is useful as a tool too demarcate things that may be out of the reach of science.

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  11. colewd: ID is about design detection. Some artifacts exhibit a stronger design signal.

    Do you have some examples of a couple of artifacts and can you show objectively that one “design signal” is “stronger” then the other?

    What units is this “design signal” measured in?

    Do you have a list of the items for which “design signals” have been determined?

    Do living organisms have stronger “design signals” then non-living objects? If so, how much stronger?

    Etc etc etc.

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  12. Nonlin.org: There’s an essay on ID. You can [still] comment there. This is Allan’s show… going down in flames.

    No, it’s an observation of fact. You don’t talk about what ID can do, ever, you only talk about your misunderstandings regarding evolution. If I thought you’d give examples of what ID can do and how/why/when I’d certainly ask on the “appropriate” thread. But we both know that’s not going to happen no matter where I ask, or you’d have done it already.

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  13. If ID is about “design detection” then when will it start doing that?

    colewd, recently you were asked about design detection and you responded with a video where you claim that Behe details the process.

    But when you are asked now you say:

    colewd: . Some artifacts exhibit a stronger design signal. ID is useful as a tool too demarcate things that may be out of the reach of science.

    But if you have information that “some artifacts” have a stronger signal then others that presupposes you have better data then a mere youtube video where the process of determining the strength of the signal is detailed.

    So you either have the specific details of “stronger signals” or you don’t. If you did, why did you link to the video instead of the details of where ID has determined that some things have “stronger signals” then other things?

    I’ll tell you why. It’s because you value making a “point” over the actual truth.

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  14. Alan Fox: How many more times? Science doesn’t deal in proofs.

    How many more times? “Evolution” is not science.

    Alan Fox: Nonlin.org: There’s an essay on ID.

    No there isn’t.

    Look it up and cut the crap.

    Alan Fox: On finding artefacts of the right age and type with the damage and distribution one finds at known sites, would I be affirming the consequent to provisionally declare I had found a likely site for the battle?

    Depends. Is that an ‘only if’? IOW, is there an alternate site?

    Corneel: This fact alone proves that evolution can account for ALL useful bases in a gene

    The fact that you think your argument is equivalent to mine is hilarious. You’re illogically jumping from genetics to “evolution”. I’m not.

    OMagain: If I thought you’d give examples of what ID can do and how/why/when I’d certainly ask on the “appropriate” thread.

    That’s your “thinking” problem.

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  15. Nonlin.org: “Evolution” is not science.

    Science is simply observing and measuring things. Counting offspring is a scientific endeavour. Proof doesn’t come into it.

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  16. Nonlin.org: Look it up and cut the crap.

    Nonlin refers to the non-existent theory of “Intelligent Design” and tells me to look it up. 🙄

    +2
  17. Nonlin.org: Depends. Is that an ‘only if’? IOW, is there an alternate site?

    In this case, anywhere on mainland Britain. For the the theory of evolution there must be alternative explanations for what we observe but I don’t know of one that is given serious consideration. Do you know of one?

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  18. Nonlin.org: The fact that you think your argument is equivalent to mine is hilarious.

    I don’t think anyone here considers what Corneel writes equivalent to what you write. 😅

    You’re illogically jumping from genetics to “evolution”. I’m not.

    You’re persistent in your wrongness, aren’t you? Genetics is the beating heart of evolutionary biology.

    +1
  19. Nonlin.org: That’s your “thinking” problem.

    That translates as “No, I can’t articulate an alternative to evolutionary theory”.

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  20. Alan Fox: I don’t think anyone here considers what Corneel writes equivalent to what you write.

    Still, Nonlin deserves credit for recognizing a parody for once. Also, he appears to have correctly reached the number 40 as the total of which two is 5%. I am mightily impressed!

    +2
  21. colewd: Everything is designed. ID is about design detection.

    But if everything is designed, what is the point of detecting it? I’ve tried a couple of sentences as follow-up but what else is there to say?

    +1
  22. Nonlin.org,

    Allan Miller: You’ll be able to tell me what it’s for on the ID viewpoint, then. And why it varies among species the way it does.

    Nonlin: You’re the one writing an OP. It’s your burden to prove something. Which you failed to do so far.

    Alternative hypotheses are very much relevant. The entire ID shtick is ‘not evolution therefore ID’. So we’re entitled to ask how that alternative provides a superior explanation.

    Allan Miller: How much waste (in your example).

    About 95% I’d say, given that you only really need the end sequences for neat excision, and assuming they aren’t self-splicing.

    Nonlin: Maybe that’s your problem, simple math. Let’s find your cure:
    If 5% is useful and another 95% on top of that is “junk”, then your waste is 95/5 = 19. This is a whopping 1900% waste. Not a “measly” 95%.

    That is an absurd way of calculating it. But whatevs, waste is waste. What’s it for?

    Of course that has a cost!

    In what terms does it have a cost? And how could an organism that shed the excess reap that cost? What mechanism could it exploit to gain an advantage? Huh? 🤔

    Imagine you had 40 hands only two of which were useful and the others just got in the way. Or your head was 20 times bigger with no increase brain power or visual, etc. acuity.

    This fact alone refutes “evolution”. For those smart enough to understand, that is.

    You would have to be incredibly dumb to think that refuted evolution.

    Allan Miller: An example without change denies change in all scenarios.

    Nonlin: Blatantly false.

    Indeed. And therefore your logic fails. Coffee/tea does not cover all design scenarios. Some of them involve change, even if coffee/tea doesn’t.

    Allan Miller: It’s not affirming the consequent, it is affirming consistency with the hypothesis.

    Nonlin: Of course it is. If that’s your only claim. To NOT be affirming the consequent, you need the ‘only if’ on top of the ‘if’.

    IOW, you need:
    “only if “evolution” were true, we would observe ABC, which we do”.
    But you can support exactly ZERO such claims.

    You’re gibbering.

    Allan Miller: Because genes ‘should’ be optimised for function. If that function is independent of morphology, then ‘why not’ is a massive cop-out.

    Nonlin: I gave examples from design. FO.

    You gave irrelevant analogies. SIUYA.

    Allan Miller: Why do nonmorphological and unexpressed genes follow morphological ones, if a Designer is at work? “That’s what a Designer would do, so Design it is”.

    Nonlin: It’s your OP. When will you defend your so-far-bogus claims?

    You don’t have many nails, do you?

    Allan Miller: You don’t even have an explanation, beyond “Why not?”.

    Nonlin: Whose OP is this again?

    It’s mine.

    Allan Miller: Translation: “I got nuthin’”

    Why “translation”? What part of “look it up”, you don’t understand?

    Haha! Just an endless succession of internet cliché. Like arguing with a basic ‘bot.

    Allan Miller: Can’t be arsed searching. If you have a question, ask away.

    Nonlin: Already did.

    I’m not going to put any effort into finding out what you want. You have a question, ask it.

    Allan Miller: “Why do ye elements combine in precise proportiiton, Mr Dalton?” “Why not?”.

    Nonlin: “Why not” is not an argument. It’s a counter to a stupid argument. Do you get the very important nuance?!?

    If that’s how one attacks stupid arguments, I will add it to my toolkit for addressing ID claims. But anyway, what’s stupid about noting, say, transition/transversion bias in genomes, and the fact that is also observed in vitro? ‘Why not’ is a feeble response.

    +2
  23. Corneel,

    Yes, I was tempted to go for another ‘100%’ gag! Funny that nonlin chooses to try and pull an attempt at mathematical superiority. Also, the expectation that selection would for-definite have eliminated that surplus implies he has some expectation that it should be subject to purifying selection, unless functional.

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  24. Flint:… detail that makes eyes glaze over.

    Ha, sorry! It’s a common problem. Anti-vax, unjustified enthusiasms for chloroquine and ivermectin, etc etc – it’s always simplistic proposal vs lengthy refutation. But it’s OK, you can say I’m wrong – that I’m ‘going down in flames’ – without knowing anything! 😁

    I’m interested in this sort of thing, but I’m totally unqualified to comment on Allan Miller’s charts. I would need several college semesters to grasp what terms like conversion, translation, transversion, and transitions even mean.

    Well, the basic principle is that the entire genome of DNA base pairs is copied in its entirety. The simplistic evolutionary expectation is thus that all parts of it should follow the same path, and hence conform to the same hierarchy, regardless what (if anything) they do. Linnaeus only had external form to go on, most of which is due to a subset of the subset of the genome that involves transcription (copying to RNA) and/or translation (converting RNA sequence to protein sequence). There’s no solid reason for things that don’t affect morphology to vary in line with those that do, beyond assuming whole-genome copying over the long term.

    Transition/transversion relates to the kinds of mutation that can occur. A and G are similar shapes, as are C and T. In the test tube, you get more mutational swaps between similar shapes than between different ones, in the ratio c2:1. You find a similar ratio when you look at both intra- and inter-species differences which proves evolution is true beyond any shadow of a doubt supports the evolutionary hypothesis.

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  25. Allan Miller: Also, the expectation that selection would for-definite have eliminated that surplus implies he has some expectation that it should be subject to purifying selection, unless functional.

    Are you implying that Nonlin made a *gasp* undisclosed assumption ?

    LOL. Loved the supernumerary hands bit btw. My inner biologist kept whispering “arthropods”.

    +1
  26. Corneel: Are you implying that Nonlin made a *gasp*undisclosed assumption ?

    Ha! Although now I’m cringing at the clumsiness of the sentence you quoted …

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  27. Allan Miller: Also wondering why he thinks I’m saying 95% in order to under-sell it …

    Because creationists like their numbers either really big or very very small. 1900% sounds twenty times as convincing as 95%.

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  28. Corneel: Because creationists like their numbers either really big or very very small. 1900% sounds twenty times as convincing as 95%.

    Leaving me twenty times as puzzled why God put it there. Still, there’ll be an analogy along in a bit to Explain All.

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  29. colewd to Flint,
    Everything is designed.

    If so then there would be no way to tell apart design from “nondesign.”

    colewd to Flint,
    ID is about design detection.

    This is nonsensical Bill. How can ID be about design detection if there’s nothing to contrast against design? Everything is designed, right?

    colewd to Flint,
    Some artifacts exhibit a stronger design signal.

    How could anything have different levels of design “signal” if everything is designed?

    colewd to Flint,
    ID is useful as a tool too demarcate things that may be out of the reach of science.

    This sentence doesn’t make sense. Leaving aside the incoherence of detecting design against a background of design, our own designs are within the reach of science. We can explain how we do it, we can explain where the energies come from, where the inputs and outputs, the behaviour of different materials, we can put it all together to improve our designs and efficiency. Design is not out of the reach of science.

    Furthermore, you’re admitting that ID is a god-of-the-gaps fallacy. While you said it poorly, what you wanted to say seems to be that ID is about finding gaps in scientific knowledge, gaps that are then filled in with “Intelligent Design”. We already knew it’s a god-of-the-gaps fallacy, but it seems like it’s taking too long to reach your mind. What I’m saying is that, even if you found it inexplicable that there’s such and such amount of information in biological systems, you’d be left with a gap in knowledge (mostly your gap, because the scientific community doesn’t have such a problem), and, even if the gap was shared by the whole scientific community, god-did-it would still be invalid as an “answer.” The best that could be done is “we’re still working on it”, or even a “we might never know.” But god-did-it? There’s no way to get there.

    Intelligent Design is not an answer either because our own intelligent designs rely, entirely, on the way nature works. Thus, intelligent design is also natural, and the information produced for and by our own designs cannot but be natural. Therefore, information cannot be out of the reach of nature.

    +2
  30. Allan Miller to Corneel:
    Leaving me twenty times as puzzled why God put it there. Still, there’ll be an analogy along in a bit to Explain All.

    The energetic costs for the extra amount of DNA have been calculated and shown to be minuscule compared to our metabolisms and many other activities. There’s also other things to consider. There’s no mechanisms for specifically deleting the extra DNA, transposons and retroviruses also evolve to become more efficient at inserting themselves into genomes, we don’t rely on the speed of our cell duplications at any stage in our development, reproduction, etc, in a way that extra DNA might slow down any of those processes, our populations are too small for random deletion of DNA to be a viable way to reduce it’s amount, etc.

    If we look at the DNA alone, it appears to be a lot of waste. If we look at the organism, the waste is minuscule and selectively neutral.

    +2
  31. Entropy: The energetic costs for the extra amount of DNA have been calculated and shown to be minuscule compared to our metabolisms and many other activities. There’s also other things to consider. There’s no mechanisms for specifically deleting the extra DNA, transposons and retroviruses also evolve to become more efficient at inserting themselves into genomes, we don’t rely on the speed of our cell duplications at any stage in our development, reproduction, etc, in a way that extra DNA might slow down any of those processes, our populations are too small for random deletion of DNA to be a viable way to reduce it’s amount, etc.

    If we look at the DNA alone, it appears to be a lot of waste. If we look at the organism, the waste is minuscule and selectively neutral.

    For sure. There’s also the selective issue – for a cost to be reaped or avoided, there has to be some kind of advantage (in terms of survival and reproduction) against current variants, not hypothetical ones. Incremental bloating is unlikely to be disadvantageous against variants in the population, even if complete removal from the endpoint would be hugely advantageous. Also there’s selection against excision because it buggers genes, and the fact that we eat organisms with bloated genomes, so get plenty of nucleotides in our diet.

    +1
  32. Alan Fox,

    Did I mention you’re clueless?
    Alan Fox,

    So is that “only if”?

    Allan Miller: So we’re entitled to ask how that alternative provides a superior explanation.

    When you theory fails, alternatives don’t even matter.

    Allan Miller: That is an absurd way of calculating it.

    In what terms does it have a cost?

    You’re absurd. And what a stupid question!

    Allan Miller: You would have to be incredibly dumb to think that refuted evolution.

    Like I said, if you’re not smart enough to understand that much, you’re beyond help.

    Allan Miller: Coffee/tea does not cover all design scenarios.

    What a stupid thing to say! From the guy that thinks everything is “change”.

    Allan Miller: You’re gibbering.

    I knew logic is gibberish to you.

    Allan Miller: You have a question, ask it.

    I would if I expected any logic from you.

    Allan Miller: Nonlin: “Why not” is not an argument. It’s a counter to a stupid argument. Do you get the very important nuance?!?

    If that’s how one attacks stupid arguments, I will add it to my toolkit for addressing ID claims.

    The fact that you learn this from me – now – at your very advanced age, should be fucking embarrassing to you. Still, it’s much better than resisting knowledge as you most often do.

    Allan Miller: Also, the expectation that selection would for-definite have eliminated that surplus implies he has some expectation that it should be subject to purifying selection, unless functional.

    Corneel: Are you implying that Nonlin made a *gasp* undisclosed assumption ?

    What a dumb thing to say! Of course, one refutes nonsense by showing an incompatibility between that nonsense (if it were true!) and reality. It’s SOP. And another basic thing you’re just learning from me?!?

    Allan Miller: You find a similar ratio when you look at both intra- and inter-species differences which proves evolution is true beyond any shadow of a doubt supports the evolutionary hypothesis.

    Doesn’t follow.

    Corneel: Allan Miller: Also wondering why he thinks I’m saying 95% in order to under-sell it …

    Because creationists like their numbers either really big or very very small. 1900% sounds twenty times as convincing as 95%.

    Desperation masquerading as cluelessness? Hilarious either way.

    Allan Miller: There’s also the selective issue – for a cost to be reaped or avoided, there has to be some kind of advantage (in terms of survival and reproduction) against current variants, not hypothetical ones. Incremental bloating is unlikely to be disadvantageous against variants in the population, even if complete removal from the endpoint would be hugely advantageous. Also there’s selection against excision because it buggers genes, and the fact that we eat organisms with bloated genomes, so get plenty of nucleotides in our diet.

    What a load of crap! Haha.

    0
  33. Nonlin.org: When you theory fails, alternatives don’t even matter.

    If there is no alternative that better explains the data we will stick with the failing theory until something better comes along. After all, that theory exists in the first place because it has explanatory power, even if it’s ‘wrong’. i.e does not model every data point.

    Until there was something better than Newton’s laws that was all we had, even if we found out that it was a failing theory in that it could not/did not describe reality as we then observed it. Until something else came along it was all there was.

    So, yes, alternatives matter. We all know why you keep saying they do not 🙂

    Those ‘gaps’ or failures spur those who notice them and who are so inclined to come up with a better theory. But that’s not you, is it? After all, alternatives don’t even matter right? So, why would you bother? You can achieve your aims by denigrating ‘evolution’ to the point of absurdity. But you can do that for the rest of your life and you won’t advance the cause for an alternative theory one jot, that’s simply not how it works.

    If your theory explains the data better then others then people will swarm to your theory. Scientists are selfish like that. But it seems you won’t even try.

    I’ve looked at your website for your alternative. It seems to be just “Intelligence Design” which as we all know explains nothing. If it did, well, you could link to it. You can’t.

    0
  34. Nonlin.org: What a load of crap! Haha.

    What a stunning rejoinder. It’s actually surprising to me anyone is still bothering with you. But such is the nature of chew-toys, they are designed to be chewed….

    0
  35. Nonlin.org: Of course, one refutes nonsense by showing an incompatibility between that nonsense (if it were true!) and reality. It’s SOP. And another basic thing you’re just learning from me?!?

    So, you are telling us that an idea can be tested by assuming, arguendo, that it is true and exploring the consequences? This is the “Standard Operating Procedure”?
    That’s a very interesting idea…
    ROFL

    +1
  36. Nonlin.org: So is that “only if”?

    Ah, I see I did not spell things out clearly enough for you with my reply “anywhere in mainland Britain”.

    The battle of Brunanburh is recorded in many near contemporary and later sources as occurring in 937 between Saxon forces led by King Æthelstan of Wessex and an alliance of Welsh, Scottish and Norse Irish forces. The site of the battle remains unknown though many possible locations have been proposed. The historical sources mention several names but none that can be clearly associated with a known location. So it is only possible to infer two possibilities; that the battle was fictional and all historical accounts are false, that the battle took place in which case all sources broadly agree on the location (somewhere in mainland Britain), the protagonists and the outcome.

    But many candidate sites have been proposed for the battle. So until or unless archaeological evidence turns up with artefacts of the correct period (late Saxon), such as weaponry carrying damage caused by combat, human remains with appropriate injuries (the battle site at Waterloo was a lucrative source for false teeth), anyone is able to hypothesize using what historical sources is available to propose a likely site. Using simple logic such as picking a point where the combatants would have all been able to get to reasonably easily (the Irish Norse came by ship from Ireland, Scots and Strath Clota Welsh from Scotland and the Saxons from Mercia and Wessex which suggests somewhere in the northwest). Some archaeological finds turn up in construction sites and, I hear, some intriguing finds have been made in the Wirral, a peninsular between the rivers Dee and Mersey. Should those finds turn out to be Saxon, Norse and Celtic and datable to around 937 AD that would strengthen the hypothesis that the battle of Brunanburh took place on the Wirral. I would not call that assuming the consequent, nor would it prove that the battle took place there. But in the absence of similar evidence from other locations, it would be a reasonable conclusion.

    That was an analogy. Similarly, modern evolutionary theory is one explanation for the observation of common descent, adaptation, speciation and extinction. There may be other theories but I’m not aware of any that fit the data as neatly as evolutionary theory does. To be fair, I’m unaware of any theory other than evolutionary theory that fits the data at all.

    0
  37. Sadly, we tried to explain this to nonlin back when he was ‘assuming the consequent’.
    His demand for “if and only if” is his way of noting that
    P1} If evolution then X,
    P2} X
    C} therefore evolution
    is assuming the consequent.
    whereas
    P1} If not evolution, then not X,
    P2} X
    C} therefore evolution
    is modus tollens
    Because he is stuck with propositional logic and thus “proof”, he is incapable of understanding that science works as follows:
    P1} If evolution, then X likely
    P2} If not evolution, then X unlikely
    P3} X
    C} therefore evolution more likely than it was before.
    Lather, rinse, repeat.
    Bayes, baby.

    0
  38. Nonlin.org,

    Allan Miller: So we’re entitled to ask how that alternative provides a superior explanation.

    Nonlin: When you theory fails, alternatives don’t even matter.

    Very coy about exposing ID to any scrutiny, aren’cha? Of course alternatives matter. If a theory fails, it needs something else.

    Allan Miller: That is an absurd way of calculating it.

    In what terms does it have a cost?

    You’re absurd.

    Fuck me, the “no you are” defence. My now-grown-up kids still say this to each other, intended ironically now.

    Allan Miller: Coffee/tea does not cover all design scenarios.

    Nonlin: What a stupid thing to say! From the guy that thinks everything is “change”.

    No, just that it is a perfectly reasonable word when comparing two highly similar but not identical genetic sequences. I know you don’t know what I’m talking about there. Science hurts the noggin. Don’t you worry about it; stick with analogies.

    Allan Miller: Nonlin: “Why not” is not an argument. It’s a counter to a stupid argument. Do you get the very important nuance?!?

    Me: If that’s how one attacks stupid arguments, I will add it to my toolkit for addressing ID claims.

    Nonlin: The fact that you learn this from me – now – at your very advanced age, should be fucking embarrassing to you. Still, it’s much better than resisting knowledge as you most often do.

    I was being ironic. As usual, sails right over your tiny head. ‘Why not?’ is generally a moronic riposte in response to a question regarding a phenomenon. I wouldn’t dream of using it ordinarily. But if you think it’s a killer, I’ll give it a whirl. Why not?

    Allan Miller: You find a similar ratio when you look at both intra- and inter-species differences which supports the evolutionary hypothesis.

    Nonlin: Doesn’t follow.

    Why not?

    Allan Miller: There’s also the selective issue – for a cost to be reaped or avoided, there has to be some kind of advantage (in terms of survival and reproduction) against current variants, not hypothetical ones. Incremental bloating is unlikely to be disadvantageous against variants in the population, even if complete removal from the endpoint would be hugely advantageous. Also there’s selection against excision because it buggers genes, and the fact that we eat organisms with bloated genomes, so get plenty of nucleotides in our diet.

    Nonlin: What a load of crap! Haha.

    You’re not even trying. You just feel you have to roll up every day and say … something. To everything. Well done. ‘Something’ duly noted.

    0
  39. Nonlin.org: What a dumb thing to say! Of course, one refutes nonsense by showing an incompatibility between that nonsense (if it were true!) and reality. It’s SOP. And another basic thing you’re just learning from me?!?

    Heh, yes, assuming the truth of a proposition to explore its entailments, indeed. SOP. I’ve been doing that quite a lot, and you’ve been pretty sniffy about it, Mr Consistency. But yeah, I just learned it from you, pat-pat-pat.

    So what’s incompatible between introns and evolution? Show your working, don’t just flap your arms.

    And introns and ID. Let’s assume its truth for an exploratory moment and wonder why they are such a large part of a protein coding region. Why not, you say? 🤔

    +1
  40. Allan Miller: You’re not even trying. You just feel you have to roll up every day and say … something. To everything. Well done. ‘Something’ duly noted.

    This is exactly my impression. Communication? Exchange of ideas? Attempting to understand other viewpoints? Is it an unattainable ideal?

    +1
  41. DNA_Jock: Because he is stuck with propositional logic and thus “proof”, he is incapable of understanding that science works as follows:
    P1} If evolution, then X likely
    P2} If not evolution, then X unlikely
    P3} X
    C} therefore evolution more likely than it was before.
    Lather, rinse, repeat.
    Bayes, baby.

    Likelihood even!

    https://en.wikipedia.org/wiki/Likelihood_function

    0
  42. DNA_Jock: So, you are telling us that an idea can be tested by assuming, arguendo, that it is true and exploring the consequences?

    Is that what you understand?!? Sad and funny!

    I notice you struggle with logic, and sometimes with math. You failed the “affirming the consequent” class, if my recollection is correct. Now, would you like me to explain it one more time? Will that help you, with a little extra effort on your part that is?

    DNA_Jock: P1} If evolution, then X likely
    P2} If not evolution, then X unlikely
    P3} X
    C} therefore evolution more likely than it was before.

    Very good. Let’s have some fun with numbers:
    1. “Likely” = 100%
    P1} If evolution, then “the sun WILL rise tomorrow”
    P2} If not evolution, then “the sun will NOT rise tomorrow”
    P3} The sun rose
    C} therefore evolution “true”???

    2. “Likely” = 0%
    P1} If evolution, then “the sun will NOT rise tomorrow”
    P2} If not evolution, then “the sun WILL rise tomorrow”
    P3} The sun rose
    C} therefore evolution “false”???

    Now you may ask: what has the sun rising to do with “evolution”? Indeed, what? And what has “evolution” to do with genetics? If you want to apply Bayes, then you need to have some numbers. Else the formula doesn’t work. What is P(sunrise | “evolution”) again? Haha.

    And of course, P2} is the ‘only if’ that I keep asking for. With a “likely” indulgence that is. Ok, fine. But where exactly is that P2} in “evolution”? Even in this attenuated form? I’d like to see ONE (1) statement anywhere of the type:
    “P2} If not evolution, then X unlikely”
    One that is backed by observations (not bullshit of the “Precambrian rabbit type!) that is. Can anyone show ONE?

    In this particular thread, the argument is (http://nonlin.org/consequent/): b. If “evolution” is true, organisms are genetically similar. Organisms are genetically similar. Therefore “evolution” is true.
    Well, if it isn’t case 1 above with “Likely” = 100%! Does this also read like ‘affirming the consequent’ to anyone else (which is nothing but the above without P2})? Because it sure does to me.

    0
  43. OMagain: If there is no alternative that better explains the data we will stick with the failing theory until something better comes along.

    Aside from being stupid, this is historically and factually false.
    Alan Fox,

    Sorry, I fell asleep half through. Was that an ‘only if’ or not?

    Allan Miller: Of course alternatives matter. If a theory fails, it needs something else.

    1. First, you must admit “theory fails”. As proved.
    2. Second, “something else” has existed from way before the failed theory. And “something else” was never disproved like your failed theory is.

    Allan Miller: I don’t see how ‘design’ evades the supposed logic trap.

    Look it up in my OP on ID. I’m steering clear of your bad argument. And when I claim “only if’ (as one MUST), I prove ‘only if’. It’s fucking elementary.

    Allan Miller: So what’s incompatible between introns and evolution? Show your working, don’t just flap your arms.

    The argument was very clear and backed by numbers. I can’t help it if you reject the basic math and logic. The conversation stops.

    Allan Miller: And introns and ID. Let’s assume its truth for an exploratory moment and wonder why they are such a large part of a protein coding region. Why not, you say?

    No. I don’t say “why not”. I say “Focus! This is your OP to defend”. When I write something, it’s rock solid (assuming we speak the same math and basic science language).

    Allan Miller: ‘Why not?’ is generally a moronic riposte in response to a question regarding a phenomenon. I wouldn’t dream of using it ordinarily. But if you think it’s a killer, I’ll give it a whirl. Why not?

    Sure is a killer of bad “theories” like your. That’s why you believe the stupid myth of “evolution”. Because you never ever asked “why not” before.

    0
  44. Nonlin.org: Was that an ‘only if’ or not?

    You are the one claiming “affirming the consequent” has some relevance. You tell me. If you can’t do your own analysis, why should I begin to take you seriously?

    0
  45. Nonlin.org,

    Allan Miller: Of course alternatives matter. If a theory fails, it needs something else.

    Nonlin: 1. First, you must admit “theory fails”. As proved.

    Well, I’ve tried ‘admitting’ it fails, but you didn’t believe me. That puts us at a bit of a convenient impasse as regards addressing your alternative. It’s a weird approach anyway, and a transparent dodge. If you were arguing for Theory B, you wouldn’t first explain why Theory A fails and then stop. Well, you would if you were a peddler of ID guff, I suppose, since that is SOP.

    2. “Something else” has existed from way before the failed theory. And “something else” was never disproved like your failed theory is.

    So let’s examine how ‘something else’ addresses introns, the widespread correlation of metabolic genes with morphological ones, or transition/transversion bias. And not by analogy; directly. None of this is in the Bible or Paley.

     

    Allan Miller: I don’t see how ‘design’ evades the supposed logic trap.
    Nonlin: Look it up in my OP on ID.

    Hahahaaa! You think I’m going to put some effort into finding the answer in your Collected Works! That’s cute.

    I’m steering clear of your bad argument. And when I claim “only if’, I prove ‘only if’. It’s fucking elementary.

    Shit analogies are not proof.

    Allan Miller: So what’s incompatible between introns and evolution? Show your working, don’t just flap your arms.
    Nonlin: The argument was very clear and backed by numbers.

    Backed by numbers? That is pathetic. You turned 95% into the arithmetically related 1900% ((95/(100-95))*100) to make it look bigger. Which demonstrated nothing. It’s a puzzle to be explained, however you choose to express the fraction. I explained why evolution would not be expected to remove the excess, and you just blinked. You hate evolution so much, you can’t bear to correctly characterise it in order to address its entailments.

    I can’t help it if you reject the basic math and logic. The conversation stops.

    Awwww. Just when it was getting interesting! 🙄

    Allan Miller: And introns and ID. Let’s assume its truth for an exploratory moment and wonder why they are such a large part of a protein coding region. Why not, you say?

    Nonlin: No. I don’t say “why not”. I say “Focus! This is your OP to defend”.

    If you reject the evolutionary expectations, which I have defended at length, the same data requires explanation (bearing in mind analogies are not explanations). It doesn’t help that you clearly don’t even understand the data I’m referring to.

    When I write something, it’s rock solid (assuming we speak the same math and basic science language).

    We don’t, clearly. It does resemble a rock, I grant you that.

     

    Allan Miller: ‘Why not?’ is generally a moronic riposte in response to a question regarding a phenomenon. I wouldn’t dream of using it ordinarily. But if you think it’s a killer, I’ll give it a whirl. Why not?

    Nonlin: Sure is a killer of bad “theories” like your. That’s why believe the stupid myth of “evolution”. Because you never ever asked “why not” before.

    That’s because I have more satisfactory tools at my disposal. But I thought I’d try your approach on for size, see how you like it when reflected back.

    +1
  46. Nonlin.org: Aside from being stupid, this is historically and factually false.

    For example?

    Can you point to where some model that explains some observed data has been abandoned in favour of nothing at all?

    narrator: He never did.

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