Intelligent Design Naturalism

That’s Gotta Hurt

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Daniel King refuses to follow the evidence regarding the implications of biological semiotics, so Upright Biped asks him:

Are you suggesting we dig up Alan Turing and test the need for a symbol system expressive enough to describe an interpreter for itself? Are you wanting to test von Neumann’s mathematical structure of self-replication, or the validity of Crick’s adapter hypothesis? Are you uncertain whether or not the anticodon-to-amino acid association is isolated from the codon-to-anticodon association? Are you wanting to test Pattee’s epistemic cut between rate-independent control and rate-based dynamics? Are you wondering if amino acids can be derived from the spatial orientation of nucleobases? Are you wanting to know if Nirenberg had to demonstrate the code in order to discover it? Shall I go on, or have you got the point yet? There is no observation that I am making that is even controversial; the observations that are important to my argument are generally considered settled science.

The outstanding question is if genetic language and natural language require the same physical conditions in order to function. Not only is a test for that question provided on my website, but the answer to the question is already part of the scientific record – put there (repeatedly) by eminently well-trained researchers working within their specialties.

Matspirit jumps in and responds:

“Representation” and “translation” are not required for life and current OOL theory doesn’t suppose they existed in the First Living Thing. Representation and translation are much faster and more flexible than direct copying and once direct copy organisms began to evolve it they dominated and replaced the old system. But representation and translation systems weren’t possible until direct copying life evolved them.

None of this should be a surprise to anybody, it’s not exactly a secret. But the “no life without representation and translation” theory does have one big thing going for it from an ID/creationist viewpoint: it makes OOL look impossibly difficult.

This is just astonishing.  The degree of materialist fideism entailed in this passage boggles the mind.  Representation and translation are absolutely essential to materialist evolutionary theory, except when they were not at a time when they could not, in principle, exist.  Then they were entirely dispensable.

Here is a pictorial representation of Matspirit’s argument:

bootstraps

And here is how you have to hold your teeth while maintaining Matspirit’s narrative:

teeth-grinding-2

To his credit, Matspirit does recognize the implications of accepting the evidence on its face.  He writes: “the ‘no life without representation and translation’ theory . . .makes OOL look impossibly difficult.”  If by “OOL” one means “materialist OOL,” that is exactly right Matspirit.  And if one is committed to the materialist narrative even at the expense of logic and evidence, this is a huge problem.  Because, as demonstrated above, it makes you say (and tell yourself that you believe) aggressively stupid things.

 

 

 

68 Replies to “That’s Gotta Hurt

  1. 1
    gpuccio says:

    I would like to ask Matspirit:

    “Representation and translation are much faster and more flexible than direct copying and once direct copy organisms began to evolve it they dominated and replaced the old system.”

    Direct copy organisms? Examples, please?

    Would you agree that the “old system” is only an abstract assumption, completely unsupported by any direct or indirect evidence?

    Just to know.

  2. 2
    mike1962 says:

    “current OOL theory”

    Hehe

  3. 3
    gpuccio says:

    Matspirit:

    And, always just to know, how would a “direct copy organism”, whatever it may be, “evolve” a whole representation and translation system, with highly symbolic connections between nucleotides and aminoacids, implemented by some 20 highly complex proteins plus some “small” machinery like the ribosome and a lot of other assets?

    IOWs, I suppose that the “direct copy” system was copying RNA to RNA (am I correct, or you mean something else?). So, in the mythical RNA world, the sequence of nucleotides was important for the information about the final RNA effectors (rybozimes, and so on). IOWs, the information was about RNA as a biological effector, and had nothing to do with proteins, aminoacids, and so on.

    So, what happens? One day the DCO (direct copy organism) decides that it is rather old fashioned to store information for the reason it is used (RNA structures which have something to do), and it would be exciting to store completely new symbolic information for some unclear future purpose, having to do with some new molecules (proteins)?

    And what about proteins? Were they present in the DCO? Did they copy themselves? How? Or did they appear suddenly?

    It is fascinating how people who seem otherwise normally intelligent can accept this kind of conjectures as though they were reasonable scientific theories. Maybe my imagination has severe limitations…

  4. 4
    Andre says:

    The problem is the possible divine foot in the door. Nothing else….

  5. 5
    Barry Arrington says:

    Gird your loins folks. Prepare for howls of indignation and cries of “you people always ask for impossible levels of detail.”

    I will respond in advance of the howls. I don’t want minute details. ANY level of detail will work. Before you can say your story is the least bit plausible, you have to demonstrate how it is in principle possible. BTW, bare, unsupported assertion such as that Matspirit put on display above does not count as a demonstration. Just sayin’.

  6. 6
    Andre says:

    Barry how could you set the bar so high by asking for actual evidence!

  7. 7
    bill cole says:

    None of this should be a surprise to anybody, it’s not exactly a secret. But the “no life without representation and translation” theory does have one big thing going for it from an ID/creationist viewpoint: it makes OOL look impossibly difficult.

    I think over the next few years 3 other origins will start to be recognized as equally hard to explain:
    -The origin of eukaryotic cell: difficult to explain the origin of the spliceosome, the nuclear pore complex and chromosome structure.

    -The origin of multicellular life: difficult to explain the origin of the ability to build complex body plans.

    -The origin of man: difficult to explain the origin of language and complex thought.

    Presently I believe that Universal Common Decent is a circular argument because of the unsolved mystery of these origins.

  8. 8
    bornagain77 says:

    Bill Cole, you may appreciate this article that Michael Egnor just posted on ENV:

    What Is Consciousness? – Michael Egnor – July 14, 2016
    Excerpt: “Why am I an I, and not an it?”
    http://www.evolutionnews.org/2.....02995.html

  9. 9
    MatSpirit says:

    Barry, thanks for the good sound arguments. Informative and to the point. That’s so much better than the childish name calling you see so much of these days.

    Gpuccio, I was referring to a ten molecule polymer I mentioned in message 128 in the Gritting you teeth thread. It reproduces itself by having each small molecule in its chain attracting an identical molecule to its side and then joining them all into a second polymer identical with the first one.

    This would be direct reproduction where the molecule copies itself directly without any DNA or other representations, signs or symbols. You can see where this idea upsets the semiotics people, but it seems to be what most of the OOL researchers seem to think happened. It goes under names like “RNA world” or “chemical evolution”.

    I don’t think the original DCO was “about” anything. It didn’t make proteins or anything else, just copies of itself. I think it was probably a polymer because just about everything alive today is made from them and because the polymer structure is perfect for evolution.

    As for how such Direct Copy Organism (thanks for that name, I’ll keep using it) would evolve the complex system we see today, I would guess that DNA backup for fragile RNA came first. Three of the four codon in DNA are identical to the ones in RNA and the fourth is a close chemical cousin. The backbones of both molecules are also chemical cousins.

    As far as proteins go, amino acids form spontaneously, botherwise on eart and in space. (Miller-Urey found five of them in their famous experiment. Modern researchers have examined vials saved from their experiment with modern instruments and brought the total up to 21.) Proteinoids (short proteins of up to 5 amino acids) form spontaneously. So I would guess that proteins of some kind were present.

  10. 10
    MatSpirit says:

    SORRY, MUST HAVE TOUCHED THE PUBLISH BUTTON.

    Look at it this way. Life as we see it today, in all its towering complexity, is so well understood that it has become intellectually irresponsible to deny that that it’s material. There is no elan vital. That idea is dead.

    So if the extravagantly complex life we see today is material and is known to have come from material causes (other life), why not believe those material causes extend all the way back until life was so simple that non living material causes could produce it?

    Finishing up, you say, “It is fascinating how people who seem otherwise normally intelligent can accept this kind of conjectures as though they were reasonable scientific theories. Maybe my imagination has severe limitations…”

    It is a fact that a lot of very intelligent people who are also very well educated and who have studied the OOL field for decades DO think that conjectures like these are reasonable. I think that if you understood the field better, you might think they were reasonable too.

    I am confident that when you do disagree you will give cogent reason for your disagreement, as above, and not childish name calling and I thank you for it.

  11. 11
    MatSpirit says:

    Barry:

    I don’t want minute details. ANY level of detail will work. Before you can say your story is the least bit plausible, you have to demonstrate how it is in principle possible. BTW, bare, unsupported assertion such as that Matspirit put on display above does not count as a demonstration. Just sayin’

    ID like to ask the same question of ID. All I’ve heard about the beginning of life from the ID camp is, “The Intelligent Designer made it and the Designer is not necessarily God.” Could we have a little more detail there?

  12. 12
    bill cole says:

    MatSpirit

    Look at it this way. Life as we see it today, in all its towering complexity, is so well understood that it has become intellectually irresponsible to deny that that it’s material. There is no elan vital. That idea is dead.

    So if the extravagantly complex life we see today is material and is known to have come from material causes (other life), why not believe those material causes extend all the way back until life was so simple that non living material causes could produce it?

    While we observe reproduction all the time as you say the great mystery is how does DNA change in order create new species especially when they have different functional DNA and protein sequences then other species.

  13. 13
    bill cole says:

    BA77
    Thanks 🙂

  14. 14
    CuriousCat says:

    I really wonder, in this case, on which side does the proof of burden lie? Or which of these views will be taken as the null hypothesis? Are we to take the RNA world as the null hypothesis, and expect statistically significant experiments or calculations to be able to reject it? Or are we going to take the view that OOL cannot be solved by the current theories as the null hypothesis, and reject this only in the existence of highly (statistically) significant results that show OOL can be explained by a RNA world. I believe most of the similar controversies (Cambrian explosion, irreducibly complex systems, parallel universes, etc.) may be viewed from this perspective. Hence, it’s more like gaining the upperhand of “status quo”, and sit at the throne of the null hypothesis, so that it becomes very difficult for the alternative view to be accepted, especially if the null hypothesis is very flexible and very story-like form (as the story told by MatSpirit). I think, somehow, naturalism has taken the luxury of occupying the null hypothesis in all cases, so it’s exceedingly difficult for ID people to defend their cases, since they are expected to falsify these naturalistic null hypotheses in all fields.

  15. 15
    bill cole says:

    Are we to take the RNA world as the null hypothesis, and expect statistically significant experiments or calculations to be able to reject it?

    The RNA world does not come close to explaining the origin of life. If you accept the RNA world as something that existed then how does that become a working cell.

    Then once you get to the first cell you need to get to the first eukaryotic cell which there is no reasonable explanation for its origin….then multicellular …then human.

    If you look at a DNA sequence that codes for a protein of 500 aa it can be falsified that it was the result of a random process.

    When 2 humans create a 3rd human it can be falsified that it is the result of a random process.

    The null hypothesis that your experimental result has random cause is not what we observe in life.

  16. 16
    gpuccio says:

    MatSpirit:

    Thank you for trying. No name calling, obviously, but I really want to comment on what you say.

    “I was referring to a ten molecule polymer I mentioned in message 128”

    OK, but a ten molecule polymer is not an organism.

    So, my point remains: Direct copy organisms? Examples, please?

    “This would be direct reproduction where the molecule copies itself directly without any DNA or other representations, signs or symbols.”

    I have no problems with simple molecules directly copying themselves in the right context (usually designed ad hoc). That still has nothing to do with living organisms.

    “You can see where this idea upsets the semiotics people, but it seems to be what most of the OOL researchers seem to think happened. It goes under names like “RNA world” or “chemical evolution”.”

    I am certainly part of the semiotic people, but strangely I don’t feel upset at all. And I am well aware that “most of the OOL researchers” believe that kind of things. Look, there is just one argument that you should not use with me: the argument of conformistic thought. I always say that I am a minority guy. I am proud of that. You see, I don’t care how many authoritative people believe one thing: for me, the only importnat thing is if I can be convinced that it is true.

    I am very firmly convinced that a very strong cognitive bias is operating in biological ideology. I understand its origins, which are maybe partly justified (the need to free science from old dogmatisms mainly connected to religion). I can understand that, but the only result of dogmatic anti-dogmatism is a new form of dogmatism. So, I beg your pardon, but the simple fact that many believe something is not, for me, a reason to believe. I like to choose the things I believe in.

    That said, let’s go to the other points.

    “I don’t think the original DCO was “about” anything. It didn’t make proteins or anything else, just copies of itself. I think it was probably a polymer because just about everything alive today is made from them and because the polymer structure is perfect for evolution.”

    Again, a replicating molecule, even if it were really spontaneously possible, is not an organism: life is made first of all of metabolism, separation of environments, far from equilibrium states, and many other things.

    However, let’s say that your “organism” is an RNA organisms. So, we are entering the myth of RNA world. OK, let’s go on.

    “As for how such Direct Copy Organism (thanks for that name, I’ll keep using it)”

    No problem, I like it too!

    “would evolve the complex system we see today, I would guess that DNA backup for fragile RNA came first.”

    I have no problems with that. RNA and DNA are similar molecules, and complementary ones. OK, the scenario has many difficulties, but I don’t want to emphasize them here. Let’s go on.

    “Three of the four codon in DNA are identical to the ones in RNA and the fourth is a close chemical cousin. The backbones of both molecules are also chemical cousins.”

    OK. The origin of nucleotides is not exactly a solved problem, but let’s go on, again.

    “As far as proteins go, amino acids form spontaneously, botherwise on eart and in space. (Miller-Urey found five of them in their famous experiment. Modern researchers have examined vials saved from their experiment with modern instruments and brought the total up to 21.) Proteinoids (short proteins of up to 5 amino acids) form spontaneously. So I would guess that proteins of some kind were present.”

    OK. Having a few aminoacids and maybe some proteinoid is not really the problem.

    Now, let’s understand where the real, big problem is:

    1) Proteins do not copy themselves directly. They can only be reproduced by the information in DNA genes, which uses the symbolic translation system. OK with that?

    2) So, even if we have a proteinoid, and even if it does something useful (very doubtful, but OK, this is the game), my simple question is: how is the information for that simple proteinoid conserved and passed from DCO to DCO? Or are new instances of the same proteinoid created each time by sheer luck? Excuse me, but I don’t understand. And how can the information in the original proteinoid “evolve”, if the information is not copied and translated from some physical storage system?

    3) And the most important point: how is it that some sequence of nucleotides at some point starts representing a sequence of aminoacids, according to some symbolic code? Remember, the sequence of nucleotides in our RNA DCO has only one function: to preserve and pass on the information for RNA enzymes.

    Now, the biochemical rules which govern RNA molecules are completely different from the biochemical rules which govern proteins. And, above all, there is no spontaneous symbolic connection between the two sets of rules.

    So, please, answer this very important point: why should a functional sequence which has a very definite function according to some set of rules, and is conserved and propagated exactly for that reason, become a sequence which has no more relationships with its initial function, but strangely starts to represent another completely different set of rules, according to a purely symbolic code, which can only work if a complex translation apparatus, including 20 aaRNA synthases, the ribosome, and many other components, is already working? This is really beyond my frail imagination.

    “Look at it this way. Life as we see it today, in all its towering complexity, is so well understood that it has become intellectually irresponsible to deny that that it’s material. There is no elan vital. That idea is dead.”

    To say that life is so well understood is really the statement of the millennium! Are you really convinced of what you are saying? I am afraid that there is no hope.

    However, while I would be happy to defend a little the “elan vital” here, I will simply emphasize that nothing in ID theory is denying that the biological information necessary for life is material, or at least implemented in material forms: our only point is that it is designed. A watch, a computer, are material objects, but the information which makes them what they are is designed. So, this is a false argument. We will discuss “elan vital” another time, for the moment let’s just discuss the origin of biological information, as we have always done.

    “So if the extravagantly complex life we see today is material and is known to have come from material causes (other life), why not believe those material causes extend all the way back until life was so simple that non living material causes could produce it?”

    Because it is simply wrong: complex functional information, even if materially implemented, has its origin in conscious intelligent representations. Always. That’s exactly the point of ID theory. Non conscious systems simply cannot generate that kind of physical organization, never have, never will.

    “It is a fact that a lot of very intelligent people who are also very well educated and who have studied the OOL field for decades DO think that conjectures like these are reasonable.”

    The conformistic thought argument again? They may think whatever they like. I don’t.

    “I think that if you understood the field better, you might think they were reasonable too.”

    Here I strongly disagree with you. I think that I understand the field well enough to have very strong and motivated convictions. Maybe I understand it better than you do, but just for fairness, let’s say that we understand the field equally well, and still we have opposite ideas. There is nothing strange in that. It’s called freedom of scientifc thought, and IMO it is the main cognitive manifestation of free will. But that’s another story.

    “I am confident that when you do disagree you will give cogent reason for your disagreement, as above, and not childish name calling and I thank you for it.”

    I have tried to satisfy your expectations. 🙂

  17. 17

    Smile. Poor atheists/Darwinists. Their house of cards is falling down all around them. Fun to watch, actually.

  18. 18
    bill cole says:

    Look at it this way. Life as we see it today, in all its towering complexity, is so well understood that it has become intellectually irresponsible to deny that that it’s material. There is no elan vital. That idea is dead.

    I have asked 4 different biochemists the question: what percentage of the eukaryotic cell do you think we understand? Everyone answers 1% or less.

  19. 19
    mike1962 says:

    Barry: “you people always ask for impossible levels of detail.”

    Yep. Us engineers wanna know the details. And not even “impossible” details. Just plausible pathways.

    They hate that.

  20. 20
    Dionisio says:

    mike1962 @19

    Barry: “you people always ask for impossible levels of detail.”

    Yep. Us engineers wanna know the details. And not even “impossible” details. Just plausible pathways.
    They hate that.

    The moment serious biologists humbly opened the doors to outsiders and invited different kinds of engineers, physicists, computer scientists, mathematicians, and their cousins to join them in multidisciplinary research teams, one could easily foresee that more trouble was ahead for the outdated Darwinian/neo-Darwinian ideas and their still influential proponents.

    We ain’t seen nothing yet. The best part is still ahead.
    As many serious biology researchers all over the world continue to report breakthrough discoveries shedding more light on the elaborate molecular and cellular choreographies orchestrated within the biological systems, the emerging big picture will confirm what the most open-minded people, logically thinking out of any imposed box, have been expecting for years.

  21. 21
    Daniel King says:

    Hi, Barry.

    Daniel King refuses to follow the evidence regarding the implications of biological semiotics…

    I followed the evidence and its implications. That’s what led me to pose the following two questions:

    Have you devised any tests of your biosemiotic hypothesis? Are any such tests conceivable?

    What I got from Upright Biped was his usual bluster, followed by more of the same, some of which you quoted in your OP above.

    I understand that neither of you have answers to those questions. That demonstrates that we’re dealing here with politics, not science. That’s fine, carry on.

    And carry the torch for reason, MatSpirit.

  22. 22
    rvb8 says:

    I see an argument so utterly dense and vague it leaves me utterly weary. I don’t know UB, but I do know he should learn to make his counter arguments to the OOL arguments far more user friendly. When I go to Science Daily (as I do quite often) I can follow the scientists description of their work, and their conclusions with some clarity. However, many of the counter arguments presented here are utterly opaque and impenetrable.
    So, a request to UB, could you please write something we educated, but amateur observers could read and say, ‘aaah that is clear rebuttal for the latest proposition in OOL which I can share in my dinner table conversation with my friends this evening.’ I would like to make the same request of Mr Torley, Seversky, and to a much lesser extent BA.
    Oh! And of the 5.2 million English articles on Wikipedia at the present, not one is entitled Biological Semiotics, can anyone explain, CLEARLY, what this is?

  23. 23
    Dionisio says:

    gpuccio @16

    To say that life is so well understood is really the statement of the millennium!

    🙂

    BTW, thank you for the very insightful comments posted @16.

  24. 24
    Barry Arrington says:

    Daniel King @ 21.

    Here’s a clue. Your inability to follow Upright Biped’s argument is not the same as his failure to make an argument. Write that down.

  25. 25

    Daniel King @ 21: Upright Biped can explain it to you, but he can’t comprehend it for you. I guess natural selection hasn’t helped you in that department.

  26. 26

    DK at 21,

    I followed the evidence and its implications.

    Really? Prove it. Tell us about the test given on Biosemiosis.org, and how you arrived at your conclusion that it doesn’t exist. Don’t waffle, give us the details of how you read the test for semiosis in the cell and concluded that there is no test for semiosis in the cell. You can’t. All you can do is sling insults, which changes nothing whatsoever of the evidence.

    rv at 22,

    There is a fundamental reason why you haven’t asked for a single clarification or explanation. Do you really think you are the first person in human history to play dumb in order to avoid something? I’ve had a pre-teen girl in California (12 yrs old I think) write me a letter and basically recite the entire argument. Somehow it didn’t take her long to figure out that if no object in the universe has any inherent meaning, then to specify something (like an amino acid) will require more than one object. Boom! She wrote to thank me for explaining how that works.

    I’m not fooled for a moment by your antics. The reason you don’t ask for a single clarification is because 1) you know very well you’re gonna get an answer, and 2) it would cause you to have to engage the evidence. It’s much better to play stupid and throw darts from a distance — a class of response that is as old as humanity itself. What is so puzzling is why you think its not stupendously obvious?

  27. 27

    GP, thank you for chiming in. You are the best.

  28. 28
    tjguy says:

    Bill @7

    I think over the next few years 3 other origins will start to be recognized as equally hard to explain:
    -The origin of eukaryotic cell: difficult to explain the origin of the spliceosome, the nuclear pore complex and chromosome structure.

    -The origin of multicellular life: difficult to explain the origin of the ability to build complex body plans.

    -The origin of man: difficult to explain the origin of language and complex thought.

    Personally, even if they claim to have an “explanation” for something, if we can’t test it, how valuable is it?

    Having an “explanation” for something is different than testing it and verifying that hypothesis.

    Now, when they can’t even come up with a feasible hypothesis, sure, that is an even greater problem, but my point is that even if they have an explanation for it, that does not necessarily mean they are right or that the problem is solved – even though they feel justified in thinking that way.

  29. 29
    MatSpirit says:

    Daniel King: “I followed the evidence and its implications.”

    Upright Biped: “Really? Prove it. Tell us about the test given on Biosemiosis.org, and how you arrived at your conclusion that it doesn’t exist.”

    Beautiful! Give him a website for a reference and tell him to find a test there and tell us why he thinks it doesn’t exist! 

    What I think Dan is looking for (and what I know I can’t find) is any reason to care about all this. Yes, information exists in cells. You learned that from science. Yes, some of that information is represented in the spatial order of the DNA/RNA molecules, you got that from science too. Yes, it takes extra molecular machinery to translate the latter information, that’s from science too.

    Nobody disputes this, it’s just plain materialistic science and that’s where you got it from. But then you drop this clanger:

    Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life’s capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity.”

    That’s what I want you back up! Prove that the DNA/RNA system we see today is the only one that ever existed. Prove that a simpler system didn’t exist long before and evolve the start of our present system.

    Give us some evidence for this beyond your mere assertion. Until then, thank you for your assertion, we have received it and nobody outside of ID is impressed.

    I do have to thank you for publishing this on biosemiosis.org.

    There are two distinct categories of semiotic systems. One category uses representations where the arrangement of the medium (like a pheromone) is reducible to the physical properties of the medium itself; [This is what I’ve been calling INTRINSIC INFORMATION]

    the other uses representations that have spatial (dimensional) orientation and are not reducible to their physical make-up (like the words on this page). [This is what I’ve been calling EXTRINSIC INFORMATION] The first type is found throughout the living kingdom. The second type is found nowhere but in recorded language and mathematics  (and in the genetic code).

    Thank you for backing me up there.

  30. 30
    gpuccio says:

    MatSpirit:

    You have very strange ideas about science and epistemology. Science is based on observed facts and on reasonable inferences from those facts.

    You say:

    “Prove that the DNA/RNA system we see today is the only one that ever existed.”

    No. The system we see today is a fact, because we can observe it. It is the only system we can observe which can do what it does.

    If you try to explain its origin by stating that simpler systems existed in the past, it’s your burden to support that hypothesis by reasonable facts and inferences. We have no reason to “prove” that your unsubstantiated assumptions are wrong. They are unsubstantiated, and that’s enough to dismiss them, unless and until you substantiate them.

    You say:

    “Prove that a simpler system didn’t exist long before and evolve the start of our present system.”

    Again, you must prove, or at least reasonably support (nothing is ever proved in empirical sciences) your hypothesis.

    This is basic epistemology. How can you discuss science, if you betray the basics of scientific thought with each new statement of yours?

  31. 31
    Dionisio says:

    gpuccio @30

    Again, you must prove, or at least reasonably support (nothing is ever proved in empirical sciences) your hypothesis.

    This is basic epistemology. How can you discuss science, if you betray the basics of scientific thought with each new statement of yours?

    Yes, that’s very clear.

    However, I strongly doubt that gpuccio’s interlocutor is willing to at least understand it.
    Hey, I could be wrong on this too. Let’s watch and see how their discussion proceeds.
    I admire Doctor GP for the patience he displays when dealing with folks who at least are perceived as not being interested in understanding (not agreeing) gpuccio’s or UB’s points.
    Understanding someone’s arguments is not necessarily agreeing with them.
    If there’s any misunderstanding then more questions are asked. It’s a simple communication rule.
    But I don’t see that here.
    On several occasions I have not understood gpuccio’s comments that are very technical -way above my capacity to understand it- so I’ve asked questions which gpuccio has answered with additional explanations or examples until I have finally understood his point, which has been clearly stated.
    Here I perceive a one way communication channel: UB and gpuccio explain clearly, ask logical questions. From the other side I don’t see anything worth reading.
    Just that pathetic.
    Oh, well. What else is new?

  32. 32
    CuriousCat says:

    Maybe this would be an unnecessary repetition of what I said above, but even I was not expecting that much of a “verification” of what I said 🙂 The whole debate has totally turned into who needs to “prove” what he/she suggests. And, as being someone who sympathizes the ID movement (having followed it for the last 2-3 years), I am sorry to say that most scientists and the majority of the public who follows the dominant views in scientific community always puts the “best” naturalist explanation (though that explanation may be too incomplete or even absurd to some) as the null hypothesis, and expects the opposite view to disprove it. And due to the very reason why the explanation is too incomplete (almost impossible to calculate, or mimic in a controlled experimental setting, etc.), it is almost impossible to reject this hypothesis. Hence, particularly in historical sciences, I believe, ideological dominance is very important, and a naturalistic “explanation” (though it may be lame) has that advantage.

  33. 33
    gpuccio says:

    CuriousCat:

    I am not sure that you use the term “null hypothesis” in a correct way.

    The “null hypothesis”, in hypothesis testing, is not a default, which is true unless proved false. It is, rather, the hypothesis that the effect (configuration) we observe has no specific cause, and is rather a random effect, usually due to sampling. So, what we do is to compute the probability of observing an effect at least as big as the one we observe in our data, if the null hypothesis is true. If the probability is lower than a pre-determined treshold, the null hypothesis is rejected.

    That has nothing to do with accepting an explanation by default, just because it is “naturalistic” (wahatever it means). That attitude can only be described as a philosophical prejudice, IOWs a cognitive bias.

  34. 34

    Matt,

    I do have to thank you for publishing this on biosemiosis.org.

    There are two distinct categories of semiotic systems. One category uses representations where the arrangement of the medium (like a pheromone) is reducible to the physical properties of the medium itself; [This is what I’ve been calling INTRINSIC INFORMATION] the other uses representations that have spatial (dimensional) orientation and are not reducible to their physical make-up (like the words on this page). [This is what I’ve been calling EXTRINSIC INFORMATION] The first type is found throughout the living kingdom. The second type is found nowhere but in recorded language and mathematics (and in the genetic code).

    Thank you for backing me up there.

    Matt, you did not read that correctly. Both categories of representations are still genuine representations, and therefore require an interpretation that is not derived from the physical properties of the medium itself. In other words, its the exact opposite of what you suppose.

    Since this data is new to you, you might want to throttle back just a bit and let the information soak in a minute

  35. 35
    Marfin says:

    Curious Cat. You may start with the belief nature did it , but once the evidence begins to stack up higher and higher against this view ,if you are being true to science you change your view.
    So in OOL experiments the evidence points to, intelligence, information , life only coming from preceding life, complexity that cannot be overcome by the random mixing of chemicals.These are the facts, you may still BELIEVE nature is all there is , but you do so not because of the evidence, but in spite of the evidence and because of your ideology.
    You then revert to silly statements like Matspirit`s “please prove something did not exist “.
    Lots of great scientific work has been achieved beginning with the imaginations of great men and women , but once the testing and experimentation starts you have to go where the evidence leads and drop the ideology.

  36. 36
    CuriousCat says:

    gpuccio:

    I am not sure that you use the term “null hypothesis” in a correct way.

    The “null hypothesis”, in hypothesis testing, is not a default, which is true unless proved false. It is, rather, the hypothesis that the effect (configuration) we observe has no specific cause, and is rather a random effect, usually due to sampling.

    Actually, no. Null hypothesis is the default, or status quo, or general (dominant) view on a problem. Under certain conditions (like Fisher used in Lady Tasting Tea) you may use the hypothesis test as a test for “chance hypothesis”: the current sample statistic may be explained without referring to the specific causes, but is likely to be observed only referring to the probability distribution of the random variable in question. However, in many other cases, hypothesis tests are used to refute the the current belief for the specific problem at hand, in favor of a research (novel) hypothesis. Typical example: the speed of light being the maximum attainable speed in the universe is a null hypothesis, and there are various experimental attempts (which have come out to be false, so far) to refute it. That’s why null hypothesis is usually taken to be an equality (BTW, being a frequentiest, I’m considering only the frequency interpretation).

    The way ID movement interprets (and utilizes) the hypothesis tests is, I believe, correct from an frequency point of view, but this is only ONE of the areas in which hypothesis tests are used. The more general application is, as I tried to point out, a fight between traditional view (null hyp., usually an equality) vs. the novel view (alternative hyp., usually an non-equality).

    Another example may illuminate the point. Say that you want to make sure that a bridge is safe for transportation of vehicles. If generally authorities (scientists, media, politicians, people, whatever you call) believe that bridge is safe, then a person who claims that bridge is not safe should prove his/her claim. Hence, the null hypothesis is that bridge is safe (a measure with some confidence limit is to be calculated for safeness limits), and the person who makes the opposite claim should show that the measurement that he/she makes will exceed these confidence limits. On the other hand, if a bridge is built for the first time in history, with many opposing scientists and people, then the null hypothesis becomes “bridge is not safe”, and the people who built the bridge should show their claim to be true by exceeding the confidence limits constructed by the null hypothesis, that the bridge is not safe. So, the proof of burden lies in opposite views for the SAME problem, but under DIFFERENT circumstances. This may seem strange, there’s an subjectivity at the very heart of the problem. It should also be noted that the very same samples and statistics may lead to different statistical results when the hypotheses are presented in two different ways.

    Now, when it comes to the problem facing ID movement, ID people are always expected to bring “proof” to why a certain mechanism (which is vaguely defined) would not work. In this scenario, ID suggestions are always taken as alternative hypotheses. This makes a serious (and unjust) challenge to ID view, since it is difficult to reject null hypotheses (you need SIGNIFICANT, to be more precise statistically significant results to do that). For the question at hand, the null hypothesis is taken to be “life started by natural processes” (the view held by many scientists), and it is up to ID people that they have to SHOW it didn’t start it that way. From this perspective, “DNA/RNA system we see today may NOT be the only one that ever existed, so a plausible trajectory for the occurrence of life may be through the RNA world” becomes the null hypothesis. I would like to emphasize that I do not support that this is how this discussion to be done; I do not like this unfair tip of balance to the side of naturalism in sciences. But that’s how it currently is. This is a serious obstacle that ID movement should overcome, I believe.

    I hope I am more clear on this.

  37. 37
    CuriousCat says:

    Marfin:
    Curious Cat. You may start with the belief nature did it , but once the evidence begins to stack up higher and higher against this view ,if you are being true to science you change your view.

    I do not think that anyone can be true to science or be honest, or we go where evidence go. We are all driven by our beliefs, theories, traditions, good habit, bad habits, etc. We think and see the universe in terms and in the light of them.

  38. 38
    bill cole says:

    CuriousCat
    Thank you for your explanation. I agree with Gpuccio’s working definition however if the null hypothesis has been expanded to default inference this is important information you are providing. Can you sight some evidence to back up your claim here so we can put your claim into context?

  39. 39
    gpuccio says:

    CuriousCat:

    Thank you for your clarifications. I must say that, as a medical doctor, I use the concept of null hypothesis only in the context of hypothesis testing. I was not aware of the contexts you describe, which however at first sight do not seem convincing epistemologically, at least to me.

    I remain convinced that in science there is no default theory, least of all the one supported by consensus, only competing explanations which have to demonstrate their own strength by explaining observed facts. IMO, the burden of proof is the same for all: to demonstrate that the proposed explanation is the best one available.

    By the way, I am a frequentist too! 🙂

  40. 40
    gpuccio says:

    CuriousCat:

    By the way, in ID a simple application of the concept of null hypothesis according to hypothesis testing is available: the null hypothesis is that biological information originated without any design intervention.

    Neo darwinism proposes a specific algorithm for that, and therefore that alogorithm can be tested according to the null hypothesis concept. IOWs, the probabilistic resources can be evaluated, as can be evaluated the contribution of NS. If the probability of observing complex functional information as we see in biological beins remains infinitesimal, even after factoring all the probabilistic resources and the possible contributions of selection (which is the absolute truth), then from all scientific perspectives the null hypothesis must be rejected, and the alternative explanation of design seriously considered as the best scientific explanation.

  41. 41
    CuriousCat says:

    Thanks for the question, bill cole..

    Here’s a quick link I’ve googled.
    http://faculty.montgomerycolle.....ds_ch9.ppt

    On page 4, it says “Null Hypothesis: A hypothesis about the parameter in question that often denotes a theoretical value, an historical value, or a production specification.”

    It also adds:
    “Alternate Hypothesis: A hypothesis that differs from the null hypothesis, such that if we reject the null hypothesis, we will accept the alternate hypothesis.”

    On page 5, it reads: “Usually the null hypothesis represents a statement of “no effect”, “no difference”, or to put another way “things haven’t changed”.

    I guess when you read “no effect” and “no difference”, this seems to validate your point, but also consider the last description: “things haven’t changed”. Also consider the first definition, it says “theoretical value”, an “historical value”, or a “production specification”.

    So, the story is something like that (including a little bit of Popper’s view). We start with a null hypothesis, usually showing ignorance. Say, we would like to do a drug trial for a disease with no known cure. Here, a bias in physicians minds are already formed, since they know (believe) that there is no cure for this disease. Suddenly some scientist come out and say that he has found a cure for the disease. What he would be expected to do is the following. Take two groups of people of sufficient size, give placebo to one group, treat the others with the cure. Our (null) expectation is that cure would not work, but that scientists expects the opposite (alternative) hypothesis. We define two variables, p1 and p2, which denote the probability of getting well after being infected with the disease with no cure and the suggested treatment. So, the architecture of the hypothesis is as follows:
    Ho (null hypothesis): p1 = p2
    H1 (alt. hyp.): p1 p2
    Here, note that though the null hypothesis looks the same, the meaning of p1, p2 are totally different. Now, the null hypothesis is the suggestion of scientist with the new treatment, when no one thought that this treatment was possible. There’s been a paradigm change, and the new paradigm is this one.

    Another example, more similar to ID case, may be given for Lady Tasting Tea. Here, for the first time, when that lady suggests that she can determine whether sugar or cream is added to the coeffe first, this sounds like an extraordinary claim. Hence the null hypothesis is “she cannot achieve what she claims”, since the status quo related with those “magical claims” dictates this view. In probabilistic terms, p (=prob that the chosen order by the lady is true) is taken to be equal to frequentist probability (=1/2). So, the architecture of the hypothesis test is as follows:
    H0: p = 1/2
    H1: p > 1/2
    Now, say that years have passed and that lady, having passed most of these tests, is now an authority, and furthermore we have scientific explanation of how she does that. Hence, people now generally believe (or know) that she will give the correct order for a given coffe. Note that I have added scientific explanation part, just to give a “rational” background for the new belief in society. Furthermore, we have a historical (or semi-theoretical) record of her success as p = 0.8.

    Suddenly, a coffee maker comes out and says that he has a new product, and the smell will mask whether milk or sugar (actually, I’ve forgot the exact story of adding milk/sugar/cream) is added first. Note that if this happened in Fisher’s time, people would not even feel the need to test this, since this was the status quo then. However, now it’s not. So the new test would be:
    H0: p = 0.8
    H1: p < 0.8

  42. 42
    CuriousCat says:

    Continued from the previous loong post 🙂
    Now back to the current discussion. In my opinion, in almost all cases I have seen related evolution, etc., the null hypothesis is always taken by the naturalist explanation, though it may very premature. Take OOL case. Before the RNA world, if we were discussing this topic, the null hypothesis would be taken by the self organization of the far-from-equilibrium systems, and ID would be expected to falsify this view. For instance MatSpirit has written:
    That’s what I want you back up! Prove that the DNA/RNA system we see today is the only one that ever existed. Prove that a simpler system didn’t exist long before and evolve the start of our present system. Give us some evidence for this beyond your mere assertion. Until then, thank you for your assertion, we have received it and nobody outside of ID is impressed.

    Note that how MatSpirit has taken the null hypothesis chair, without anybody realizing 🙂 (no offence, just kidding). My question is how is this view justified in gaining the status quo? The last sentence is also a striking one, I believe. “Nobody outside of ID is impressed”. It is because most scientists believe that there’s a naturalistic explanation (for historical, or whatever reasons).

    Or you may take the typical claim: “Show that Darwinian evolution would not yield the current complex mechanism”. Now again, this view has taken the luxury of having the null hypothesis. You cannot falsify it because the suggested mechanism is not very detailed, we cannot simulate or experiment in the required time or spatial scales.

    I hope I didn’t bore anyone. This is probably my text record for ID discussions. 🙂

  43. 43
    CuriousCat says:

    I don’t know what happened, but my first post has been pretty much messed up! After the statement:
    H1 (alt. hyp.): p1 p2 (which should actually have been p1 is less than p2), one paragraph is gone!

    For those who read, please just skip to the 2nd example, related with the lady tasting tea.

  44. 44
    Daniel King says:

    Barry:

    Here’s a clue. Your inability to follow Upright Biped’s argument is not the same as his failure to make an argument. Write that down.

    Thank you for your condescension, but you take liberty in assuming a lack of understanding on my part. I’m satisfied that Upright made an argument. And I’ll say that it’s a good one.

    But that’s not the point. The point is that making an argument is just the start of an investigation, and I’m asking for at least one (just one) next possible step in testing the argument. That’s how science works.

  45. 45
    Daniel King says:

    Upright Biped:

    Tell us about the test given on Biosemiosis.org, and how you arrived at your conclusion that it doesn’t exist.

    I’ve been there and I don’t see a test.

    Would it kill you to post it here?

    Think of all the electrons we might save.

  46. 46
    Mung says:

    I’ll be impressed if Daniel King ever manages to actually state the biosemiotic hypothesis.

    To date I’ve seen no evidence that he is either capable of or willing to do so. Yet he continues to claim that he knows it is wrong.

  47. 47
    bill cole says:

    CuriousCat
    Thanks for the detailed explanation by no you are by no means the longest post 🙂

    That’s what I want you back up! Prove that the DNA/RNA system we see today is the only one that ever existed. Prove that a simpler system didn’t exist long before and evolve the start of our present system. Give us some evidence for this beyond your mere assertion. Until then, thank you for your assertion, we have received it and nobody outside of ID is impressed.

    Note that how MatSpirit has taken the null hypothesis chair, without anybody realizing 🙂 (no offence, just kidding). My question is how is this view justified in gaining the status quo? The last sentence is also a striking one, I believe. “Nobody outside of ID is impressed”. It is because most scientists believe that there’s a naturalistic explanation(for historical, or whatever reasons).

    I think in this case it is a little early because a hypothesis about how life started has not been established. Without a hypothesis that it happened without cause (randomly) and this is how it happened. Can we have a null hypothesis at all? People who understand the problem of life realize that simple and life are opposing terms. For life to occur ( the ability rapidly convert outside energy to work rapidly and continuously plus self replication) at the molecular level requires more complexity than man currently has ever devised on his own. The basic components of life like enzymes, replication systems, and an energy generating system etc are highly interdependent components of the system. The idea that this came form a simpler past has failed as a viable argument at this point and I do get any argument form evolutionary biologists any more. They claim evolution starts with first life.

  48. 48
    CuriousCat says:

    I think our main disagreement lies in the following point:

    bill cole
    I think in this case it is a little early because a hypothesis about how life started has not been established.

    gpucio
    I remain convinced that in science there is no default theory, least of all the one supported by consensus, only competing explanations which have to demonstrate their own strength by explaining observed facts. IMO, the burden of proof is the same for all: to demonstrate that the proposed explanation is the best one available.

    The views you pronounce seem to be in accordance with what Meyers calls inference to the best explanation method. Given that science progresses via this method, Meyer (and very successfully) demonstrates that ID should be regarded as a scientific theory, and the best one yet to explain OOL and Cambrian explosion. But my question is why is this very well argued view not accepted by the majority of scientific community? The reason I believe is that inference to the best explanation is not how science works, or at least for most cases.

    I believe that a combination of Popper-Kuhn view is the best explanation of progress in science. Scientists do not want to let go of the existing theories easily. And I believe these views are akin to hypothesis testing (Popper method) and likelihood function (inference to the best explanation). In likelihood functions, we use the parameter estimates, which best fit to the existing underlying distribution. However, there’s a serious difference between explanations in scientific theories and this method. In science, explanations are not considered simultaneously, but in a historical order. Say that someone comes up with a theory 100 years ago. After the initial tests, if that theory still survives, that theory becomes the null hypothesis (status quo). After 50 years of testing (and no significant falsification of the null hypothesis), a new theory is suggested. I guess, in your opinions, these two hypothesis are to be compared on equal grounds for their explanation power. However, this is not what is actually observed. Scientists would be reluctant to let go of the old theory in favor of the new one. There would be a bias for old theory. So it is not a simple inference to the best explanation. If there are not observations which refute the first theory, scientists would not adopt the new theory, although it may have higher explanatory power. I think the very good example would be parallel universe speculation, which has a higher explanatory power, but cannot replace the standard view.

    So one may ask, why do scientists tend to stick with older and working hypotheses? Apart from psychological reasons, I believe there’s a very good statistical explanation: Old theories are tested over and over again. and these theories are BEFORE this set of data are collected. For the null hypothesis that nothing can be faster than light, for instance, many experiments and new data, possibly not anticipated when this theory was first constructed, have been accumulated and used to falsify H0. It has still survived these tests. If a person comes with a new theory, even with a better explanation power, but suggests that there are things faster than light, it should be realized he/she has constructed this theory AFTER the data. Hence, it is not simply a matter of explanation, but this new hypothesis (though explains all the current data, or even more) has NOT passed the tests, the old theory has passed. It is constructed using the very same data, used to test the old hypothesis.

    For the technical details, one may refer to a well written paper on the difference of hypotheses after or before the data:
    https://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjFo_Pkz_fNAhVIBSwKHZDaAx4QFggaMAA&url=http%3A%2F%2Fwww2.psych.ubc.ca%2F~schaller%2F528Readings%2FKerr1998.pdf&usg=AFQjCNE78DvIq0OOx8x2KR9u_jMbY4ge_A&bvm=bv.127178174,bs.1,d.bGs

    Again, coming to the current discussion, since different naturalist theories have passed too many tests, scientists use ANY naturalistic theory as a null hypothesis (which is actually not related with the statistical reasoning I’ve given, since this should apply to a single scientific theory, not to a philosophical preference) and do not take new (especially non-naturalistic) theories on equal grounds with a naturalistic one, though this new theory has a higher explanation power.

    As a note, let’s see what MatSpirit has written:
    So if the extravagantly complex life we see today is material and is known to have come from material causes (other life), why not believe those material causes extend all the way back until life was so simple that non living material causes could produce it?

    He reasons that since theories on evolution has worked, it is expected that OOL can be explained by mechanistic principles. When ID community says that for OOL we have a better explanation (for the current data, a higher likelihood function), this does not persuade the scientific community, since they do not want to let go of their previously working (and ideally tested, but for evolution case, not so much tested) theory.

    Overall, I think the main problem lies, as pointed out by Gpuccio, in epistemological views.

  49. 49
    gpuccio says:

    CuriousCat:

    I can generally agree with what you say at #48. But I would like to make a couple of comments.

    IMO, inference to the best explanation describes well how science should work. And indeed, in many cases, does work.

    But in many cases, as you suggest, science works differently. Kuhn and Feyerabend have reasoned very well on those aspects.

    Now, I believe, as I have said, that appeal to consensus is a very tricky driving force in science, and is the cause of many cognitive biases.

    Still, I can accept in a very general way your concept that well assessed theories should have some “authority” in the face of new, extravagant ones. That is simply common sense.

    But it does not apply to neo darwinism. Indeed, here the situation is completely different:

    1) The neo darwinian explanation has never explained anything in terms of complex functional biological information. It is completely conjectural about that problem. It is not supported by any facts, nor has it passed any tests. Almost all the “successes” of neo darwinian evolutionary theory are simply confirmations of common descent, never confirmations of any capability of the theory to explain complex functional information.

    2) The assumption that science has explained many thing in a naturalistic way, and therefore we should be confident that even biological information will be explained in a naturalistic way, is completely wrong, for two important reasons:

    a) If we have succeeded in explaining some things in a way, there are no reasons to believe that we can explain completely different things in the same way. This is a very simple, but important concept. Biological realities are very different from other contexts. That has always been recognized in the course of human thought.

    b) But the most important point is: what does “naturalistic” mean? I have always rejected the word. ID theory is in now way “non naturalistic”. It just states that there are fundamental differences between designed things and non designed things, and that in many cases we can make a safe inference to design.

    Now, what is “non natural” in that? Are computers supernatural entities?

    ID simply infers a conscious designer for biological information. We are conscious designers. Are we supernatural entities?

    Now, the usual objection is: but a designer of biological information must be supernatural. OK, what does that mean? Let’s say that there are conscious entities in reality that can design biological things, and of which we have at present no knowledge or understanding. Are they “supernatural”? Even if they are part of reality?

    Were quantum wave functions supernatural when nobody had the least idea that something like that could exist?

    The simple truth is: “natural”, “nature” and “naturalistic” have no unequivocal meaning. In a sense, they have no meaning at all.

    The really bad meaning that most people seem to give to those words is: we can accept only explanations which are in accord with our present view of reality.

    Must I emphasize how such an attitude is completely unscientific?

  50. 50
    bill cole says:

    CuriousCat

    The views you pronounce seem to be in accordance with what Meyers calls inference to the best explanation method. Given that science progresses via this method, Meyer (and very successfully) demonstrates that ID should be regarded as a scientific theory, and the best one yet to explain OOL and Cambrian explosion. But my question is why is this very well argued view not accepted by the majority of scientific community? The reason I believe is that inference to the best explanation is not how science works, or at least for most cases.

    This is quite accurate. As it turns out Darwin also used inference to the best explanation to extrapolate the data he collected to hypothesize that natural selection could explain life’s diversity. Many evolutionary biologists, in fact almost all I meet on the pro evolutionary blogs no longer believe that natural selection alone explains diversity. Neutral theory is an additional hypothesis, natural genetic engineering is another.

    Both intelligent design and a stochastic theory of evolution are in the same boat. You can make an inference from the evidence but there is no mechanism that you can test to validate transition from one specie to another.

    Universal Common Decent is an untested hypothesis and in big trouble because there are origin events like the first eukaryotic cell that cannot be explained by stochastic processes because of the massive amount of new DNA sequences that have to become organized to build these cells.

  51. 51
    Daniel King says:

    Mung @ 46 would

    …be impressed if Daniel King ever manages to actually state the biosemiotic hypothesis.

    Upright Biped quoting Howard H Pattee on the Gritting Your Teeth thread:

    Biosemiotics is the study of all forms of signification and communication. It recognizes that life is distinguished from the nonliving world by its dependence on signs and symbols.

    Mung:

    Yet he continues to claim that he knows it is wrong.

    I don’t remember saying it is wrong. I’m just waiting for somebody to tell me what it’s good for scientifically.

  52. 52
    CuriousCat says:

    gpuccio:
    I agree with most of what you have written. I again emphasize that I have brought that topic into attention not that I believe it is the right method to follow, but it’s the method (if there’s any method at all), which I believe to be followed in the scientific community. As I have said, that’s the main obstacle that ID community have to overcome.

    bill cole:
    As it turns out Darwin also used inference to the best explanation to extrapolate the data he collected to hypothesize that natural selection could explain life’s diversity.
    That’s the point I disagree with Stephen Meyer’s analysis. I believe, at the time, highly influenced by the surrounding philosophical tendencies, there was a bias towards mechanistic (or naturalist. I agree the term is vague, but that’s another discussion) explanations, and that’s how Darwin’s views were borne and accepted by the scientific community. Since then from the perspective of scientific community, intelligent design and stochastic theory of evolution are not in the same boat, but ID is constantly trying to shake the boat in which evolution is sitting. Again I’d like to point out that this is not how it should be, but that’s unfortunately the way it is.

  53. 53
    bill cole says:

    CuriousCat
    Here is an independent discussion (of Meyer) of inference to the best explanation as used by Darwin. This paper has surprised many evolutionary biologists.

    Van Fraassen’s Critique of Inference to the Best Explanation
    Samir Okasha*

  54. 54

    DK at 45

    I’ve been there and I don’t see a test.

    That’s hard to believe. On the front page of my website I present the necessary material conditions of semiosis, under the title “There are four material conditions required to confirm and instance of translated information”.

    I think it would be difficult not to see these material conditions as the basis of an empirical test, particularly since that is the way they are presented. But I go further, and present them specifically as a test in a section entitled “A Scientific Hypothesis of Design”. This is a page that begins with the words “The validity of any test proposing to identify the action of an unknown intelligence…”

    So yes, I find it hard to believe you don’t notice the test, or the fact that the test has already been fully and repeatedly answered in the literature. Frankly, your response has all the earmarks of avoidance, which is typically the set-up for a dramatic dismissal. I’d be delighted to be shown otherwise.

  55. 55
    CuriousCat says:

    bill cole
    Thanks very much for the paper. I have just taken a quick look, it seems quite interesting. Probably, I’ll be reading it tonight.

  56. 56
    MatSpirit says:

    Gpuccio @ 16:

    I’m using the online dictionaries definition of organism: “an individual animal, plant, or single-celled life form.” Wrap the molecule up in a membrane if you wish.

    I’m defining “life” as anything that reproduces itself. This isn’t a perfect definition. Mules don’t reproduce, but they’re clearly alive, for example, but it works pretty well for sub cellular life.

    I applaud your declaration of non conformity. The western world admires those who break away from conventional thought and boldly think ideas of their own. Galileo comes to mind. The problem is that for every Galileo, there are at least a thousand deluded souls working out a new route to China in their basements. You have to keep those odds in mind.

    I agree with you that there’s a very strong cognitive bias at work here, but I think it’s held by those who believe God made life and are going to keep believing that no matter what the evidence. If I didn’t think that, reading this site and observing the twists and turns of the true believer’s minds would soon convince me otherwise.

    Proteins: Remember I have no reason to think the first living thing used proteins, but if they did, small proteins are known to self assemble and would have been available for use without having to manufacture them, just as humans use vitamin c from their environment instead of manufacturing it.

    If a cell did find a way to manufacture proteins, that would have opened up a vast new protein deficient area to live in, giving that cell a clear advantage over its compatriots.

    As for how the manufacturing was accomplished, without knowing what life was like at that time, I can’t say except that the proteins were probably much simpler, using only a few amino acids, and the manufacturing was probably much simpler too. (And slower and less efficient – lots of advantages to be had for newly evolved improvements.)

    So, please, answer this very important point: why should a functional sequence which has a very definite function according to some set of rules, and is conserved and propagated exactly for that reason, become a sequence which has no more relationships with its initial function, but strangely starts to represent another completely different set of rules, according to a purely symbolic code, which can only work if a complex translation apparatus, including 20 aaRNA synthases, the ribosome, and many other components, is already working? This is really beyond my frail imagination.

    I quoted that paragraph because your thinking seems to be a little confused here. You seem to be implying that the organism would somehow switch it’s function from self-copying to protein synthesis. It would me far more likely to keep its self copying function at all costs (on pain of extinction) and add protein manufacturing to its repertoire. I also doubt that protein manufacture started with a full 20 amino acids. Two or three of the most common ones would be more likely.

    GP:

    “To say that life is so well understood is really the statement of the millennium! Are you really convinced of what you are saying? I am afraid that there is no hope.

    Go to http://www.uncommondescent.com.....l-biology/ on this site and see what Craig Ventor says about that:

    We know about two-thirds of essential biology. We’re missing a third,” Venter said.

    And we’ve got the other third boxed in. As far as elan vital or anything non-physical about life is concerned, the debate is over. You lost.

    I don’t think there’s much reason to reply to the rest of the message. You don’t believe evolution can generate CSI, it’s well established that it can, you pride yourself on your independence of thought and I’m not holding my breath until you find that new route to China. Good luck on your quest.

  57. 57

    You don’t believe evolution can generate CSI, it’s well established that it can

    What is required for evolution, Matt? Or do you think that evolution (rv+ns) occurs without any physical or organizational requirements of any kind whatsoever?

  58. 58

    Matt, it’s interesting that you want to cite Venter, who has reduced a cell down to its minimal functional state within a tightly controlled environment (below which the cell fails), while you demand that Life can thrive far below that level — apparently without limits of any kind. Your imagination ignores experimental results, and it seems to never even occur to you.

    a short passage from a previous conversation discussing Venter’s minimal cell:

    The central assumption is that translation can be reduced and made simpler, and simpler, and simpler still, to the point that it’s clearly simple enough to spontaneously come into being. That’s the overarching theory, and whatever findings we have that can help circle the wagons will be used to do exactly that. And that’s fine as far as it goes, but it literally does nothing whatsoever to negate the mountain of (rigorous) physical evidence that says an autonomous or perpetual translation system doesn’t get any simpler than what is required to specify itself in a medium and translate that medium into functional effects. Nature shows us precisely how specification and translation occur. Our understanding of it is entirely coherent. Nature shows us that discontinuous association is what establishes a medium, and that the coordination of many associations is what enables the capacity to describe the system in a transcribable memory. This is what von Neumann referred to as the “threshold of complexity”, beneath which the system degrades. This is what is required to bridge Pattee’s “epistemic cut” between rate-dependent construction and rate-independent control. It’s Polanyi’s classic “boundary condition”, and is the physical reason Crick proposed the “adapter hypothesis”. It’s what Venter left untouched in the minimal cell.

    And yet, in every debate on the matter, in every research initiative, in every praiseworthy publication of any kind whatsoever, the immediate assumption is that no such threshold exist. Complexity — of the kind capable of specifying the genetic translation system — is assumed to form spontaneously. Reduction below a point of complexity that nature clearly demonstrates to us as physically and logically necessary (which is specifically referred to in the publications of truly gifted researchers) is intellectually obligatory.

    But without semiosis you have a dynamical process that establishes no medium and has no physical means to specify anything from that medium. It doesn’t have the organization (the systematic capacity) required to break the bonds of determinism and do something locally interesting — like organize a system or describe itself in combinatorial permutations, both of which it must do. The belief that a translation apparatus can be dynamically “specified” from the surface properties of its constituent parts over time has failed. The concept hasn’t been falsified, it’s been invalidated. But it hasn’t been invalidated because we’ve tested every possible combination of matter. It’s been invalidated because we know what is necessary, and at every level, it’s the wrong paradigm.

  59. 59
    gpuccio says:

    MatSpirit:

    Briefly (it is probably not worthwhile to spend much time with this).

    “Wrap the molecule up in a membrane if you wish.”

    A molecule wrapped in a membrane is not a cell.

    “I’m defining “life” as anything that reproduces itself. This isn’t a perfect definition.”

    Definitely. Life is much more.

    “The problem is that for every Galileo, there are at least a thousand deluded souls working out a new route to China in their basements. You have to keep those odds in mind.”

    I like those odds. I like challenges.

    “I agree with you that there’s a very strong cognitive bias at work here, but I think it’s held by those who believe God made life and are going to keep believing that no matter what the evidence. If I didn’t think that, reading this site and observing the twists and turns of the true believer’s minds would soon convince me otherwise.”

    Let’s say that there are two very strong cognitive biases at work here. I like neither.

    “Proteins: Remember I have no reason to think the first living thing used proteins, but if they did, small proteins are known to self assemble and would have been available for use without having to manufacture them, just as humans use vitamin c from their environment instead of manufacturing it.”

    So, you are saying that at this state those proteins were not part of the information in the cell, just an environmental resource. OK. let’s go on.

    “If a cell did find a way to manufacture proteins, that would have opened up a vast new protein deficient area to live in, giving that cell a clear advantage over its compatriots.”

    The problem is not only how to manufacture a protein. The problem is how to store and transmit the information. They are two different problems. You seem to completely ignore the second.

    “As for how the manufacturing was accomplished, without knowing what life was like at that time, I can’t say except that the proteins were probably much simpler, using only a few amino acids, and the manufacturing was probably much simpler too. (And slower and less efficient – lots of advantages to be had for newly evolved improvements.)”

    Again, the problem is not so much how to manufacture, but where is the information. Remember, proteins cannot pass their information. They are not genetic material.

    “I quoted that paragraph because your thinking seems to be a little confused here.”

    Maybe. Let’s see.

    “You seem to be implying that the organism would somehow switch it’s function from self-copying to protein synthesis. It would me far more likely to keep its self copying function at all costs (on pain of extinction) and add protein manufacturing to its repertoire. I also doubt that protein manufacture started with a full 20 amino acids. Two or three of the most common ones would be more likely.”

    Again, you miss the point completely. Of course, the organism must retain its direct copy function. The problem is: how did the system to store information for proteins (the genetic code) arise from nucleic acids whose only function was to copy themselves to effect functions according to the rules of nucleic acids?

    I will try to be more clear. Let’s say that we have a sequence of, say, 1000 nucleotides. That sequence is functional because it effects the function of a rybozime. OK?

    So, that sequence is passed and preserved by selection because it is functional. But its function has nothing to do with the future genetic code, least of all with protein sequences and their possible function. OK?

    Now, what I am asking is: how can RV + NS generate, from sequences like that, new sequences which acquire a symbolic value, so that they can store and transmit the information for proteins? Especially if you consider, that the translation of that coded infotmation implies the ribosome and 20 very complex proteins?

    The problem here is not if the original proteins were simple (I don’t believe they were), but rather where was the information for those proteins stored before the genetic code existed (you will accept that there was some time when it still did not exist).

    Or, if you prefer, if proteins still did not exist as a form of functional information stored in the cell and transmitted, and the genetic code arose first, then how could the genetic code evolve to store symbolically an information which was nowhere to be found?

    These are very precise questions, and I would appreciate an answer. Possibly something better than “without knowing what life was like at that time, I can’t say”.

    Regarding Venter, you are completely equivocating his statement. He was simply saying that two thirds of the genes which were retained in his “minimal” prokaryote were in some way known genes, while the function of about one third remained unknown. That is completely different from saying that we know how a prokaryotic cell works. If you cannot understand the difference, there is really no hope.

    For example, we know exactly all the cells of C. elegans, and in particular all the neuronal connections. But in no way we understand hoe C. elegans works. least of all how its nervous system works. Please, read sonmething at the wormbook site:

    http://www.wormbook.org/

    and see for yourself.

    “As far as elan vital or anything non-physical about life is concerned, the debate is over. You lost.”

    I have not even started that debate with you, and I have already lost? 🙂

    “I don’t think there’s much reason to reply to the rest of the message.”

    Strangely, I would agree with you: my expectations about your answers have become very low.

    “You don’t believe evolution can generate CSI”

    It can’t.

    “it’s well established that it can”

    Examples, please.

    “you pride yourself on your independence of thought”

    I do.

    “and I’m not holding my breath until you find that new route to China.”

    Never expected that from you. I can go on while you continue breathing.

    “Good luck on your quest.”

    Thank you. It’s a great quest.

  60. 60
    bornagain77 says:

    MatSpirit, among many other false claims, also falsely claims that,,,

    “As far as elan vital or anything non-physical about life is concerned, the debate is over. You lost.”

    That is an interesting claim for MatSpirit to make since non-local, beyond space-time matter-energy, quantum entanglement has now been found in molecular biology on a massive scale. In every DNA and protein molecule.

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1141908409155424/?type=2&theater

    Quantum entanglement, via quantum non-locality, simply is not reducible to any matter-energy explanation.

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Moreover, it is important to learn that ‘non-local’, beyond space and time, quantum entanglement (A. Aspect, A. Zeilinger, etc..) is its own independent entity that is separate from matter-energy and that it can be used as a ‘quantum information channel’,,,

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

    Moreover, classical information is found to be a subset of quantum entanglement/information by the following:

    “What happens is this classical information (of DNA) is embedded, sandwiched, into the quantum information (of DNA). And most likely this classical information is never accessed because it is inside all the quantum information. You can only access the quantum information or the electron clouds and the protons. So mathematically you can describe that as a quantum/classical state.”
    Elisabeth Rieper – Classical and Quantum Information in DNA – video (Longitudinal Quantum Information resides along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    Scientists show how to erase information without using energy – January 2011
    Excerpt: Until now, scientists have thought that the process of erasing information requires energy. But a new study shows that, theoretically, information can be erased without using any energy at all. Instead, the cost of erasure can be paid in terms of another conserved quantity, such as spin angular momentum.,,, “Landauer said that information is physical because it takes energy to erase it. We are saying that the reason it (information) is physical has a broader context than that.”, Vaccaro explained.
    http://www.physorg.com/news/20.....nergy.html

    New Scientist astounds: Information is physical – May 13, 2016
    Excerpt: Recently came the most startling demonstration yet: a tiny machine powered purely by information, which chilled metal through the power of its knowledge. This seemingly magical device could put us on the road to new, more efficient nanoscale machines, a better understanding of the workings of life, and a more complete picture of perhaps our most fundamental theory of the physical world.
    http://www.uncommondescent.com.....-physical/

    Matter, energy… knowledge: – May 11, 2016
    Running a brain-twisting thought experiment for real shows that information is a physical thing – so can we now harness the most elusive entity in the cosmos?
    https://www.newscientist.com/article/mg23030730-200-demon-no-more-physics-most-elusive-entity-gives-up-its-secret/

  61. 61
    bornagain77 says:

    As well, Quantum Information is also found to be ‘conserved’:

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Finding conserved Quantum Information/Entanglement in molecular biology on a massive scale should be very disturbing for those who are atheistic in their philosophical basis, and have spent years fighting tooth and nail against God, since such a finding is very suggestive to the fact that we do indeed have an eternal soul that lives beyond the death of our material bodies:

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video
    https://www.youtube.com/watch?v=iIyEjh6ef_8

    Verse:

    Mark 8:37
    Or what can anyone give in exchange for their soul?

  62. 62
    Origenes says:

    Matspirit @56,

    Matspirit:
    I agree with you that there’s a very strong cognitive bias at work here, but I think it’s held by those who believe God made life and are going to keep believing that no matter what the evidence.

    There is exactly zero evidence for your position.

    Matspirit:

    Gpuccio:
    “To say that life is so well understood is really the statement of the millennium! Are you really convinced of what you are saying? I am afraid that there is no hope.

    Go to http://www.uncommondescent.com.....l-biology/ on this site and see what Craig Ventor says about that:
    We know about two-thirds of essential biology. We’re missing a third,” Venter said.
    And we’ve got the other third boxed in. As far as elan vital or anything non-physical about life is concerned, the debate is over. You lost.

    I’m afraid that you’ve completely misunderstood what Ventor is saying here. He is saying that when constructing Syn 3.0 — 473 genes — two-thirds of the genes have known functions.

    “The other challenge had to do with those 149 mystery genes. Because the functions of the genes are unknown, the researchers didn’t know they were needed until they were gone. That shows how far geneticists still have to go in understanding how life works.”

    IOWs Ventor says that two-thirds of the genes of Syn 3.0 are understood wrt function. To be clear, he is not saying that two-thirds of biology is understood, as you seem to think. Understanding the functions of Syn 3.0 genes is what Venter terms ‘knowing essential biology’, well good for him … Meanwhile, evolutionary biology is nowhere near understanding two-thirds of epi-genetics, embryonal development, the evolution of biosemiosis, body plans and so forth.

  63. 63
    Daniel King says:

    Upright Biped:

    So yes, I find it hard to believe you don’t notice the test…

    I saw the word “test,” but I didn’t see a test. Instead, I saw an iteration of the original claim in a different format. Looks like circular reasoning.

    …or the fact that the test has already been fully and repeatedly answered in the literature

    Fully answered? That can’t be science.

    Repeatedly in the literature? In the Howard H Pattee theoretical literature? T’aint science, McGee.

  64. 64
    Daniel King says:

    Upright Biped:

    Frankly, your response has all the earmarks of avoidance, which is typically the set-up for a dramatic dismissal.

    Thank you for judging me and trying to save my soul.

  65. 65

    (the dramatic dismissal)

    You couldn’t be more obvious, DK. Nice job.

  66. 66
    bill cole says:

    I’m defining “life” as anything that reproduces itself. This isn’t a perfect definition. Mules don’t reproduce, but they’re clearly alive, for example, but it works pretty well for sub cellular life.

    Reproduction is just a piece and maybe thats why you think the simple to complex path is still valid. You need to convert either directly or indirectly solar energy into work at a nano scale with continuous uninterrupted production. Right now minimum life is 473 genes. Thats where the evidence is. Also there is no known path from 473 genes to cells like ours with 5000 plus genes.

  67. 67
    EugeneS says:

    Nice thread. It is amusing to see people denying the obvious truth that naturalism cannot explain how nature began to be. Pathetic denialism of the obvious.

  68. 68
    EugeneS says:

    In defence of what is termed here in the thread as cognitive bias, I would just acknowledge the simple fact that since naturalism does not hold water in the area of how everything came into existence, we are necessarily in the metaphysical realm. Theistic metaphysics appeals to me because it naturally accommodates meaning.

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