That’s Gotta Hurt

_{Barry Arrington

July 14, 2016

Intelligent Design, Naturalism}

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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:

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

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.

Comments

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.EugeneS_{July 19, 2016
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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.EugeneS_{July 18, 2016
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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.bill cole_{July 16, 2016
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(the dramatic dismissal) You couldn't be more obvious, DK. Nice job.Upright BiPed_{July 16, 2016
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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.Daniel King_{July 16, 2016
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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.Daniel King_{July 16, 2016
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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 https://uncommondescent.com/news/venter-missing-a-third-of-essential-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.Origenes_{July 16, 2016
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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/2011-03-quantum-no-hiding-theorem-experimentally.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?
bornagain77_{July 16, 2016
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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/highlight/121029_hidden_influences.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/releases/2011/06/110601134300.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/2011-01-scientists-erase-energy.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. https://uncommondescent.com/news/new-scientist-astounds-information-is-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/
bornagain77_{July 16, 2016
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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.gpuccio_{July 16, 2016
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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.
Upright BiPed_{July 16, 2016
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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?Upright BiPed_{July 16, 2016
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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 https://uncommondescent.com/news/venter-missing-a-third-of-essential-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.MatSpirit_{July 16, 2016
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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.CuriousCat_{July 16, 2016
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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.Upright BiPed_{July 16, 2016
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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*bill cole_{July 16, 2016
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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.CuriousCat_{July 16, 2016
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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.Daniel King_{July 16, 2016
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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.bill cole_{July 16, 2016
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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?gpuccio_{July 16, 2016
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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.CuriousCat_{July 16, 2016
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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.bill cole_{July 15, 2016
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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.Mung_{July 15, 2016
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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.Daniel King_{July 15, 2016
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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.Daniel King_{July 15, 2016
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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.CuriousCat_{July 15, 2016
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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. :)CuriousCat_{July 15, 2016
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Thanks for the question, bill cole.. Here's a quick link I've googled. http://faculty.montgomerycollege.edu/maronne/Ma116-brase-brase/POWER-PT-9/brase_9e_lectureaids_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 < 0.8CuriousCat_{July 15, 2016
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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.gpuccio_{July 15, 2016
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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! :)gpuccio_{July 15, 2016
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