The Demise of Intelligent Design

At last?

Back in 2007, I predicted that the idea of “Intelligent Design” would soon fade into obscurity. I wrote:

My initial assessment of ID in my earliest encounter with an ID proponent* was that ID would be forgotten within five years, and that now looks to me an over-generous estimate.

*August, 2005

I was wrong. Whilst the interest in “Intelligent Design” (ID) as a fruitful line of scientific enquiry has declined from the heady days of 2005 (or perhaps was never really there) there remain diehard enthusiasts who maintain the claim that ID has merit and is simply being held back by the dark forces of scientism. William Dembski; the “high priest” of ID has largely withdrawn from the fray but his ideas have been promoted and developed by Robert Marks and Winston Ewert. In 2017 (with Dembski as a co-author) they published Introduction to Evolutionary Informatics, which was heralded as a new development in the ID blogosphere. However, the claim that this represents progress has been met with scepticism.

But the issue of whether ID was ever really scientific has remained as the major complaint of those who dismiss it. Even ID proponents have admitted this to be a problem. Paul Nelson, a prominent (among ID proponents) advocate of ID famously declared in 2004:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’ – but, as yet, no general theory of biological design.

Whilst some ID proponents – Ann Gauger, Douglas Axe are perhaps most prominent among them – have tried to develop ID as science, the general scientific community and the wider world have remained unimpressed.

Then a new young vigorous player appears on the field. Step forward, Eric Holloway! Dr Holloway has produced a number of articles published at Mind Matters – a blog sponsored by the Discovery Institute (the paymasters of ID) on artificial and “natural” intelligence. He has also been quite active here and elsewhere defending ID and I have had to admire his persistence in arguing his case for ID, especially as the whole concept is, in my view, indefensible.

But! Do I see cracks appearing? I happened to glance at the blog site formerly run by William Dembski, Uncommon Descent, and noticed an exchange of comments on a thread entitled Once More from the Top on “Mechanism” The post author is Barry Arrington, current owner of UD and a lawyer by trade, usually too busy to produce a thoughtful or incisive piece (and this is no different). However, the comments get interesting when Dr Holloway joins in at comment 48. He writes:

If we can never be sure we account for all chance hypotheses, then how can we be sure we do not err when making the design inference? And even if absolute certainty is not our goal, but only probability, how can we be confident in the probability we derive?

Eric continues with a few more remarks that seem to raise concern among the remaining regulars. ( ” Geeze you are one confused little pup EricMH.” “Has a troll taken over Eric’s account?) and later comments:

But since then, ID has lost its way and become enamored of creationism vs evolution, apologetics and the culture wars, and lost the actual scientific aspect it originally had. So, ID has failed to follow through, and is riding on the cultural momentum of the original claims without making progress.

Dr Holloway continues to deliver home truths:

I would most like to be wrong, and believe that I am, but the ID movement, with one or two notable exceptions, has not generated much positive science. It seems to have turned into an anti-Darwin and culture war/apologetics movement. If that’s what the Discovery Institute wants to be, that is fine, but they should not promote themselves as providing a new scientific paradigm.

I invite those still following the fortunes of ID to read on, though I recommend scrolling past comments by ET and BA77. Has Dr Holloway had a road-to-Damascus moment? Is the jig finally up for ID? I report – you decide!

ETA link

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823 thoughts on “The Demise of Intelligent Design

  1. And Nelson does it again here: https://youtu.be/Mf01GXUl-mg?t=2650

    Ohh!!! The authors are so puzzled! this should be impossible if common descent is true! Let’s put aside the fact the they actually advance an explanation for DNA topoisomerase V.

    Facts:
    – Nelson never tells us why orphans should be impossible if common descent is true
    – Nelson only provides “testimony” from apparently puzzled scientists
    – Nelson doesn’t even mention the explanations offered by the authors he quotes, ignoring their work and why they don’t actually believe there’s a problem with CD.
    – Nelson fails to look at the big picture, as if orphan genes are going to make the other 80% of genes go away magically.
    – Nelson offers no alternative scientific explanation for ANY of the things he presents as problems to common descent, except for the omnipresent, IDiotic, argument from analogy

    Just another day in the creationist office. Yawn

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  2. Corneel: Do you agree the nested hierarchy of species exists?

    1. As a convenient informational retrieval system? Sure. (See the NCBI nested hierarchy in daily use at GenBank, for instance.)

    2. As a reliable predictor of characters yet to be observed? Hell no. Assume UCD and CD, and anything can happen along the branches of a phylogeny.

    If the nested hierarchy could perform at task (2), Joe Felsenstein should have been able to ace my little thought experiment, with a perfect score.

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  3. BruceS: Any stochastic/deterministic processes can be simulated on TM but human intelligence cannot according to Eric. Hence intelligence could produce non-stochastic processes, according to Eric.

    I’m usually amused (sometimes irritated) when Intelligent Design advocates are so certain that “intelligence” could not possibly be simulated on a Turing machine. This despite that the ID, rather ironically, at no point has ever developed a theory of what intelligence is or what design is. ID proponents have no understanding at all that there are whole branches of study devoted to understanding intelligence and understanding design, and needless to say there is no serious interest in understanding how laws of physics work or whether there is a computational description of neurophysiological activity. Yet despite their vast and nearly total ignorance, they insist that ID is a scientific theory and that the burden is entirely on those who maintain otherwise. And that is why ID belongs in the same Big Tent with astrology, phrenology, and homeopathy — with cranks and quacks of every appellation.

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  4. Paul Nelson: 1. As a convenient informational retrieval system? Sure. (See the NCBI nested hierarchy in daily use at GenBank, for instance.)

    2. As a reliable predictor of characters yet to be observed? Hell no. Assume UCD and CD, and anything can happen along the branches of a phylogeny.

    If the nested hierarchy could perform at task (2), Joe Felsenstein should have been able to ace my little thought experiment, with a perfect score.

    Thanks. In line with the general theme of this thread, do you believe that Design theory has to come up with an alternative explanation to common descent in explaining the nested hierarchy? If so, what alternative would you propose?

    As an aside: your #1 and #2 contradict, since you cannot build a classification system without it being informative with respect to the characters used to make the classification.

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  5. Kantian Naturalist,

    Oh what silly nonsense. If you are claiming intelligence is well studied and understood, why in the world would they need their own unique definition of it to claim a Turing machine can’t produce it? You have already said it is understood.

    You are not a serious thinker so you don’t get to decide where ID belongs. Your post is quackery.

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  6. Kantian Naturalist: I’m usually amused (sometimes irritated) when Intelligent Design advocates are so certain that “intelligence” could not possibly be simulated on a Turing machine. This despite that the ID, rather ironically, at no point has ever developed a theory of what intelligence is or what design is. ID proponents have no understanding at all that there are whole branches of study devoted to understanding intelligence and understanding design, and needless to say there is no serious interest in understanding how laws of physics work or whether there is a computational description of neurophysiological activity. Yet despite their vast and nearly total ignorance, they insist that ID is a scientific theory and that the burden is entirely on those who maintain otherwise. And that is why ID belongs in the same Big Tent with astrology, phrenology, and homeopathy — with cranks and quacks of every appellation.

    The point is that in order to create information we need something that is non-stochastic, a halting oracle, etc. Stochastic processes cannot create CSI type information metrics, which is well defined and proven in traditional information theory without having to bring ID into the picture. We perceive there is CSI all around us, and humans appear to generate gobs of it, so we must infer there is a non-stochastic process behind it all, either proximately in the human mind, or ultimately in some meta-mind. But somewhere there must be a non-stochastic process terminating the chain. It is simple logical deduction.

    Fields that try to reduce intelligence and design to stochastic processes are merely missing the big question: where does the information come from, since it cannot be stochastic processes? It doesn’t matter whether these other fields use the same words ‘mind’ ‘design’ ‘intelligence’ etc. Behind the words there is a fundamental problem, and ID is trying to solve the problem, or at least eliminate incorrect solutions such as Darwinism and methodological naturalism so the door is opened to better ideas. I don’t see any other disciplines addressing this big question. They are just using buzzwords to get grant money, and are not bold enough to look outside the stochastic presumption. Or, more cynically, it is precisely the impossibility of the endeavor that makes it attractive, since a problem that is never solved is a bottomless source of funding. It is the old proverb of people only looking for their keys under the streetlight, when they need to get a flashlight and look in their front lawn, or perhaps just reach into their pocket. If you are then paying some contractors to find your keys under the streetlight, they are not going to tell you the key is not there, because that would end their contract.

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  7. Corneel,

    As an aside: your #1 and #2 contradict, since you cannot build a classification system without it being informative with respect to the characters used to make the classification.

    The classification system is built primarily on the signal and not the noise. It can be informative but not reliably predictive depending on how much noise there is.

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  8. colewd: He just does not understand the limits of his knowledge.

    BWAHAHAHAHA!

    Bill are you trying to break every Irony-meter on the whole planet? 😀

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  9. colewd:
    keiths,

    I listened to the part about Weiss this am.There maybe some subtile spin in his comment.Is there anyone here who has not used some spin in their arguments.

    LOL! Here we go again. It’s not to quote-mine and drastically misrepresent what a scientist actually believes, it’s just “subtle spin”.

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  10. Dazz:

    Let’s put aside the fact the they actually advance an explanation for DNA topoisomerase V.

    I didn’t mention Patrick Forterre’s explanation, because it doesn’t actually solve the problem — it only moves the puzzle to the virosphere, where orphans predominate. The actual origin of Topo V is still unknown.

    Here’s what Forterre hypothesized, in the 2006 paper I cited (my emphasis):

    “The restricted phylogenetic distribution of Topo V raises the question of its origin: if Topo V is such a wonderful enzyme, why was Mother Nature so mean as to limit its presence to a single archaeal species? Considering the extreme complexity of Topo V, it cannot have originated from scratch in the M. kandleri lineage. At this point, it should be acknowledged that without the pioneering biochemical work of Alexei Slesarev and co-workers, Topo V would only be another of the myriad of orphan proteins that populate the genosphere, and whose number increases linearly with the sequencing of new genomes. In my opinion, many of these orphans might have a viral origin, in agreement with the huge number of viruses in the biosphere and in line with the fact that most genes encoded in the genomes of large DNA viruses have no homologues in current databases. In such a scenario, Topo V might have been recently transferred from a virus to the archaeal lineage leading to M. kandleri.”

    (From P. Forterre, “DNA topoisomerase V: a new fold of mysterious origin,” Trends in Biotechnology 24 [2006]:24-27; p. 25)

    dazz continues:

    – Nelson never tells us why orphans should be impossible if common descent is true

    Since common descent doesn’t rule out anything, orphans are entirely possible if common descent is true. So is their absence, which was the case prior to the mid-1990s, and the DNA sequencing revolution. When someone can tell me what UCD forbids, and why…we might be able to see if orphans should exist or not.

    – Nelson only provides “testimony” from apparently puzzled scientists

    All the scientists I know are puzzled by something: it’s part of their job description (problem-solving).

    – Nelson doesn’t even mention the explanations offered by the authors he quotes, ignoring their work and why they don’t actually believe there’s a problem with CD.

    Questioning UCD / CD is a rare move in evolutionary theory, for all sorts of reasons. Earlier in the talk, I explain why UCD / CD have the centrality they do, in the thinking of most biologists. But the whole point of my talk is to suggest that biologists now have data which should lead them to ask questions about UCD / CD — which, while still a minority move, is happening with increasing frequency.

    But the viewer of the my talk should not need me to hold his hand, and reassure him that all is well with his favorite theory, UCD / CD. All is not well.

    – Nelson fails to look at the big picture, as if orphan genes are going to make the other 80% of genes go away magically.

    Most genes are orphans. You need to turn your percentages around. Looking just at prokaryotes:

    “These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes…The ORFans represent the bulk of the genes in the microbial genomic universe. Considering their extremely rapid turnover revealed here, taking into account the available estimates of the total number of microbial species and extrapolating the present findings to bacteria, we roughly estimate the size of this universe. Conservatively assuming 10exp6 to 10exp7 microbial species (some recent estimates are as high as 10exp11 species), an average genome size of 2,000 genes and 10% of ORFans without overlap between species, the genetic universe can be estimated to consist of at least 2 × 10exp8 to 2 × 10exp9 unique genes.”

    Yuri I. Wolf et al., “Two fundamentally different classes of microbial genes,” Nature Microbiology 7 Nov 2016, pp. 1-6; p. 1, 3.

    – Nelson offers no alternative scientific explanation for ANY of the things he presents as problems to common descent, except for the omnipresent, IDiotic, argument from analogy

    Point taken, dazz. (long sigh) My talk failed to spell out any ID approach to the same data. Bad habits (bash the mainstream theory, call it a day) die hard.

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  11. Bill doing what Bill does. He’s bought Nelson’s crap wholesale and he’s now parroting his signal-to-noise slogan as if he knew what it means

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  12. Adapa,

    LOL! Here we go again. It’s not to quote-mine and drastically misrepresent what a scientist actually believes, it’s just “subtle spin”

    People will ignore your and Dazz’s failing attempt to discredit Paul. But feel free to keep at it. It is entertaining 🙂 As an alternative you guys could try and understand the substance of his arguments.

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  13. Adapa: An honest person did.A dishonest Creationist knee-jerk defends another dishonest Creationist quote-miner without bothering to read the thread or watch the video in question.

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  14. colewd: The classification system is built primarily on the signal and not the noise. It can be informative but not reliably predictive depending on how much noise there is.

    I think the problem word here is “reliably”.

    Suppose you were to ask me who is the taller person, Sam or Kim. As an additional piece of information you tell me that Sam is a man and Kim is a woman. Can I now “reliably” predict who is the tallest? Given the standard you and Paul hold me to, a perfect score, probably not.

    Yet men as a group are still taller than women. This is a solid fact, despite the fact that one can pick lots of “surprising” examples.

    Welcome to the wonderful world of statistical thinking.

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  15. dazz,

    Bill doing what Bill does. He’s bought Nelson’s crap wholesale and he’s now parroting his signal-to-noise slogan as if he knew what it means

    Why don’t you first try to understand the arguments. You last comment looked like the product of a pre schooler.

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  16. Corneel,

    I think the problem word here is “reliably”.

    Suppose you were to ask me who is the taller person, Sam or Kim. As an additional piece of information you tell me that Sam is a man and Kim is a woman. Can I now “reliably” predict who is the tallest? Given the standard you and Paul hold me to, a perfect score, probably not.

    Yet men as a group are still taller than women. This is a solid fact, despite the fact that one can pick lots of “surprising” examples.

    Welcome to the wonderful world of statistical thinking.

    This would be more interesting if you could tie the analogy to heredity.

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  17. Paul Nelson:
    Memo to the Quote-Mining Thought Police:

    Memo to dishonest quote-mining Creationists:

    Why didn’t Nelson provide this Weiss assessment in his Creationist lecture?

    [2]”Whatever the specifics, orphan genes are exceptions that test the rule, because the only reason they’re recognized in the first place is that they are genes: they have the sequence-based structures of coding regions, splicing, transcription start and stop signals, and so on, as we know them from the rest of life. So while they may be unique in the world today, they were not dropped to earth from outer space. Orphan genes require no suspension of the rules of life and make no rent in the connected fabric of life. Indeed, understanding them actually shows the Darwinian method in action.”

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  18. colewd: This would be more interesting if you could tie the analogy to heredity.

    … which Joe did.

    Joe Felsenstein: Thanks Paul, but no, I won’t do that. It would be too easy for you to pick and choose among cases and present me only with ones where there were surprising differences. Similarly, on a smaller scale, I could present you with sites in a stretch of DNA where humans had “A”, and ask you to guess the base in the Chimpanzee. And it would always not be “A”, if I chose the right sites.

    Of course if I chose the sites more representatively, “A” would be more common than “C” or “G” or “T”. Have your students tried cases like that? Have they also tried to see whether the trees inferred from one protein locus are very similar to the trees inferred from others? I know a data set with about 14,000 protein loci, each of which is aligned across 116 mammalian species, and which has trees automatically inferred for each locus. Your students might look at those trees to see whether, say, apes and humans form a clade on them. Or whether they are all wildly different.

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  19. colewd:
    dazz,

    Why don’t you first try to understand the arguments.You last comment looked like the product of a pre schooler.

    Or you could try to understand the solid rebuttal half a dozen people have explained to you instead of doing your usual Bill hand-waving denial.

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  20. dazz[1]: Let’s put aside the fact the they actually advance an explanation for DNA topoisomerase V.

    Facts:
    [2]– Nelson never tells us why orphans should be impossible if common descent is true
    [3]– Nelson only provides “testimony” from apparently puzzled scientists
    [4]– Nelson doesn’t even mention the explanations offered by the authors he quotes, ignoring their work and why they don’t actually believe there’s a problem with CD.
    [5]– Nelson fails to look at the big picture, as if orphan genes are going to make the other 80% of genes go away magically.
    [6]– Nelson offers no alternative scientific explanation for ANY of the things he presents as problems to common descent, except for the omnipresent, IDiotic, argument from analogy

    1. I didn’t mention Forterre’s explanation for the origin of Topo V, because it doesn’t actually solve the problem, but simply moves the puzzle to the virosphere, where orphans predominate. Here’s what Forterre hypothesized in 2006 (my emphasis):

    “The restricted phylogenetic distribution of Topo V raises the question of its origin: if Topo V is such a wonderful enzyme, why was Mother Nature so mean as to limit its presence to a single archaeal species? Considering the extreme complexity of Topo V, it cannot have originated from scratch in the M. kandleri lineage. At this point, it should be acknowledged that without the pioneering biochemical work of Alexei Slesarev and co-workers, Topo V would only be another of the myriad of orphan proteins that populate the genosphere, and whose number increases linearly with the sequencing of new genomes. In my opinion, many of these orphans might have a viral origin, in agreement with the huge number of viruses in the biosphere and in line with the fact that most genes encoded in the genomes of large DNA viruses have no homologues in current databases.

    2. Orphans may be entirely possible if common descent (meaning universal common descent, UCD) is true. So is their total absence, which was the case before the mid-1990s, and the DNA sequencing revolution. We can only know if orphans are possible, or not, when we know what UCD rules out, which is not the case today.

    3. Every scientist I know is puzzled by something. Comes with the job description (you know — problem-solving and all that).

    4. As I noted with Forterre’s explanation for the origin of Topo V, the “solutions” offered don’t actually address the deeper puzzle: where the gene and its protein product come from? And I explained the centrality of UCD / CD in my talk, so its status as an empirical given for most evolutionary biologists is not at issue. The viewer should not need me to hold his or her hand, however, reassuring them that all is well with UCD. All is not well.

    5. Most genes are orphans. You need to turn your percentages around. Looking just at the prokaryotic genomic universe, for instance:

    “These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes…The ORFans represent the bulk of the genes in the microbial genomic universe. Considering their extremely rapid turnover revealed here, taking into account the available estimates of the total number of microbial species and extrapolating the present findings to bacteria, we roughly estimate the size of this universe. Conservatively assuming 10exp6 to 10exp7 microbial species (some recent estimates are as high as 10exp11 species), an average genome size of 2,000 genes and 10% of ORFans without overlap between species, the genetic universe can be estimated to consist of at least 2 × 10exp8 to 2 × 10exp9 unique genes.”

    (Yuri Wolf et al., 2016, “Two fundamentally different classes of microbial genes,” Nature Microbiology 7 November, pp. 1-6; p. 1, p. 3)

    6. Point taken, dazz. (long sigh here) My talk failed to give a coherent ID account of the same data. Bad habits — namely, attack the mainstream theory, call it a day — die hard.

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  21. Paul Nelson: I didn’t mention Patrick Forterre’s explanation, because it doesn’t actually solve the problem — it only moves the puzzle to the virosphere, where orphans predominate. The actual origin of Topo V is still unknown

    Enjoyed moving the goalposts much? No, you didn’t omit their proposed explanation because it moves the problem one step further (it doesn’t, because the origin of the DNA topoisomerase V in the virosphere is an entirely different question). You did it because it undermines your thesis that orphan genes pose a threat to common descent. Obviously. And what’s with this nonsense about needing to know the origin of something or else you can’t know anything about it? It’s like claiming there’s no way to find carrots, and if someone replies “try at a grocery store” you complain that just pushes the problem one step further “where did they get them from? huh? huh?”. Creationist absurdity

    Paul Nelson: Since common descent doesn’t rule out anything, orphans are entirely possible if common descent is true. So is their absence, which was the case prior to the mid-1990s, and the DNA sequencing revolution. When someone can tell me what UCD forbids, and why…we might be able to see if orphans should exist or not.

    LOL, common descent forbids organisms being poofed into existence out of nowhere. Which we all know is the reason why you’re so enraged that it’s a fact. And wait a minute, are you saying now that CD doesn’t predict that orphan genes won’t exist? WTF? Stop the presses! Weren’t you claiming that we shouldn’t expect to see those if CD were true? What happened there?

    Paul Nelson: But the whole point of my talk is to suggest that biologists now have data which should lead them to ask questions about UCD / CD — which, while still a minority move, is happening with increasing frequency.

    How would they be able to do that if CD doesn’t predict anything as you just claimed above? Confused much? Here’s another fact: you’re just projecting. It’s your ID crap what doesn’t predict jack shit.

    Paul Nelson:while still a minority move, is happening with increasing frequency.

    In your dreams

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  22. Paul Nelson: Signal + noise = all the observations.

    Paul, obviously if there’s still signal, then we can infer common descent. Please take a moment to think.

    Yes, the further back in time we go, the weaker the signal becomes. That’s to be expected. But, so far, with all species hitherto discovered we can still detect it. The noise becomes larger, and eventually will drown out the signal for some loci in some species with very deep branches. But other loci still show signal, so we can still infer CD.

    If there was no signal left, in any loci, then CD would run into a problem. But you can’t complain that we infer CD when there’s still some signal there.

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  23. colewd:
    Corneel,

    I mean where there is confirming evidence of heredity.

    That’s right Bill, you tell ’em! Modern science has no confirming evidence of heredity between parents and their offspring. 😀

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  24. colewd: I mean where there is confirming evidence of heredity.

    I do not understand what you mean. I guess your signal-to-noise ratio has dropped below the point where you can reliably get your message across.

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  25. Paul Nelson:
    My talk failed to give a coherent ID account of the same data.

    When will the Biologic Institute or BIO-Complexity be publishing this coherent ID account of the same data?

    BTW “the Designer made this pattern of orphan genes JUST BECAUSE!” is neither coherent nor science.

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  26. colewd:
    BruceS,

    Let’s look at a process of manufacturing a nail that is 100 mm with a specification of plus or minus 1 millimeter.Depending on the control of the process I would expect a mean length around 100 mm with a distribution around 99 and 101 mm.The shape of this bell curve will fill out over time as my numbers go up.I would also expect outliers to be rejected outside the spec.as numbers go up.The filling out of the bell curve is convergence if I understand it correctly.

    You are agreeing with me right? I take you to be assuming a Gaussian distn (bell curve). I am not sure what you mean by “the shape will fill out” but perhaps you mean the sequence of overall sample means and variances will better approximate the true parameters of the (assumed) iid Normal variables. And you can do statistical tests with estimates — that’s quality control theory. That will allow you to verify that the manufacturing process is meeting the 100 mm +- 1 numbers you quote, which I am taking as the quality standards being checked.

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  27. Corneel: Welcome to the wonderful world of statistical thinking.

    But descent with modification as a biological process is not “statistical,” in the sense you mean (i.e., some fuzziness expected).

    It is or is not the case that your biological mother is who she is — namely, a unique organism. And so on, all the way back to the Last Universal Common Ancestor (LUCA).

    So whatever statistical methods we employ, they must be able to answer the following question without equivocation:

    Did LUCA exist or not?

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  28. Paul Nelson: It should not be possible for me to pick surprising cases, if UCD, when that historical geometry is coupled with its multiple auxiliary theories, were truly predictive, in the sense of excluding possible states of affairs.

    This is complete nonsense. It is entirely conceivable that you could find an organism with a set of characters that show no detectable relationship to anything else.

    No significant sequences similarities above that expected from chance, no structural similarities, different chiralities. You could find an organism with a radically different genetic code implemented by a translation system with components completely unlike those known. A different molecular machine responsible for catalyzing peptide bonds, very different from the ribosome we know. Protein-based molecules carrying out functions analogous to tRNA, and so on. Perhaps a different genetic polymer, like TNA or PNA. Or DNA or RNA with opposite chirality, or different nucleobases than the AGCT(U) we know.

    For such an organism, we would have no reason to infer common ancestry.

    The fact that such an organism has not been found is not evidence it couldn’t exist in principle. The fact that all known life is utilizing the same, highly similar core translation system components, which is responsible for implementing essentially the same genetic code (with minor variants implemented by mutated versions of translation system components, such as altered tRNAs or tRNA-synthetases) is signal. The fact that individual translation system components, when subjected to phylogenetic analysis, yield phylogenetic trees with a statistically significant level of similar topology, is also signal. The fact that some less central components have managed to mutate beyond the point where signal is detectable doesn’t somehow magically make the core translation and genetic code signal disappear and not count.

    The same goes for many individual genetic loci which biologists don’t think are directly related(are not homologous). While the species in which these molecules are found are still thought to be related by common descent, the molecules for which no such signal can be detected are not invoked as evidence for common descent for that very reason. But there is still signal in other attributes and characters.

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  29. Kantian Naturalist: I’m usually amused (sometimes irritated) when Intelligent Design advocates are so certain that “intelligence” could not possibly be simulated on a Turing machine.

    Based on other exchanges with him, some at PS, I understand that Eric believes that human intelligence can solve the halting problem, which TMs cannot do.

    There may be physical universes (involving Malament-Hogarth spacetime — see link), where so-called hypercomputers exist which could solve the halting problem (essentially by doing infinite work in finite time)
    https://plato.stanford.edu/entries/computation-physicalsystems/#Hyp

    ETA: But, as you say, there is no evidence that possibility applies to our universe.

    Scott Aaronson has a fine set of lectures on the Church-Turing thesis, its modern (physical) version, and what quantum computers bring to the picture over TMs.
    https://www.scottaaronson.com/blog/?p=4301

    While I am pushing Scott, here his view on Google’s claims of quantum supremacy. (Short version: Google’s claim is valid).
    https://www.scottaaronson.com/blog/?p=4317

    I agree with you and Joe F that ID’s only content is its mathematical criticism of current science — there is no positive scientific explanation advanced to explain what we observe. But Eric and is ID colleagues do not accept the conclusions of Joe F, Jeff S, etc that ID’s criticisms fail and that armchair math is not science. So iIt comes down to who to trust and why. I trust the scientific community because of its processes as captured in the Mertonian norms.
    https://en.wikipedia.org/wiki/Mertonian_norms

    Eric and others have resorted to conspiracy theory to explain the rejection of ID by mainstream biology. I take this as an admission of defeat — they cannot advance good reasons to be taken seriously by the scientific community and so have to resort to QAnon/No Moon Landing tactics.

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  30. BruceS,

    You are agreeing with me right? I take you to be assuming a Gaussian distn (bell curve). I am not sure what you mean by “the shape will fill out” but perhaps you mean the sequence of overall sample means and variances will better approximate the true parameters of the (assumed) iid Normal variables. And you can do statistical tests with estimates — that’s quality control theory. That will allow you to verify that the manufacturing process is meeting the 100 mm +- 1 numbers you quote, which I am taking as the quality standards being checked.

    You got it. Filling out the shape simply means when enough data points are in we will see the bell curve based on the law of large numbers. Eric’s last explanation to KN was helpful to me.

    If there was 1 part outside the curve limits (called control limits) out of 6 million that is what 6 sigma (six SD’s from the mean) is all about if you heard this term thrown around.

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  31. Paul Nelson:

    Did LUCA exist or not?

    The scientific consensus based on all the available evidence is yes. Of course like all scientific findings that conclusion is subject to change based on the introduction of additional contradictory evidence. HINT: ORFan genes are not contradictory evidence.

    When will you be publishing your coherent ID explanation for ORFan genes instead of just flinging mud and misrepresenting other scientists?

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  32. BruceS,

    I agree with you and Joe F that ID’s only content is its mathematical criticism of current science — there is no positive scientific explanation advanced to explain what we observe.

    To me ID’s interesting claim is mind as a mechanism. I think this has legs as it is a known causal mechanism of what we are observing in biology. I think where Eric’s work is interesting is starting the path of understanding why minds can produce information.

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  33. dazz: Weren’t you claiming that we shouldn’t expect to see those if CD were true?

    Exactly — but only by using a definition of UCD regulated by the Principle of Continuity (PrC). PrC rules out orphans as observed in their current abundance and essential functional roles, if they must descend from LUCA.

    UCD by itself does not, however, which explains why most biologists continue to hold UCD even in the presence of potentially billions of orphans. UCD in that mode rules out nothing.

    You need to get out more, dazz:

    “Recent advances from genomics refute the ideas of gradualism, exclusive vertical inheritance, evolution selecting the fittest, a common ancestor and the TOL [Tree of Life]. Indeed, there may not be any two genes that have the same evolutionary tree.”

    From here (open access):

    https://www.frontiersin.org/articles/10.3389/fcimb.2012.00113/full

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  34. colewd:
    BruceS,

    You got it.

    So how would this apply to Eric’s proposed tests for a stochastic process?

    It seems to me that control theory requires that we are dealing with a manufacturing process which produces outputs where a certain measured variable is being tested to ensure it is within spec.

    I don’t see a way of applying that to testing for a stochastic process. As per my upthread post, I am not even clear on how such a test could be done. Or what it even means.

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  35. colewd: To me ID’s interesting claim is mind as a mechanism. I think this has legs as it is a known causal mechanism of what we are observing in biology. I think where Eric’s work is interesting is starting the path of understanding why minds can produce information.

    It’s still a non-starter unless and until you come up with a mechanism for a “mind” to physically manipulate matter into the desired configuration. Then you need positive evidence a “mind” actually DID direct the physical construction.

    Just because a mind CAN think of a specific sequence isn’t evidence a mind DID produce a specific sequence. Known evolutionary processes are capable of producing the genetic sequences we see now no matter how much you deny reality.

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  36. Rumraket: It is entirely conceivable that you could find an organism with a set of characters that show no detectable relationship to anything else.

    OK, let’s try this.

    Suppose I found an organism where 1/3 of its experimentally-demonstrated essential molecular hardware “had no detectable relationship to anything else.”

    Would that count?

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  37. Adapa,

    Just because a mind CAN think of a specific sequence isn’t evidence a mind DID produce a specific sequence. Known evolutionary processes are capable of producing the genetic sequences we see now no matter how much you deny reality.

    This is not a supported claim. If you make it again my only choice is to ignore it.

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  38. Paul Nelson: Exactly — but only by using a definition of UCD regulated by the Principle of Continuity (PrC).PrC rules out orphans as observed in their current abundance and essential functional roles, if they must descend from LUCA.

    UCD by itself does not, however, which explains why most biologists continue to hold UCD even in the presence of potentially billions of orphans. UCD in that mode rules out nothing.

    You should save this sort of empty rhetoric for your ignorant ID-Creationist audiences. Your bullshit doesn’t sell with anyone who has any knowledge of biology or genetics.

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  39. Paul Nelson:

    Joe Felsenstein: Thanks Paul, but no, I won’t do that. It would be too easy for you to pick and choose among cases and present me only with ones where there were surprising differences.

    But that’s just the point. QED.

    It should not be possible for me to pick surprising cases, if UCD, when that historical geometry is coupled with its multiple auxiliary theories, were truly predictive, in the sense of excluding possible states of affairs.

    Nelson should recall the case I discussed: I take human DNA sequences, look at the corresponding Chimpanzee sequences, and for the sites where the human sequence has an A, find the ones where the Chimpanzee has a G, and present the seminar students with only those sites. Would my ability to do that disprove common descent?

    In effect, Paul Nelson has acknowledged that yes, he chose cases that were like that. And now his argument is that if there is not perfect predictability of the base in chimpanzees from the base in humans, that common descent should be rejected.

    I repeat, if we choose sites that have an A in humans, but we do not pick and choose those that also have a G in chimps, we do get a signal of common descent. Because although we find all four bases (A, C, G, T) at the sites in chimps, among them, A’s are substantially more frequent. If anyone doubts that, I can make a table for a small data set and show it here. (This works for about 100 million years back, at which point the excess of A’s gets hard to detect. Earlier than that, we have to use DNA sequences that change especially slowly or use protein sequences instead.)

    I did not expect Nelson’s argument to be that silly. It is just as silly as arguing that life on Earth is less than 10,000 years old.

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  40. colewd:
    Adapa,

    This is not a supported claim.If you make it again my only choice is to ignore it.

    You ignore the rest of science with your willful ignorance, why should this be any different?

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  41. Joe Felsenstein:
    I did not expect Nelson’s argument to be that silly.It is as silly as arguing that life on Earth is less than 10,000 years old.

    I was under the impression Paul Nelson is a YEC. Is that wrong?

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  42. Adapa: I was under the impression Paul Nelson is a YEC.Is that wrong?

    As far as I know, he is, or at least thinks that life on earth is young. Which is why I threw in that gratuitous remark.

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  43. BruceS,

    I don’t see a way of applying that to testing for a stochastic process. As per my upthread post, I am not even clear on how such a test could be done. Or what it even means.

    I think Eric means by a stochastic process is simply a linear process that delivers an output. The non stochastic process can essentially create the linear process. A computer can execute a novel algorithm but can it create one?

    Taken the next step is DNA evidence of a non stochastic process.

    2+
  44. BruceS,

    In 1942, Robert K. Merton introduced “four sets of institutional imperatives taken to comprise the ethos of modern science… communism…

    That’s as far as most creationists here will read, LOL

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  45. Joe Felsenstein: As far as I know, he is, which is why I threw in that gratuitous remark.

    Ah, got it. My coffee hasn’t cut in yet. 🙂

    Paul Nelson, how old is life on Earth and how do you know?

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  46. On the EricMH statement that random processes converge: does that means that when we have idealized independent coin tosses, that we expect them to converge to, say, Heads? They don’t — you keep getting both Heads and Tails. The Law of Large Numbers applies to means, not to individual tosses.

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  47. Joe Felsenstein,

    On the EricMH statement that random processes converge: does that means that when we have idealized independent coin tosses, that we expect them to converge to, say, Heads? They don’t — you keep getting both Heads and Tails. The Law of Large Numbers applies to means, not to individual tosses.

    As the number of trials goes up the ratio of H to T will approach 1. Some how I don’t think this is news to you 🙂

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  48. colewd: As the number of trials goes up the ratio of H to T will approach 1. Some how I don’t think this is news to you

    Not news, law of large numbers. But I think EricMH said that the process converges, not that means (or ratios) of total counts converged.

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