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A Materialist Gets It (Almost)

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A recent exchange with Allan Keith illustrates how materialists have allowed their intellect to become literally enslaved to their metaphysical commitments.  Allan proves one can understand the logic fully and even accept the logic.  And then turn right around and deny the conclusions compelled by the logic.  Let’s see how:

We will pick up the exchange where Allan has admitted that we have countless trillions of examples of functional complexity, semiosis and irreducible complexity caused by humans.

___________________________________________________________

Barry:

You admit that we have countless trillions of examples of functional complexity, semiosis and irreducible complexity from humans. So far so good.

What is it about humans that enables them to cause those things Allan? Intelligence.

So now we have countless trillions of examples of functional complexity, semiosis and irreducible complexity from humans on account of their intelligence.

We have observed exactly ZERO instances of any other cause accounting for functional complexity, semiosis and irreducible complexity.

Put it together Allan. Human intelligence is the only certainly known source of functional complexity, semiosis and irreducible complexity.

Therefore, when we see functional complexity, semiosis and irreducible complexity whose origins we do not know, we have a choice:

1 Attribute it to the only cause known with certainty to produce it, i.e. intelligence.
2 Attribute it to causes that have never been observed producing it.

Answer 1 is obviously best.

Allan responds:

Option 1 does not follow from your logic. The logical option 1 would be:  Attribute it to the only cause known with certainty to produce it, i.e. Human intelligence.

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I understand Allan’s metaphysical commitments prevent him from following the logic beyond a certain point, but his response is still very sad.  I wonder if he ever gets tired of wearing those blinkers.

What is wrong with Allan’s reply?  It steadfastly ignores the glaringly obvious fact that intelligence (not the more narrow “human intelligence”) is the causal factor.

In other words, the thing about humans that makes them a special case is not that they are a member of the Animalia kingdom, or the Chordata phylum, or the Mammalia class, or the Primate order, or the Homo genus or the Homo sapiens species.  The thing that distinguishes humans is reflected in the name of the species.  (“Homo sapiens” means literally “wise man.”) The distinguishing characteristic of the species is intelligence.

It is that characteristic and nothing else that accounts for the ability of Homo sapiens to cause functional complexity, semiosis and irreducible complexity.*

Now it is certainly true that the species Homo sapiens is the only species of which we have observational evidence that it causes functional complexity, semiosis and irreducible complexity.  Allan seems to believe that fact compels the conclusion that we can infer only “human design” from an observed instance of functional complexity, semiosis and irreducible complexity.

Nonsense.  Not even Allan’s fellow materialists agree with him:

BEN STEIN: What do you think is the possibility that Intelligent Design might turn out to be the answer to some issues in genetics or in Darwinian evolution.

DAWKINS: Well, it could come about in the following way. It could be that at some earlier time, somewhere in the universe, a civilization evolved, probably by some kind of Darwinian means, probably to a very high level of technology, and designed a form of life that they seeded onto perhaps this planet. Um, now that is a possibility, and an intriguing possibility. And I suppose it’s possible that you might find evidence for that if you look at the details of biochemistry, molecular biology, you might find a signature of some sort of designer. . . . And that Designer could well be a higher intelligence from elsewhere in the universe.  But that higher intelligence would itself have had to have come about by some explicable, or ultimately explicable process. It couldn’t have just jumped into existence spontaneously. That’s the point

Dawkins understands, as Allan apparently does not, that it is the intelligence, not its instantiation in any particular species, that is important when it comes to inferring design.

UPDATE:

To his credit, Allan now admits the obvious:

Design inference is based almost solely on a comparison to human design. This can certainly be used to infer design in biology . . .

But he cannot resist adding an unwarranted disclaimer:

. . . but with only one known source of intelligence as a frame of reference, the inference is weak. That is statistical reality speaking, not me. But even a weak inference can strengthen support for ID if there were other avenues of examination that support ID.

Why does Allan consider the inference weak?  Because his metaphysical commitments, not logic, compel that conclusion.  Again, here is the logic:

  1. Object X exhibits functional complexity, semiosis and irreducible complexity.
  2. The ONLY KNOWN CAUSE of functional complexity, semiosis and irreducible complexity is design by an intelligent agent.
  3. Inferring to best explanation, the only known cause of functional complexity, semiosis and irreducible complexity (i.e., intelligent design) is the cause of the functional complexity, semiosis or  irreducible complexity in Object X.

Allan insists the inference is “weak,” even though he admits the inference as to cause is to the only known cause of the phenomenon.  Why?  Statistics.  Nonsense.  It is not a statistical analysis.  It is a logical analysis.

 

 

 

_____________

*Let’s not get bogged down with beavers and bees.  The international space station is obviously different in kind and not merely degree from a beaver dam.  Anyone who denies this disqualifies themselves from being considered serious.

 

Comments
There isn't any evidence that nylonase was the product of blind and mindless processes. There isn't even any way to test the claim. That makes it an unscientific claim.ET
March 26, 2018
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EugeneS The answer is very simple: it would not have been a code. Which is exactly what Dr Venema (a Christian by the way) is arguing. The use of the word 'code' conveys connotations that are liable to misinterpretation. https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-meyer-yarus-and-the-direct-templating-hypothesis Some one said that these posts had been debunked, I didn't see that. I erroneously latched onto a series or critiques made by Dr Gauger about a book Dr Venema had written.JVL
March 26, 2018
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JVL:
Read through the articles.
Already have, you lose. And you cannot make your case
Well, I guess you’ll just have to live with the vast majority of biologists disagreeing with you then.
They don't have a viable alternative so I can easily live with that. They don't even have a methodology to test their claims so I can easily live with that.
Well, that lengthy series of posts I was quoting from say otherwise.
No, they don't and again you cannot make your case so you loseET
March 26, 2018
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Eric, "then they are exactly an example of necessity creating specified complexity" I don't understand the "then" bit. Necessity cannot create anything, least of all specified complexity. Necessity/regularity corresponds to 0 information. If you have an unfair coin, you know before you toss it, if it will land on heads or tails. Choice between physically equivalent states is a valid causal factor. Choice causation is not physical but formal and does not (apparently) happen in inanimate nature, without the aid of intelligence. Decision making boils down to choice contingency as opposed to necessity or chance. The human mind is choice contingent causation in relation to complex functional things we create.EugeneS
March 26, 2018
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So, anti-Darwinism is certainly science. But, positive ID is not science, at this point in time. It is still in the philosophy camp.
Science is in the philosophy camp. Andrewasauber
March 26, 2018
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@tribune7 @ 174, how do you know it takes intelligence to generate specified complexity? The only argument I ever see from the ID side is: humans are the only sources of specified complexity we know of. Great! But, if humans are artificial intelligences, then they are exactly an example of necessity creating specified complexity, which contradicts the explanatory filter. ID only makes sense if the human mind is somehow beyond computation, i.e. not necessity, but we don't know that is the case. Thus, the primary positive argument for ID doesn't work. That being said, the negative arguments against Darwinism are devastating. So, anti-Darwinism is certainly science. But, positive ID is not science, at this point in time. It is still in the philosophy camp.EricMH
March 26, 2018
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JVL
No natural law restricts the possibility-space of a written (or spoken) text. Jesper Hoffmeyer, Claus Emmeche (1991). Code-duality and the semiotics of nature. In On Semiotic Modeling, M. Anderson and F. Merrell (eds.), 117-166. Berlin: Mouton de Gruyter.
Semiotic interactions do not take place of physical necessity. Kalevi Kull (1999). Biosemiotics in the twentieth century: A view from biology. Semiotica 127 (1/4), 385 - 414.
Laws are valued because they express the maximum possible regularity of events. Symbols, by contrast, are valued as information carriers, and information capacity is measured by the minimum regularity of events.[...] The most convincing general argument for this irreducible complementarity of dynamical laws and measurement structures comes again from von Neumann (Neumann 1955). He calls the system being measured, S, and the measuring device, M, that must provide the initial conditions for the dynamic laws of S. Since M is also a physical system obeying the same laws as S, we may try a unified description by considering the combined physical system (S+M). But then we will need a new measuring device, M', to provide the initial conditions for a larger system (S+M). This leads to an infinite regress; but the main point is that even though any measuring device, M, can in principle be described by the universal laws, the fact is that if you choose to do so you will lose the function of M as a measuring device. This demonstrates that laws cannot describe the semantic function of measurement even if they can correctly and completely describe the physics of the measuring device. Howard Pattee (2001). Irreducible and complementary semiotic forms, Semiotica, 134-1/4 (2001), 341-358.
EugeneS
March 26, 2018
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JVL "But what if the genetic code had a chemical basis?" The answer is very simple: it would not have been a code. Regarding suggested reading, also, try http://bio-complexity.org where people post their research papers specifically related to intelligent design. Okay, it is not peer-reviewed (as far as I know) but there is interesting stuff there. "Stay tuned for more results I guess!!" Thank you. I am tuned, but I am not holding my breath :)EugeneS
March 26, 2018
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And another critique of her stance on Nylonase: http://theskepticalzone.com/wp/is-it-easy-to-get-a-new-protein-a-reply-to-ann-gauger/JVL
March 26, 2018
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Actually, I see now that many of these discussions are regarding Dr Gauger's evaluation of a book written by Dr Venema. Another article here: https://skeptic78240.wordpress.com/tag/ann-gauger/JVL
March 26, 2018
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Upright Biped Here is my question: Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place? I have no idea and I suspect no one else does either. I don't think anyone was around at the time. Unless it was your designer . . . . Origenes Why is it that you want us to read thoroughly debunked articles about protein folds written by someone, Venema, who does not know what protein folds are? I didn't know anyone had 'debunked' those articles. Actually, it's not clear the articles were 'debunked'. Dr Gauger participates in the following discussion. https://discourse.biologos.org/t/ann-gaugers-latest-salvo-against-dennis-venemas-arguments-against-an-original-pair-of-human-beings/36790/62 It doesn't address all the issues but clearly people are taking issue with Dr Gauger. Oh and there's this as well. https://www.quora.com/Is-Ann-Gauger-correct-in-her-rebuttal-of-the-claim-that-nylonase-is-an-example-of-a-new-enzyme-arising-from-a-random-frameshift-mutation Things are never crystal clear are they?JVL
March 26, 2018
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F/N: Pertinent works to was it March 2017:
BIBLIOGRAPHIC AND ANNOTATED LIST OF PEER-REVIEWED PUBLICATIONS SUPPORTING INTELLIGENT DESIGN UPDATED MARCH, 2017 PART I: INTRODUCTION While intelligent design (ID) research is a new scientific field, recent years have been a period of encouraging growth, producing a strong record of peer-reviewed scientific publications. In 2011, the ID movement counted its 50th peer-reviewed scientific paper and new publications continue to appear. As of 2015, the peer-reviewed scientific publication count had reached 90. Many of these papers are recent, published since 2004, when Discovery Institute senior fellow Stephen Meyer published a groundbreaking paper advocating ID in the journal Proceedings of the Biological Society of Washington. There are multiple hubs of ID-related research. Biologic Institute, led by molecular biologist Doug Axe, is "developing and testing the scientific case for intelligent design in biology." Biologic conducts laboratory and theoretical research on the origin and role of information in biology, the fine-tuning of the universe for life, and methods of detecting design in nature. Another ID research group is the Evolutionary Informatics Lab, founded by senior Discovery Institute fellow William Dembski along with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University. Their lab has attracted graduate-student researchers and published multiple peer-reviewed articles in technical science and engineering journals showing that computer programming ”points to the need for an ultimate information source qua intelligent designer." Other pro-ID scientists around the world are publishing peer-reviewed pro-ID scientific papers. These include biologist Ralph Seelke at the University of Wisconsin Superior, Wolf-Ekkehard Lonnig who recently retired from the Max Planck Institute for Plant Breeding Research in Germany, and Lehigh University biochemist Michael Behe. These and other labs and researchers have published their work in a variety of appropriate technical venues, including peer-reviewed scientific journals, peer-reviewed scientific books (some published by mainstream university presses), trade-press books, peer-edited scientific anthologies, peer-edited scientific conference proceedings and peer-reviewed philosophy of science journals and books. These papers have appeared in scientific journals such as Protein Science, Journal of Molecular Biology, Theoretical Biology and Medical Modelling, Journal of Advanced Computational Intelligence and Intelligent Informatics, Complexity, Quarterly Review of Biology, Cell Biology International, Physics Essays, Rivista di Biologia / Biology Forum, Physics of Life Reviews, Quarterly Review of Biology, Journal of Bacteriology , Annual Review of Genetics, and many others. At the same time, pro-ID scientists have presented their research at conferences worldwide in fields such as genetics, biochemistry, engineering, and computer science. Collectively, this body of research is converging on a consensus: complex biological features cannot arise by unguided Darwinian mechanisms, but require an intelligent cause. Despite ID’s publication record, we note parenthetically that recognition in peer-reviewed literature is not an absolute requirement to demonstrate an idea’s scientific merit. Darwin’s own theory of evolution was first published in a book for a general and scientific audience -- his Origin of Species -- not in a peer-reviewed paper. Nonetheless, ID’s peer-reviewed publication record shows that it deserves -- and is receiving -- serious consideration by the scientific community. The purpose of ID’s budding research program is thus to engage open-minded scientists and thoughtful laypersons with credible, persuasive, peer-reviewed, empirical data supporting intelligent design. And this is happening. ID has already gained the kind of scientific recognition you would expect from a young (and vastly underfunded) but promising scientific field . . .
Click the link. KFkairosfocus
March 26, 2018
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Abel: https://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-6-27kairosfocus
March 26, 2018
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AK, 226 (attn, JVL):
I have two degrees in chemistry and have run an accredited testing lab for over twenty years. What would you like to know?
This implies that you have significant exposure to statistical thermodynamics and certainly enough to understand the configuration state issues at the heart of the matter. Where, for D/RNA, the chaining chemistry is at right angles to the informational element, in effect serving as a backbone to hang the informational sequence. In which context ANY of A, G, C, T/U (this last distinguishing D/R) can follow any other. This provides the freedom of physical succession thus high contingency required for information storing. This is then imposed upon by coding rules and patterns, which -- attn, JVL -- are NOT physically forced. Were they physically forced, there would be absence of freedom of state for symbols or characters in the strings. Consequently, we have dialects of the standard genetic code, e.g. Mitochondrial DNA. IIRC there are about two dozen known dialects. Where also in recent years, there has been insertion of two extra elements by researchers, X and Y if memory serves. There is of course the well-known double-helix structure for DNA, where two complementary strings fit together much like elements of a zipper. Proteins are coded for by using three-letter codons, with a start element and several stop elements. This gives 64 possibilities distributed across 20 main AA's (yes there are oddball cases that we need not elaborate). Some results suggest that there are regulatory implications from code choice. The issue is further multiplied by deep isolation of several thousand protein fold domains in the config space for AA's. Beyond, lies wider organic chemistry including handedness [chirality] of molecules. All of this underscores what I have emphasised. We have digital, alphanumerical code [using prong height in a chain] that functions algorithmically in the heart of the life processes of the living cell. This implies semiotics and communication systems, language, cybernetics, mathematics. All to be addressed before there is a functioning metabolic automaton with integral code using von Neumann self-replication facility. The cell. All of this is chock full of functionally specific complex organisation and associated information (FSCO/I for convenient short). Such has just one empirically warranted, known adequate cause: intelligently directed configuration, aka design. The observation base is trillions, there are zero credible exceptions that we have actually observed. This is backed up by needle in haystack search challenge in relevant config spaces which readily exceed 500 - 1,000 bits of complexity, thus 3.27*10^150 to 1.07*10^301 possibilities. The atomic resources of sol system or observed cosmos are about 10^57 to 10^80 atoms. Factoring in organic chem, 10^-12 to 10^-15 s for interactions allows us to say treat each atom as an observer and allow shuffles of 500 - 1,000 bits [think strings of coins or a weak paramagnetic substance in a B-field such that there are 2 alignments]. Scan for 10^17 s, and see how negligible a fraction of the space of possibilities will be explored. This gives context for the search challenge and shows just how conservative the thresholds of 500 and 1,000 bits are. This sets what Abel has termed a set of plausibility bounds, in the spirit of Borel's work on the effective zero chance in stat thermodynamics. As I have noted, random text search exercises have found ASCII strings of about 20 - 25 characters, a factor of 10^100 short of the low end of the threshold for FSCO/I. A space of 10^50 can be searched (IIRC Borel thought 10^30 was a good threshold), but 10^150 - 301 is a different matter. This outline gives context for seeing why the empirical observation makes sense. Now, I have to taper off due to RW issues for a little while. KFkairosfocus
March 26, 2018
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JVL: If de novo protein-coding genes such as nylonase can come into being from scratch, as it were, then it is demonstrably the case that new protein folds can be formed by evolutionary mechanisms without difficulty ... Read through the articles.
Why is it that you want us to read thoroughly debunked articles about protein folds written by someone, Venema, who does not know what protein folds are?
Venema: "Nylonase is chock full of protein folds— exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life."
“Chock full of protein folds”? What? Surely, nylonase has only one single fold …. Ann Gauger:
Unfortunately, Venema doesn’t have the story straight. Nylonase has a particular fold, a particular three-dimensional, stable shape. Most proteins have a distinct fold — there are several thousand kinds of folds known so far, each with a distinct topology and structure. Folds are typically made up of small secondary structures called alpha helices and beta strands, which help to assemble the tertiary structure — the fold as a whole. Venema seems unclear about what a protein fold is, and the distinction between secondary and tertiary structures. Nylonase is not “chock full of folds.” No structural biologist would describe nylonase as “chock full of protein folds.” Indeed, no protein is “chock full of folds.” Perhaps Venema was referring to the smaller units of secondary structure I mentioned above, the alpha helices or beta strands. But it would appear he doesn’t know what a protein fold is.
Origenes
March 26, 2018
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Well well well. Kick a mule hard enough and it'll stand up. Suddenly JVL knows elementary biology 101. The problem is, he answered a question I didn't ask. So I'll ask again: We know that aminoacyl synthetases are the finite set of complex proteins that establish the genetic code. Their task in the cell is to perform a double-recognition and bind a particular amino acid to a particular tRNA adapter prior to the act of translation. We can all conceive of their significance to the system. They are synthesized from nucleic memory, and it stands to reason that there was once a time in earth’s history that none of the set of aaRS had ever been synthesized from that memory. Here is my question: Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place? I'll check back this evening to see if you've attempted to answer.Upright BiPed
March 26, 2018
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EugeneS I admit that this is down to personal views, but the bottom up explanation will never work. It just does not happen that way. Bifurcation is not a proper choice but for chemistry based software to come about decisions need to be made. There is no way for a decision making system to appear other than by decision making. Not in this world, at least. Stay tuned for more results I guess!!JVL
March 26, 2018
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EugeneS You probably want me to show you the words “intelligent design” in black and white, no less. I agree that ID is not mainstream but to dismiss it as not being an item on the scientific agenda would not be fair. There is a certain caveat that goes with peer review as an objective criterion for separation science from non-science because there is a noticeable influence of consensus on peer review. And consensus, in certain circumstances, could be a science stopper. I didn't dismiss it, I merely asked for some guidance so I could find the pertinent work more quickly. Not everything that is formally labeled ‘evolutionary’ in the preface is in fact counter-design. Evolution itself as a thesis is not necessarily counter-design as such (putting aside the question about what evolution can actually physically achieve in nature). So I guess a reader should learn to read between the lines nowadays. It reminds me of the times of the Soviet Union when to get something published you had to mention Marx, Engels and Lenin, together with the decisions of the most recent Communist party congress upfront, even if your paper was to do with particle physics or inorganic chemistry ???? But reading between the lines might lead to mis-interpretations. This series of articles I've been reading on BioLogos (starting here: https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-introduction) is very clear and open about addressing many of the issues brought up here and so I don't have to interpret it. here is no bona fide naturalistic explanation to semiotic state. Here ‘naturalistic’ means ’caused ultimately by any combination of the four basic types of physical interactions’. But what if the genetic code had a chemical basis? There is a load of literature on the thesis of complementarity of sign and matter (that organization does not reduce to natural regularities alone). You need to do you homework yourself, I am afraid. There’s Pierce, Pattee, Polanyi, von Neumann, Abel and many others. And yes, there are recent peer-reviewed things. So I suggest you look into the peer-reviewed literature hard enough ???? I'll see what I can find. gpuccio That is the important point. Non design systems are incapable to generate complex functional information and symbolic codes. But what if the genetic code had a basis in chemistry? That very well could be the case in which case . . . The absolute absence of any other sources for those features, except for human design, makes the inference absolutely strong, and not weak! It demonstrates that conscious understanding and purpose are absolutely necessary to produce that kind of outcome. You are defeating your own argument. I think the jury is still out owing to the large amount of research still on going. It's pretty exciting actually. Like I said, I'm really enjoying this series of articles on BioLogos https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-introduction There the argument is made that the genetic code seems to have at least a partial chemical basis in which case it's not arbitrary. That would change things it seems.JVL
March 26, 2018
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JVL "Later, tRNAs would be added to the system, allowing for other amino acids—amino acids that cannot directly bind mRNA—to be added to the code." Ok, how? (c) James Tour Given that, what is the chemical basis for this later extension? When/how does a core of chemical reactions decide to extend itself? "Decide" = "choose from among chemical/energy alternatives". There is hardly any chemical bias in nucleotide polymerization. Correct me if I am wrong, but the bias that exists is too weak to account for an entirely chemical source of the mRNA's information carrying capacity. This lack of bias is in fact what makes information translation possible. Without that it would not have been possible for mRNAs to carry information at all. I admit that this is down to personal views, but the bottom up explanation will never work. It just does not happen that way. Bifurcation is not a proper choice but for chemistry based software to come about decisions need to be made. There is no way for a decision making system to appear other than by decision making. Not in this world, at least.EugeneS
March 26, 2018
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JVL and Allan Keith:
Human made codes are linguistic and human made algorithms are mathematical. You are till relying on comparison to a single source to make your inference. As such, it remains a weak inference.
Excuse nme, I have already said that the real issue is exactly that: we are relying on a single source because there are no others! That is the important point. Non design systems are incapable to generate complex functional information and symbolic codes. The absolute absence of any other sources for those features, except for human design, makes the inference absolutely strong, and not weak! It demonstrates that conscious understanding and purpose are absolutely necessary to produce that kind of outcome. You are defeating your own argument.gpuccio
March 26, 2018
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JVL "I haven’t seen that suggestion in the peer reviewed literature, any hints as to where I might find an explanation?" You probably want me to show you the words "intelligent design" in black and white, no less. I agree that ID is not mainstream but to dismiss it as not being an item on the scientific agenda would not be fair. There is a certain caveat that goes with peer review as an objective criterion for separation science from non-science because there is a noticeable influence of consensus on peer review. And consensus, in certain circumstances, could be a science stopper. Not everything that is formally labeled 'evolutionary' in the preface is in fact counter-design. Evolution itself as a thesis is not necessarily counter-design as such (putting aside the question about what evolution can actually physically achieve in nature). So I guess a reader should learn to read between the lines nowadays. It reminds me of the times of the Soviet Union when to get something published you had to mention Marx, Engels and Lenin, together with the decisions of the most recent Communist party congress upfront, even if your paper was to do with particle physics or inorganic chemistry ;) There is no bona fide naturalistic explanation to semiotic state. Here 'naturalistic' means 'caused ultimately by any combination of the four basic types of physical interactions'. Semiosis, in physical terms, is a local effect of the organization of the system, i.e. boundary conditions on the motion of particles of matter in the system, not of the motion itself. There is a load of literature on the thesis of complementarity of sign and matter (that organization does not reduce to natural regularities alone). You need to do you homework yourself, I am afraid. There's Pierce, Pattee, Polanyi, von Neumann, Abel and many others. And yes, there are recent peer-reviewed things. So I suggest you look into the peer-reviewed literature hard enough ;)EugeneS
March 26, 2018
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Upright Biped I’m assuming you already know that the dynamic properties of a codon do not determine which amino acid is specified by that codon. This sounds pretty pertinent:
One of the key challenges for abiogenesis research is to explain the origin of the genetic code—how it came to be that certain codons specify certain amino acids. Recall that tRNA molecules recognize and bind codons on mRNA through their anticodons—and bring the correct amino acid for that codon to the ribosome in the process. One feature of the tRNA system is that there is no direct chemical or physical connection between an amino acid and its codon or anticodon. Amino acids are connected to tRNA molecules at the “acceptor stem” section (the yellow region in the above diagram). Moreover, the acceptor stem is the same sequence for every tRNA, regardless of what amino acid it carries. Connecting the proper amino acids to their tRNA molecules is the job of a set of protein enzymes called aminoacyl tRNA synthetases. These enzymes recognize free amino acids and their proper tRNA molecules and specifically connect them together. Because there is no direct interaction between an amino acid and its codon, in principle it seems that any codon could have been assigned to any amino acid. If so, how might this system have arisen without any chemical connections to guide its formation? Significantly, the lack of a direct chemical or physical connection between amino acids and their codons or anticodons forms a critical part of the Intelligent Design (ID) argument that the “genetic code” is in fact a genuine code of the sort that is determined and manufactured by a designing intelligence, and is not the product of what scientists would call a natural origin. This argument rests on the claim that since there is no physical connection between amino acids and codons (or anticodons) in the present-day system, the “genetic code” is an arbitrary, symbolic code – that the list of codons and their corresponding amino acids are not connected through chemistry. Since there is no connecting chemistry, so the argument goes, then there is no chemical path that could bring the system into being. And if there is no material, chemical process that can bring it into being, then it must have its origin through another means—such as by a designing intelligence that produced it directly, and not through a material process. Meyer lays out his argument for an arbitrary genetic code on pages 247-248 of Signature (emphases mine). Self-organizational theories have failed to explain the origin of the genetic code for several reasons. First, to explain the origin of the genetic code, scientists need to explain the precise set of correspondences between specific nucleotide triplets in DNA (or codons on the messenger RNA) and specific amino acids (carried by transfer RNA). Yet molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond. This means that forces of chemical attraction between amino acids and these groups of bases do not explain the correspondences that constitute the genetic code… Thus, chemical affinities between nucleotide codons and amino acids do not determine the correspondences between codons and amino acids that define the genetic code. From the standpoint of the properties of the constituents that comprise the code, the code is physically and chemically arbitrary. All possible codes are equally likely; none is favored chemically. Here we can see Meyer’s argument clearly: in order to provide a material explanation for the origin of the genetic code, scientists need to explain how the specific correspondences between codons and amino acids came about. But, as he notes, there is no physical connection between them in the present system that can explain the correspondences. The code is arbitrary—and for Meyer, this indicates design. Crisps or chips? Having recently returned from a family vacation in Europe, my kids and I have a new appreciation for this line of argument. Travelling to the UK put our family into a similar, yet distinct linguistic context. Learning the words for various things in the UK was part of the fun. For example, the kids soon learned that if they wanted a bag of potato chips, they needed to ask for “crisps” instead of “chips”—“chips” being what they thought of as “French fries” (though curiously retained in the common UK/North American construction, “fish and chips”). Now, does it matter if a group settles on “chips” or “crisps”? No, not really—what matters is that people know what you are talking about. In principle, any word could be used for thinly sliced and deep-fried potatoes, as long as everyone in the group agreed on what that word meant. Languages thus have an element of arbitrariness to them, and manufactured codes even more so. In fact, a human code benefits from arbitrary associations in that it makes it much harder to crack. I recall reading Meyer’s argument for an arbitrary code when Signature first came out in 2009, and being surprised by it. The reason for my surprise was simple: in 2009 there was already a detailed body of scientific work that demonstrated exactly what Meyer claimed had never been shown.[1] Though Meyer claimed that “molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond” this was simply not the case. One hypothesis about the origin of the genetic code is that the tRNA system is a later addition to a system that originally used direct chemical interactions between amino acids and codons. In this hypothesis, amino acids would directly bind to their codons on mRNA, and then be joined together by a ribozyme (the ancestor of the present-day ribosome). This hypothesis is called “direct templating”, and it predicts that at least some amino acids will directly bind to their codons (or perhaps anticodons, since the codon/anticodon pairing could possibly flip between the mRNA and the tRNA). So, is there evidence that amino acids can bind directly to their codons or anticodons on mRNA? Meyer’s claim notwithstanding, yes—very much so! Several amino acids do in fact directly bind to their codon (or in some cases, their anticodon), and the evidence for this has been known since the late 1980s in some cases. Our current understanding is that this applies only to a subset of the 20 amino acids found in present-day proteins. In this model, then, the original code used a subset of amino acids in the current code, and assembled proteins directly on mRNA molecules without tRNAs present. Later, tRNAs would be added to the system, allowing for other amino acids—amino acids that cannot directly bind mRNA—to be added to the code. The fact that several amino acids do in fact bind their codons or anticodons is strong evidence that at least part of the code was formed through chemical interactions— and, contra Meyer, is not an arbitrary code. The code we have—or at least for those amino acids for which direct binding was possible—was indeed a chemically favored code. And if it was chemically favored, then it is quite likely that it had a chemical origin, even if we do not yet understand all the details of how it came to be. As such, building an apologetic on the presumed future failings of abiogenesis research, when current research already undercuts one’s thesis, seems to me as problematic for Meyer in 2009 as it did for Edwards in 1696. Do unanswered questions remain? Of course. Should we bank on them never being answered? Or would it be more wise to frame our apologetics on what we know, rather than what we don’t know?[2]
JVL
March 25, 2018
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ET t didn’t come from scratch. And there isn’t any evidence it was via a copying error or mistake- no evidence for the blind watchmaker Read through the articles. And yet without the actual scientific theory of evolution to check he could be just making it all up. I bet he equivocates throughout the book- equivocating “evolution” with “evolution by means of blind and mindless processes”. Perhaps you should wait until you read what he actually says. 1- The people who disagree don’t have a viable alternative 2- Intelligent Design has evidence in biology- plenty there- and from other scientific venues as well. And again those who disagree don’t have any viable alternatives- things just happen isn’t an alternative Well, I guess you'll just have to live with the vast majority of biologists disagreeing with you then. It seems quote apparent that unguided processes have clearly been eliminated from consideration. There isn’t even any testable hypotheses Well, that lengthy series of posts I was quoting from say otherwise. Where? Not in peer-review Have you read all the pertinent papers? The strong inference to design, supported with compelling evidence from multiple other disciplines, has been made. What are the alternatives and how can we test them? You're going to get a big thick textbook all about it soon. Origenes Venema’s nylonase story has been thoroughly debunked by Ann Gauger in a series of articles. Seems like a lot of people disagree. Eric Anderson If you are sincerely interested in the issue (as opposed to some commentators who are just regurgitating the latest OOL news report they read), let me know and I’ll take a few minutes to point you to a few additional things on this site to read. I'm enjoying the BioLogos series of articles very much at the moment but thanks. kairosfocus JVL, if one has not shown causal adequacy of a claimed causal factor then one is simply speculating. There is just one observationally known adequate cause of codes, text that functions algorithmically and associated execution machinery. That observation is no accident, given the config space needle in haystack search challenge. This more than warrants an inference on tested, reliable sign to that cause, intelligently directed configuration. The BioLogos series spends quite a bit of time discussing what kind of 'code' DNA is. You should read it, it's very interesting. And backed up with recent research. Upright Biped JVL, you say you’ve never seen anything convincing, but you also say you can’t engage in a Biology 101 observation (of half-century old settled science) because you’re “not familiar with the current stage of research in that particular sub-field”. I've take Biology 101 and that topic wasn't covered. I'm not ashamed to say I don't understand something. Are either of the two of you familiar with the Periodic Table of Elements? It’s a table that list all the chemical elements in the known universe, arranged by their atomic number. For instance the table includes such elements as Iron, Oxygen, Helium, Barium, Neodymium, and 113 others. It is from these basic elements that all material objects in the universe are made. Of course, I have a tea cup with the periodic table on it. So now let me ask about your familiarity with DNA? It’s a series of four different nucleobases attached to a long sugar-phosphate backbone. It’s often called “the information molecule” because it holds the genetic information that tells an organism how to build and maintain itself across its lifespan. It was first understood how it holds that information in 1953, and it exist in every cell of your body. Are either of you familiar with this? Good heavens, we are being a bit condescending aren't we? Yes, I am familiar with DNA. How many discrete arrangements of matter does the cellular translation apparatus use to specify a particular amino acid from among alternatives during protein synthesis? Oh go on, tell us!! Look, I'm sure you are heading towards some important point in which case it would be nice if you just made it and then I could check and see what other make of it. That makes sense yes?JVL
March 25, 2018
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I'm assuming you already know that the dynamic properties of a codon do not determine which amino acid is specified by that codon.Upright BiPed
March 25, 2018
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How many discrete arrangements of matter does the cellular translation apparatus use to specify a particular amino acid from among alternatives during protein synthesis?Upright BiPed
March 25, 2018
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UB,
Are either of the two of you familiar with the Periodic Table of Elements?
I have two degrees in chemistry and have run an accredited testing lab for over twenty years. What would you like to know?Allan Keith
March 25, 2018
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Okay okay, let's just assume that at least one of you is familiar with the Periodic Table of Elements and coincidentally also understands the axiom that there is no inherent meaning in matter. So now let me ask about your familiarity with DNA? It's a series of four different nucleobases attached to a long sugar-phosphate backbone. It's often called "the information molecule" because it holds the genetic information that tells an organism how to build and maintain itself across its lifespan. It was first understood how it holds that information in 1953, and it exist in every cell of your body. Are either of you familiar with this?Upright BiPed
March 25, 2018
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JVL and AK, Are either of the two of you familiar with the Periodic Table of Elements? It's a table that list all the chemical elements in the known universe, arranged by their atomic number. For instance the table includes such elements as Iron, Oxygen, Helium, Barium, Neodymium, and 113 others. It is from these basic elements that all material objects in the universe are made. Are you familiar with the axiom in science that none of those elements refers to anything else? This is to say that they have no inherent "meaning". A philosopher might say that they have no "stands for" relation to anything else in the universe. They just are what they are. Ever heard of that? Is there any chance that either of you are familiar with and understand that observation, which is again, axiomatic throughout the sciences?Upright BiPed
March 25, 2018
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This conversation has moved on considerably since this morning. This looks just exactly like trying to convince one of those science deniers that NASA actually did land on the moon. There is no amount of argument that can penetrate a willfully closed mind. JVL, you say you've never seen anything convincing, but you also say you can't engage in a Biology 101 observation (of half-century old settled science) because you're "not familiar with the current stage of research in that particular sub-field". Good grief.Upright BiPed
March 25, 2018
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Evidence for Intelligent Design in the details of ATP synthase- the external tether: Take a look at the the architecture and subunit composition of ATP synthase. Notice the external tethering that has nothing to do with the function of either subunit but without it there isn't any ATP synthase. And it has to be the proper length. Details. Sometimes the devil is in the and sometimes the design inference is confirmed by them.ET
March 25, 2018
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